Untitled

2010 KRIBB Article Abstracts 

Corresponding Articles Indexed in SCIE 

Contents 

01 Division of Bioconvergence Technology 

BioNanotechnology Research Center 

Aging Research Center 

Brain Research Center 

Integrative Omics Research Center 

BioMonitoring Research Center 

19 Division of Translational Research 

Medical Genomics Research Center 

Development and Differentiation Research Center 

Medical Proteomics Research Center 

39 Division of Biosystems Research 

Industrial Biotechnology & Bioenergy Research Center 

Plant Systems Engineering Research Center 

Industrial Bio-materials Research Center 

Environmental Biotechnology Research Center 

75 Division of Leading R&D 

Korean Bioinformation Center 

Viral Infectious Disease Research Center 

AI Control Material Research Center 

International Biological Material Research Center 

DAEJEON-KRIBB-FHCRC Research Cooperation Center 

Kinomics Based Cancer Research World Class Institute 

83 Korea Biological Resource Center 

Microbial Resource Center 

Plant Resource Center 

Human Derived Material Center 

Genome Resource Center 

Animal Model Resource Center

Korea Research Institute of Bioscience & Biotechnology 

99 Bio-Therapeutics Research Institute 

Therapeutic Antibody Research Center 

Stem Cell Research Center 

Immune Modulator Research Center 

Molecular Cancer Research Center 

Chemical Biology Research Center 

123 Division of Bio-Infra Structure 

Bio-Evaluation Center 

Korea National Primate Research Center 

Biomedical Mouse Resource Center 

Biotechnology Process Engineering Center 

137 Jeonbuk Branch Institute 

Microbe-based Fusion Technology Research Center 

Eco-Friendly Biomaterial Research Center 

Bioindustrial Process Center 

151 Indexes 

Corresponding Author Index 

Journal Index 

Keyword Index

2010 

KRIBB Article Abstracts 

Corresponding Articles 

Indexed in SCIE 

Division of Bioconvergence Technology 



Brain Research Center 



Korea Research Institute of Bioscience and Biotechnology

www.kribb.re.kr

Article 1 

Detection of mutant p53 using field-effect 

transistor biosensor 

Article 2 

Fabrication of a structure-specific RNA binder 

for array detection of label-free microRNA 

Anal Chim Acta. 2010 Apr; 665(1):79-83. 

Angew Chem Int Ed Engl. 2010 Nov; 49(46):8662-5. 

Han SH, Kim SK, Park K, Yi SY, Park HJ, Lyu HK, Kim 

M * , Chung BH * 

* Correspondence: kimm@kribb.re.kr chungbh@kribb.re.kr 


We assessed the abilities of wild p53 and mutant p53 proteins 

to interact with the consensus DNA-binding sequence using 

a MOSFET biosensor. This is the first report in which mutant 

p53 has been detected on the basis of DNA-protein interaction 

using a FET-type biosensor. In an effort to evaluate the 

performance of this protocol, we constructed the core domain 

of wild p53 and mutant p53 (R248W), which is DNA-binding-defective. 

After the immobilization of the cognate DNA 

to the sensing layer, wild p53 and mutant p53 were applied 

to the DNA-coated gate surface, and subsequently analyzed 

using a semiconductor analyzer. As a consequence, a significant 

up-shift in drain current was noted in response to 

wild p53, but not mutant p53, thereby indicating that sequence-specific 

DNA-protein interactions could be successfully 

monitored using a field-effect-based biosensor. These 

data also corresponded to the results obtained using surface 

plasmon resonance (SPR) measurements. Taken together, 

our results show that a FET-type biosensor might be promising 

for the monitoring of mutant p53 on the basis of its 

DNA-binding activity, providing us with very valuable insights 

into the monitoring for diseases, particularly those 

associated with DNA-protein binding events. 

PMID: 20381694 

Lee JM, Cho H, Jung Y * 

* Correspondence: ywjung@kribb.re.kr 


Like an antibody: A novel structure-specific RNA-binding 

protein was designed to stably and specifically bind to surface-bound 

microRNAs. By acting like an antibody, this 

RNA binder enabled the universal detection of hybridized 

microRNAs on array surfaces (see picture) without any enzymatic 

amplification or labeling reactions. 

PMID: 20922734 

Keywords: Biosensor; Electron spin resonance; Liver; 

Microarrays; MicroRNA; Myocardium; 

Oligonucleotides; Protein design; RNA recognition; 

RNA probes 

Keywords: Biosensor; DNA-binding domain; Metal oxide 

semiconductor; Mutant p53; Mutation; Surface 

plasmon resonance; Tumor suppressor protein 

2010 KRIBB Article Abstracts | 3 |

Article 3 

Characterization of alcohol dehydrogenase 1 of 

the thermotolerant methylotrophic yeast 

Hansenula polymorpha 

Appl Microbiol Biotechnol. 2010 Sep; 88(2):497-507. 

Suwannarangsee S, Oh DB, Seo JW, Kim CH, Rhee SK, 

Kang HA, Chulalaksananukul W, Kwon O * 

* Correspondence: oskwon@kribb.re.kr 


The thermotolerant methylotrophic yeast Hansenula polymorpha 

has recently been gaining interest as a promising 

host for bioethanol production due to its ability to ferment 

xylose, glucose, and cellobiose at elevated temperatures up 

to 48 degrees C. In this study, we identified and characterized 

alcohol dehydrogenase 1 of H. polymorpha (HpADH1). 

HpADH1 seems to be a cytoplasmic protein since no N-terminal 

mitochondrial targeting extension was detected. 

Compared to the ADHs of other yeasts, recombinant 

HpADH1 overexpressed in Escherichia coli exhibited much 

higher catalytic efficiency for ethanol oxidation along with 

similar levels of acetaldehyde reduction. HpADH1 showed 

broad substrate specificity for alcohol oxidation but had an 

apparent preference for medium chain length alcohols. Both 

ADH isozyme pattern analysis and ADH activity assay indicated 

that ADH1 is the major ADH in H. polymorpha 

DL-1. Moreover, an HpADH1-deleted mutant strain produced 

less ethanol in glucose or glycerol media compared to 

wild-type. Interestingly, when the ADH1 mutant was complemented 

with an HpADH1 expression cassette, the resulting 

strain produced significantly increased amounts of ethanol 

compared to wild-type, up to 36.7 g l(-1). Taken together, 

our results suggest that optimization of ADH1 expression 

would be an ideal method for developing H. polymorpha 

into an efficient bioethanol production strain. 

PMID: 20635082 

Keywords: Acetaldehyde; ADH1; Alcohol dehydrogenase; 

Ethanol production; Glycerol fermentation; 

Hansenula polymorpha; Oxidation-reduction; 

Pichia; Substrate specificity 

Article 4 

Construction of an in vitro trans-sialylation 

system: surface display of Corynebacterium 

diphtheriae sialidase on Saccharomyces 

cerevisiae 

Appl Microbiol Biotechnol. 2010 Oct; 88(4):893-903. 

Kim S, Oh DB, Kwon O * , Kang HA 



Sialidases can be used to transfer sialic acids from sialoglycans 

to asialoglycoconjugates via the trans-glycosylation reaction 

mechanism. Some pathogenic bacteria decorate their 

surfaces with sialic acids which were often scavenged from 

host sialoglycoconjugates using their surface-localized 

enzymes. In this study, we constructed an in vitro trans-sialylation 

system by reconstructing the exogenous sialoglycoconjugate 

synthesis system of pathogens on the surfaces 

of yeast cells. The nanH gene encoding an extracellular 

sialidase of Corynebacterium diphtheriae was cloned into 

the yeast surface display vector pYD1 based on the 

Aga1p-Aga2p platform to immobilize the enzyme on the 

surface of the yeast Saccharomyces cerevisiae. The surface-displayed 

recombinant NanH protein was expressed as 

a fully active sialidase and also transferred sialic acids from 

pNP-α-sialoside, a sialic acid donor substrate, to human-type 

asialo-N-glycans. Moreover, this system was capable of attaching 

sialic acids to the glycans of asialofetuin via α(2,3)- 

or 

α(2,6)-linkage. The cell surface-expressed 

C. diphtheriae 

sialidase showed its potential as a useful whole cell biocatalyst 

for the transfer of sialic acid as well as the hydrolysis 

of N-glycans containing α(2,3)- and α(2,6)-linked sialic acids 

for glycoprotein remodeling. 

PMID: 20711574 

Keywords: Asialoglycoproteins; Cell surface display; 

Corynebacterium diphtheriae; Genetic vectors; In 

vitro trans-sialylation; NanH; Neuraminidase; 

Saccharomyces cerevisiae; Sialidase; 

Sialoglycoconjugate 

| 4 | 2010 KRIBB Article Abstracts

Article 5 

Perfluorodecalin/[InGaP/ZnS quantum dots] 

nanoemulsions as 19F MR/optical imaging 

nanoprobes for the labeling of phagocytic and 

nonphagocytic immune cells 

Biomaterials. 2010 Jun; 31(18):4964-71. 

Lim YT, Cho MY, Kang JH, Noh YW, Cho JH, Hong KS, 

Chung JW, Chung BH * 

* Correspondence: chungbh@kribb.re.kr 


Multimodal imaging contrast agents with unique magnetic 

resonance (MR) and optical imaging capabilities have great 

potentials in the diagnosis and therapy of disease. Using 

a rational materials design approach, the bimodal imaging 

contrast agent, perfluorodecalin (PFD)/[InGaP/ZnS quantum 

dots (QDs)] composite nanoemulsions is developed in this 

study. (19)F molecules in the PFD/[InGaP/ZnS QDs] nanoemulsions 

provide a (19)F-based MR imaging capability, 

while fluorescent QDs dispersed in PFD nanodroplets provide 

an optical imaging modality. This study also demonstrates 

that these bimodal imaging contrast agents can be delivered 

easily into both phagocytic and nonphagocytic immune cells. 

Internalization of multifunctional PFD/[InGaP/ZnS QDs] 

nanoemulsions into immunotherapeutic cells permits the labeled 

cells to be imaged by both magnetic resonance and 

fluorescence imaging with little effect on cell viability and 

function. The results of our study highlight the potential 

of PFD/[InGaP/ZnS QDs] nanoemulsion as a bimodal imaging 

nanoprobe for molecular imaging in immune cell-based 

cancer therapies. 

PMID: 20346494 

Keywords: Cell imaging; Fluorine; Fluorocarbons; Immune 

cell; Intracellular delivery; Macrophages; Molecular 

imaging; Nanoparticle; Perfluorocarbon; Quantum 

dots 

Article 6 

Enhanced immobilization of hexa-arginine-tagged 

esterase on gold nanoparticles using 

mixed self-assembled monolayers 

Bioprocess Biosyst Eng. 2010 Jan; 33(1):165-9. 

Jeong J, Lee CS, Chung SJ, Chung BH * 



Mixed self-assembled monolayers (MSAMs) composed of 

diverse ligands offer a mechanism for the specific binding 

of biomolecules onto solid surfaces. In this study, we examined 

the formation of MSAMs on gold nanoparticles (AuNPs) 

and the immobilization of hexa-arginine-tagged esterase 

(Arg(6)-esterase) on the surfaces of the resulting particles. 

The functionalization of AuNPs with MSAMs was achieved 

by introducing a mixture of tethering and shielding ligands 

into an AuNP solution. The formation of self-assembled 

monolayers (SAMs) on the AuNP surface was characterized 

by UV/visible spectroscopy, transmission electron microscopy, 

and Fourier-transform infrared spectroscopy. 

Arg(6)-esterase was immobilized in a highly specific manner 

onto AuNPs treated with mixed SAMs (MSAM-AuNPs) by 

providing a shielding ligand which reduce the non-specific 

adsorption of enzymes caused by hydrophobic interaction 

compared to AuNPs treated with single-component SAMs 

(SSAM-AuNPs). Moreover, Arg(6)-esterase immobilized on 

MSAM-AuNPs showed substantially enhanced catalytic activity 

up to an original activity compared to that on 

SSAM-AuNPs (58%). 

PMID: 19639343 

Keywords: Catalysis; Enzyme activity; Enzyme 

immobilization; Esterases; Gold nanoparticles; 

Mixed self-assembled monolayer; Peptides 


Article 7 

A dual gold nanoparticle conjugate-based lateral 

flow assay (LFA) method for the analysis of troponin 

I 

Biosens Bioelectron. 2010 Apr; 25(8):1999-2002. 

Choi DH, Lee SK, Oh YK, Bae BW, Lee SD, Kim S, Shin 

YB * , Kim MG * 

Article 8 

Extracellular hydrogen peroxide contributes to oxidative 

glutamate toxicity 

Brain Res. 2010 Nov; 1359:291-7. 

Ha JS, Lim HM, Park SS * 

* Correspondence: sspark@kribb.re.kr 


* Correspondence: ybshin@kribb.re.kr mgkim@kribb.re.kr 


For signal amplification without an additional operation step 

in a gold nanoparticle (AuNP)-based lateral flow assay 

(LFA), a new and simple method utilizing two AuNP-antibody 

conjugates was developed. The 1st conjugate was the 

AuNP immobilized with an anti-troponin I antibody and 

blocked with bovine serum albumin (BSA), and the 2nd 

conjugate was the AuNP immobilized with an anti-BSA 

antibody and blocked with human serum albumin. The two 

conjugates were encapsulated in different pads, respectively. 

A scheme of the LFA system is described in the part A 

of first figure. The size of the two conjugates was very 

critical in the detection sensitivity of troponin I. When 10nm 

for the 1st and 40 nm for the 2nd were used, the detection 

sensitivity increased about a 100-fold compared to the conventional 

LFA. We could detect as low as 0.01 ng/mL troponin 

I in 10 min using the dual AuNP conjugate-based LFA, 

which was successfully applied in the analysis of serum 

samples of patients with myocardial infarction. 

PMID: 20167468 

Keywords: Biosensing techniques; Flow injection analysis; 

Gold; Immunoassay; Lateral flow assay; Myocardial 

infarction; Nanoparticles; Nanotechnology; 

Troponin I 

Oxidative glutamate toxicity is characterized by the inhibition 

of cystine uptake, the depletion of intracellular glutathione, 

and increased levels of intracellular reactive oxygen species, 

factors that lead to neuronal injury. We found that the presence 

of extracellular catalase protected cultured neuronal 

cells, such as HT22, SH-SY5Y and PC12 cells, from glutamate-induced 

cytotoxicity. Extracellular hydrogen peroxide 

(H₂O ₂) accumulated in a time- and concentration-depend - 

ent manner in HT22 cells during prolonged exposure to 

glutamate. To investigate the involvement of NADPH oxidase 

in glutamate-induced H₂O₂ 

generation, we used small 

interference RNA (siRNA). Knockdown of Nox2 and Nox4 

expression reduced H₂O₂ 

accumulation and increased cell 

survival. siRNA specific for Nox4 reduced the production 

of H₂O₂ 

by ~74% compared with control siRNA. 

Furthermore, H₂O₂ 

accumulation was also suppressed by 

U0126, a MEK/ERK inhibitor, in a concentration-dependent 

manner. These results suggest that glutamate triggers the 

Nox-dependent generation of extracellular H₂O₂ via 

ERK1/2 activation, which contributes to oxidative glutamate 

toxicity. 

PMID: 20816674 

Keywords: Enzyme activation; Erk activation; Extracellular 

space; Hydrogen peroxide; NADPH oxidase; 

Neurotransmitter agents; Oxidative glutamate 

toxicity; Oxidative stress; Signal transduction 


Article 9 

Complete separation of triangular gold nanoplates 

through selective precipitation under CTAB micelles 

in aqueous solution 

Article 10 

Label-free and naked eye detection of PNA/DNA 

hybridization using enhancement of gold nanoparticles 

Chem Commun (Camb). 2010 May; 46(18):3164-6. 

Chem Commun (Camb). 2010 May; 46(19):3315-7. 

Ha TH * , Kim YJ, Park SH 

Kim SK, Cho H, Jeong J, Kwon JN, Jung Y, Chung BH * 

* Correspondence: taihwan@kribb.re.kr 




Triangular gold nanoplates in CTAB solution were selectively 

precipitated on a glass wall in ambient conditions 

and the nanoplates could be easily recovered by a brief 

sonication. 

PMID: 20424761 

Keywords: Cetrimonium compounds; Chemical 

precipitation; Gold nanoparticle; Metal 

nanoparticles; CTAB micelles; Water 

We demonstrated a new method for the labelfree detection 

of DNA using the gold enhancement process after inducing 

the electrostatic interaction between the positively charged 

gold nanoparticles and the negatively charged target DNA 

hybridized to the neutral PNA capture probes. Among the 

various sizes of gold nanoparticles, 4 nm gold nanoparticles 

were found to exhibit the optimal response. In this method, 

the target-bound spot can be visualized by the naked eye 

or by using a commercialized optical grayscale flatscanner. 

The grayscale levels were proportional to the concentration 

of the target DNA within the range of 10 pM to 100 nM, 

exhibiting comparable sensitivity to the fluorescence method. 

It is expected that this novel method offers the potential 

for label-free DNA detection in a cost-effective manner. 

Utilizing a gold enhancement process after inducing electrostatic 

interaction between positively charged gold nanoparticles 

and negatively charged target DNA hybridized to 

neutral PNA capture probes, a new method for label-free 

detection of DNA was developed and successfully applied 

to detect H5-type DNA. 

PMID: 20361103 

Keywords: DNA; Gold; In situ hybridization; Metal 

nanoparticles; Particle size; Peptide nucleic acids; 

Static electricity; Surface properties 


Article 11 

An iminocoumarin-based fluorescent probe for 

the selective detection of dual-specific protein tyrosine 

phosphatases 

Article 12 

Nox4-dependent H2O2 production contributes to 

chronic glutamate toxicity in primary cortical neurons 

Chemistry. 2010 May; 16(18):5297-300. 

Exp Cell Res. 2010 Jun; 316(10):1651-61. 

Kim TI, Jeong MS, Chung SJ * , Kim Y. 

* Correspondence: sjchung@kribb.re.kr 


The fluorescencebased assays are attractive tools to achieve 

label-free phosphatase activity measurements due to their 

high sensitivity, rapid detection, and applicability to 

high-throughput screening (HTS) for PTP inhibitors and 

activators. We report the design, synthesis, and application 

of a fluorescent probe for the detection of PTP activity with 

high sensitivity and selectivity and low background signal. 

The chemical structure of probe 1 is based on the donor– ac- 

ceptor dye, 9-(dicyanovinyl)julolidine (DCVJ). The feasibility 

of proposed detection Scheme is demonstrated by investigating 

the photophysical properties of iminocoumarin iminocoumarin 

dye 2 in aqueous media. The chemical stability 

of probe 1 was studied in HEPES buffer (10 mm, pH 7.8) 

containing 2% DMSO. 

The selectivity of probe 1 for PTPs was investigated by 

measuring the fluorescence increase upon incubating with 

PTPs. The probe 1 has been shown to be a turn-on fluorescent 

probe with a high on/off ratio that is selective for dual-specific 

PTPs. Probe 1 shows considerable stability to unwanted hydrolysis 

in aqueous environment at physiologically relevant 

pH and minimized nonspecific interactions with biological 

macromolecules, such as albumin. Probe 1 thus represents 

a new tool for the identification of potential therapeutic targets 

as well as fundamental biochemical research. A fluorescent 

probe for monitoring the activity of dual-specific 

protein tyrosine phosphatases (PTPs) has been developed. 

Selective enzymatic hydrolysis and subsequent intramolecular 

cyclization results in a highly fluorescent iminocoumarin 

fluorophore. 

PMID:20373316 

Ha JS, Lee JE, Lee JR, Lee CS, Maeng JS, Bae YS, Kwon 

KS * , Park SS * 

* Correspondence: kwonks@kribb.re.kr sspark@kribb.re.kr 


Reactive oxygen species (ROS) can trigger neuronal cell 

death and has been implicated in a variety of neurodegenerative 

diseases as well as brain ischemia. Here, we 

demonstrate that chronic (but not acute) glutamate toxicity 

in primary cortical neuronal cultures is associated with hydrogen 

peroxide (H(2)O(2)) accumulation in the culture medium 

and that neurotoxicity can be eliminated by external catalase 

treatment. Neuronal cultures in Ca(2+)-free medium or treated 

with BAPTA showed reduced glutamate-induced 

H(2)O(2) generation, indicating that H(2)O(2) generation 

is Ca(2+)-dependent. Pharmacological and genetic approaches 

revealed that NADPH oxidase plays a role in glutamate-induced 

H(2)O(2) generation and that activation of 

NMDA and AMPA receptors is involved in this H(2)O(2) 

generation. The Nox4 siRNA reduced NMDA-induced 

H(2)O(2) production by 54% and cytotoxicity in parallel, 

suggesting that Nox4-containing NADPH oxidase functions 

NMDA receptor-mediated H(2)O(2) production resulting in 

neurotoxicity. These findings suggest that the modulation 

of NADPH oxidase can be used as a new therapeutic strategy 

for glutamate-induced neuronal diseases. 

PMID: 20363222 

Keywords: Cerebral cortex; Chronic exposure; DNA 

primers; Glutamate toxicity; H2O2; Hydrogen 

peroxide; NADPH oxidase; Neurons; Nox4; Reactive 

oxygen species 

Keywords: Coumarins; Cyclization; Dual specificity; 

Fluorescent probes; Intramolecular cyclizations; 

Protein tyrosine phosphatases; Selective detection 


Article 13 

The Drosophila homolog of methionine sulfoxide 

reductase A extends lifespan and increases nuclear 

localization of FOXO 

Article 14 

Identification and functional characterization of 

the NanH extracellular sialidase from 

Corynebacterium diphtheriae 

FEBS Lett. 2010 Aug; 584(16):3609-14. 

J Biochem. 2010 Apr; 147(4):523-33. 

Chung H, Kim AK, Jung SA, Kim SW, Yu K * , Lee JH 

Kim S, Oh DB, Kwon O * , Kang HA 

* Correspondence: kweonyu@kribb.re.kr 




Methionine sulfoxide reductase A (msrA) was previously 

found to increase resistance to oxidative stress and longevity 

in animals. We identified Drosophila msrA (dmsrA), a 

Drosophila homolog of human msrA, as a downstream effector 

of forkhead box O (FOXO) signaling in Drosophila, 

which enhances resistance to oxidative stress and increases 

survival under stressed conditions. Additionally, overexpression 

of dmsrA in neurons extended the lifespan of 

flies. Moreover, overexpression of dmsrA in fat body cells 

caused FOXO to translocate to the nucleus, implying that 

this possible positive feedback loop between dmsrA and 

FOXO could potentiate the antioxidant activity of dmsrA 

and increase the lifespan in Drosophila. 

PMID:20655917 

Keywords: Antioxidant enzyme; Drosophila; Forkhead box 

O; Lifespan; Longevity; Methionine sulfoxide 

reductase A; Oxidative stress; Transcription; 

Translocation 

Corynebacterium diphtheriae, a pathogenic Gram-positive 

bacterium, contains sialic acids on its cell surface, but no 

genes related to sialic acid decoration or metabolism have 

been reported in C. diphtheriae. In the present study, we 

have identified a putative sialidase gene, nanH, from C. 

diphtheriae KCTC3075 and characterized its product for 

enzyme activity. Interestingly, the recombinant NanH protein 

was secreted as a catalytically active sialidase into the periplasmic 

space in Escherichia coli, while the short region 

at its C-terminus was truncated by proteolysis. We reconstructed 

a truncated NanH protein (His(6)-NanH( ΔN)) 

devoid of its signal sequence as a mature enzyme fused 

with the 6xHis tag at the N-terminal region. The purified 

His(6)-NanH( ΔN) can cleave α-2,3- and α-2,6-linked sialic 

acid from sialic acid-containing substrates. In addition, even 

though the efficiency was low, the recombinant His(6)-NanH 

( ΔN) was able to catalyse the transfer of sialic acid using 

several sialoconjugates as donor, suggesting that the reversible 

nature of C. diphtheriae NanH can be used for the 

synthesis of sialyl oligosaccharides via transglycosylation 

reaction. 

PMID: 20007980 

Keywords: Bacterial proteins; Corynebacterium 

diphtheriae; Extracellular protein; Glycosylation; 

Kinetics; Neuraminidase; Peptide mapping; 

Periplasm; Sialic acid; Sialidase; 

Sialoglycoconjugate 


Article 15 

Soluble CD93 induces differentiation of monocytes 

and enhances TLR responses 

J Immunol. 2010 Oct; 185(8):4921-7. 

Jeon JW, Jung JG, Shin EC, Choi HI, Kim HY, Cho ML, 

Kim SW, Jang YS, Sohn MH, Moon JH, Cho YH, Hoe 

KL, Seo YS, Park YW * 

Article 16 

Fabrication of nanochannels by anisotropic wet 

etching on silicon-on-insulator wafers and their 

application to DNA stretch 

J Nanosci Nanotechnol. 2010 Jan; 10(1):637-42. 

Kim SK, Cho H, Park HK, Kim JH, Chung BH * 


* Correspondence: ywpark@kribb.re.kr 


The cell surface protein CD93 is known to be involved 

in the regulation of phagocytosis and cell adhesion. Although 

typically membrane-bound, a soluble form of CD93 (sCD93) 

has recently been identified. Currently, however, the role 

of sCD93 in monocyte function is unknown. In the current 

study, we analyzed the functional effects of sCD93 on THP-1 

monocytic cells and human primary monocytes. Various 

forms of recombinant human sCD93 were used to investigate 

the effects of this molecule on both human primary monocytes 

and a monocytic cell line, THP-1. We found that sCD93 

induced differentiation of monocytes to macrophage-like 

cells, as evidenced by activated cell adhesion and increased 

phagocytic activities. In addition, this differentiation resulted 

in an enhanced response to TLR stimulation in terms of 

differentiation marker expression and proinflammatory cytokine 

production. Furthermore, sCD93 enhanced LPS-stimulated 

TNF-α 

production even prior to monocyte 

differentiation. To investigate a possible role for sCD93 in 

the pathogenesis of chronic inflammatory diseases, we assessed 

the concentration of sCD93 in synovial fluid from 

patients with rheumatoid arthritis and found it to be significantly 

increased compared with synovial fluid from patients 

with osteoarthritis. Together, these data revealed a 

function for sCD93 that may have implications in inflammation 

and inflammatory diseases including rheumatoid 

arthritis. 

PMID:20861352 


We report a new approach to fabricate nanochannels on 

silicon-on-insulator (SOI) wafers using conventional micromachining 

techniques. Proper selection of the size of the 

photomask-window and the thickness of the top silicon layer 

is necessary to obtain nano-sized regions. Silicon anisotropic 

wet etching followed by an additional reactive-ion-etching 

(RIE) process and a second silicon wet etching step resulted 

in long channels (1 cm) of about 200 nm width and 100 

nm depth. Finally, we demonstrated the ability of the nanochannels 

to stretch random coiled DNA by applying YOYO-1 

stained 

λ-DNA to the nanochannel sealed by PDMS polymer 

using fluorescence microscopy. This fabrication method provides 

a basis for simple and cost-effective mass production 

of nanochannels with controllable dimensions. It is therefore 

expected that the nanochannels fabricated have great potential 

for biological applications. 

PMID:20352904 

Keywords: Anisotropy; DNA stretch; Microscopy, 

fluorescence; Microtechnology; Nanochannel; 

Nanostructures; Nanotechnology; SiliconSOI wafer 

Keywords: Arthritis, rheumatoid; Cell differentiation; 

Cytokines; Enzyme-linked immunosorbent; 

Inflammation; Membrane glycoproteins; Monocytes; 

Synovial fluid; Toll-like receptors 


Article 17 

Enhanced biomolecular detection based on localized 

surface plasmon resonance (LSPR) using 

enzyme-precipitation reaction 

Article 18 

Microglial peroxiredoxin V acts as an inducible 

anti-inflammatory antioxidant through cooperation 

with redox signaling cascades 

J Nanosci Nanotechnol. 2010 May; 10(5):3246-9. 

J Neurochem. 2010 Jul; 114(1):39-50. 

Lee SW, Ahn J, Kim MG, Shin YB * , Lee JJ, Lim KP, Kim 

KB 

* Correspondence: ybshin@kribb.re.kr 


An enzyme-catalyzed precipitation reaction was employed 

as a means to increase the change in the LSPR signal after 

intermolecular bindings between antigens and antibodies occurred 

on gold nanodot surfaces. The gold nanodot array 

with an diameter of 175 nm and a thickness of 20 nm was 

fabricated on a glass wafer using thermal nanoimprint 

lithography. The human interleukin (hIL) 5 antibody was 

immobilized on the gold nanodot, followed by binding of 

hIL 5 to the anti-hIL 5. Subsequently, a biotinylated anti-hIL 

5 and a alkaline phosphatase conjugated with streptavidin 

were simultaneously introduced. A mixture of 5-bromo-4-chloro-3-indolyl 

phosphate p-toluidine (BCIP) and nitro 

blue tetrazolium (NBT) was then used for precipitation, 

which resulted from the biocatalytic reaction of the alkaline 

phosphatase on gold nanodot. The LSPR spectra were obtained 

after each binding process. Using this analysis, the 

enzyme-catalyzed precipitation reaction on gold nanodots 

was found to be effective in amplifying the change in the 

peak wavelength of LSPR after molecular bindings. 

PMID:20358932 

Keywords: Biopolymers; Biosensing techniques; 

Enzyme-catalyzed precipitation; Equipment design; 

Immunoassay; Metalloproteins; Nanodot; 

Nanoimprint lithography (NIL); Nanotubes; Surface 

plasmon resonance 

Sun HN, Kim SU, Huang SM, Kim JM, Park YH, Kim 

SH, Yang HY, Chung KJ, Lee TH, Choi HS, Min JS, Park 

MK, Kim SK, Lee SR, Chang KT, Lee SH, Yu DY * , Lee 

DS 

* Correspondence: dyyu10@kribb.re.kr 


Reactive oxygen species (ROS) actively participate in microglia-mediated 

pathogenesis as pro-inflammatory molecules. 

However, little is known about the involvement of specific 

antioxidants in maintaining the microglial oxidative balance. 

We demonstrate that microglial peroxiredoxin (Prx) 5 expression 

is up-regulated by lipopolysaccharide (LPS) through 

activation of the ROS-sensitive signaling pathway and is 

involved in attenuation of both microglial activation and 

nitric oxide (NO) generation. Unlike in stimulation of oxidative 

insults with paraquat and hydrogen peroxide, Prx V 

expression is highly sensitive to LPS-stimulation in 

microglia. Reduction of ROS level by treatment with either 

NADPH oxidase inhibitor or antioxidant ablates LPS-mediated 

Prx V up-regulation in BV-2 microglial cells and is 

closely associated with the activation of the c-jun N-terminal 

kinase (JNK) signaling pathway. This suggests the involvement 

of ROS/JNK signaling in LPS-mediated Prx V 

induction. Furthermore, NO induces Prx V up-regulation 

that is ablated by the addition of inducible nitric oxide synthase 

inhibitor or deleted mutation of inducible nitric oxide 

synthase in LPS-stimulated microglia. Therefore, these results 

suggest that Prx V is induced by cooperative action 

among the ROS, RNS, and JNK signaling cascades. 

Interestingly, knockdown of Prx V expression causes the 

acceleration of microglia activation, including augmented 

ROS generation and JNK-dependent NO production. In summary, 

we demonstrate that Prx V plays a key role in the 

microglial activation process through modulation of the balance 

between ROS/NO generation and the corresponding 

JNK cascade activation. 

PMID: 20345759 

Keywords: C-jun N-terminal kinase; Lipopolysaccharide; 

Microglia; Mutation; NADPH oxidase; Nitric oxide; 

Peroxiredoxin V; Reactive oxygen species; Signal 

transduction 


Article 19 

Synthesis and characterization of various-shaped 

C60 microcrystals using alcohols as antisolvents 

J Phys Chem C. 2010 Aug; 114(30):12976-81. 

Jeong J, Kim WS, Park SI, Yoon TS, Chung BH * 



Solvent-based synthetic methods of fullerene nano/microstructures 

are known to enhance and utilize unique optical 

and electrical properties of fullerene structures. Here, we 

report the systematic synthesis and characterization of various-shaped 

fullerene microcrystals using alcohols as antisolvents 

in drowning-out crystallization. The microcrystals 

are formed in one-, two-, and three-dimensional structures 

depending on the alcohol type, and the size and shape of 

the microcrystals are also varied by the C60 concentration 

and the volume ratio of the solvents. X-ray diffraction patterns 

demonstrate that the crystalline structures differ from the 

chain lengths of alcohols. It is suggested that the formation 

mechanisms are driven by supersaturation related to the C60 

solubility in alcohols. This crystallization could allow for 

production of C60 microcrystals with the desired shape and 

crystalline structure, leading to potential applications in optoelectronics 

and photoconducting devices. 

Keywords: Anti-solvents; Crystalline structure; Formation 

mechanism; Fullerene structure; Optical and 

electrical properties; Potential applications; 

Synthetic methods; Three-dimensional structure 

Article 20 

Addressable micropatterning of multiple proteins 

and cells by microscope projection photolithography 

based on a protein friendly photoresist 

Langmuir. 2010 Jul; 26(14):12112-8. 

Kim M, Choi JC, Jung HR, Katz JS, Kim MG * , Doh J 

* Correspondence: mgkim@kribb.re.kr 


We report a new method for the micropatterning of multiple 

proteins and cells with micrometer-scale precision. 

Microscope projection photolithography based on a new protein-friendly 

photoresist, poly(2,2-dimethoxy nitrobenzyl 

methacrylate-r-methyl methacrylate-r-poly(ethylene glycol) 

methacrylate) (PDMP), was used for the fabrication of multicomponent 

protein/cell arrays. Microscope projection lithography 

allows precise registration between multiple patterns 

as well as facile fabrication of microscale features. Thin 

films of PDMP became soluble in near-neutral physiological 

buffer solutions upon UV exposure and exhibited excellent 

resistance to protein adsorption and cell adhesion. By harnessing 

advantages in microscope projection photolithography 

and properties of PDMP thin films, we could successfully 

fabricate protein arrays composed of multiple proteins. 

Furthermore, we could extend this method for the patterning 

of two different types of immune cells for the potential 

study of immune cell interactions. This technique will in 

general be useful for protein chip fabrication and 

high-throughput cell-cell communication study. 

PMID:20565061 

Keywords: Cell-cell communications; Facile fabrication; 

Methyl methacrylates; Micro patterning; 

Poly(ethylene glycol) methacrylate; Projection 

lithography; Protein adsorption; Protein arrays; 

Protein chip; UV exposure 


Article 21 

Analysis of a genome-wide set of gene deletions 

in the fission yeast Schizosaccharomyces pombe 

Nat Biotechnol. 2010 Jun; 28(6):617-23. 

Kim DU, Hayles J, Kim D, Wood V, Park HO, Won M, 

Yoo HS, Duhig T, Nam M, Palmer G, Han S, Jeffery L, 

Baek ST, Lee H, Shim YS, Lee M, Kim L, Heo KS, Noh 

EJ, Lee AR, Jang YJ, Chung KS, Choi SJ, Park JY, Park 

Y, Kim HM, Park SK, Park HJ, Kang EJ, Kim HB, Kang 

HS, Park HM, Kim K, Song K, Song KB, Nurse P, Hoe 

KL * 

* Correspondence: kwanghoe@kribb.re.kr 


We report the construction and analysis of 4,836 heterozygous 

diploid deletion mutants covering 98.4% of the fission 

yeast genome providing a tool for studying eukaryotic 

biology. Comprehensive gene dispensability comparisons 

with budding yeast--the only other eukaryote for which a 

comprehensive knockout library exists--revealed that 83% 

of single-copy orthologs in the two yeasts had conserved 

dispensability. Gene dispensability differed for certain pathways 

between the two yeasts, including mitochondrial translation 

and cell cycle checkpoint control. We show that fission 

yeast has more essential genes than budding yeast and that 

essential genes are more likely than nonessential genes to 

be present in a single copy, to be broadly conserved and 

to contain introns. Growth fitness analyses determined sets 

of haploinsufficient and haploproficient genes for fission 

yeast, and comparisons with budding yeast identified specific 

ribosomal proteins and RNA polymerase subunits, which 

may act more generally to regulate eukaryotic cell growth. 

PMID: 20473289 

Keywords: Cell cycle; Deletion mutants; Essential gene; 

Eukaryotic cells; Fission yeast; Gene deletion; 

Orthologs; Ribosomal proteins; RNA polymerase; 

Schizosaccharomyces pombe 

Article 22 

Efficient selection of IgG Fc domain-binding peptides 

fused to fluorescent protein using E. coli 

expression system and dot-blotting assay 

Peptides. 2010 Feb; 31(2):202-6. 

Jeong YJ, Kang HJ, Bae KH, Kim MG * , Chung SJ * 

* Correspondence: mgkim@kribb.re.kr sjchung@kribb.re.kr 



Antibody purification technology is of particular industrial 

importance due to the rapidly increasing use of antibodies 

in protein purification, diagnostic and therapeutic 

applications. Such purification has mostly relied on affinity 

chromatography using Protein A or Protein G as affinity 

ligands. Several synthetic ligands have also been developed 

to overcome the disadvantages associated with protein affinity 

ligands, which include high cost, low stability and possible 

contamination if the proteins have been expressed in bacteria. 

In the present study, a convenient selection method for new 

peptides binding to the IgG Fc domain was developed. The 

method includes the construction of a DNA library fused 

to the 5'-position of the eGFP gene expressed from a constitutive 

vector, expression of the library in Escherichia coli, 

fluorescence-based screening, and determination of the antibody-binding 

affinities of selected peptides using surface 

plasmon resonance. With this method, five novel peptides 

were identified as new affinity ligands for the IgG Fc domain, 

and the binding affinities were appropriate for antibody 

purification. This method is a convenient alternative to phage 

or bacterial surface display and can be used in the routine 

biochemistry laboratory. 

PMID: 20025916 

Keywords: Escherichia coli; Goats; Green fluorescent 

proteins; Immunoblotting; Immunoglobulin Fc 

fragments; Immunoglobulin G; Oligopeptides; 

Protein binding; Recombinant fusion proteins; 

Surface plasmon resonance 


Article 23 

Poly(arylene ether)s with trifluoromethyl groups 

via meta-activated nitro displacement reaction 

Polymer. 2010 Sep; 51(20):4477-83. 

Chung IS * , Kim KH, Lee YS, Kim SY 

* Correspondence: cis123@kribb.re.kr 


New poly(arylene ether)s with pendent trifluoromethyl 

groups were synthesized from 2,2'-bis(trifluoromethyl)-4,4'-dinitro-1,1'-biphenyl 

with several 

bisphenols. The nitro leaving group activated by the trifluoromethyl 

group at meta position was quantitatively displaced 

with phenolate ions, resulting in high molecular weight 

polymers. The quantum mechanical calculation of the energy 

state suggested that the nitro displacement reaction activated 

by the trifluoromethyl group at meta position is an energetically 

favorable process. The polymers having weight average 

molecular weight of 42,100-95,000 g/mol and molecular 

weight distribution of 2.65-2.95 were obtained. The polymers 

were amorphous and dissolved in a wide range of organic 

solvents. Transparent and flexible films were obtained by 

solution casting. The resulting polymers are thermally stable, 

and Tgs of the polymers are in the range of 176-199 °C 

depending on their molecular structure. All of the synthesized 

polymers show refractive indices in the range of 1.592-1.624 

with low birefringence below 0.006. 

Keywords: Bisphenols; Displacement reactions; Flexible 

films; Meta positions; Poly(arylene ether)s; 

Quantum-mechanical calculation; SNAr reaction; 

Synthesized polymers; Trifluoromethyl group 

Article 24 

Large-scale expression in Escherichia coli and 

efficient purification of precursor and active caspase-7 

by introduction of thrombin cleavage sites 

Protein Expr Purif. 2010 Jan; 69(1):29-33. 

Lee YM, Kang HJ, Jang M, Kim M, Bae KH * , Chung SJ * 

* Correspondence: khbae@kribb.re.kr sjchung@kribb.re.kr 



Caspases are a family of cysteine proteases that have critical 

roles in the apoptotic pathway. Caspase-7 is a well-known 

apoptotic effector that cleaves a variety of cellular substrates, 

and is known to be an important target in the treatment 

of many diseases. For efficient research, large amounts of 

the protein are required. However, it has been difficult to 

obtain sufficient quantities of either the precursor or active 

caspase-7 from Escherichia coli strain. In the present study, 

we constructed thrombin-activatable caspase-7 precursors by 

changing the auto-activation sites of the caspase-7 precursor 

into sequences susceptible to thrombin cleavage. These engineered 

precursors were highly expressed as soluble proteins 

in E. coli, and were easily purified by affinity chromatography 

(to levels of 10-15 mg per liter of E. coli culture), and 

were then readily activated by treatment with thrombin. In 

vitro cleavage assays and kinetic analyses revealed that the 

engineered active caspase-7 proteins had characteristics similar 

to those of wild-type caspase-7. This novel method is 

valuable for obtaining both precursor and active caspase-7, 

thereby contributing to the development of caspase-7-specific 

drugs to treat various diseases, including cancer and neurodegenerative 

conditions. 

PMID: 19782754 

Keywords: Biocatalysis; Blotting, caspase 7; Enzyme 

activation; Escherichia coli; HL-60 cells; Kinetics; 

Mutant proteins; Poly(ADP-ribose) polymerases; 

Protein precursors; Protein structure, specificity; 

Thrombin 


Article 25 

A new palm-sized surface plasmon resonance 

(SPR) biosensor based on modulation of a light 

source by a rotating mirror 

Sensor Actuator B. 2010; 150(1):1-6. 

Shin YB, Kim HM, Jung Y, Chung BH * 



A novel surface plasmon resonance (SPR) sensing scheme 

was devised to develop a palm-sized SPR biosensor device. 

In this system, the beam from a diode laser (as the incident 

light source) is modulated using a rotating mirror. The reflected 

light from the gold chip is then captured using a 

CMOS image sensor, controlled by a notebook PC via a 

USB interface. This provides a portable POCT SPR sensor 

device which enables label-free and real-time analyses. This 

method can also eliminate the deterioration in image quality 

of the reflected laser light, originating from the coherency 

of the laser source. The sensing response of the system to 

the bulk refractive index was calibrated using various concentrations 

of glycerol solution. As a result, the SPR sensor 

was able to detect a 

∼2.5 × 10-6 RIU change in the refractive 

index of the solution without implementing any of data processing 

techniques. The performance of the sensor was tested 

by monitoring the binding of PSA to its antibody in real-time 

to verify its potential applicability in analyzing biomolecular 

interactions. The results obtained from a series of tests confirmed 

the practicality of the sensor for the on-site detection 

of a variety of substances in biology, diagnosis, the environment, 

and defense. 

Keywords: Biomolecular interactions; Biosensor; CMOS 

image sensor; Diode lasers; Handheld; Modulation 

by rotating mirror; SPR biosensor; Surface plasmon 

resonance (SPR); USB interface 

Article 26 

Monitoring of C-reactive protein using ion sensitive 

field effect transistor biosensor 

Sensor Lett. 2010 Apr; 8(2):233-7. 

Park HJ, Kim SK, Park K, Yi SY, Chung JW, Chung BH, 

Kim M * 

* Correspondence: kimm@kribb.re.kr 


An ion sensitive field effect transistor (ISFET) as a transducer, 

more precisely an immunologically modified-FET 

(immuno-FET) device, was utilized for the detection of the 

C-reactive protein (CRP), a potent marker for inflammation 

or cardiac risk. The ISFET biosensor investigated in this 

study was fabricated via a standard CMOS process. Anti-CRP 

monoclonal antibody was covalently attached to the gate 

surface using the self-assembled monolayer (SAM) method. 

The response of anti- CRP antibody to CRP was evaluated 

via the measurement of the electrical features of the ISFET 

device. As a consequence, a considerable reduction in drain 

current was clearly noted upon CRP binding to anti-CRP 

antibody on the gate, which can be explained by the charge 

effect, in which negatively charged CRP is predominantly 

responsible for the current drop in the n-type ISFET. The 

FET measurement was also verified by surface plasmon resonance 

(SPR) analysis. Collectively, our data convincingly 

showed that the FET-type biosensor is potentially applicable 

to the detection of CRP via antigen-antibody binding events 

on the gate surface. 

Keywords: Antigen-antibody binding; Antigen-antibody 

interaction; Biosensor; C-reactive protein; Charge 

effect; FET-type biosensors; Immuno-FET; ISFET; 

Standard CMOS process 


Article 27 

Signal amplification by enzymatic reaction in an 

immunosensor based on localized surface plasmon 

resonance (LSPR) 

Article 28 

A highly sensitive enzyme-amplified immunosensor 

based on a nanoporous niobium oxide 

(Nb2O5) electrode 

Sensors. 2010 Mar; 10(3):2045-53. 

Sensors. 2010 May; 10(5):5160-70. 

Lee TH, Lee SW, Jung JA, Ahn J, Kim MG, Shin YB * 

Lee CS, Kwon D, Yoo JE, Lee BG, Choi J, Chung BH * 

* Correspondence: ybshin@kribb.re.kr 




An enzymatic reaction was employed as a means to enhance 

the sensitivity of an immunosensor based on localized surface 

plasmon resonance (LSPR). The reaction occurs after intermolecular 

binding between an antigen and an antibody on 

gold nano-island (NI) surfaces. For LSPR sensing, the gold 

NI surface was fabricated on glass substrates using vacuum 

evaporation and heat treatment. The interferon- γ(IFN- γ) cap- 

ture antibody was immobilized on the gold NIs, followed 

by binding of IFN-γ to the antibody. Subsequently, a bio- 

tinylated antibody and a horseradish peroxidase (HRP) conjugated 

with avidin were simultaneously introduced. A solution 

of 4-chloro-1-naphthol (4-CN) was then used for precipitation; 

precipitation was the result of the enzymatic reaction 

catalyzed the HRP on gold NIs. The LSPR spectra were 

obtained after each binding process. Using this method, the 

enzyme-catalyzed precipitation reaction on the gold NI surface 

was found to effectively amplify the change in the 

signal of the LSPR immunosensor after intermolecular 

binding. 

Keywords: Enzyme-catalyzed precipitation; Gold 

nano-island; Immunosensor; Localized surface 

plasmon resonance (LSPR) 

We report on the development of an enzyme-amplified sandwich-type 

immunosensor based on a thin gold film sputtered 

on an anodic nanoporous niobium oxide (Au@Nb2O5) 

electrode. The electrocatalytic activity of enzymatically amplified 

electroactive species and a stable electrode consisting 

of Au@Nb2O5 were used to obtain a powerful signal amplification 

of the electrochemical immunobiosensor. The method 

using this electrochemical biosensor based on an Au@Nb2O5 

electrode provides a much better performance than those 

based on conventional bulk gold or niobium oxide electrodes. 

Our novel approach does not require any time-consuming 

cleaning steps to yield reproducible electrochemical signals. 

In addition, the strong adhesion of gold films on the niobium 

oxide electrodes offers a very stable substrate during electrochemical 

biosensing. Cyclic voltammetry measurements indicate 

that non-specific binding of proteins to the modified 

Au@Nb2O5 surface is sufficiently low to be ignored in 

the case of our novel system. Finally, we demonstrated the 

ability of the biosensor based on an Au@Nb2O5 offering 

the enhanced performance with a high resolution and 

sensitivity. Therefore, it is expected that the biosensor based 

on an Au@Nb2O5 has great potential for highly efficient 

biological devices. 

Keywords: Electrochemical biosensor; Enzyme; Gold film; 

Immunosensor; Nb2O5; Niobium oxide 


Article 29 

Proteolytic fluorescent signal amplification on 

gold nanoparticles for a highly sensitive and rapid 

protease assay 

Article 30 

HBx-induced reactive oxygen species activates 

hepatocellular carcinogenesis via dysregulation of 

PTEN/Akt pathway 

Small. 2010 Jan; 6(1):126-31. 

World J Gastroenterol. 2010 Oct; 16(39):4932-7. 

Kim JH, Chung BH * 

Ha HL, Yu DY * 





A new strategy for highly sensitive and rapid protease assay 

is developed by mediating proteolytic formation of oligonucleotide 

duplexes and using the duplexes for signal 

amplification. In the presence of matrix metalloprotease-2 

(MMP-2), fragmentation of the intact DNA-peptide on gold 

nanoparticles (GNP) by hydrolytic cleavage of a peptide 

bond within the substrate allows diffusion of DNA away 

from the GNP and the formation of a DNA/RNA heteroduplex, 

leading to digestion of RNA by RNase H. Because 

of the high quenching efficacy of GNP to the fluorophore 

in RNA and multiple digestions of the RNA, the fluorescence 

signal recovery is amplified. This method permits the assessment 

of the activity of MMP-2 at concentrations as low 

as 10 pM within 4 h. Compared with the reported protease 

nanosensors using quantum dots, GNP, and magnetic nanoparticles 

with the same peptide sequence, the assay time 

of this method is sixfold faster and the limit of detection 

is 100-fold more sensitive. The formulations for proteolytic 

formations of oligonucleotides duplexes for signal amplification 

on GNP could lead to the development of more sensitive 

and rapid protease assay techniques, thus extending the role 

of proteases as therapeutic targets and disease indicators. 

PMID: 19904765 

Keywords: Fluorescence signals; FRET; Gold nanoparticle; 

Heteroduplex; Hydrolytic cleavage; Limit of 

detection; Magnetic nanoparticles; Oligonucleotide 

duplexes; Protease assay; Quantum dot; Therapeutic 

targets 

AIM: To investigate the role of hepatitis B virus X-protein 

(HBx)-induced reactive oxygen species (ROS) on liver carcinogenesis 

in HBx transgenic mice and HepG2-HBx cells. 

METHODS: Cell growth rate was analyzed, and through 

western blotting, mitogenic signaling was observed. 

Endogenous ROS from wild and HBx transgenic mice and 

HepG2-Mock and HBx cells were assayed by FACScalibur. 

Identification of oxidized and reduced phosphatase and tensin 

homolog (PTEN) was analyzed through N-ethylmaleimide 

alkylation, nonreducing electrophoresis. 

RESULTS: We observed that the cell-proliferation-related 

phosphoinositide 3-kinase/Akt pathway is activated by HBx 

in vivo and in vitro. Increased ROS were detected by HBx. 

Tumor suppressor PTEN, via dephosphorylation of Akt, was 

oxidized and inactivated by increased ROS. Increased oxidized 

PTEN activated the mitogenic pathway through 

over-activated Akt. However, treatment with ROS scavenger 

N-acetyl cysteine can reverse PTEN to a reduced form. 

Endogenously produced ROS also stimulated HBx 

expression. 

CONCLUSION: HBx induced ROS promoted Akt pathways 

via oxidized inactive PTEN. HBx and ROS maintained a 

positive regulatory loop, which aggravated carcinogenesis. 

PMID: 20954279 

Keywords: Akt; Flow cytometry; Hep G2 cells; Hepatitis 

B virus X protein; Hepatocellular carcinoma; Liver 

neoplasms; Phosphatase and tensin homolog; PTEN 

Phosphohydrolase; Reactive oxygen species; Signal 

Transduction 


Article 31 

Oxidative stress and antioxidants in hepatic pathogenesis 

World J Gastroenterol. 2010 Dec; 16(48):6035-43. 

Ha HL, Shin HJ, Feitelson MA, Yu DY * 



Long term hepatitis B virus (HBV) infection is a major 

risk factor in pathogenesis of chronic liver diseases, including 

hepatocellular carcinoma (HCC). The HBV encoded proteins, 

hepatitis B virus X protein and preS, appear to contribute 

importantly to the pathogenesis of HCC. Both are associated 

with oxidative stress, which can damage cellular molecules 

like lipids, proteins, and DNA during chronic infection. 

Chronic alcohol use is another important factor that contributes 

to oxidative stress in the liver. Previous studies reported 

that treatment with antioxidants, such as curcumin, silymarin, 

green tea, and vitamins C and E, can protect DNA from 

damage and regulate liver pathogenesis-related cascades by 

reducing reactive oxygen species. This review summarizes 

some of the relationships between oxidative stress and liver 

pathogenesis, focusing upon HBV and alcohol, and suggests 

antioxidant therapeutic approaches. 

PMID:21182217 

Keywords: Alcohol; Antioxidant; Carcinoma, 

hepatocellular; Chronic liver disease; Hepatitis B 

virus; Hepatitis B virus X protein; Liver neoplasms; 

Oxidative stress; Risk factors; Trans-activators 


2010 




Division of Translational Research 




Korea Research Institute of Bioscience and Biotechnology 


www.kribb.re.kr

Article 32 

Development of a nanoparticle-based FRET sensor 

for ultrasensitive detection of phytoestrogen 

compounds 

Analyst. 2010 Nov; 135(11):2879-86. 

Dumbrepatil AB, Lee SG, Chung SJ, Lee MG, Park BC, 

Kim TJ, Woo EJ * 

* Correspondence: ejwoo@kribb.re.kr 


Phytoestrogens are plant compounds that mimic the actions 

of endogenous estrogens. The abundance of these chemicals 

in nature and their potential effects on health require the 

development of a convenient method to detect 

phytoestrogens. We have developed a nanoparticle (NP)-conjugated 

FRET probe based on the human estrogen receptor 

α 

(ER) ligand-binding domain (LBD) to detect 

phytoestrogens. The NP-conjugated FRET probe showed fluorescence 

signals for genistein, resveratrol and daidzein compounds 

with Δ ratios of 1.65, 2.60 and 1.37 respectively, 

which are approximately six times greater compared to individual 

FRET probes. A significantly higher signal for resveratrol 

versus genistein and daidzein indicates that the 

probe can differentiate between antagonistic phytoalexin substances 

and agonistic isoflavone compounds. NP-conjugated 

probes demonstrated a wide dynamic range, ranging from 

10(-18) to 10(-1) M with EC(50) values of 9.6 × 10(-10), 

9.0 × 10(-10) and 9.2 × 10(-10) M for genistein, daidzein 

and resveratrol respectively, whereas individual probes detected 

concentrations of 10(-13) to 10(-4) M for phytoestrogens 

compounds. The time profile revealed that the 

NP-conjugated probe is stable over 30 h and there is not 

a significant deviation in the FRET signal at room 

temperature. These data demonstrate that conjugation of a 

FRET probe to nanoparticles is able to serve as an effective 

FRET sensor for monitoring bioactive compounds with significantly 

increased sensitivity, dynamic range and stability. 

PMID: 20877819 

Article 33 

Inhibitory activities of anthraquinones from Rubia 

akane on phosphatase regenerating liver-3 

Arch Pharm Res. 2010 Nov; 33(11):1747-51. 

Moon MK, Han YM, Lee YJ, Lee LH, Yang JH, Kwon 

BM * , Kim DK 

* Correspondence: kwonbm@kribb.re.kr 


The methanolic extract of the roots of Rubia akane 

(Rubiaceae) was found to show inhibitory activity on phosphatase 

of regenerating liver-3 (PRL-3). Bioassay-guided 

fractionation of the methanolic extract resulted in the isolation 

of two anthraquinone compounds, 2-methyl-1,3,6-trihydroxy-9,10-anthraquinone-3-O-(6'-O-acetyl)-α-rhamnosyl(1 

→2)-β-glucoside and 2-methyl-1,3,6-trihydroxy-9,10-an- 

thraquinone, as inhibitors on PRL-3. These compounds inhibited 

PRL-3 in a dose-dependent manner with IC₅₀ 

values 

of 5.2 and 1.3 

PMID:21116777 

μg/mL, respectively. 

Keywords: Anthraquinones; Antineoplastic agents; Cell 

line, tumor; Cell proliferation; Glucosides; Neoplasm 

proteins; Plant roots; Protein tyrosine phosphatases; 

Rubia akane, rubiaceae 

Keywords: Binding sites; Estrogen receptor 

resonance energy; Fluorescent dyes; 

α; Fluorescence 

Genistein; 

Isoflavones; Ligands; Nanoparticles; 

Phytoestrogens; Sensitivity and specificity; Stilbenes 


Article 34 

Tristetraprolin regulates the stability of HIF-1α 

mRNA during prolonged hypopia 

Biochem Biophys Res Commun. 2010 Jan; 391(1):963-8. 

Kim TW, Yim S, Choi BJ, Jang Y, Lee JJ, Sohn BH, Yoo 

HS, Yeom YI * , Park KC * 

* Correspondence: yeomyi@kribb.re.kr kpark@kribb.re.kr 


Hypoxia-inducible factor-1 (HIF-1) is a transcription factor 

involved in the cancer cell adaptation to hypoxia, a leading 

cause of tumor malignancy. Thus, control of HIF-1α ex- 

pression may assist in treatment of cancer. The expression 

of HIF-1α 

is finely regulated via alterations in not only 

HIF-1α 

protein stability but also mRNA stability. However, 

the molecular mechanisms of regulation of HIF-1α 

mRNA 

stability have not yet been fully elucidated. Here, we show 

that tristetraprolin (TTP) protein, of which the mRNA expression 

level is downregulated in most of hepatocellular 

carcinoma tissues, bound directly to the 3'-UTR of HIF-1α 

mRNA containing eight putative TTP-binding motifs, 

AU-rich elements (AUUUA), to downregulate stability. 

Furthermore, TTP expression was induced in hypoxic cells, 

and overexpression of TTP repressed the hypoxic induction 

of HIF-1α 

protein. Taken together, these data suggest that 

TTP is a modulator of HIF-1α 

expression during hypoxia 

and may play a physiological role in regulation between 

cellular adaptation and apoptosis in prolonged hypoxia. In 

addition, cancer cells may benefit from the downregulation 

of TTP, which subsequently increases HIF-1α 

expression 

and assists with the adaptation of cancer cells to hypoxia. 

PMID: 19962963 

Keywords: AU-rich element; Carcinoma, hepatocellular; 

Cell hypoxia; HIF-1 α; Liver neoplasms; Response 

elements; RNA stability; Tristetraprolin; TTP; UTR 

Article 35 

Increase of RhoB in 

γ-radiation-induced apoptosis 

is regulated by c-Jun N-terminal kinase in Jurkat 

T cells 

Biochem Biophys Res Commun. 2010 Jan; 391(2):1182-6. 

Kim CH, Won M, Choi CH, Ahn J, Kim BK, Song KB, 

Kang CM, Chung KS * 

* Correspondence: kschung@kribb.re.kr 


The Ras-related small GTP-binding protein RhoB is known 

to be a pro-apoptotic protein and immediate-early inducible 

by genotoxic stresses. In addition, JNK activation is known 

to function in 

γ-radiation-induced apoptosis. However, it 

is unclear how JNK activation and 

γ-radiation-dependent 

RhoB induction are related. Here we verified the relationship 

between JNK activation and RhoB induction. RhoB induction 

by 

γ-radiation occurred at the transcriptional level and tran- 

scriptional activation of RhoB was concomitant with an increase 

in RhoB protein. 

γ-Radiation-induced RhoB ex- 

pression was markedly attenuated by pretreatment with a 

JNK-specific inhibitor, SP600125, but not by a p38 MAPK 

inhibitor, SB203580. Inhibition of JNK caused a decrease 

in early apoptotic cell death that correlated with RhoB 

expression. However, PI3K inhibition had no significant effects, 

indicating that the AKT survival pathway was not 

involved. The siRNA knockdown of JNK resulted in a decrease 

in RhoB expression and the siRNA knockdown of 

RhoB restored cell growth even in the 

γ-irradiated cells. 

These results suggest that RhoB regulation involves the JNK 

pathway and contributes to the early apoptotic response of 

Jurkat T cells to 

PMID:19995557 

γ-radiation. 

Keywords: Apoptosis; Gamma rays; 

γ-Radiation; JNK; 

Jurkat; Protein kinase B; RhoB; Small interfering; 

T-Lymphocytes 


Article 36 

Oxidative stress-enhanced SUMOylation and aggregation 

of ataxin-1: Implication of JNK pathway 

Article 37 

Molecular interaction between HAX-1 and XIAP 

inhibits apoptosis 

Biochem Biophys Res Commun. 2010 Mar; 393(2):280-5. 

Biochem Biophys Res Commun. 2010 Mar; 393(4):794-9. 

Ryu J, Cho S, Park BC * , Lee DH 

* Correspondence: parkbc@kribb.re.kr 


Although the polyglutamine protein ataxin-1 is modified by 

SUMO at multiple sites, the functions of such modification 

or how it is regulated are still unknown. Here we report 

that SUMO-1 or Ubc9 over-expression stimulated the aggregation 

of ataxin-1 and that oxidative stress, such as hydrogen 

peroxide treatment, further enhanced SUMO conjugation 

and aggregation of ataxin-1. Accordingly, co-treatment with 

antioxidant N-acetyl-cysteine attenuated the effect of oxidative 

stress. Ataxin-1, which can activate c-Jun N-terminal 

kinase (JNK) pathway by itself, strongly associated with 

apoptosis signal-regulating kinase 1 (ASK1) while not interacting 

with JNK. Finally, treatment of JNK-specific inhibitor 

caused a reduction in the oxidant-enhanced SUMOylation 

and aggregation of ataxin-1. Together these results indicate 

that SUMO modification of ataxin-1 promotes the aggregation 

of ataxin-1 and that oxidative stress and JNK pathway 

play roles in this process. 

PMID:20132795 

Keywords: ASK1; Ataxin-1; Cell line; JNK; Nerve tissue 

proteins; Oxidative stress; Polyglutamine diseases; 

SUMO-1 

Kang YJ, Jang M, Park YK, Kang S, Bae KH, Cho S, Lee 

CK, Park BC, Chi SW * , Park SG * 

* Correspondence: swchi@kribb.re.kr sgpark@kribb.re.kr 


Caspase-3 is an important executor caspase that plays an 

essential role in apoptosis. Recently, HS1-associated protein 

X1 (HAX-1) was found to be a substrate of caspase-3. 

Although HAX-1 has serve multifunctional roles in cellular 

functions such as cell survival and calcium homeostasis, 

the detailed functional mechanism of HAX-1 remains still 

unclear. In this study, we performed proteomic experiments 

to identify the HAX-1 interactome. Through immunoprecipitation 

and 2D gel electrophoresis, we identified 

X-linked inhibitor of apoptosis protein (XIAP) as a novel 

HAX-1-interacting protein. By performing the GST 

pull-down assay, we defined the interaction domains in 

HAX-1 and XIAP, showing that HAX-1 binds to the BIR2 

and BIR3 domains of XIAP whereas XIAP binds to the 

C-terminal domain of HAX-1. In addition, surface plasma 

resonance experiments showed that both BIR2 and BIR3 

domains of XIAP bind to HAX-1 with affinity similar to 

that of full-length XIAP, indicating that either domain is 

necessary and sufficient for tight binding to HAX-1. Taken 

together with the observation that HAX-1 suppresses the 

polyubiquitination of XIAP, the cell viability assay results 

suggest that the formation of the HAX-1-XIAP complex 

inhibits apoptosis by enhancing the stability of XIAP against 

proteosomal degradation. 

PMID: 20171186 

Keywords: Apoptosis; Caspase 3; Cell line; HAX-1; Protein 

interaction; Proteomics; Ubiquitination; XIAP 


Article 38 

NDRG2 is one of novel intrinsic factors for regulation 

of IL-10 production in human myeloid cell 

Biochem Biophys Res Commun. 2010 Jun; 396(3):684-90. 

Choi SC, Kim KD, Kim JT, Oh SS, Yoon SY, Song EY, 

Lee HG, Choe YK, Choi I, Lim JS, Kim JW * 

* Correspondence: wjkim@kribb.re.kr 


Article 39 

LW6, a novel HIF-1 inhibitor, promotes proteasomal 

degradation of HIF-1α via upregulation of 

VHL in a colon cancer cell line 

Biochem Pharmacol. 2010 Oct; 80(7):982-9. 

Lee K, Kang JE, Park SK, Jin Y, Chung KS, Kim HM, 

Lee K, Kang MR, Lee MK, Song KB, Yang EG, Lee JJ, 

Won M * 

* Correspondence: misun@kribb.re.kr 

N-myc downstream-regulated gene 2 (NDRG2) implicated 

in cellular growth and differentiation was previously reported 

as it is specifically expressed in primary and in vitro-differentiated 

dendritic cells (DCs) from monocytes and CD34(+) 

progenitor cells. However, its function has yet to be investigated 

in DCs. Here, the novel NDRG2 function about modulation 

of cytokines in DC was observed in this study. The 

secretion of IL-10 was not found in the monocyte-derived 

DC cells with high level of NDRG2 expression, but IL-10 

was abundantly secreted up to 1ng/ml in the monocyte-derived 

macrophages with low level of NDRG2 expression, 

and further confirmed that the expression of IL-10 

was dramatically increased in NDRG2-silenced DCs under 

presence of LPS, and significantly reduced in the 

NDRG2-overexpressed U937 cells under stimulation of 

PMA. The secretion of IL-12p70 was significantly reduced 

in the siNDRG2 introduced DC cells. The intracellular signaling 

of IL-10 secretion was markedly inhibited by SB203580, 

inhibitor of p38 MAPK, in the LPS-activated DCs and phosphorylation 

of p38 MAPK was decreased in the NDRG2 

introduced U937 cells under PMA-stimulation. Taken together, 

NDRG2 might have a pivotal role as one of intrinsic 

factors for the modulation of p38 MAPK phosphorylation, 

and subsequently involve in controlling of IL-10 production. 

PMID: 20438703 

Keywords: DC differentiation; IL-10; Myeloid cell; 

NDRG2 (N-myc downstream-regulated gene 2); p38 

MAPK; U937 cell line 


Hypoxia-inducible factor HIF-1 is responsible for radiation 

resistance and poor prognosis in cancer therapy. As part 

of our drug discovery program, a novel HIF inhibitor, LW6, 

was identified as a small compound that inhibits the accumulation 

of HIF-1 α. We found that LW6 decreased HIF-1α 

protein expression without affecting HIF-1β 

expression. 

MG132, a proteasome inhibitor, protected HIF-1α 

from 

LW6-induced proteasomal degradation, indicating that LW6 

affects the stability of the HIF-1α 

protein. We found that 

LW6 promoted the degradation of wild type HIF-1 α, but 

not of a DM-HIF-1 α with modifications of P402A and P564A, 

at hydroxylation sites in the oxygen-dependent degradation 

domain (ODDD). LW6 did not affect the activity of prolyl 

hydroxylase (PHD), but induced the expression of von 

Hippel-Lindau (VHL), which interacts with prolyl-hydroxylated 

HIF-1α 

for proteasomal degradation. In the presence 

of LW6, knockdown of VHL did not abolish HIF-1 α protein 

accumulation, indicating that LW6 degraded HIF-1α via regulation 

of VHL expression. In mice carrying xenografts of 

human colon cancer HCT116 cells, LW6 demonstrated strong 

anti-tumor efficacy in vivo and caused a decrease in HIF-1α 

expression in frozen-tissue immunohistochemical staining. 

These data suggest that LW6 may be valuable in the development 

of a HIF-1α 

inhibitor for cancer treatment. 

PMID:20599784 

Keywords: (aryloxyacetylamino)Benzoic acid; Colonic 

Neoplasms; HIF-1 α; Hypoxia; Prolyl hydroxylation; 

Von-Hippel-Lindau 


Article 40 

Gene delivery using a derivative of the protein 

transduction domain peptide, K-Antp 

Article 41 

OIP5 is a highly expressed potential therapeutic 

target for colorectal and gastric cancers 

Biomaterials. 2010 Mar; 31(7):1858-64. 

BMB Rep. 2010 May; 43(5):349-54. 

Min SH, Kim DM, Kim MN, Ge J, Lee DC, Park IY, Park 

KC, Hwang JS, Cho CW, Yeom YI * 

* Correspondence: yeomyi@kribb.re.kr 


Due to their intracellular permeability, protein transduction 

domains (PTDs) have been widely used to deliver proteins 

and peptides to mammalian cells. However, their performance 

in gene delivery has been relatively poor. To improve 

the efficiency of PTD-mediated gene delivery, we synthesized 

a new peptide, KALA-Antp (K-Antp), which contains 

the sequences for PTD of the third 

α-helix of Antennapedia 

(Antp) homeodomain and the fusogenic peptide KALA. In 

this configuration, Antp is designed to provide the cell permeation 

capacity and nuclear localization signal, while the 

KALA moiety to promote cellular entry of the peptide-DNA 

complex. An optimal K-Antp/DNA formula was nearly 

400-600 fold more efficient than Antp or poly-lysine-Antp 

(L-Antp) in gene delivery, and comparable or superior to 

a commercial liposome. The K-Antp-mediated plasmid DNA 

transfection not only exhibited temperature sensitivity, reflecting 

the involvement of an endocytosis-mediated gene 

transfer mechanism similar to other known PTDs, but also 

temperature insensitivity, suggesting the role of an energy-independent 

mechanism. Incorporation of an endosomolytic 

polymer polyethylenimine (PEI) into the system or treatment 

with chloroquine further increased the efficiency of 

K-Antp-mediated gene delivery. These results demonstrate 

the potential of the combinatorial use of KALA, Antp and 

PEI in the development of efficient PTD-derived gene 

carriers. 

PMID: 19954838 

Chun HK, Chung KS, Kim HC, Kang JE, Kang MA, Kim 

JT, Choi EH, Jung KE, Kim MH, Song EY, Kim SY, Won 

M * , Lee HG * 

* Correspondence: misun@kribb.re.kr hglee@kribb.re.kr 


Previously, we reported that overexpression of Opa 

(Neisseria gonorrhoeae opacity-associated)-interacting protein 

5 (OIP5) caused multi-septa formation and growth defects, 

both of which are considered cancer-related 

phenotypes. To evaluate OIP5 as a possible cancer therapeutic 

target, we examined its expression level in 66 colorectal 

cancer patients. OIP5 was upregulated about 3.7-fold in tumors 

and over 2-fold in 58 out of 66 colorectal cancer patients. 

Knockdown of OIP5 expression by small interfering RNA 

specific to OIP5 (siOIP5) resulted in growth inhibition of 

colorectal and gastric cancer cell lines. Growth inhibition 

of SNU638 by siOIP5 caused an increase in sub-G1 DNA 

content, as measured by flow cytometry, as well as an apoptotic 

gene expression profile. These results indicate that 

knockdown of OIP5 may induce apoptosis in cancer cells. 

Therefore, we suggest that OIP5 might be a potential cancer 

therapeutic target, although the mechanisms of OIP5-induced 

carcinogenesis should be elucidated. 

PMID: 20510019 

Keywords: Apoptosis; Chromosomal proteins; Colorectal 

cancer; Gastric cancer; Gene expression profiling; 

LINT-25; OIP5; Therapeutic target 

Keywords: Antennapedia peptide (Antp); Fusogenic 

peptide; Gene delivery; KALA; KALA-Antp 

(K-Antp); Protein transduction domain (PTD) 


Article 42 

Epigenetic modification of retinoic acid-treated 

human embryonic stem cells 

Article 43 

Obovatol attenuates microglia-mediated neuroinflammation 

by modulating redox regulation 

BMB Rep. 2010 Dec; 43(12):830-5. 

Br J Pharmacol. 2010 Apr; 159(8):1646-62. 

Cheong HS, Lee HC, Park BL, Kim H, Jang MJ, Han YM, 

Kim SY, Kim YS * , Shin HD 

Ock J, Han HS, Hong SH, Lee SY, Han YM, Kwon BM * , 

Suk K 

* Correspondence: yongsung@kribb.re.kr 


* Correspondence: kwonbm@kribb.re.kr 


Epigenetic modification of the genome through DNA methylation 

is the key to maintaining the differentiated state of 

human embryonic stem cells (hESCs), and it must be reset 

during differentiation by retinoic acid (RA) treatment. A 

genome-wide methylation/gene expression assay was performed 

in order to identify epigenetic modifications of 

RA-treated hESCs. Between undifferentiated and RA-treated 

hESCs, 166 differentially methylated CpG sites and 2,013 

differentially expressed genes were discovered. Combined 

analysis of methylation and expression data revealed that 

19 genes (STAP2, VAMP8, C10orf26, WFIKKN1, ELF3, 

C1QTNF6, C10orf10, MRGPRF, ARSE, LSAMP, CENTD3, 

LDB2, POU5F1, GSPT2, THY1, ZNF574, MSX1, SCMH1, 

and RARB) were highly correlated with each other. The results 

provided in this study will facilitate future investigations 

into the interplay between DNA methylation and gene expression 

through further functional and biological studies. 

PMID:21189161 

Keywords: Cell differentiation; CpG islands; DNA 

methylation; Epigenetic modification; Gene 

expression; Human embryonic stem cell; Retinoic 

acid 

BACKGROUND AND PURPOSE: Obovatol isolated from 

the medicinal herb Magnolia obovata exhibits a variety of 

biological activities. Here, the effect of obovatol and its 

mechanism of action on microglial activation, neuroinflammation 

and neurodegeneration were investigated. 

EXPERIMENTAL APPROACH: In microglial BV-2 cells 

stimulated with lipopolysaccharide (LPS), we measured nitric 

oxide (NO) and cytokine production, and activation of intracellular 

signalling pathways by reverse transcription-polymerase 

chain reaction and Western blots. Cell 

death was assayed in co-cultures of activated microglia (with 

bacterial LPS) and neurons and in LPS- induced neuroinflammation 

in mice in vivo. 

KEY RESULTS: Obovatol inhibited microglial NO production 

with an IC50 value of 10 μM. Obovatol also inhibited 

microglial expression of proinflammatory cytokines and inducible 

nitric-oxide synthase, which was accompanied by 

the inhibition of multiple signalling pathways such as nuclear 

factor κ B, signal transducers and activators of transcription 

1, and mitogen-activated protein kinases. In addition, obovatol 

protected cultured neurons from microglial toxicity and 

inhibited neuroinflammation in mice in vivo. One molecular 

target of obovatol in microglia was peroxiredoxin 2 (Prx2), 

identified by affinity chromatography and mass spectrometry. 

Obovatol enhanced the reactive oxygen species 

(ROS)-scavenging activity of Prx2 in vitro, thereby suppressing 

proinflammatory signalling pathways of microglia where 

ROS plays an important role. 

CONCLUSIONS AND IMPLICATIONS: Obovatol is not 

only a useful chemical tool that can be used to investigate 

microglial signalling, but also a promising drug candidate 

against neuroinflammatory diseases. Furthermore, our results 

indicate that Prx2 is a novel drug target that can be exploited 

for the therapeutic modulation of neuroinflammatory 

signalling. 

PMID:20397299 

Keywords: Biphenyl compounds; Coculture techniques; 

Microglia; Neuroinflammation; Neuroprotection; 

Obovatol; Peroxiredoxin 2 


Article 44 

Synthesis and biological evaluation of KRIBB3 

analogues on a proliferation of HCT-116 colorectal 

cancer cells 

Article 45 

Genome-wide identification of chemosensitive 

single nucleotide polymorphism markers in colorectal 

cancers 

Bull Kor Chem Soc. 2010 Dec; 31(12):3800-2. 

Cancer Sci. 2010 Apr; 101(4):1007-13. 

Lee S * , Kim J, Min JH, Yoon KS, Shin KD, Kwon BM, 

Han DC * 

Kim JC, Kim SY, Cho DH, Roh SA, Choi EY, Jo YK, 

Jung SH, Na YS, Kim TW, Kim YS * 

* Correspondence: sangku@kribb.re.kr dchan@kribb.re.kr 



KRIBB3 showed inhibition of proliferation of HCT-116 colorectal 

cancer cells with GI50 value of 0.1 

μM and showed 

6 times stronger inhibitory activity than nocodazol. 

Nocodazole is a well known anti-mitotic chemical and we 

used it as a control compound. We synthesized a series 

of diaryl isoxazole derivatives by modifying alkoxy and hydroxyl 

group in the aryl moiety of KRIBB3, and evaluated 

their antiproliferative activity on the proliferation of 

HCT-116 colorectal cancer cells. Inhibitory activity of diaryl 

isoxazole derivatives against proliferaction of HCT-116 colorectal 

cancer cells was evaluated by measurement of the 

amount of WST-1 formazan formed by adding cell proliferation 

reagent WST-1. The presence of free hydroxyl 

hydrogen in the B-aryl moiety of KRIBB3 analogues decreased 

the efficiency of antiproliferative activity. In conclusion, 

analogues of KRIBB3 were synthesized and their 

inhibitory activities on proliferaction of HCT-116 colorectal 

cancer cells were evaluated. 

Keywords: Anti-mitotic; HCT-116 colorectal cancer cells; 

Inhibition; Isoxazole; KRIBB3; Proliferation; SAR 



Improved methods for predicting chemoresponsiveness involving 

the identification of polymorphic markers is highly 

desirable, considering narrow therapeutic index and frequent 

resistance to anti-cancer regimens. The genome-wide screening 

of chemosensitive single nucleotide polymorphisms 

(SNPs) was undertaken in association with in vitro chemosensitivity 

assays in 104 colorectal cancer patients for the 

initial screening step. Allele frequency, linkage disequilibrium, 

potential function, and Hardy-Weinberg equilibrium 

of the candidate SNPs were then determined for the 

identifying step. Finally, clinical association analysis in the 

other 260 evaluable patients or cell viability assays of transfected 

RKO cells was used to verify candidate SNPs for 

the validation step. In total, 12 SNPs to six regimens were 

initially chosen during the screening and identifying steps. 

In patients receiving fluoropyrimidine-based adjuvant chemotherapy, 

the substitution alleles of GPC5 rs553717 (AA) 

correlated significantly with tumor recurrence and shorter 

disease-free survival (P = 0.019 and 0.023, respectively). 

Interestingly, RKO cells expressing mutant GPC5 showed 

enhanced cell death in response to 5-FU in cytotoxicity 

assays. Patients that were homozygous for the reference alleles 

SSTR4 rs2567608 (AA) and EPHA7 rs2278107 (TT) 

showed lower disease control rates in response to irinotecan 

and oxaliplatin regimens, respectively, than those with substitution 

alleles (P = 0.022 and 0.014, respectively). Thus, 

we identified chemosensitive SNP markers using a novel 

three step process of genome-wide analysis consisting of 

in vitro screening, identification, and validation. The candidate 

chemosensitive SNP markers identified in our study, 

including those identified in vitro, can now be further verified 

in a large cohort study. 

PMID:20085586 

Keywords: Antineoplastic agents; Biological markers; 

Chemotherapy; Colorectal neoplasms; Disease-free 

survival; Fluorouracil; Gene frequency; Linkage 

disequilibrium; Polymorphism, Single nucleotide 


Article 46 

Identification of endothelial cell-specific molecule-1 

as a potential serum marker for colorectal 

cancer 

Article 47 

Frequent silencing of popeye domain-containing 

genes, BVES and POPDC3, is associated with 

promoter hypermethylation in gastric cancer 

Cancer Sci. 2010 Oct; 101(10):2248-53. 

Carcinogenesis. 2010 Sep; 31(9):1685-93. 

Ji NY, Kim YH, Jang YJ, Kang YH, Lee CI, Kim JW, 

Yeom YI, Chun HK, Choi YH, Kim JH, Kim JW, Lee HG * , 

Song EY * 

Kim M, Jang HR, Haam K, Kang TW, Kim JH, Kim SY, 

Noh SM, Song KS, Cho JS, Jeong HY, Kim JC, Yoo HS, 

Kim YS * 

* Correspondence: hglee@kribb.re.kr eysong@kribb.re.kr 




No ideal serum markers for screening colorectal cancer 

(CRC) have been identified. The aim of this study was to 

determine the usefulness of endothelial cell-specific molecule-1 

(ESM-1) as a serum marker for CRC. Illumina microarray 

was carried out to search CRC-related biomarkers. 

cDNA microarray detected that ESM-1 was one of the overexpressed 

genes in CRC. Overexpression of ESM-1 mRNA 

was confirmed in tissues of CRC by RT-PCR and real-time 

PCR. Immunohistochemical staining showed strong expression 

of ESM-1 in the cytoplasm of tumor cells. 

Overexpression of ESM-1 in human serum with CRC was 

found by Western blot analysis. For quantitative analysis 

of ESM-1 in serum, we determined the ESM-1 levels in 

serum specimens using an ELISA kit. We showed that the 

ESM-1 levels in the serum of patients with CRC were significantly 

elevated (70.1 ± 29.7 pg/mL) compared to healthy 

subjects (29.7 ± 14.9 pg/mL). The accuracy, sensitivity, and 

specificity of ESM-1 for CRC were 0.94, 99%, and 73%, 

respectively, by receiver operating characteristics curve 

analysis. The positive predictive value and negative predictive 

value were 63% and 95%, respectively. The likelihood 

ratios of a positive or negative test result were 73 and 0.27, 

respectively. When analyzed with a Cox regression model, 

a higher serum ESM-1 level ( ≥76.0 pg/mL) was correlated 

with poor prognosis. This study suggests that expression 

of ESM-1 is increased in tissue and serum of CRC patients 

and that ESM-1 can be used as a potential serum marker 

for the early detection of CRC. 

PMID: 20735430 

Keywords: Colorectal neoplasms; Neoplasm proteins; 

Proportional hazards models; Proteoglycans; 

Sensitivity and specificity; Tumor markers 

The Popeye domain-containing (POPDC) genes BVES, 

POPDC2 and POPDC3 encode proteins that regulate cell-cell 

adhesion and cell migration during development. Herein, 

we report the frequent downregulation of BVES and POPDC3 

by promoter hypermethylation in gastric cancer. POPDC 

expression in 11 gastric cancer cell lines and 96 paired gastric 

tumor and normal adjacent tissues was analyzed with quantitative 

reverse transcription-polymerase chain reaction. The 

methylation status of BVES and POPDC3 was analyzed with 

methylated DNA immunoprecipitation sequencing, bisulfite 

sequencing and pyrosequencing. Expression of BVES and 

POPDC3 was downregulated in 73% of the gastric cancer 

cell lines and in 69% (BVES) and 87% (POPDC3) of the 

gastric cancer tissues. The BVES and POPDC3 promoter 

regions were hypermethylated in the gastric cancer cell lines 

in which they were silenced. Combined treatment with a 

DNA methylation inhibitor and a histone deacetylase inhibitor 

strongly induced BVES and POPDC3 expression. 

BVES and POPDC3 were hypermethylated in 69% (BVES) 

and 64% (POPDC3) of the gastric cancer tissues. We knocked 

down POPDC3 expression with short hairpin RNAs and 

examined the consequences on cell migration and invasion. 

Knockdown of POPDC3 in SNU-216 cells caused increased 

cell migration and invasion. Thus, epigenetic inactivation 

of BVES and POPDC3 occurs frequently in gastric tumors 

and may promote gastric cancer cell migration and invasion. 

PMID: 20627872 

Keywords: Apoptosis; Cell adhesion; Cell proliferation; 

DNA methylation; Gene silencing; Histone 

deacetylase inhibitors; Membrane proteins; Muscle 

proteins; POPDC3; Stomach neoplasms 


Article 48 

Annexin A4 interacts with the NF- κB p50 subunit 

and modulates NF-κB transcriptional activity in 

a Ca2+-dependent manner 

Cell Mol Life Sci. 2010 Jul; 67(13):2271-81. 

Jeon YJ, Kim DH, Jung H, Chung SJ, Chi SW, Cho S, 

Lee SC, Park BC, Park SG * , Bae KH * 

Article 49 

Change in serum proteome during allogeneic hematopoietic 

stem cell transplantation and clinical 

significance of serum C-reactive protein and haptoglobin 

Exp Mol Med. 2010 Sep; 42(9):651-61. 

Ryu J, Lee SR, Park SG, Kang S, Kim HJ, Park BC * 

* Correspondence: sgpark@kribb.re.kr khbae@kribb.re.kr 


* Correspondence: parkbc@kribb.re.kr 


Previously, we identified annexin A4 (ANXA4) as a candidate 

substrate of caspase-3. Proteomic studies were performed 

to identify interacting proteins with a view to determining 

the roles of ANXA4. ANXA4 was found to interact 

with the p105. Subsequent studies revealed that ANXA4 

interacts with NF-κB through the Rel homology domain 

of p50. Furthermore, the interaction is markedly increased 

by elevated Ca(2+) levels. NF-κB transcriptional activity 

assays demonstrated that ANXA4 suppresses NF-κB tran- 

scriptional activity in the resting state. Following treatment 

with TNF-α or PMA, ANXA4 also suppressed NF-κB tran- 

scriptional activity, which was upregulated significantly early 

after etoposide treatment. This difference may be due to 

the intracellular Ca(2+) level. Additionally, ANXA4 translocates 

to the nucleus together with p50, and imparts greater 

resistance to apoptotic stimulation by etoposide. Our results 

collectively indicate that ANXA4 differentially modulates 

the NF-κB signaling pathway, depending on its interactions 

with p50 and the intracellular Ca(2+) ion level. 

PMID: 20237821 

Keywords: Annexin A4; Ca2+; Cell line; Etoposide; Hela 

cells; NF-kB; Protein structure, tertiary; RNA 

interference; Transcriptional activation; Tumor 

necrosis factor-α 

Successful hematopoietic stem cell transplantation (HSCT) 

involves the restoration of hematopoietic function after engraftment, 

arising from the differentiation and proliferation 

of hematopoietic stem cells. Several factors could influence 

the course of allogeneic-HSCT (allo-HSCT). Therefore, 

knowledge of serum proteome changes during the allo-HSCT 

period might increase the efficacy of diagnosis and disease 

prevention efforts. This study conducted proteomic analyses 

to find proteins that were significantly altered in response 

to allo-HSCT. Sera from five representative patients who 

underwent allo-HSCT were analyzed by 2-dimensional gel 

electrophoresis and liquid chromatography tandem mass 

spectrometry, and were measured on a weekly basis before 

and after allo-HSCT in additional 78 patients. Fourteen protein 

spots showing changes in expression were further examined, 

and most proteins were identified as acute phase proteins 

(APPs). Studies of 78 additional patients confirmed that C-reactive 

protein (CRP) and haptoglobin undergo expression 

changes during allo-HSCT and thus may have the potential 

to serve as representative markers of clinical events after 

allo-HSCT. Maximal CRP level affected the development 

of major transplant-related complications (MTCs) and other 

problems such as fever of unknown origin. Particularly, an 

increase in CRP level 21 days after allo-HSCT was found 

to be an independent risk factor for MTC. Maximal haptoglobin 

and haptoglobin level 14 days after allo-HSCT were 

predictive of relapses in underlying hematologic disease. 

Our results indicated that CRP and haptoglobin were significantly 

expressed during allo-HSCT, and suggest that their 

level can be monitored after allo-HSCT to assess the risks 

of early transplant-related complications and relapse. 

PMID: 20716902 

Keywords: Adolescent; Biological markers; C-reactive 

protein; Haptoglobin; Hematopoietic stem cell; 

Proteomics; Recurrence; Transplantation 

conditioning; Transplantation, homologous 


Article 50 

Crystal structure of ED-Eya2: insight into dual 

roles as a protein tyrosine phosphatase and a transcription 

factor 

Article 51 

Indole-3-carbinol induces apoptosis through p53 

and activation of caspase-8 pathway in lung cancer 

A549 cells 

FASEB J. 2010 Feb; 24(2):560-9. 

Food Chem Toxicol. 2010 Mar; 48(3):883-90. 

Jung SK, Jeong DG, Chung SJ, Kim JH, Park BC, Tonks 

NK, Ryu SE, Kim SJ * 

* Correspondence: ksj@kribb.re.kr 


Eya proteins are transcription factors that play pivotal roles 

in organ formation during development by mediating interactions 

between Sine Oculis (SO) and Dachshund (DAC). 

Remarkably, the transcriptional activity of Eya proteins is 

regulated by a dephosphorylating activity within its Eya domain 

(ED). However, the molecular basis for the link between 

catalytic and transcriptional activities remains unclear. Here 

we report the first description of the crystal structure of 

the ED of human Eya2 (ED-Eya2), determined at 2.4-A 

resolution. In stark contrast to other members of the haloacid 

dehalogenase (HAD) family to which ED-Eya2 belongs, the 

helix-bundle motif (HBM) is elongated along the back of 

the catalytic site. This not only results in a structure that 

accommodates large protein substrates but also positions 

the catalytic and the SO-interacting sites on opposite faces, 

which suggests that SO binding is not directly affected by 

catalytic function. Based on the observation that the 

DAC-binding site is located between the catalytic core and 

SO binding sites within ED-Eya2, we propose that catalytic 

activity can be translated to SO binding through DAC, which 

acts as a transcriptional switch. We also captured at two 

stages of reaction cycles-acyl-phosphate intermediate and 

transition state of hydrolysis step, which provided a detailed 

view of reaction mechanism. The ED-Eya2 structure defined 

here serves as a model for other members of the Eya family 

and provides a framework for understanding the role of Eya 

phosphatase mutations in disease. 

PMID: 19858093 

Choi HS, Cho MC, Lee HG * , Yoon DY 

* Correspondence: hglee@kribb.re.kr 


Indole-3-carbinol (I3C) has anti-tumor effects in various cancer 

cell lines. However, the anti-tumor effect of I3C on 

human lung cancers has been rarely reported. We investigated 

the anti-tumor effects and its mechanism of I3C on human 

lung carcinoma A549 cell line. Treatment of the A549 cells 

with I3C significantly reduced cell proliferation, increased 

formations of fragmented DNA and apoptotic body, and 

induced cell cycle arrest at G0/G1 phase. I3C increased not 

only the protein levels of cyclin D1, phosphorylated p53, 

and p21 but also the expression of Fas mRNA. Cleavage 

of caspase-9, -8, -3 and PARP also was increased by I3C. 

Treatment with wortmannin significantly suppressed both 

I3C-induced Ser15 phosphorylation and accumulation of p53 

protein. The inhibition of caspase-8 by z-IETD-FMK significantly 

decreased cleavage of procaspase-8,-3 and PARP 

in I3C-treated A549 cells. Taken together, these results demonstrate 

that I3C induces cell cycle arrest at G0/G1 through 

the activation of p-p53 at Ser 15 and induces caspase-8 

mediated apoptosis via the Fas death receptor. This molecular 

mechanism for apoptotic effect of I3C on A549 lung carcinoma 

cells may be a first report and suggest that I3C may 

be a preventive and therapeutic agent against lung cancer. 

PMID:20060030 

Keywords: Anticarcinogenic agents; A549; Apoptosis; 

Caspase 8; Cell cycle arrest; Fas ligand protein; Flow 

cytometry; Indole-3-carbinol; Lung cancer 

Keywords: Amino acid sequence; Branchio-oto-renal 

syndrome; Catalytic domain; Crystallization; Eyes 

absent phosphatase; Halo-acid dehalogenase 


Article 52 

Purification and characterization of a novel fibrinolytic 

enzyme from chive (Allium tuberosum) 

Food Sci Biotech. 2010 Jun; 19(3):697-702. 

Chung DM, Choi NS, Maeng PJ, Chun HK, Kim SH * 

* Correspondence: shkim@kribb.re.kr 


A novel Allium tuberosum fibrinolytic enzyme (ATFE) was 

purified from the leaf of chive by ion exchange chromatography 

followed by gel filtration. The molecular mass and 

iso-electric point (pI) of ATFE were 90 kDa and 4.0 by 

using 1- or 2-D fibrin zymography, respectively. ATFE was 

optimally active at pH 4.0 and 40oC. ATFE had a high 

degrading activity for the Aα-chain of human fibrinogen 

and hydrolyzed the Bβ-chain slowly, but did not affect the 

γ-chain, indicating that it is a α-fibrinogenase. The proteolytic 

activity of ATFE was inhibited completely by phenylmethylsulfonyl 

fluoride (PMSF), indicating that this enzyme 

belongs to the serine protease class. ATFE was also inhibited 

by the 1 

μM of Cu2+. ATFE exhibited high specificity for 

Meo-Suc-Arg-Pro-Tyr-pNA (S-2586), a synthetic chromogenic 

substrate for chymotrypsin. The first 20 amino acid 

residues of the N-terminal sequence of ATFE were determined 

as TTKSWNFIGFDETSKXTTYE, which is 60% 

identical with subtilisin-like serine protease from Narcissus 

pseudonarcissus. 

Keywords: Allium tuberosum; Fibrin zymography; 

Fibrinolytic enzyme; Phenylmethylsulfonyl fluoride; 

Proteolytic activities; Serine protease; 

Subtilisin-like; Zymography 

Article 53 

Functional switching of TGF- β1 signaling in liver 

cancer via epigenetic modulation of a single CpG 

site in TTP promoter 

Gastroenterology. 2010 May; 138(5):1898-908. 

Sohn BH, Park IY, Lee JJ, Yang SJ, Jang YJ, Park KC, 

Kim DJ, Lee DC, Sohn HA, Kim TW, Yoo HS, Choi JY, 

Bae YS, Yeom YI * 

* Correspondence: yeomyi@kribb.re.kr 


BACKGROUND & AIMS: Acquisition of resistance to the 

antiproliferative effect of transforming growth factor (TGF)- 

β1 is crucial for the malignant progression of cancers. In 

this study, we sought to determine whether deregulated expression 

of tristetrapolin (TTP), a negative posttranscriptional 

regulator of c-Myc, confers resistance to the antiproliferative 

effects of TGF-β1 on liver cancer cells. 

METHODS: The epigenetics of TTP promoter regulation 

and its effects on TGF-β1 signaling were examined in hep- 

atocellular carcinoma (HCC) cell lines and patient tissues. 

RESULTS: TTP was down-regulated in HCC cell lines 

(10/11), compared with normal liver, as well as in tumor 

tissues (19/24) from paired HCC specimens. Methylation 

of a specific single CpG site located within the TGF-β1-re 

- 

sponsive region (TRR) of the TTP promoter was significantly 

associated with TTP down-regulation in both HCC cell lines 

and tumor tissues (r = -0.606383, P < .001). The singly 

methylated CpG site was specifically bound by a transcriptional 

repressor complex consisting of 

MECP2/c-Ski/DNMT3A and abolished the TGF-β1-induced 

as well as basal-level expression of TTP. The epigenetic 

inactivation of TTP led to an increased half-life of c-Myc 

mRNA and blocked the cytostatic effect of TGF-β1. 

Statistically significant correlations were observed between 

the single CpG site methylation and expression levels of 

TTP or c-Myc in clinical samples of HCC. 

CONCLUSIONS: Abrogation of the post-transcriptional regulation 

of c-Myc via methylation of a specific single CpG 

site in the TTP promoter presents a novel mechanism for 

the gain of selective resistance to the antiproliferative signaling 

of TGF-β1 in HCC. 

PMID: 20038433 

Keywords: Carcinoma, hepatocellular; CpG islands; DNA 

methylation; HCC; Liver neoplasms; Methylation; 

TGF-β1; 

Transfection; TTP 


Article 54 

Phosphorylation of serine-10 of histone H3 shields 

modified lysine-9 selectively during mitosis 

Article 55 

Genome-wide association of serum bilirubin levels 

in Korean population 

Genes Cells. 2010 Apr; 15(3):181-92. 

Hum Mol Genet. 2010 Sep; 19(18):3672-8. 

Jeong YS, Cho S, Park JS, Ko Y, Kang YK * 

* Correspondence: ykkang@kribb.re.kr 


Post-translational modifications of histones play important 

roles in regulating chromatin dynamics and epigenetic inheritance 

during mitosis. The epigenetic significance and 

stability of histone H3-lysine 9 (H3K9) modifications have 

been well studied in interphase cells, whereas not as much 

in mitotic cells. Here, we inspected mitosis-coupled alterations 

in the global modifications of H3K9. Signals for H3K9 

mono-, di-methylation and acetylation became invisible as 

cells entered mitosis in contrast to the pattern observed for 

H3-serine 10 phosphorylation (H3S10ph). Treatment with 

the aurora-B inhibitor ZM447439 or expression of the dominant 

negative mutant Aur-B(K106R) resulted in prometaphase 

chromosomes that lacked signals for H3S10ph but 

were positive for H3K9 modifications. Trimethylation was 

the sole K9 modification that remained consistently detectable 

throughout the cell cycle. This phenomenon was specific 

for H3K9-S10, as this pattern was not observed at 

H3K27-S28. Methylated H3K27 remained detectable 

throughout the cell cycle, despite phosphorylation of the 

adjacent H3S28. Contrastingly, our dot-blot experiment using 

synthetic peptides showed that phosphorylation of serine 

residue basically kept adjacent lysine from antibody access. 

Together, these results suggest that phosphorylation of serine 

residue occurs in a selective manner, being influenced by 

the types of modifications and the nature of neighboring 

lysine residues. 

PMID: 20070858 

Keywords: Acetylation; Anaphase; Cell cycle arrest; 

Epigenetics; Immunocytochemistry; Mitosis; 

Prometaphase; Protein depletion; Protein expression; 

Protein phosphorylation; Protein stability 

Kang TW, Kim HJ, Ju H, Kim JH, Jeon YJ, Lee HC, Kim 

KK, Kim JW, Lee S, Kim JY, Kim SY * , Kim YS * 

* Correspondence: kimsy@kribb.re.kr yongsung@kribb.re.kr 


A large-scale, genome-wide association study was performed 

to identify genetic variations influencing serum bilirubin levels 

using 8841 Korean individuals. Significant associations 

were observed at UGT1A1 (rs11891311, P = 4.78 x 10(-148)) 

and SLCO1B3 (rs2417940, P = 1.03 x 10(-17)), which are 

two previously identified loci. The two single-nucleotide 

polymorphisms (SNPs) were replicated (rs11891311, P = 

3.18 x 10(-15)) or marginally significant (rs2417940, P = 

8.56 x 10(-4)) in an independent cohort of 1096 individuals. 

In a conditional analysis adjusted for the top UGT1A1 variant 

(rs11891311), another variant in UGT1A1 (rs4148323, P = 

1.22 x 10(-121)) remained significant; this suggests that in 

UGT1A1 at least two independent genetic variations influence 

the bilirubin levels in the Korean population. The protein 

coding variant rs4148323, which is monomorphic in 

European-derived populations, may be specifically associated 

with serum bilirubin levels in Asians (P = 2.56 x 

10(-70)). The SLCO1B3 variant (rs2417940, P = 1.67 x 

10(-18)) remained significant in a conditional analysis for 

the top UGT1A1 variant. Interestingly, there were significant 

differences in the associated variations of SLCO1B3 between 

Koreans and European-derived populations. While the variant 

rs2417940 at intron 7 of SLCO1B3 was more significantly 

associated in Koreans, variants rs17680137 (P = 0.584) and 

rs2117032 (P = 2.76 x 10(-5)), two of the top-ranked SNPs 

in European-derived populations, did not reach the genome-wide 

significance level. Also, variants in SLCO1B1 

did not reach genome-wide significance in Koreans. Our 

result supports the idea that there are considerable ethnic 

differences in genetic association of bilirubin levels between 

Koreans and European-derived populations. 

PMID: 20639394 

Keywords: Adolescent; Bilirubin; Cohort studies; Genetic 

variation; Glucuronosyltransferase; Organic anion 

transporters; Polymorphism, single nucleotide 


Article 56 

Drosophila G9a is implicated in germ cell 

development 

Article 57 

Active loss of DNA methylation in two-cell stage 

goat embryos 

Insect Mol Biol. 2010 Feb; 19(1):131-9. 

Int J Dev Biol. 2010; 54(8-9):1323-8. 

Lee KS, Yoon J, Park JS, Kang YK * 

Park JS, Lee D, Cho S, Shin ST, Kang YK * 





In Drosophila ovaries, germline stem cells (GSCs) divide 

asymmetrically in the germaria to produce daughter GSCs 

and cystoblasts. Single cystoblasts differentiate to form germline 

cysts with 16 germline cells, all of which are connected 

by the fusome, a vesiculated structure critical for oocyte 

specification. We here show that histone H3K9 methyltransferase 

dg9a is associated with spectrosome/fusome formation 

in the germarium; dG9a(13414) mutant ovaries have 

disorganized spectrosome/fusome in about half the germaria, 

with reduced levels of hu-li tai shao and alpha-SPECTRIN 

proteins. We found that the amount of germline cells within 

cysts was reduced and that oocyte determination often failed 

in egg chambers of the dG9a(13414) mutant ovaries. These 

results suggest that a mutation in dG9a gene gives rise to 

anomalous spectrosome/fusome structures, which in turn lead 

to faulty germ-cell development in Drosophila ovaries. 

PMID:20002223 

Keywords: dG9a; Drosophila; Fusome; Germline cell; 

Histone methylation; Mutation; Oocytes; Oogenesis; 

Ovary; Spectrosome 

Early mammalian embryos are thought to gain nuclear totipotency 

through DNA methylation reprogramming (DMR). By 

this process, DNA methylation patterns acquired during gametogenesis 

that are unnecessary for zygotic development 

are erased. The DMR patterns of various mammalian species 

have been studied; however, they do not seem to have a 

conserved pattern. We examined early goat embryos to find 

conforming rules underlying mammalian DMR patterns. 

Immunocytochemical results showed that the overall level 

of DNA methylation was not greatly changed during the 

pronucleus stage. At the two-cell stage, active demethylation 

occurred and simultaneously affected both parental DNAs, 

resulting in a global loss of 5-methylcytosine. The level 

of DNA methylation was lowest in the four-cell stage, with 

increased de novo methylation during the eight-cell stage. 

Histone H3-lysine 9 was gradually trimethylated in the 

sperm-derived chromatin, continuing from the pronucleus 

stage through the two-cell stage. This goat DMR pattern 

is novel and distinct from the DMRs of other mammalian 

species. The more mammalian species we included for DMR 

analysis, the more multifarious patterns we obtained, adding 

an extra diversity each time to the known mammalian DMR 

patterns. Nevertheless, the evolutionary significance and developmental 

consequence of such diverse DMR patterns are 

currently unknown. 

PMID:20563995 

Keywords: Azacitidine; DMR; Embryo, Mammalian; 

Enzyme Inhibitors; Epigenetics; Goats; Histone 

methylation; Immunohistochemistry; Lysine; 

Preimplantation development; Reprogramming; 

Zygote 


Article 58 

Proteomic analysis of oxidative stress-induced 

neuronal cell death by using two-dimensional 

fluorescence difference gel electrophoresis 

Int J Mol Med. 2010 Dec; 26(6):829-35. 

Kim EY, Yoon TS, Bahn YJ, Jeong DG, Park MR, Chung 

SJ, Park SG, Park BC, Lee SC, Ryu SE, Bae KH * 

* Correspondence: khbae@kribb.re.kr 


Oxidative stress has been implicated in a number of neurological 

disorders, including cerebral ischemia and neuro-degenerative 

diseases. Comprehensive proteomic studies 

were carried out using an immortalized mouse hippocampal 

cell line, HT22, exhibiting oxidative stress-mediated cell 

death upon glutamate treatment. Two-dimensional fluorescence 

difference gel electrophoresis (2D DIGE) of subcellular 

organelle fractions revealed that significant numbers 

of proteins showed quantitative changes during HT22 cell 

death, among which a total of 51 proteins were identified 

by mass spectrometry. The identified proteins indicate that 

HT22 cell death occurs through perturbations in mitochondrial 

function, changes in translational elongation machinery, 

and translocation of proteins across subcellular organelles. 

This list of proteins may shed light on oxidative stress-mediated 

neuronal cell death. 

PMID:21042776 

Keywords: Cell death; Cytoskeletal proteins; 

Electrophoresis, gel; Hippocampus; HT22; Neurons; 

Oxidative stress; Peptide elongation factors; 

Proteomics; Reactive oxygen species; Spectrometry 

Article 59 

Enigma negatively regulates p53 through MDM2 

and promotes tumor cell survival in mice 

J Clin Invest. 2010 Dec; 120(12):4493-506. 

Jung CR, Lim JH, Choi Y, Kim DG, Kang KJ, Noh SM, 

Im DS * 

* Correspondence: imdongsu@kribb.re.kr 


The human E3 ubiquitin ligase murine double minute 2 

(MDM2) targets the tumor suppressor p53 for ubiquitination 

and degradation but also promotes its own ubiquitination 

and subsequent degradation. As the balance between MDM2 

and p53 levels plays a crucial role in regulating cell proliferation 

and apoptosis, we sought to identify factors selectively 

inhibiting MDM2 self-ubiquitination. Here we have 

shown that the LIM domain protein Enigma directly interacts 

with MDM2 to form a ternary complex with p53 in vitro 

and in human hepatoma and colon carcinoma cell lines and 

mouse embryonic fibroblasts. We found that Enigma elicited 

p53 degradation by inhibiting MDM2 self-ubiquitination and 

increasing its ubiquitin ligase activity toward p53 in cells. 

Moreover, mitogenic stimuli such as serum, FGF, and HGF 

increased Enigma transcription via induction of serum response 

factor (SRF), leading to MDM2 stabilization and 

subsequent p53 degradation. We observed similar results 

in the livers of mice treated with HGF. In humans, we found 

SRF and Enigma coexpressed with MDM2 but not p53 in 

several liver and stomach tumors. Finally, we showed that 

Enigma promoted cell survival and chemoresistance by suppressing 

p53-mediated apoptosis in both cell lines and a 

mouse xenograft model. Our findings suggest a role for 

Enigma in tumorigenesis and uncover a mechanism whereby 

mitogens attenuate p53 antiproliferative activity through an 

SRF/Enigma/MDM2 pathway. 

PMID: 21060154 

Keywords: Apoptosis; Colorectal neoplasms; p21; 

Intracellular signaling; Neoplasms; Proto-oncogene 

proteins c-mdm2; Small interfering; Signal 

transduction; Stomach neoplasms; p53; 

Ubiquitination 


Article 60 

A new fibrinolytic enzyme (55 kDa) from Allium 

tuberosum: purification, characterization, and 

comparison 

Article 61 

Proteomic analysis of pancreata from mini-pigs 

treated with streptozotocin as a type I diabetes 

models 

J Med Food. 2010 Dec; 13(6):1532-6. 

J Microbiol Biotechnol. 2010 Apr; 20(4):817-20. 

Chung DM, Choi NS, Chun HK, Maeng PJ, Park SB, Kim 

SH * 

Lee PY, Park SG, Kim EY, Lee MS, Chung SJ, Lee SC, 

Yu DY, Bae KH * 

* Correspondence: shkim@kribb.re.kr 


* Correspondence: khbae@kribb.re.kr 


Chives have been used both as food and as medicine. 

Previously, two fibrinolytic enzymes, ATFE-I (90 kDa) and 

ATFE-II (55 kDa), were identified in chives (Allium tuberosum), 

a perennial herb. In the present work, ATFE-II was 

purified by ion-exchange chromatography followed by gel 

filtration. In addition, the enzyme properties of ATFE-I and 

ATFE-II were compared. The molecular mass and isoelectric 

point (pI value) of ATFE-II were 55 kDa and pI 4.0, respectively, 

as revealed using one- or two-dimensional fibrin 

zymography. ATFE-II was optimally active at pH 7.0 and 

45°C. ATFE-II degraded the Aα-chain of human fibrinogen 

but did not hydrolyze the Bβ-chain or the γ-chain, indicating 

that the enzyme is an 

α-fibrinogenase. The proteolytic activity 

of ATFE-II was completely inhibited by 1 

μM leupeptin, 

indicating that the enzyme belongs to the cysteine protease 

class. ATFE-II was also inhibited by 1 

μM Fe²(+). ATFE-II 

exhibited high specificity for MeO-Suc-Arg-Pro-Tyr-p-nitroaniline 

(S-2586), a synthetic chromogenic substrate of 

chymotrypsin. Thus proteolytic enzymes from A. tuberosum 

may be useful as thrombolytic agents. 

PMID: 20954802 

Type 1 diabetes mellitus (T1DM) is an autoimmune disease 

characterized by extreme insulin deficiency due to an overall 

reduction in the mass of functional pancreatic 

β-cells. Several 

animal models have been used to study T1DM. Among them, 

mini-pig seems to be a useful model of diabetes because 

of its similarities in anatomy and physiology to humans. 

The purpose of this study is to analyze differentially expressed 

pancreatic proteins in streptozotocin (STZ)-induced 

mini-pig T1DM model. The pancreas proteins from mini-pigs 

treated with STZ were separated by 2-dimensional gel electrophoresis 

and eleven protein spots were found to be altered 

significantly compared with control mini-pigs. The data in 

this study from proteomic analysis provide a valuable resource 

for the further understanding of T1DM 

pathomechanism. 

PMID: 20467259 

Keywords: Diabetes mellitus; Electrophoresis, gel; 

Mini-pig; Pancreas; Proteomics; Streptozocin; 

Swine; T1DM 

Keywords: Cysteine endopeptidases; Cysteine proteinase 

inhibitors; Ferrous compounds; Fibrinogen; 

Hydrogen-ion concentration; Isoelectric point; 

Isoenzymes; Leupeptins; Oligopeptides; 

Thrombolytic therapy; Thrombosis 


Article 62 

Structural insights on the new mechanism of trehalose 

synthesis by trehalose synthase TreT from 

Pyrococcus horikoshii 

J Mol Biol. 2010 Nov; 404(2):247-59. 

Woo EJ * , Ryu SI, Song HN, Jung TY, Yeon SM, Lee HA, 

Park BC, Park KH, Lee SB. 



Many microorganisms produce trehalose for stability and 

survival against various environmental stresses. Unlike the 

widely distributed trehalose-biosynthetic pathway, which utilizes 

uridine diphosphate glucose and glucose-6-phosphate, 

the newly identified enzyme trehalose glycosyltransferring 

synthase (TreT) from hyperthermophilic bacteria and archaea 

synthesizes an 

α, α-trehalose from nucleoside diphosphate 

glucose and glucose. In the present study, we determined 

the crystal structure of TreT from Pyrococcus horikoshii 

at 2.3 Å resolution to understand the detailed mechanism 

of this novel trehalose synthase. The conservation of essential 

residues in TreT and the high overall structural similarity 

of the N-terminal domain to that of trehalose phosphate 

synthase (TPS) imply that the catalytic reaction of TreT 

for trehalose synthesis would follow a similar mechanism 

to that of TPS. The acceptor binding site of TreT shows 

a wide and commodious groove and lacks the long flexible 

loop that plays a gating role in ligand binding in TPS. The 

observation of a wide space at the fissure between two domains 

and the relative shift of the N-domain in one of the 

crystal forms suggest that an interactive conformational 

change between two domains would occur, allowing a more 

compact architecture for catalysis. The structural analysis 

and biochemical data in this study provide a molecular basis 

for understanding the synthetic mechanism of trehalose, or 

the nucleotide sugar in reverse reaction of the TreT, in extremophiles 

that may have important industrial implications. 

PMID: 20888836 

Keywords: Amino acid substitution; Catalytic domain; 

Glycosyltransferase; Mutant proteins; Pyrococcus 

horikoshii; Trehalose synthase; TreT; X-ray structure 

Article 63 

Leukocyte common antigen-related (LAR) tyrosine 

phosphatase positively regulates osteoblast 

differentiation by modulating extracellular signal-regulated 

kinase (ERK) activation 

Mol Cells. 2010 Oct; 30(4):335-40. 

Kim WK, Bae KH, Choi HR, Kim DH, Choi KS, Cho YS, 

Kim HD, Park SG, Park BC, Ko Y, Lee SC * 

* Correspondence: lesach@kribb.re.kr 


Protein tyrosine phosphatases (PTPs) are pivotal regulators 

of key cellular functions, including cell growth, differentiation, 

and adhesion. Previously, we reported that leukocyte 

common antigen-related (LAR) tyrosine phosphatase 

promotes osteoblast differentiation in MC3T3-E1 preosteoblast 

cells. In the present study, the mechanism of the regulatory 

action of LAR on osteoblast differentiation was 

investigated. The mineralization of extracellular matrix and 

calcium accumulation in MC3T3-E1 cells were markedly 

enhanced by LAR overexpression, and these effects were 

further increased by treatment with a MEK inhibitor. In 

addition, LAR overexpression dramatically reduced extracellular 

signal-regulated kinase (Erk) activation during 

osteoblast differentiation. In contrast, a marginal effect of 

the inactive LAR mutant on Erk activation was detected. 

Expression of osteoblast-related genes such as ALP, BSP, 

DLX5, OCN, and RUNX2, was increased by LAR overexpression 

during osteoblast differentiation. On he basis of 

these results, we propose that LAR functions as a positive 

regulator of osteoblast differentiation by modulating ERK 

activation. Therefore, LAR phosphatase could be used as 

a novel regulatory target protein in many bone-associated 

diseases, including osteoporosis. 

PMID: 20811813 

Keywords: Differentiation; ERK; Extracellular matrix; 

LAR tyrosine phosphatase; Osteoblast; 

Phosphorylation; Protein tyrosine phosphatases 


Article 64 

Structural features of the Nostoc punctiforme debranching 

enzyme reveal the basis of its mechanism 

and substrate specificity 

Article 65 

Structural rationale for the short branched substrate 

specificity of the glycogen debranching enzyme 

GlgX 

Proteins. 2010 Feb; 78(2):348-56. 

Proteins. 2010 Jun; 78(8):1847-55. 

Dumbrepatil AB, Choi JH, Park JT, Kim MJ, Kim TJ, Woo 

EJ * , Park KH 

Song HN, Jung TY, Park JT, Park BC, Myung PK, Boos 

W, Woo EJ * , Park KH 





The debranching enzyme Nostoc punctiforme debranching 

enzyme (NPDE) from the cyanobacterium Nostoc punctiforme 

(PCC73102) hydrolyzes the 

α-1,6 glycosidic linkages 

of malto-oligosaccharides. Despite its high homology to cyclodextrin/pullulan 

(CD/PUL)-hydrolyzing enzymes from 

glycosyl hydrolase 13 family (GH-13), NPDE exhibits a 

unique catalytic preference for longer malto-oligosaccharides 

(>G8), performing hydrolysis without the transgylcosylation 

or CD-hydrolyzing activities of other GH-13 enzymes. To 

investigate the molecular basis for the property of NPDE, 

we determined the structure of NPDE at 2.37-A resolution. 

NPDE lacks the 

typical N-terminal domain of other 

CD/PUL-hydrolyzing enzymes and forms an elongated dimer 

in a head-to-head configuration. The unique orientation of 

residues 25-55 in NPDE yields an extended substrate binding 

groove from the catalytic center to the dimeric interface. 

The substrate binding groove with a lengthy cavity beyond 

the -1 subsite exhibits a suitable architecture for binding 

longer malto-oligosaccharides (>G8). These structural results 

may provide a molecular basis for the substrate specificity 

and catalytic function of this cyanobacterial enzyme, distinguishing 

it from the classical neopullulanases and 

CD/PUL-hydrolyzing enzymes. 

PMID:19768689 

Keywords: Bacterial proteins; Crystal structure; 

Cyclodextrin/pullulan-hydrolyzing; 

Debranching 

enzyme; Dimerization; Neopullulanase; Protein 

conformation; Protein multimerization 

Glycogen serves as major energy storage in most living 

organisms. GlgX, with its gene in the glycogen degradation 

operon, functions in glycogen catabolism by selectively catalyzing 

the debranching of polysaccharide outer chains in 

bacterial glycosynthesis. GlgX hydrolyzes 

α-1,6-glycosidic 

linkages of phosphorylase-limit dextrin containing only three 

or four glucose subunits produced by glycogen 

phosphorylase. To understand its mechanism and unique 

substrate specificity toward short branched 

α-polyglucans, 

we determined the structure of GlgX from Escherichia Coli 

K12 at 2.25 A resolution. The structure reveals a monomer 

consisting of three major domains with high structural similarity 

to the subunit of TreX, the oligomeric bifunctional 

glycogen debranching enzyme (GDE) from Sulfolobus. In 

the overlapping substrate binding groove, conserved residues 

Leu270, Asp271, and Pro208 block the cleft, yielding a shorter 

narrow GlgX cleft compared to that of TreX. Residues 

207-213 form a unique helical conformation that is observed 

in both GlgX and TreX, possibly distinguishing GDEs from 

isoamylases and pullulanases. The structural feature observed 

at the substrate binding groove provides a molecular explanation 

for the unique substrate specificity of GlgX for 

G4 phosphorylase-limit dextrin and the discriminative activity 

of TreX and GlgX toward substrates of varying lengths. 

PMID:20187119 

Keywords: Amino acid sequence; Catalytic domain; 

Escherichia coli proteins; Glycogen debranching 

enzyme; Hydrolysis; Protein structure; Sequence 

alignment; Substrate specificity; Surface properties 


Article 66 

Iloprost, a prostacyclin analogue, stimulates 

meiotic maturation and early embryonic 

development in pigs 

Reprod Fertil Dev. 2010; 22(2):437-47. 

Kim JS, Chae JI, Song BS, Lee KS, Choo YK, Chang KT, 

Park H, Koo DB * 

* Correspondence: Retirement 


Oviduct fluid contains various cytokines and growth factors 

that enhance the embryo development during the preimplantation 

period. In hatched embryos, prostacyclin 

(PGI(2)) improves implantation, but its role during oocyte 

maturation and early embryo development remains 

contentious. Therefore, in the present study, we examined 

the effects of a PGI(2) analogue (iloprost) on meiotic maturation 

and early embryonic development in pigs, as well on 

the structural integrity, mitochondrial membrane potential 

and apoptosis in blastocysts. First, meiotic maturation in 

pig oocytes was examined in the presence of increasing 

concentrations of iloprost (1, 5 and 10 muM). After IVM, 

a higher proportion of iloprost-treated compared with untreated 

oocytes was in MII (90.0% v. 65.7%, respectively; 

P < 0.05). In addition, protein kinase A activity increased 

in iloprost-treated oocytes, indicating increased intracellular 

cAMP concentrations. After 22 h iloprost treatment (44 h 

total incubation time), western blotting demonstrated increased 

expression of extracellular signal-regulated kinase 

(ERK) 1/2, phosphorylated (p-) ERK1/2, cAMP response 

element-binding protein (CREB), p-CREB and cyclo-oxygenase-2, 

indicating activation of the mitogen-activated protein 

kinase and PGI(2) pathways. In addition, the frequency 

of polyspermy decreased in iloprost-treated oocytes (19.9%) 

compared with control (35.8%), whereas the rate of blastocyst 

formation increased (P < 0.05). Terminal deoxynucleotidyl 

transferase-mediated dUTP nick-end labelling (TUNEL) 

showed that the number of nuclei containing fragmented 

DNA at the blastocyst stage decreased in the iloprost-treated 

group compared with control (1.2% v. 3.6%, respectively). 

In conclusion, iloprost appears to play a direct role in porcine 

oocyte maturation by enhancing blastocyst structure and 

survival. 

PMID:20047729 

Keywords: Apoptosis; Blastocyst development; 

Cyclooxygenase 2; DNA primers; Embryonic 

development; Fertilization in vitro; Iloprost; Meiosis; 

Oocytes; Signal transduction; Sus scrofa 

Article 67 

Rapamycin promotes the osteoblastic differentiation 

of human embryonic stem cells by blocking 

the mTOR pathway and stimulating the 

BMP/Smad pathway 

Stem Cells Dev. 2010 Apr; 19(4):557-68. 

Lee KW, Yook JY, Son MY, Kim MJ, Koo DB, Han YM, 

Cho YS * 

* Correspondence: june@kribb.re.kr 


Studies revealed that PI3K/AKT/mTOR signaling is important 

in the regulation of human embryonic stem cell 

(hESC) self-renewal and differentiation. However, its action 

on osteogenic differentiation of hESCs is poorly understood. 

We tested the effects of pharmacological PI3K/AKT/mTOR 

inhibitors on their potential to induce osteogenic differentiation 

of hESCs. Under feeder-free culture conditions, 

rapamycin (an mTOR inhibitor) potently inhibited the activities 

of mTOR and p70S6K in undifferentiated hESCs; however, 

LY294002 (a PI3K inhibitor) and an AKT inhibitor 

had no effects. Treatment with any of these inhibitors 

down-regulated the hESC markers Oct4 and Nanog, but only 

rapamycin induced the up-regulation of the early osteogenic 

markers BMP2 and Runx2. We also observed that hESCs 

differentiated when treated with FK506, a structural analog 

of rapamycin, but did not exhibit an osteogenic phenotype. 

Increases in Smad1/5/8 phosphorylation and Id1-4 mRNA 

expression indicated that rapamycin significantly stimulated 

BMP/Smad signaling. After inducing both hESCs and human 

embryoid bodies (hEBs) for 2-3 weeks with rapamycin, osteoblastic 

differentiation was further characterized by the expression 

of osteoblastic marker mRNAs and/or proteins 

(osterix, osteocalcin, osteoprotegerin, osteonectin, and bone 

sialoprotein), alkaline phosphatase activity, and alizarin red 

S staining for mineralized bone nodule formation. No significant 

differences in the osteogenic phenotypes of rapamycin-differentiated 

hESCs and hEBs were detected. Our results 

suggest that, among these 3 inhibitors, only rapamycin functions 

as a potent stimulator of osteoblastic differentiation 

of hESCs, and it does so by modulating rapamycin-sensitive 

mTOR and BMP/Smad signaling. 

PMID: 19642865 

Keywords: Embryonic stem cells; Enzyme inhibitors; 

Immunosuppressive agents; Morpholines; Octamer 

transcription factor-3; Osteoblasts; Osteogenesis; 

Proto-oncogene proteins c-akt; Sirolimus; Smad 

proteins; Tacrolimus 


2010 




Division of Biosystems Research 







www.kribb.re.kr

Article 68 

Template-blocking PCR: an advanced PCR technique 

for genome walking 

Anal Biochem. 2010 Mar; 398(1):112-6. 

Bae JH, Sohn JH * 

* Correspondence: sohn4090@kribb.re.kr 


This article describes the development of an improved method 

for the isolation of genomic fragments adjacent to a known 

DNA sequence based on a cassette ligation-mediated polymerase 

chain reaction (PCR) technique. To reduce the nonspecific 

amplification of PCR-based genome walking, the 

3' ends of the restriction enzyme-digested genomic DNA 

fragments were blocked with dideoxynucleoside triphosphate 

(ddNTP) and ligated with properly designed cassettes. The 

modified genomic DNA fragments flanked with cassettes 

were used as a template for the amplification of a target 

gene with a gene-specific primer (GSP) and a cassette primer 

(CP). The ddNTP blocking of the genomic DNA ends significantly 

reduced the nonspecific amplification and resulted 

in a simple and rapid walking along the genome. The efficiency 

of the template-blocking PCR method was confirmed 

by a carefully designed control experiment. The method was 

successfully applied for the cloning of the PGK1 promoter 

from Pichia ciferrii and two novel cellulase genes from 

Penicillium sp. 

PMID: 19903447 

Keywords: Cassette ligation-mediated PCR; Cellulase; 

Chromosome walking; Dideoxynucleosides; 

Genome walking; Genomics; Phosphoglycerate 

kinase; Template-blocking PCR 

Article 69 

Genome-wide screening and identification of factors 

affecting the biosynthesis of prodigiosin by 

Hahella chejuensis, using Escherichia coli as a 

surrogate host 

Appl Environ Microbiol. 2010 Mar; 76(5):1661-8. 

Kwon SK, Park YK, Kim JF * 

* Correspondence: jfk@kribb.re.kr 


A marine bacterium, Hahella chejuensis, recently has attracted 

attention due to its lytic activity against a red-tide 

dinoflagellate. The algicidal function originates from its red 

pigment, prodigiosin, which also exhibits immunosuppressive 

or anticancer activity. Genome sequencing 

and functional analysis revealed a gene set contained in 

the hap gene cluster that is responsible for the biosynthesis 

of prodigiosin. To screen for the factors affecting the prodigiosin 

biosynthesis, we constructed a plasmid library of the 

H. chejuensis genomic DNA, introduced it into Escherichia 

coli strains harboring the hap cluster, and observed changes 

in production of the red pigment. Among the screened clones, 

hapXY genes whose products constitute a two-component 

signal transduction system were elucidated as positive regulators 

of the pigment production. In addition, an Hfq-dependent, 

noncoding region located at one end of the hap cluster 

was confirmed to play roles in regulation. Identification of 

factors involved in the regulation of prodigiosin biosynthesis 

should help in understanding how the prodigiosin-biosynthetic 

pathway is organized and controlled and also aid 

in modulating the overexpression of prodigiosin in a heterologous 

host, such as E. coli, or in the natural producer, H. 

chejuensis. 

PMID: 20038694 

Keywords: Biosynthetic pathways; DNA, bacterial; 

Escherichia coli; Gammaproteobacteria; Gene 

library; Genes, bacterial; Molecular sequence data; 

Multigene family; Plasmids; Prodigiosin 


Article 70 

Characterization of an adenylate cyclase gene 

(cyaB) deletion mutant of Corynebacterium glutamicum 

ATCC 13032 

Appl Microbiol Biotechnol. 2010 Jan; 85(4):1061-8. 

Cha PH, Park SY, Moon MW, Subhadra B, Oh TK, Kim 

E, Kim JF * , Lee JK 



Genome analysis of C. glutamicum ATCC 13032 has showed 

one putative adenylate cyclase gene, cyaB (cg0375) which 

encodes membrane protein belonging to class III adenylate 

cyclases. To characterize the function of cyaB, a deletion 

mutant was constructed, and the mutant showed decreased 

level of intracellular cyclic AMP compared to that of 

wild-type. Interestingly, the cyaB mutant displayed growth 

defect on acetate medium, and this effect was reversed by 

complementation with cyaB gene. Similarly, it showed 

growth defect on glucose-acetate mixture minimal medium, 

and the utilization of glucose was retarded in the presence 

of acetate. The deletion mutant retained the activity of glyoxylate 

bypass enzymes. Additionally, the mutant could grow 

on ethanol but not on propionate medium. The data obtained 

from this study suggests that adenylate cyclase plays an 

essential role in the acetate metabolism of C. glutamicum, 

even though detailed regulatory mechanisms involving 

cAMP are not yet clearly defined. The observation that glyoxylate 

bypass enzymes are derepressed in cyaB mutant indicates 

the involvement of cAMP in the repression of aceB 

and aceA. 

PMID: 19568747 

Keywords: Acetate metabolism; Adenylate cyclase; 

Bacterial proteins; CAMP; Cloning, molecular; 

Corynebacterium glutamicum; CyaB; Cyclic AMP 

Article 71 

Silencing of SlFTR-c, the catalytic subunit of ferredoxin:thioredoxin 

reductase, 

induces pathogenesis-related 

genes and pathogen resistance in 

tomato plants 

Biochem Biophys Res Commun. 2010 Sep; 399(4):750-4. 

Lim CJ, Kim WB, Lee BS, Lee HY, Kwon TH, Park JM, 

Kwon SY * 

* Correspondence: sykwon@kribb.re.kr 


As a heterodimeric protein, ferredoxin:thioredoxin reductase 

(FTR) catalyses the light-dependant activation of several 

photosynthetic enzymes. The active site of the catalytic subunit 

of FTR contains a redox-active disulfide and a [4Fe-4S] 

center. We isolated the catalytic subunit gene of FTR, designated 

SlFTR-c, from tomato (Solanum lycopersicum L.). 

SlFTR-c transcripts were detected in all tissues examined, 

including roots, leaves, flowers, fruits, and seeds. 

Interestingly, virus-induced gene silencing (VIGS) of 

SlFTR-c resulted in necrotic lesions with typical cell death 

symptoms and reactive oxygen species (ROS) production 

in tomato leaves. Moreover, these SlFTR-c-silenced plants 

displayed enhanced disease resistance against bacterial pathogens, 

specifically Pseudomonas syringae pv. tomato DC3000, 

by the induction of defense-related genes (SlPR-1, SlPR-2, 

SlPR-5, SlGlucA, SlChi3, and SlChi9). Taken together, it 

seems that SlFTR-c works as a regulator of programmed 

cell death (PCD) and pathogen resistance in tomato plants. 

PMID: 20705057 

Keywords: Catalytic subunit; Defense response; Lesion 

mimics; Solanum lycopersicum; Virus-induced gene 

silencing (VIGS) 


Article 72 

Lavandulyl flavonoids from Sophora flavescens 

suppress lipopolysaccharide-induced activation of 

nuclear factor-κ 

B and mitogen-activated protein 

kinases in RAW264.7 cells 

Biol Pharm Bull. 2010; 33(6):1019-23. 

Han JM, Jin YY, Kim HY, Park KH, Lee WS, Jeong TS * 

* Correspondence: tsjeong@kribb.re.kr 


Oxidized low-density lipoprotein (oxLDL) and reactive oxygen 

species (ROS) play key roles in the early stage of 

atherosclerosis. Nitric oxide (NO) and ROS are responsible 

for regulation of the transcriptional pathways of nuclear 

Factor-κB (NF-κB) and mitogen-activated protein kinase 

(MAPK), key regulators of cellular inflammatory and immune 

responses. Previously, we examined LDL-antioxidant 

activities of the nine flavonoids isolated from Sophora 

flavescens. Among these, two lavandulyl flavonoids, kurarinone 

(1) and kuraridin (2) inhibited inducible nitric oxide 

synthase (iNOS)-dependent NO production and ROS generation, 

and suppressed remarkably the expression of inflammatory 

cytokines, CCL2, tumor necrosis factor (TNF)- α, 

interleukin (IL)-1 β, and iNOS in lipopolysaccharide 

(LPS)-stimulated RAW264.7 macrophages. Moreover, compounds 

1 and 2 attenuated NF-κB activation by inhibition 

of IκBα 

proteolysis and p65 nuclear translocation, as well 

as phosphorylation of extracellular signal-regulated kinase 

(ERK)1/2, c-Jun N-terminal kinase (JNK), and p38 MAP 

kinases. 

PMID: 20522970 

Article 73 

Ellagic acid protects hepatocytes from damage 

by inhibiting mitochondrial production of reactive 


Biomed Pharmacother. 2010 Apr; 64(4):264-70. 

Hwang JM, Cho JS, Kim TH, Lee YI * 

* Correspondence: yilee@kribb.re.kr 


The aim of this experiment is to investigate the antioxidative 

and antiapoptotic roles of ellagic (EA) acid in in vitro and 

in in vivo experiment. We measured protective properties 

of EA against oxidative stress-induced hepatocyte damage 

in vitro and Concanavalin (ConA)-induced liver damage in 

vivo. EA, a potent antioxidant, exhibited protective properties 

against oxidative stress-induced hepatocyte damage by preventing 

vitamin k3 (VK3)-induced reactive oxygen species 

(ROS) productions, apoptotic and necrotic cellular damage 

and mitochondrial depolarization, which is a main cause 

of ROS production. EA also protects against cell death and 

elevation of glutathione (GSH), alanine transaminase (ALT) 

and asparatate transaminase (AST) in Con A-induced fulminant 

liver damage in mice. These results show that antioxidant 

and cytoprotective properties of EA prevent liver 

damage induced by various type of oxidative stress. 

PMID: 20347566 

Keywords: Antioxidant; Apoptosis; Concanavalin A; 

Cytoprotective effect; Ellagic acid; Glutathione; 

Hepatocytes; Mitochondrial depolarization; Reactive 


Keywords: 

Lavandulyl flavonoid; Mitogen-acti-vated 

protein kinase; Nitric oxide; Nuclear factor-κB; 

Reactive oxygen species; Sophora flavescens 


Article 74 

Synthesis and antifungal activity of a novel series 

of 13-(4-isopropylbenzyl)berberine derivatives 

Bioorg Med Chem Lett. 2010 Nov; 20(22):6551-4. 

Park KD, Cho SJ, Moon JS, Kim SU * 

* Correspondence: kimsu@kribb.re.kr 


By replacing the methyl group of 13-(4-isopropylbenzyl)berberine 

2 with various acyl, alkyl, and benzyl 

groups via the demethylated intermediate, 13-(4-isopropylbenzyl)berberrubine 

4, a novel series of 9-O-alkyl-13-(4-isopropylbenzyl)berberine 

derivatives was synthesized 

and examined for antifungal activities against various 

human pathogenic fungi. The introduction of various alkyl 

groups led to enhanced antifungal activity but that of acyl 

groups resulted in decrease of the activity. Among them, 

9-O-butyl-13-(4-isopropylbenzyl)berberine 6d exhibited the 

most potent antifungal activities against Cryptococcus neoformans, 

Candida species (MIC=0.25-1 μg/ml), and 

Aspergillus species (MIC=2-4 

μg/ml). The compound was 

found to be relatively safe up to 900 mg/kg in oral administration 

to mice. 

PMID: 20932752 

Keywords: 13-(4-Isopropylbenzyl)berberine; Antifungal 

activity; Aspergillus; Berberine derivatives; 

Candida; Cryptococcus neoformans; Human 

pathogenic fungi; Microbial sensitivity tests 

Article 75 

Novel intracellular GH10 xylanase from Cohnella 

laeviribosi HY-21: biocatalytic properties and alterations 

of substrate specificities by site-directed 

mutagenesis of Trp residues 

Bioresour Technol. 2010 Nov; 101(22):8814-21. 

Kim DY, Han MK, Oh HW, Bae KS, Jeong TS, Kim SU, 

Shin DH, Kim IH, Rhee YH, Son KH * , Park HY * 

* Correspondence: sonkh@kribb.re.kr hypark@kribb.re.kr 


The novel intracellular GH10 xylanase (iXylC) gene 

(1023-bp) of Cohnella laeviribosi HY-21 encoded a protein 

consisting of 340 amino acids with a deduced molecular 

mass of 39,330Da and a calculated pI of 5.81. The primary 

structure of iXylC was 70% identical to that of Geobacillus 

sp. GH10 enzyme (GenBank accession number: EDV78425). 

Xylanolytic activity of the His-tagged iXylC overproduced 

in Escherichia coli BL21 was stimulated by 2.2-fold in the 

presence of 0.5% non-ionic detergents. iXylC produced a 

mixture of xylooligosaccharides (xylobiose to xylooctaose) 

from xylotriose and xylotetraose used as the hydrolytic 

substrate. In addition, it exhibited considerable cleavage activities 

for p-nitrophenylxylopyranoside (PNP-xylopyranoside) 

and PNP-cellobioside, indicating that iXylC is a unique 

GH10 enzyme. The hydrolytic activity (57.8IUmL(-1)) of 

iXylC toward PNP-xylopyranoside increased to 8.3-fold by 

W217A and W315A mutations, while mutations of W133A, 

W295A, and W303A abolished the hydrolytic activity of 

the enzyme. 

PMID: 20615688 

Keywords: Cohnella laeviribosi HY-21; Endo-1,4-β 

Xylanases; Intracellular GH10 xylanase; 

Paenibacillus; Site-directed mutagenesis; 

Transxylosylation; Xylooligosaccharides 


Article 76 

Selection of microalgae for lipid production under 

high levels carbon dioxide 

Article 77 

Comparison of several methods for effective lipid 

extraction from microalgae 

Bioresour Technol. 2010 Jan; 101(Suppl 1):S71-4. 

Bioresour Technol. 2010 Jan; 101(Suppl 1):S75-7. 

Yoo C, Jun SY, Lee JY, Ahn CY, Oh HM * 

Lee JY, Yoo C, Jun SY, Ahn CY, Oh HM * 

* Correspondence: heemock@kribb.re.kr 




To select microalgae with a high biomass and lipid productivity, 

Botryococcus braunii, Chlorella vulgaris, and 

Scenedesmus sp. were cultivated with ambient air containing 

10% CO(2) and flue gas. The biomass and lipid productivity 

for Scenedesmus sp. with 10% CO(2) were 217.50 and 20.65 

mg L(-1)d(-1) (9% of biomass), while those for B. braunii 

were 26.55 and 5.51 mg L(-1)d(-1) (21% of biomass). With 

flue gas, the lipid productivity for Scenedesmus sp. and B. 

braunii was increased 1.9-fold (39.44 mg L(-1)d(-1)) and 

3.7-fold (20.65 mg L(-1)d(-1)), respectively. Oleic acid, a 

main component of biodiesel, occupied 55% among the fatty 

acids in B. braunii. Therefore, the present results suggested 

that Scenedesmus sp. is appropriate for mitigating CO(2), 

due to its high biomass productivity and C-fixation ability, 

whereas B. braunii is appropriate for producing biodiesel, 

due to its high lipid content and oleic acid proporton. 

PMID: 19362826 

Keywords: 10% CO2; Algae; Biomass; Bioreactors; 

Carbon dioxide; Fatty acids; Flue gas; Lipid 

metabolism; Microalgae; Total lipid 

Various methods, including autoclaving, bead-beating, microwaves, 

sonication, and a 10% NaCl solution, were tested 

to identify the most effective cell disruption method. The 

total lipids from Botryococcus sp., Chlorella vulgaris, and 

Scenedesmus sp. were extracted using a mixture of chloroform 

and methanol (1:1). The lipid contents from the three 

species were 5.4-11.9, 7.9-8.1, 10.0-28.6, 6.1-8.8, and 

6.8-10.9 g L(-1) when using autoclaving, bead-beating, microwaves, 

sonication, and a 10% NaCl solution, respectively. 

Botryococcus sp. showed the highest oleic acid productivity 

at 5.7 mg L(-1)d(-1) when the cells were disrupted using 

the microwave oven method. Thus, among the tested methods, 

the microwave oven method was identified as the most 

simple, easy, and effective for lipid extraction from 

microalgae. 

PMID: 19386486 

Keywords: Algae; Biodiesel; Biomass; Bioreactors; Cell 

disruption; Chemical fractionation; Chloroform; 

Lipid extraction; Microalgae 


Article 78 

Isolation and identification of FR198248, a hydroxylated 

1,3-dihydroisobenzofuran, from 

Aspergillus flavipes as an inhibitor of peptide deformylase 

Biosci Biotechnol Biochem. 2010; 74(2):390-3. 

Kwon YJ, Zheng CJ, Kim WG * 

* Correspondence: wgkim@kribb.re.kr 


Two highly hydroxylated 1,3-dihydroisobenzofurans, 

FR198248 (1) and FR202306 (2), were isolated as peptide 

deformylase (PDF) inhibitors from Aspergillus flavipes. 

Compounds 1 and 2 inhibited Staphylococus aureus PDF 

with IC(50) values of 3.6 and 2.5 

μM , respectively, and 

also showed antibacterial activity with an MIC value of 

25 microg/ml. In contrast, 6-O-methyl derivative 3 of compound 

2 was inactive against both PDF and S. aureus. 

PMID: 20139618 

Keywords: 1,3-dihydroisobenzofuran; Amidohydrolases; 

Antibacterial; Aspergillus flavipes; Benzofurans; 

Inhibitory concentration 50; Microbial sensitivity 

tests; Peptide deformylase; Staphylococcus aureus 

Article 79 

Cyanobactericidal effect of Rhodococcus sp. isolated 

from eutrophic lake on Microcystis sp. 

Biotechnol Lett. 2010 Nov; 32(11):1673-8. 

Lee YK, Ahn CY, Kim HS, Oh HM * 



A bacterium, which was observed in all cultivations of 

Microcystis sp., was isolated and designated as Rhodococcus 

sp. KWR2. The growth of bloom-forming cyanobacteria, 

including four strains of Microcystis aeruginosa and 

Anabaena variabilis, was suppressed by up to 75-88% by 

2% (v/v) culture broth of KWR2 after 5 days. But KWR2 

did not inhibit eukaryotic algae, Chlorella vulgaris and 

Scenedesmus sp. An extracellular algicidal substance produced 

by KWR2 showed a cyanobactericidal activity of 94% 

and was water-soluble with a molecular weight of lower 

than 8 kDa. 

PMID: 20640876 

Keywords: Algicide; Anabaena variabilis; Anti-bacterial 

agents; Antibiosis; Bloom; Chlorella vulgaris; 

Cyanobacteria; Microbial viability; Microcystis; 

Rhodococcus; Scenedesmus 


Article 80 

Complete reductive dechlorination of tetrachloroethene 

to ethene by anaerobic microbial enrichment 

culture developed from sediment 

Biotechnol Lett. 2010 Dec; 32(12):1829-35. 

Kim BH, Baek KH, Cho DH, Sung Y, Koh SC, Ahn CY, 

Oh HM, Kim HS * 

* Correspondence: hkim@kribb.re.kr 


A mixed, anaerobic microbial enrichment culture, AMEC-4P, 

was developed that uses lactate as the electron donor for 

the reductive dechlorination of tetrachloroethene (PCE) to 

ethene. AMEC-4P consistently and completely converted 

2 μM PCE to cis-1,2-dichloroethene ( cis-DCE) within 13 

days, and the intermediate, cis-DCE, was then completely 

dechlorinated to ethene after 130 days. Dechlorination rates 

for PCE to cis-DCE, cis-DCE to VC, and VC to ethene 

were 243, 27, and 41 

μmol/l/day, respectively. 

Geobacter 

lovleyi and a Dehalococcoides sp. were identified from their 

16S rRNA sequences to be the dominant phylotypes in 

AMEC-4P. 

PMID: 20714784 

Keywords: Anaerobic microbial enrichment; Anaerobiosis; 

Bacteria; Chlorine; Dechlorination; Microbial 

community analysis; Oxidation-reduction; 

Tetrachloroethene 

Article 81 

Classification of rice (Oryza sativa L. Japonica 

nipponbare) immunophilins (FKBPs, CYPs) and 

expression patterns under water stress 

BMC Plant Biol. 2010 Nov; 10:253. 

Ahn JC, Kim DW, You YN, Seok MS, Park JM, Hwang 

H, Kim BG, Luan S, Park HS * , Cho HS * 

* Correspondence: hspark@kribb.re.kr hscho@kribb.re.kr 



BACKGROUND: FK506 binding proteins (FKBPs) and cyclophilins 

(CYPs) are abundant and ubiquitous proteins belonging 

to the peptidyl-prolyl cis/trans isomerase (PPIase) 

superfamily, which regulate much of metabolism through 

a chaperone or an isomerization of proline residues during 

protein folding. They are collectively referred to as immunophilin 

(IMM), being present in almost all cellular 

organs. In particular, a number of IMMs relate to environmental 

stresses. 

RESULTS: FKBP and CYP proteins in rice (Oryza sativa 

cv. Japonica) were identified and classified, and given the 

appropriate name for each IMM, considering the ortholog-relation 

with Arabidopsis and Chlamydomonas or molecular 

weight of the proteins. 29 FKBP and 27 CYP genes 

can putatively be identified in rice; among them, a number 

of genes can be putatively classified as orthologs of 

Arabidopsis IMMs. However, some genes were novel, did 

not match with those of Arabidopsis and Chlamydomonas, 

and several genes were paralogs by genetic duplication. 

Among 56 IMMs in rice, a significant number are regulated 

by salt and/or desiccation stress. In addition, their expression 

levels responding to the water-stress have been analyzed 

in different tissues, and some subcellular IMMs located by 

means of tagging with GFP protein. 

CONCLUSION: Like other green photosynthetic organisms 

such as Arabidopsis (23 FKBPs and 29 CYPs) and 

Chlamydomonas (23 FKBs and 26 CYNs), rice has the highest 

number of IMM genes among organisms reported so 

far, suggesting that the numbers relate closely to 

photosynthesis. Classification of the putative FKBPs and 

CYPs in rice provides the information about their evolutional/functional 

significance when comparisons are drawn 

with the relatively well studied genera, Arabidopsis and 

Chlamydomonas. In addition, many of the genes upregulated 

by water stress offer the possibility of manipulating the stress 

responses in rice. 

PMID: 21087465 

Keywords: Cell nucleus; Cyclophilins; Cytoplasm; 

Immunophilins; Microscopy, fluorescence; Oryza 

sativa; Phylogeny; Protein isoforms; Sodium 

chloride; Tacrolimus binding proteins; Tobacco 


Article 82 

Exogenous sucrose utilization and starch biosynthesis 

among sweet potato cultivars 

Article 83 

Differential responses of sweetpotato peroxidases 

to heavy metals 

Carbohydr Res. 2010 Jan; 345(1):55-60. 

Chemosphere. 2010 Sep; 81(1):79-85. 

Ahn YO, Kim SH, Kim CY, Lee JS, Kwak SS, Lee HS * 

Kim YH, Lee HS, Kwak SS * 

* Correspondence: hslee@kribb.re.kr 


* Correspondence: sskwak@kribb.re.kr 


Three sweetpotato cultivars were investigated for their starch 

content and amylose/amylopectin ratio. Ym starch contains 

87.2% amylopectin and 12.8% amylose, when total starch 

was calculated as 100%. The Zm cultivar contains 33.6% 

amylopectin and 18.2% amylose, and its total starch was 

calculated as 51.8% of that of Ym. The Hm cultivar contains 

39.1% amylopectin and 30.5% amylose, and its total starch 

was 69.6%. We analyzed the expression levels of starch 

and sucrose biosynthesis-related genes including AGPases 

a, b, and c; sucrose synthases I and II; starch synthase I; 

GBSS I; and SBEs I and II. All genes tested in this experiment 

were detected only in Ym, while several genes showed very 

faint or no expression in Zm and Hm. We also measured 

tissue-specific expression of these genes in whole plants 

of Ym. Most of the genes are expressed in the stem and 

roots of the plants. Expression profiles of starch synthesis-related 

genes of the sweetpotato leaves were investigated 

after supplementing the different concentrations of 

sucrose solution. All genes in Ym were clearly induced by 

sucrose, but the expression levels of some of these genes 

did not change in Zm and Hm. The total starch content 

of Ym, Zm, and Hm gradually increased over time on addition 

of 3%, 6%, and 9% sucrose concentrations. The greatest 

accumulation was observed in Ym at 48h, and it was almost 

2.24 times higher than that of the (0%) control, while Zm 

and Hm showed 1.76 and 1.91 times higher levels of starch, 

respectively. These results indicate that cooperative expression 

of all related genes is essential for starch biosynthesis 

from sucrose. This is the first report on different sucrose 

contents and the efficiency with which exogenous sucrose 

switches on gene expression of starch biosynthesis-related 

genes among cultivars. 

PMID: 19896120 

Keywords: Amylopectin; Amylose; Gene expression 

regulation; Ipomoea batatas; Organ specificity; 

Starch; Starch biosynthesis; Sucrose; Sucrose 

feeding; Sweetpotato 

Oxidative stress is one of the major causes of damage in 

plants exposed to different types of environmental stress, 

including heavy metals. Accumulation of heavy metals in 

plants can disrupt many cellular functions and plant growth. 

To assess the contribution of oxidative stress to heavy metal 

toxicity in plants, young sweetpotato plants (Ipomoea batatas) 

were treated with increasing concentrations of Cd, Cu 

and Zn, and grown in half Murashige and Skoog nutrient 

solution culture. Plant growth was significantly inhibited 

and internal metal content was increased in a dose-dependent 

manner for each metal. The generation of H(2)O(2) in leaves 

and fibrous roots correlated positively with metal dose. The 

specific activity of peroxidases (PODs) in fibrous roots was 

markedly enhanced by metal treatment, whereas in leaves, 

activity was low and only slightly affected by metal treatment. 

Analysis of 13 POD genes revealed differential expression 

of PODs in response to heavy metals. Several genes for 

acidic PODs (swpa2, swpa3 and swpa4) and basic PODs 

(swpb1, swpb3 and swpab4) were strongly expressed under 

all metal treatment conditions in leaves or fibrous roots. 

The expression of swpa1 was increased in leaves and fibrous 

roots by Cd and Cu treatment, whereas swpb5 expression 

was reduced by all metals in fibrous roots. These results 

indicate that increased H(2)O(2) levels in response to heavy 

metal stress are closely linked to an improved antioxidant 

defense capability mediated by POD. 

PMID: 20638101 

Keywords: Biodegradation, environmental; Bio-indicator; 

Heavy metal stress; Hydrogen peroxide; Ipomoea 

batatas; Oxidative stress; Peroxidase; 

Phytoremediation; Reactive oxygen species; 

Sweetpotato 


Article 84 

Antibody responses in mice stimulated by various 

doses of the potato-derived major surface antigen 

of hepatitis B virus 

Article 85 

Annual variation of Microcystis genotypes and 

their potential toxicity in water and sediment from 

a eutrophic reservoir 

Clin Vaccine Immunol. 2010 Dec; 17(12):2029-32. 

FEMS Microbiol Ecol. 2010 Oct; 74(1):93-102. 

Youm JW, Won YS, Jeon JH, Moon KB, Kim HC, Shin 

KS, Joung H, Kim HS * 

* Correspondence: hyuns@kribb.re.kr 


The ability of potato-derived major surface antigen of hepatitis 

B virus (P-HBsAg) to elicit antibody responses to different 

dosages of P-HBsAg ranging from 0.02 to 30 

μg ad- 

ministered orally in mice was examined. All immunized 

groups produced specific serum IgG and fecal IgA antibodies 

against P-HBsAg, even at low levels (

Article 86 

Isolation and identification of pentagalloylglucose 

with broad-spectrum antibacterial activity from 

Rhus trichocarpa Miquel 

Food Chem. 2010 Nov; 123(2):501-6. 

Cho JY, Sohn MJ, Lee J, Kim WG * 



Rhus trichocarpa Miquel has been utilised both as a food 

and for medicinal purposes. In this study, we determined 

that the methanol extracts of the stem and leaf portions 

of R. trichocarpa inhibited the growth of both Gram-negative 

and Gram-positive bacteria. The active constituent was isolated, 

and identified via mass spectrometry and NMR as 

1,2,3,4,6-penta-O-galloyl-β-d-glucose. The compound also 

evidenced a broad spectrum of antibacterial activity against 

both Gram-negative and Gram-positive bacteria including 

Staphylococcus aureus (both methicillin-resistant S. aureus 

and quinolone-resistant S. aureus), Bacillus subtilis, 

Streptococcus mutans, Escherichia coli, Salmonella typhimurium, 

and Pseudomonas aeruginosa with MRC values of 

16-32 μg/ml, whereas gallate failed to inhibit the growth 

of Gram-negative bacteria, even at a concentration of 128 

μg/ml. The antibacterial activity of penta-O-galloylglucose 

was restored by the addition of Fe2+, whereas gallate was 

not, thereby indicating that its antibacterial activity could 

be attributable to the chelation of iron. The results of the 

time-kill study against S. aureus and E. coli revealed that 

penta-O-galloylglucose exhibited bacteriostatic activity. 

These findings indicate that the extracts of R. trichocarpa 

as well as its active component, penta-O-galloylglucose, may 

have profound potential for the control of both Gram-positive 

and negative pathogens. 

Article 87 

A Computational Simulation Study of 

Benzamidine Derivatives Binding to 

Arginine-Specific Gingipain (HRgpA) from 

Periodontopathogen Porphyromonas gingivalis 

Int J Mol Sci. 2010 Sep; 11(9):3252-65. 

Kim D, Lee DS * 

* Correspondence: daesilee@kribb.re.kr 


We have shown that the binding free energy calculation 

from molecular dynamics can be adapted successfully to 

cysteine proteinases, such as arginine-specific gingipain 

(HRgpA) from Porphyromonas gingivalis. The binding free 

energy obtained is in good agreement with the available 

experimental data for eight benzamidine derivatives including 

urea and ether linker. The calculations showed that the 

electrostatic energies between HRgpA and inhibitors were 

important in determining the relative affinities of the inhibitors 

to the HRgpA, with an average binding free energy 

of about -5 kcal/mol. The average structures of the eight 

complexes suggest that benzamidine inhibitors interact with 

Asp387, His435, and Cys468 by hydrogen bonding and with 

Trp508 by hydrophilic interactions that are essential for the 

activities of benzamidine inhibitors. It can therefore be expected 

that the method provides a reliable tool for the investigation 

of new HRgpA inhibitors. This finding could significantly 

benefit the future design of HRgpA inhibitors. 

PMID: 20957091 

Keywords: Arg-gingipain; Drug protein binding; Free 

energy; Hydrophilicity; Molecular dynamics; 

Porphyromonas gingivalis; Static electricity; 

Structural homology 

Keywords: Antibacterial activity; Bacillus subtilis; 

Bacteriostatic; Mass spectrometry; 

Penta-O-galloylglucose; Pseudomonas aeruginosa; 

Rhus trichocarpa; Salmonella typhimurium; 

Staphylococcus aureus; Streptococcus mutans 


Article 88 

Jeotgalibacillus salarius sp. nov., isolated from 

a marine saltern, and reclassification of 

Marinibacillus marinus and Marinibacillus campisalis 

as Jeotgalibacillus marinus comb. nov. 

and Jeotgalibacillus campisalis comb. nov., respectively 

Int J Syst Evol Microbiol. 2010 Jan; 60(1):15-20. 

Yoon JH * , Kang SJ, Schumann P, Oh TK 

* Correspondence: jhyoon@kribb.re.kr 


A Gram-variable, motile and rod-shaped bacterial strain, 

ASL-1 T , was isolated from a marine saltern located on the 

coast of the Yellow Sea, Korea. A neighbour-joining phylogenetic 

tree based on 16S rRNA gene sequences showed that 

strain ASL-1 T clustered with Jeotgalibacillus alimentarius 

YKJ-13 T and that this cluster joined the clade comprising 

the type strains of two Marinibacillus species. Strain ASL-1 T 

exhibited 16S rRNA gene sequence similarity values of 97.3 

% to J. alimentarius YKJ-13 T and 96.5 % to the type strains 

of Marinibacillus marinus and Marinibacillus campisalis. 

The chemotaxonomic properties of strain ASL-1 T were similar 

to those of one or two of the genera Jeotgalibacillus 

and Marinibacillus. The peptidoglycan type was A1α 

linked 

directly through L-lysine as the diamino acid. Strain ASL-1 T 

contained MK-7 as the predominant menaquinone with the 

presence of a significant amount of MK-8. The predominant 

fatty acid was anteiso-C 15:0. The DNA G+C content was 

42.9 mol%. Differential phenotypic properties, together with 

the phylogenetic and genetic distinctiveness, revealed that 

strain ASL-1 T could be differentiated from J. alimentarius 

and the two Marinibacillus species. On the basis of the 

data presented, strain ASL-1 T represents a novel species within 

the genus Jeotgalibacillus, for which the name 

Jeotgalibacillus salarius sp. nov. is proposed. The type strain 

is ASL-1 T (=KCTC 13257 T =CCUG 56751 T ). It is also proposed 

that Marinibacillus marinus and Marinibacillus campisalis 

be reclassified as Jeotgalibacillus marinus comb. nov. 

(type strain 581 T =DSM 1297 T =ATCC 29841 T =CCUG 

28884 T =CIP 103308 T =LMG 6930 T ) and Jeotgalibacillus 

campisalis comb. nov. (type strain SF-57 T =KCCM 

41644 T =JCM 11810 T ), respectively. 

PMID: 19643870 

Article 89 

Jannaschia seohaensis sp. nov., isolated from a 

tidal flat sediment 


Yoon JH * , Kang SJ, Park S, Oh KH, Oh TK 



A Gram-negative, motile and pleomorphic bacterial strain, 

SMK-146 T , was isolated from a tidal flat sediment of the 

Yellow Sea, Korea, and its taxonomic position was 

investigated. Strain SMK-146 T grew optimally at pH 7.0-8.0 

and 30 degrees C. It contained Q-10 as the predominant 

ubiquinone and C(18 : 1) ω7c and 11-methyl C(18 : 1) ω7c 

as the major fatty acids. The major polar lipids were phosphatidylcholine, 

phosphatidylglycerol and 

phosphatidylethanolamine. The DNA G+C content was 68.4 

mol%. Phylogenetic analysis based on 16S rRNA gene sequences 

showed that strain SMK-146 T belongs to the genus 

Jannaschia. Strain SMK-146 T exhibited 16S rRNA gene sequence 

similarity values of 95.3-97.0 % to the type strains 

of the five recognized Jannaschia species. The mean 

DNA-DNA relatedness value between strain SMK-146 T and 

Jannaschia seosinensis KCCM 42114 T , the closest phylogenetic 

neighbour, was 17 %. Differential phenotypic properties 

also revealed that strain SMK-146 T differs from the recognized 

Jannaschia species. On the basis of phenotypic, phylogenetic 

and genetic data, strain SMK-146 T represents a novel 

species of the genus Jannaschia, for which the name 

Jannaschia seohaensis sp. nov. is proposed. The type strain 

is SMK-146 T (=KCTC 22172 T =CCUG 55326 T ). 

PMID: 19648318 

Keywords: Base composition; DNA, bacterial; DNA, 

ribosomal; Fatty acids; Geologic sediments; 

Molecular sequence data; Phylogeny; 

Rhodobacteraceae; RNA, ribosomal, 16S; Seawater 

Keywords: Bacillales; Base composition; DNA, Bacterial; 

DNA, ribosomal; Fatty acids; Geologic sediments; 

Molecular sequence data; Phylogeny; RNA, 

ribosomal, 16S; Seawater 


Article 90 

Gaetbulicola byunsanensis gen. nov., sp. nov., 

isolated from tidal flat sediment 

Article 91 

Algoriphagus lutimaris sp. nov., isolated from a 




Yoon JH * , Kang SJ, Jung YT, Oh TK 

Park S, Kang SJ, Oh KH, Oh TK, Yoon JH * 





A Gram-negative, non-motile and pleomorphic bacterial 

strain, SMK-114 T , which belongs to the class 

Alphaproteobacteria, was isolated from a tidal flat sample 

collected in Byunsan, Korea. Strain SMK-114 T grew optimally 

at pH 7.0-8.0 and 25-30 degrees C and in the presence 

of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree 

based on 16S rRNA gene sequences showed that strain 

SMK-114 T formed a cluster with Octadecabacter species, 

with which it exhibited 16S rRNA gene sequence similarity 

values of 95.2-95.4 %. This cluster was part of the clade 

comprising Thalassobius species with a bootstrap resampling 

value of 76.3 %. Strain SMK-114 T exhibited 16S rRNA 

gene sequence similarity values of 95.1-96.3 % to members 

of the genus Thalassobius. It contained Q-10 as the predominant 

ubiquinone and C(18 : 1) ω7c as the major fatty acid. 

The DNA G+C content was 60.0 mol%. On the basis of 

phenotypic, chemotaxonomic and phylogenetic data, strain 

SMK-114 T is considered to represent a novel species in a 

new genus for which the name Gaetbulicola byunsanensis 

gen. nov., sp. nov. is proposed. The type strain of 

Gaetbulicola byunsanensis is SMK-114 T (=KCTC 

22632 T =CCUG 57612 T ). 

PMID: 19648332 



Molecular sequence data; Phylogeny; 

Rhodobacteraceae; RNA, ribosomal, 16S; Seawater 

A Gram-negative, non-motile, non-spore-forming bacterial 

strain, S1-3 T , was isolated from a tidal flat sediment on 

the west coast of Korea and its taxonomic position was 

investigated. Strain S1-3 T grew optimally at 30 degrees C 

and in the presence of 2 % (w/v) NaCl. Strain S1-3 T contained 

MK-7 as the predominant menaquinone and C(16 : 1) ω7c 

and/or iso-C(15 : 0) 2-OH and iso-C(15 : 0) as the major 

fatty acids. The DNA G+C content was 41.4 mol%. 

Phylogenetic analyses based on 16S rRNA gene sequences 

revealed that strain S1-3 T fell within the clade comprising 

Algoriphagus species, clustering with Algoriphagus halophilus 

IMSNU 14013 T , with which it exhibited 99.6 % 

16S rRNA gene sequence similarity. The 16S rRNA gene 

sequence similarity between strain S1-3 T and the type strains 

of other Algoriphagus species was 94.0-97.1 %. Differential 

phenotypic properties and phylogenetic and genetic distinctiveness 

of strain S1-3 T demonstrated that this strain is 

distinguishable from the other Algoriphagus species as well 

as A. halophilus. On the basis of phenotypic, chemotaxonomic, 

phylogenetic and genetic data, strain S1-3 T is 

considered to represent a novel species of the genus 

Algoriphagus, for which the name Algoriphagus lutimaris 

sp. nov. is proposed. The type strain is S1-3 T (=KCTC 22630 T 

=CCUG 57608 T ). 

PMID: 19648320 

Keywords: Bacteroidetes; DNA, bacterial; DNA, 



ribosomal, 16S; Seawater 


Article 92 

Lysinibacillus xylanilyticus sp. nov., a xylan-degrading 

bacterium isolated from forest humus 

Article 93 

Virgibacillus byunsanensis sp. nov., isolated from 

a marine solar saltern 

Int J Syst Evol Microbiol. 2010 Feb; 60(2):281-6. 


Lee CS, Jung YT, Park S, Oh TK, Yoon JH * 

Yoon JH * , Kang SJ, Jung YT, Lee KC, Oh HW, Oh TK 





A novel xylan-degrading bacterium, designated XDB9 T , was 

isolated from forest humus collected from Gyeryong 

Mountain in Korea. Cells were Gram-positive, aerobic, motile 

and endospore-forming rods. A neighbour-joining phylogenetic 

tree based on 16S rRNA gene sequences showed that 

strain XDB9 T was most closely related to members of the 

genus Lysinibacillus. 16S rRNA gene sequence similarities 

between strain XDB9 T and the type strains of species of 

the genus Lysinibacillus ranged from 98.0 to 98.5 %. The 

cell-wall peptidoglycan type of strain XDB9 T was A4 α, which 

is based on L-Lys-D-Asp. Strain XDB9 T contained iso-C(15 

: 0) and C(16 : 1) ω7c alcohol as the major fatty acids and 

MK-7 as the predominant menaquinone. The major polar 

lipids were diphosphatidylglycerol, phosphatidylglycerol and 

phosphatidylethanolamine. The DNA G+C content was 37.2 

mol%. The DNA-DNA hybridization results and differential 

phenotypic properties showed that strain XDB9 T could be 

distinguished from recognized species of the genus 

Lysinibacillus. It was concluded that strain XDB9 T represents 

a new taxon for which the name Lysinibacillus xylanilyticus 

sp. nov. is proposed. The type strain is XDB9 T (=KCTC 

13423 T =CCUG 57438 T ). 

PMID: 19651743 

Keywords: Bacillaceae; Base composition; Base sequence; 

DNA, bacterial; Korea; Molecular sequence data; 

Phylogeny; RNA, bacterial; RNA, ribosomal, 16S; 

Sequence homology; Soil microbiology; Trees; 

Xylans 

A Gram-variable, motile, endospore-forming and rod-shaped 

bacterial strain, ISL-24 T , was isolated from a marine solar 

saltern of the Yellow Sea, Korea, and its taxonomic position 

was investigated by a polyphasic study. Strain ISL-24 T grew 

optimally at pH 7.0-8.0, at 30-37 degrees C and in the presence 

of 8 % (w/v) NaCl. It contained MK-7 as the predominant 

menaquinone and anteiso-C(15 : 0) as the predominant 

fatty acid. The DNA G+C content was 37.6 mol%. A phylogenetic 

analysis based on 16S rRNA gene sequences showed 

that strain ISL-24 T fell within the genus Virgibacillus, clustering 

with Virgibacillus carmonensis LMG 20964 T and 

Virgibacillus necropolis LMG 19488 T , with a bootstrap resampling 

value of 92.3 %, and exhibiting 97.3 and 97.4 

% 16S rRNA gene sequence similarity, respectively, to these 

strains. Strain ISL-24 T exhibited 94.8-96.8 % 16S rRNA 

gene sequence similarity to the type strains of the other 

Virgibacillus species. Mean DNA-DNA relatedness values 

between strain ISL-24 T and V. carmonensis DSM 14868 T 

and V. necropolis DSM 14866 T were 11 and 19 %, 

respectively. Differential phenotypic properties of strain 

ISL-24 T , together with the phylogenetic and genetic distinctiveness, 

revealed that this strain is different from recognized 

Virgibacillus species. On the basis of phenotypic, phylogenetic 

and genetic data, strain ISL-24 T represents a novel 

species of the genus Virgibacillus, for which the name 

Virgibacillus byunsanensis sp. nov. is proposed. The type 

strain is ISL-24 T (=KCTC 13259 T =CCUG 56754 T ). 

PMID: 19651717 

Keywords: Bacillaceae; Base composition; Base sequence; 

DNA, bacterial; Korea; Molecular sequence data; 

Phylogeny; RNA, bacterial; RNA, ribosomal, 16S; 

Seawater; Sequence homology; Water microbiology 


Article 94 

Alkalibacillus flavidus sp. nov., isolated from a 

marine solar saltern 

Article 95 

Lutibacter maritimus sp. nov., isolated from a 



Int J Syst Evol Microbiol. 2010 Mar; 60(3):610-4. 

Yoon JH * , Kang SJ, Jung YT, Lee MH, Oh TK 

Park S, Kang SJ, Oh TK, Yoon JH * 





A Gram-stain-positive, motile, rod-shaped bacterial strain, 

ISL-17 T , was isolated from a marine solar saltern of the 

Yellow Sea, Korea, and its taxonomic position was investigated 

by means of a polyphasic study. Strain ISL-17 T grew 

optimally at pH 8.5-9.0, at 37 degrees C and in the presence 

of approximately 10 % (w/v) NaCl. It contained meso-diaminopimelic 

acid as the diagnostic diamino acid in the peptidoglycan, 

MK-7 as the predominant menaquinone and 

iso-C(15 : 0), anteiso-C(15 : 0) and iso-C(16 : 0) as the 

major fatty acids. The DNA G+C content was 48.1 mol%. 

Phylogenetic analysis based on 16S rRNA gene sequences 

showed that strain ISL-17 T fell within the genus 

Alkalibacillus, clustering with Alkalibacillus salilacus 

BH163 T with a bootstrap resampling value of 100 %. Strain 

ISL-17 T exhibited 98.2 % 16S rRNA gene sequence similarity 

to A. salilacus BH163 T and 95.8-96.5 % similarity to the 

type strains of the other Alkalibacillus species. The mean 

DNA-DNA relatedness value between strain ISL-17 T and 

A. salilacus KCTC 3916 T was 19 %. The phenotypic properties 

of strain ISL-17 T , together with its phylogenetic and 

genetic distinctiveness, enable this strain to be differentiated 

from recognized Alkalibacillus species. On the basis of phenotypic, 

phylogenetic and genetic data, strain ISL-17 T represents 

a novel species within the genus Alkalibacillus, for 

which the name Alkalibacillus flavidus sp. nov. is proposed; 

the type strain is ISL-17 T (=KCTC 13258 T =CCUG 56753 T ). 

PMID: 19651725 

A Gram-staining-negative, aerobic, non-motile, non-gliding, 

yellow-pigmented and rod-shaped bacterial strain, designated 

S7-2 T , was isolated from a tidal flat sediment at Saemankum 

on the west coast of Korea and investigated using a polyphasic 

taxonomic approach. Strain S7-2 T grew optimally at pH 

7.0-8.0, at 25-30 degrees C and in the presence of 2 % 

(w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene 

sequences showed that strain S7-2 T clustered with Lutibacter 

litoralis CF-TF09 T , a member of the family 

Flavobacteriaceae, with which it showed 95.8 % 16S rRNA 

gene sequence similarity. It contained MK-6 as the predominant 

menaquinone and iso-C(15 : 0) and C(15 : 1) 

ω6c 

as the major fatty acids. The major polar lipids of strain 

S7-2 T and L. litoralis JCM 13034 T were phosphatidylethanolamine 

and three unidentified lipids. The DNA G+C content 

was 34.6 mol%. Differential phenotypic properties and phylogenetic 

distinctiveness suggested that strain S7-2 T represents 

a novel species of the genus Lutibacter, for which the name 

Lutibacter maritimus sp. nov. is proposed. The type strain 

is S7-2 T (=KCTC 22635 T =CCUG 57524 T ). 

PMID: 19654353 

Keywords: DNA, bacterial; DNA, ribosomal; Fatty acids; 

Flavobacteriaceae; Geologic sediments; Molecular 

sequence data; Phylogeny; RNA, ribosomal, 16S; 

Seawater 

Keywords: Bacillaceae; Base composition; DNA, bacterial; 

Korea; Molecular sequence data; Phylogeny; RNA, 

bacterial; RNA, ribosomal, 16S; Seawater; Sequence 

homology; Sodium chloride; Water microbiology 


Article 96 

Planococcus salinarum sp. nov., isolated from 

a marine solar saltern, and emended description 

of the genus Planococcus 

Article 97 

Description of Olleya aquimaris sp. nov., isolated 

from seawater, and emended description of the 

genus Olleya Mancuso Nichols et al. 2005 

Int J Syst Evol Microbiol. 2010 Apr; 60(4):754-8. 

Int J Syst Evol Microbiol. 2010 Apr; 60(4):887-91. 

Yoon JH * , Kang SJ, Lee SY, Oh KH, Oh TK 

Lee SY, Park S, Oh TK, Yoon JH * 





A Gram-positive, non-motile and coccoid-, short rod- or 

rod-shaped bacterial strain, ISL-16 T , was isolated from a 

marine solar saltern in Korea and its taxonomic position 

was investigated using a polyphasic taxonomic approach. 

Strain ISL-16 T grew optimally at pH 7.0-8.0, at 30 degrees 

C and in the presence of 2 % (w/v) NaCl. Phylogenetic 

analysis based on 16S rRNA gene sequences showed that 

strain ISL-16 T joined the cluster comprising species of the 

genus Planococcus. Its 16S rRNA gene sequence contained 

the same signature nucleotides as those defined for the genus 

Planococcus. Strain ISL-16 T exhibited 16S rRNA gene sequence 

similarity values of 96.9-98.2 % to the type strains 

of species of the genus Planococcus. Strain ISL-16 T contained 

MK-8 and MK-7 as the predominant menaquinones and anteiso-C(15 

: 0), C(16 : 1) ω7c alcohol and anteiso-C(17 : 0) 

as the major fatty acids. The DNA G+C content was 48.3 

mol%. DNA-DNA relatedness values between strain ISL-16 T 

and the type strains of species of the genus Planococcus 

were 15-28 %. Differential phenotypic properties, together 

with its phylogenetic and genetic distinctiveness, enabled 

strain ISL-16 T to be differentiated from recognized species 

of the genus Planococcus. On the basis of the data presented, 

strain ISL-16 T is considered to represent a novel species 

of the genus Planococcus, for which the name Planococcus 

salinarum sp. nov. is proposed. The type strain is ISL-16 T 

(=KCTC 13584 T =CCUG 57753 T ). An emended description 

of the genus Planococcus is also given. 

PMID: 19656937 

Keywords: Bacillales; Base composition; DNA, ribosomal; 

Genes, rRNA; Geologic sediments; Molecular 

sequence data; Nucleic acid hybridization; 

Phenotype; Phylogeny; Republic of Korea; RNA, 

ribosomal, 16S; Seawater; Species specificity 

A Gram-stain-negative, non-flagellated, motile (by gliding), 

yellow-pigmented, rod-shaped bacterial strain, designated 

L-4 T , was isolated from seawater of Baekdo harbour in the 

East Sea, Korea. Strain L-4 T grew optimally at 37 degrees 

C, at pH 6.5-7.0 and in the presence of 2 % (w/v) NaCl. 


showed that strain L-4 T clustered with Olleya marilimosa 

CAM030 T , a member of the family Flavobacteriaceae. Strain 

L-4 T exhibited 16S rRNA gene sequence similarity values 

of 97.2 % to O. marilimosa CAM030 T and less than 95.8 

% to other members of the family Flavobacteriaceae. Strain 

L-4 T and O. marilimosa CIP 108537 T contained MK-6 as 

the predominant menaquinone. The fatty acid and polar lipid 

profiles of strain L-4 T were similar to those of O. marilimosa 

CIP 108537 T . The DNA G+C content of strain L-4 T was 

35 mol% and DNA-DNA relatedness between strain L-4 T and 

O. marilimosa CIP 108537 T was 7 %. Differential phenotypic 

properties, together with its phylogenetic and genetic distinctiveness, 

enable strain L-4 T to be distinguished from O. 

marilimosa . On the basis of these data, strain L-4 T is considered 

to represent a novel species of the genus Olleya for 

which the name Olleya aquimaris sp. nov. is proposed; the 

type strain is L-4 T (=KCTC 22661 T =CCUG 58074 T ). An 

emended description of the genus Olleya is also provided. 

PMID: 19661521 

Keywords: DNA, ribosomal; Flavobacteriaceae; Genes, 

rRNA; Genotype; Molecular sequence data; Nucleic 

acid hybridization; Phenotype; Phylogeny; Republic 

of Korea; RNA, ribosomal, 16S; Seawater; Species 

specificity 


Article 98 

Roseivivax lentus sp. nov., isolated from a tidal 

flat sediment, and emended description of the genus 

Roseivivax Suzuki et al. 1999 

Article 99 

Pseudoruegeria lutimaris sp. nov., isolated from 

a tidal flat sediment, and emended description 

of the genus Pseudoruegeria 

Int J Syst Evol Microbiol. 2010 May; 60(5):1113-7. 

Int J Syst Evol Microbiol. 2010 May; 60(5):1177-81. 

Park S, Kang SJ, Oh TK, Yoon JH * 

Jung YT, Kim BH, Oh TK, Yoon JH * 





A Gram-negative-staining, aerobic, non-motile and rod-shaped 

bacterial strain, S5-5 T , was isolated from a tidal flat sediment 

at Saemankum on the west coast of Korea and subjected 

to a polyphasic taxonomic investigation. Strain S5-5 T grew 

optimally at pH 7.5-8.0, at 30 degrees C and in the presence 

of 2 % (w/v) NaCl. It did not produce bacteriochlorophyll 

a. Phylogenetic analyses based on 16S rRNA gene sequences 

showed that strain S5-5 T is phylogenetically closely related 

to the genus Roseivivax, joining the cluster comprising the 

two recognized Roseivivax species. The 16S rRNA gene 

sequence similarity between strain S5-5 T and members of 

the genus Roseivivax was in the range 95.0-96.7 %. Strain 

S5-5 T contained Q-10 as the predominant ubiquinone and 

C(18 : 1) ω7c and 11-methyl C(18 : 1) ω7c as the major 

fatty acids. The DNA G+C content was 68.2 mol%. 

Differential phenotypic properties, together with the phylogenetic 

distinctiveness, demonstrated that strain S5-5 T could 

be differentiated from Roseivivax species. On the basis of 

the data presented, strain S5-5 T is considered to represent 

a novel species of the genus Roseivivax, for which the name 

Roseivivax lentus sp. nov. is proposed. The type strain is 

S5-5 T (=KCTC 22708 T =CCUG 57755 T ). 

PMID: 19666792 


ribosomal; Genes, rRNA; Geologic sediments; 

Molecular sequence data; Phenotype; Phylogeny; 

Republic of Korea; Rhodobacteraceae; RNA, 


A Gram-negative-staining, non-motile and rod-shaped bacterial 

strain, HD-43 T , was isolated from a tidal flat sediment 

collected from Hwang-do, an island of Korea. Strain HD-43 T 

grew optimally at pH 7.0-8.0, at 30 degrees C and in the 

presence of 2 % (w/v) NaCl. Phylogenetic analyses based 

on 16S rRNA gene sequences showed that strain HD-43 T 

clustered with Pseudoruegeria aquimaris SW-255 T . It exhibited 

96.6 % 16S rRNA gene sequence similarity and 79.4 

% gyrB sequence similarity with P. aquimaris SW-255 T . 

Strain HD-43 T contained Q-10 as the predominant ubiquinone 

and C(18 : 1) ω7c as the major fatty acid. The major polar 

lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, 

an unidentified aminolipid, an unidentified 

glycolipid and an unidentified lipid. The DNA 

G+C content was 73.5 mol%. The mean DNA-DNA relatedness 

between strain HD-43 T and P. aquimaris SW-255 T was 

5 %. Differential phenotypic properties demonstrated that 

strain HD-43 T is clearly distinguishable from P. aquimaris. 

On the basis of phenotypic, chemotaxonomic and phylogenetic 

data, strain HD-43 T is considered to represent a novel 

species of the genus Pseudoruegeria, for which the name 

Pseudoruegeria lutimaris sp. nov. is proposed. The type 

strain is HD-43 T (=KCTC 22690 T =CCUG 57754 T ). 

PMID: 19667391 

Keywords: Base composition; DNA gyrase; DNA, 

bacterial; DNA, ribosomal; Genes, rRNA; Genotype; 

Geologic sediments; Molecular sequence data; 

Nucleic acid hybridization; Phenotype; Phylogeny; 

Republic of Korea; Rhodobacteraceae; RNA, 



Article 100 

Nocardioides daedukensis sp. nov., a halotolerant 

bacterium isolated from soil 

Int J Syst Evol Microbiol. 2010 Jun; 60(6):1334-8. 

Yoon JH * , Park S, Kang SJ, Lee JS, Lee KC, Oh TK 



A Gram-positive, non-motile and rod- or coccoid-shaped 

bacterial strain, MDN22 T , was isolated from a soil sample 

from Korea. Strain MDN22 T grew optimally at pH 7.0-8.0, 

at 30 degrees C and in the presence of 0-0.5 % (w/v) NaCl. 


showed that strain MDN22 T was phylogenetically most closely 

related to the genera Nocardioides and Marmoricola. In 

the neighbour-joining phylogenetic tree, strain MDN22 T was 

most closely related to Nocardioides jensenii KCTC 9134 T , 

with which it exhibited 98.3 % 16S rRNA gene sequence 

similarity. The strain exhibited 93.1-96.9 % and 95.3-95.9 

% 16S rRNA gene sequence similarities to the type strains 

of other species of the genera Nocardioides and Marmoricola, 

respectively. The chemotaxonomic properties of strain 

MDN22 T were consistent with those of the genus 

Nocardioides; the cell-wall peptidoglycan type was based 

on ll-2,6-diaminopimelic acid, the predominant menaquinone 

was MK-8(H(4)) and the major fatty acids were iso-C(16 

: 0) and C(17 : 1). The DNA G+C content was 68.7 mol%. 

DNA-DNA relatedness data and differential phenotypic properties 

suggested that strain MDN22 T could be differentiated 

from N. jensenii and Nocardioides dubius. On the basis of 

the data obtained, strain MDN22 T is considered to represent 

a novel species of the genus Nocardioides, for which the 

name Nocardioides daedukensis sp. nov., is proposed. The 

type strain is MDN22 T (=KCTC 19601 T =CCUG 57505 T ). 

PMID: 19667373 

Keywords: Actinomycetales; DNA, bacterial; Molecular 

sequence data; Phenotype; Phylogeny; RNA, 

bacterial; RNA, ribosomal, 16S; Soil microbiology 

Article 101 

Rhizobium soli sp. nov., isolated from soil 

Int J Syst Evol Microbiol. 2010 Jun; 60(6):1387-93. 

Yoon JH, Kang SJ, Yi HS, Oh TK, Ryu CM * 

* Correspondence: cmryu@kribb.re.kr 


A Gram-negative, non-motile, pale-yellow, rod-shaped bacterial 

strain, DS-42 T , was isolated from a soil in Korea and 

its taxonomic position was investigated by a polyphasic 

study. Strain DS-42 T grew optimally at 25 degrees C and 

pH 7.0-8.0. Strain DS-42 T did not form nodules on three 

different legumes, and the nodD and nifH genes were also 

not detected by PCR. Strain DS-42 T contained Q-10 as the 

predominant ubiquinone. The major cellular fatty acid was 

C(18 : 1) ω7c. The DNA G+C content was 60.8 mol%. 

Phylogenetic analyses based on 16S rRNA, atpD and recA 

gene sequences showed that strain DS-42 T belonged to the 

genus Rhizobium. Strain DS-42 T showed 16S rRNA gene 

sequence similarity of 94.1-97.7 % to the type strains of 

recognized Rhizobium species. DNA-DNA relatedness between 

strain DS-42 T and the type strains of Rhizobium huautlense, 

R. galegae, R. loessense and R. cellulosilyticum was 

13-19 %, indicating that strain DS-42 T was distinct from 

them genetically. Strain DS-42 T can also be differentiated 

from these four phylogenetically related Rhizobium species 

by various phenotypic properties. On the basis of phenotypic 

properties, phylogenetic distinctiveness and genetic data, 

strain DS-42 T is considered to represent a novel species 

of the genus Rhizobium, for which the name Rhizobium 

soli sp. nov. is proposed. The type strain is DS-42 T (=KCTC 

12873 T =JCM 14591 T ). 

PMID: 19671727 

Keywords: Anti-bacterial agents; Enzymes; Fatty acids; 

Hexoses; Molecular sequence data; Phylogeny; 

Republic of Korea; Rhizobium; Soil microbiology 


Article 102 

Thalassobacillus hwangdonensis sp. nov., isolated 

from a tidal flat sediment 

Article 103 

Photobacterium gaetbulicola sp. nov., a lipolytic 

bacterium isolated from a tidal flat sediment 

Int J Syst Evol Microbiol. 2010 Sep; 60(9):2108-12. 

Int J Syst Evol Microbiol. 2010 Nov; 60(11):2587-91. 

Lee SY, Oh TK, Yoon JH * 



A Gram-staining-positive, endospore-forming, motile, 

rod-shaped bacterium, strain AD-1 T , was isolated from a 

tidal flat sediment of the coast of Hwangdo on the Yellow 

Sea, Korea. Strain AD-1 T grew optimally at pH 7.0-7.5 and 

40 degrees C and in the presence of 5-10 % (w/v) NaCl. 

Phylogenetic analysis based on 16S rRNA gene sequences 

showed that strain AD-1 T was most closely related to 

Thalassobacillus devorans G-19.1 T (98.0 % sequence similarity) 

and Thalassobacillus cyri HS286 T (97.8 %). The 

cell-wall peptidoglycan was based on meso-diaminopimelic 

acid and MK-7 was the predominant menaquinone. The major 

polar lipids were diphosphatidylglycerol, phosphatidylglycerol 

and two unidentified lipids. The major fatty acids (>10 

% of total fatty acids) were iso-C(15 : 0), iso-C(17 : 0) 

and anteiso-C(15 : 0). The DNA G+C content of strain AD-1 T 

was 45.2 mol%. It appears reasonable to classify strain AD-1 T 

as a member of the genus Thalassobacillus. There were 

differences in fatty acid profiles and phenotypic and genetic 

characteristics between strain AD-1 T and the type strains 

of the two Thalassobacillus species. On the basis of the 

data presented, strain AD-1 T represents a novel species within 

the genus Thalassobacillus, for which the name 

Thalassobacillus hwangdonensis sp. nov. is proposed. The 

type strain is AD-1 T (=KCTC 13254 T =CCUG 56607 T ). 

PMID: 19854876 

Keywords: Bacillaceae; DNA, bacterial; DNA, ribosomal; 

Fatty acids; Geologic sediments; Molecular sequence 

data; Phylogeny; RNA, ribosomal, 16S; Seawater 

Kim YO, Kim KK, Park S, Kang SJ, Lee JH, Lee SJ, Oh 

TK, Yoon JH * 



A Gram-negative, motile, non-spore-forming and lipolytic 

bacterial strain, designated Gung47 T , was isolated from a 

tidal flat on the west coast of Korea. Strain Gung47 T grew 

optimally at 30 °C and with 2-5 % (w/v) NaCl. Phylogenetic 

analyses based on 16S rRNA gene sequences revealed that 

strain Gung47 T belonged to the genus Photobacterium. Strain 

Gung47 T exhibited 98.1 % 16S rRNA gene sequence similarity 

with Photobacterium rosenbergii LMG 22223 T and 

94.3-96.3 % similarity with other type strains of species of 

the genus Photobacterium. Strain Gung47 T exhibited 47 % 

DNA-DNA relatedness to P. rosenbergii LMG 22223 T . Strain 

Gung47 T contained Q-8 as the predominant ubiquinone and 

C(16 : 1) ω 7c and/or iso-C(15 : 0) 2-OH, C(16 : 0) and 

C(18 : 1) ω7c as the major fatty acids. In this study, two close - 

ly related type strains, P. rosenbergii LMG 22223 T and 

Photobacterium halotolerans LMG 22194 T , were also found 

to have Q-8 as the predominant ubiquinone. The DNA G+C 

content of strain Gung47 T was 50.6 mol%. The differential 

phenotypic properties together with the phylogenetic and 

genetic distinctiveness of strain Gung47 T demonstrated that 

this strain is distinguishable from recognized Photobacterium 

species. Therefore, strain Gung47 T is considered to represent 

a novel species of the genus Photobacterium, for which 

the name Photobacterium gaetbulicola sp. nov. is proposed. 

The type strain is Gung47 T (=KCTC 22804 T =CCUG 

58399 T ). 

PMID:20023056 

Keywords: Bacterial typing techniques; Base composition; 

DNA, bacterial; Geologic sediments; Molecular 

sequence data; Photobacterium; Phylogeny; RNA, 

ribosomal, 16S; Seawater; Sodium chloride 


Article 104 

Oceanobacillus locisalsi sp. nov., isolated from 

a marine solar saltern 

Int J Syst Evol Microbiol. 2010 Dec; 60(12):2758-62. 

Lee SY, Oh TK, Kim W, Yoon JH * 



A Gram-stain-variable, motile, moderately halophilic bacterial 

strain, CHL-21 T , was isolated from a marine solar saltern 

and its taxonomic position was investigated using a polyphasic 

approach. Optimal growth of strain CHL-21 T occurred 

at 30-37 °C, at pH 7.0-7.5 and in the presence of 5-10 

% (w/v) NaCl. In phylogenetic trees based on 16S rRNA 

gene sequences, strain CHL-21 T fell within the cluster comprising 

members of the genera Oceanobacillus, 

Ornithinibacillus and Paucisalibacillus. Strain CHL-21 T exhibited 

97.1-97.2 % 16S rRNA gene sequence similarity to 

the type strains of the two subspecies of Oceanobacillus 

oncorhynchi and 92.0-94.7 % 16S rRNA gene sequence similarity 

to the type strains of other members of the genus 

Oceanobacillus and members of the genera Ornithinibacillus 

and Paucisalibacillus. Mean DNA-DNA reassociation values 

between strain CHL-21 T and the type strains of the two 

subspecies of Oceanobacillus oncorhynchi were 19-21 %. 

The cell-wall peptidoglycan of strain CHL-21 T was based 

on meso-diaminopimelic acid, MK-7 was the predominant 

menaquinone, and anteiso-C(15 : 0) and anteiso-C(17 : 0) 

were the major fatty acids. The DNA G+C content was 

39.8 mol%. Differential phenotypic properties, including facultatively 

anaerobic growth and acid production from substrates, 

together with its phylogenetic and genetic distinctiveness, 

demonstrated that strain CHL-21 T is distinguishable 

from recognized Oceanobacillus species. On the basis of 

data presented, strain CHL-21 T represents a novel species 

within the genus Oceanobacillus, for which the name 

Oceanobacillus locisalsi sp. nov. is proposed; the type strain 

is CHL-21 T (=KCTC 13253 T =CCUG 56608 T ). 

PMID: 20061491 

Keywords: Anaerobic bacterium; Bacillus; Bacterial cell 

wall; Bacterial strain; DNA base composition; Gene 

sequence; Gram staining; Halophilic bacterium; 

Marine bacterium; Oceanobacillus locisalsi; 

Oceanobacillus oncorhynchi; Ornithinibacillus; 

Paucisalibacillus; Phenotype; Phylogenetic tree 

Article 105 

Paracoccus fistulariae sp. nov., a lipolytic 

bacterium isolated from bluespotted cornetfish, 

Fistularia commersonii 


Kim YO, Kong HJ, Park S, Kang SJ, Kim KK, Moon DY, 

Oh TK, Yoon JH * 



A Gram-stain-negative, non-motile, non-spore-forming and 

short rod- or rod-shaped bacterial strain, designated 22-5 T , 

was isolated from a bluespotted cornetfish, Fistularia commersonii, 

and subjected to taxonomic study. Strain 22-5 T 

grew optimally at 30&emsp14;°C and in the presence of 

2-5 % (w/v) NaCl. Phylogenetic analyses based on 16S 

rRNA gene sequences revealed that strain 22-5 T belonged 

to the genus Paracoccus and joined the cluster comprising 

Paracoccus homiensis DD-R11 T and Paracoccus zeaxanthinifaciens 

ATCC 21588 T , with which strain 22-5 T exhibited 

97.4 and 96.9 % 16S rRNA gene sequence similarity, 

respectively. Strain 22-5 T exhibited 94.0-96.6 % 16S rRNA 

gene sequence similarity with the other type strains of species 

of the genus Paracoccus. Strain 22-5 T contained Q-10 as 

the predominant menaquinone and C(18 : 1) ω7c as the pre- 

dominant fatty acid. In this study, P. zeaxanthinifaciens 

KCTC 22688 T also contained Q-10 as the predominant isoprenoid 

quinone. The DNA G+C content of strain 22-5 T 

was 63.6 mol%. Strain 22-5 T exhibited 44 and 32 % 

DNA-DNA relatedness to P. homiensis KACC 11518 T and 

P. zeaxanthinifaciens KCTC 22688 T , respectively. On the 

basis of phenotypic, phylogenetic and genetic data, strain 

22-5 T is considered to represent a novel species of the genus 

Paracoccus, for which the name Paracoccus fistulariae sp. 

nov. is proposed. The type strain is 22-5 T (=KCTC 22803 T 

=CCUG 58401 T ). 

PMID:20097797 

Keywords: Bacterial strain; Bacterium isolation; DNA 

sequence; Fistularia commersonii; Nucleotide 

sequence; Paracoccus; Paracoccus fistulariae; 

Paracoccus zeaxanthinifaciens; Phenotype; 

Phylogeny; Sequence homology 


Article 106 

Qualitative and quantitative detection of agricultural 

microorganisms expressing iturin and mop 

cyclase in soils 

J Agric Food Chem. 2010 Dec; 58(24):12657-63. 

Kim SE, Moon JS, Choi WS, Lee EN, Lee SH, Kim SU * 



The environmental release of genetically engineered microorganisms 

(GEMs) to improve agriculture or remediate environmental 

hazards has raised concern over the fate of the 

organisms and their engineered genes. To detect the microorganisms 

released into the environment at the molecular 

level, Bacillus subtilis KB producing iturin and Pseudomonas 

fluorescens MX1 carrying the moc (mannityl opine catabolism) 

region from the Agrobacterium tumefaciens were employed 

as model microorganisms. Using specific fusion primers 

and the TaqMan probes, qualitative and quantitative 

detections of the model organisms by PCR and real-time 

PCR were conducted employing a small-scale soil-core device 

and pots during the six month period. The data indicate 

that the model bacteria can be easily detected by qualitative 

and quantitative methods in the test systems employed, and 

they do not give significant impacts on the other bacteria 

in soils on the Southern blotting analysis, although long-term 

observation may be needed. 

PMID: 21077680 

Keywords: Agricultural microorganism; Genetically 

modified organism (GMO); Horizontal gene transfer; 

Iturin; Mop cyclase; PGPR; Real-time PCR; 

Soil-core device 

Article 107 

Signature gene expression profile of triclosan-resistant 

Escherichia coli 

J Antimicrob Chemother. 2010 Jun; 65(6):1171-7. 

Yu BJ, Kim JA, Pan JG * 

* Correspondence: jgpan@kribb.re.kr 


OBJECTIVES: To gain further insight into the defence mechanisms 

against triclosan in a mutant derived from an 

Escherichia coli strain carrying the triclosan-resistant target 

enzyme, FabI(G93V). 

METHODS: An E. coli imp4231 FabI(G93V) strain was 

constructed by replacing intact fabI with a linear DNA cassette, 

fabI(G93V)-CmR, that contains a single mutation, GGT 

to GTT, at codon 93 of fabI(G93V) and a chloramphenicol 

resistance gene (CmR) as a marker for the mutant allele 

by a Red-mediated recombination system. Using this E. coli 

imp4231 FabI(G93V) strain, nitrosoguanidine (NTG) mutagenesis 

was performed to generate E. coli IFNs [imp4231 

FabI(G93V) treated with NTG] displaying higher MICs of 

triclosan than its parent strain. The genes overexpressed in 

E. coli IFN4 were identified by DNA microarray analysis. 

RESULTS: An E. coli imp4231 FabI(G93V) strain displays 

approximately 400-fold increased MICs of triclosan (MIC 

approximately 8 mg/L) compared with the parent strain (MIC 

approximately 0.02 mg/L). Furthermore, E. coli IFN4 has 

the highest MIC of triclosan (MIC approximately 80 mg/L). 

DNA microarray analysis of E. coli IFN4 shows that many 

genes involved in the biosynthesis of membrane proteins, 

including transporters, reductases/dehydrogenases and stress 

response regulators, were highly expressed in the mutant. 

CONCLUSIONS: These results strongly indicate that E. coli 

IFN cells might protect themselves from triclosan by activating 

various defence mechanisms, such as (i) changing efflux 

activities; (ii) capturing the triclosan; and (iii) increasing 

the expression of important regulators or metabolic enzymes. 

PMID: 20410062 

Keywords: Anti-infective agents; DNA microarray; Drug 

resistance, bacterial; E. coli; FabI; Microbial 

sensitivity tests; Mutagenesis; Mutagens; Mutant 

proteins; Triclosan MIC 


Article 108 

Adsorption of turbid materials by the cyanobacterium 

Phormidium parchydematicum 

J Appl Phycol. 2010 Apr; 22(2):181-6. 

Kim CJ, Jung YH, Ahn CY, Lee YK, Oh HM * 



The present study investigated the adsorption of turbid materials 

such as clays, by microalgae. Among six tested microalgae, 

including Chlorophyceae and Cyanophyceae, a cyanobacterium, 

Phormidium parchydematicum strain KCTC 

10851BP, and unicellular alga, Chlorella vulgaris strain 

UTEX 265, showed a higher turbidity-removal efficiency 

(TRE) of 99% and 93%, respectively, for clay-containing 

water after 24 h, which was much higher than the 36% 

for the control. The TREs of all the treatments were >95% 

after 24 h, except for the treatment with a lower algal density 

and optical density (OD) = 0.1. Phormidium parchydematicum 

demonstrated a slightly higher TRE than a polyaluminum 

chloride coagulant (Al13(OH)28Cl9SO4) for a turbid field 

water. Scanning electron microscope (SEM) observations 

revealed a dense adsorption of clay particles to the surface 

of P. parchydematicum. Thus, it would appear that P. parchydematicum 

and C. vulgaris can be used for clay removal 

in turbid water by sedimentation through microalgae-clay 

flocculation. 

Article 109 

Genome sequence of the polymyxin-producing 

plant-probiotic rhizobacterium Paenibacillus polymyxa 

E681 

J Bacteriol. 2010 Nov; 192(22):6103-4. 

Kim JF, Jeong H, Park SY, Kim SB, Park YK, Choi SK, 

Ryu CM, Hur CG, Ghim SY, Oh TK, Kim JJ, Park CS, 

Park SH * 

* Correspondence: shpark@kribb.re.kr 


Paenibacillus polymyxa E681, a spore-forming, low-G+C, 

Gram-positive bacterium isolated from the rhizosphere of 

winter barley grown in South Korea, has great potential 

for agricultural applications due to its ability to promote 

plant growth and suppress plant diseases. Here we present 

the complete genome sequence of P. polymyxa E681. Its 

5.4-Mb genome encodes functions specialized to the plant-associated 

lifestyle and characteristics that are beneficial to 

plants, such as the production of a plant growth hormone, 

antibiotics, and hydrolytic enzymes. 

PMID: 20851896 

Keywords: DNA, bacterial; Genome, bacterial; Hordeum; 

Hydrolases; Molecular sequence data; Paenibacillus; 

Plant growth regulators; Plant roots; Polymyxins; 

Republic of Korea; Soil microbiology 

Keywords: Algae; Chlorella vulgaris; Chlorophyceae; 

Clay; Cyanobacteria; Phormidium 

parchydematicum; Turbid material 


Article 110 

Draft genome sequence of Streptomyces clavuligerus 

NRRL 3585, a producer of diverse secondary 

metabolites 

Article 111 

Crystal structure of SmcR, a quorum-sensing 

master regulator of Vibrio vulnificus, provides 

insight into its regulation of transcription 

J Bacteriol. 2010 Dec; 192(23):6317-8. 

J Biol Chem. 2010 Apr; 285(18):14020-30. 

Song JY, Jeong H, Yu DS, Fischbach MA, Park HS, Kim 

JJ, Seo JS, Jensen SE, Oh TK, Lee KJ, Kim JF * 

Kim Y, Kim BS, Park YJ, Choi WC, Hwang J, Kang BS, 

Oh TK, Choi SH, Kim MH * 



* Correspondence: mhk8n@kribb.re.kr 


Streptomyces clavuligerus is an important industrial strain 

that produces a number of antibiotics, including clavulanic 

acid and cephamycin C. A high-quality draft genome sequence 

of the S. clavuligerus NRRL 3585 strain was produced 

by employing a hybrid approach that involved Sanger sequencing, 

Roche/454 pyrosequencing, optical mapping, and 

partial finishing. Its genome, comprising four linear replicons, 

one chromosome, and four plasmids, carries numerous 

sets of genes involved in the biosynthesis of secondary 

metabolites, including a variety of antibiotics. 

PMID: 20889745 

Keywords: Biosynthetic pathways; Chromosomes, 

bacterial; DNA, bacterial; Genome, bacterial; 

Molecular sequence data; Plasmids; Sequence 

analysis, DNA; Streptomyces 

Quorum sensing has been implicated as an important global 

regulatory system controlling the expression of numerous 

virulence factors in bacterial pathogens. SmcR, a homologue 

of Vibrio harveyi LuxR, has been proposed as a quorum-sensing 

master regulator of Vibrio vulnificus, an opportunistic 

human pathogen. Previous studies demonstrated that SmcR 

is essential for the survival and pathogenesis of V. vulnificus, 

indicating that inhibiting SmcR is an attractive approach 

to combat infections by the bacteria. Here, we determined 

the crystal structure of SmcR at 2.1 A resolution. The protein 

structure reveals a typical TetR superfamily fold consisting 

of an N-terminal DNA binding domain and a C-terminal 

dimerization domain. In vivo and in vitro functional analysis 

of the dimerization domain suggested that dimerization of 

SmcR is vital for its biological regulatory function. The 

N-terminal DNA recognition and binding residues were assigned 

based on the protein structure and the results of in 

vivo and in vitro mutagenesis experiments. Furthermore, protein-DNA 

interaction experiments suggested that SmcR may 

have a sophisticated mechanism that enables the protein to 

recognize each of its many target operators with different 

affinities. 

PMID:20178981 

Keywords: Bacterial proteins; Crystallography, X-ray; 

Mutagenesis; Protein folding; Protein structure; 

Quorum sensing; Repressor proteins; 

Trans-activators; Transcription, genetic; Vibrio 

vulnificus 


Article 112 

Development of a stationary phase-specific autoinducible 

expression system in Bacillus subtilis 

J Biotechnol. 2010 Aug; 149(1-2):16-20. 

Lee SJ, Pan JG, Park SH, Choi SK * 

* Correspondence: sookeun@kribb.re.kr 


Bacillus thuringiensis produces crystal proteins (Cry) that 

account for up to 25% of the dry cell weight during the 

stationary phase. The high-level expression and stationary 

phase-specific autoinduction of the cry gene led to development 

of a cry promoter-based Bacillus expression system. 

Among the various cry promoters, cry3Aa promoter was 

selected by comparing the lacZ expression levels in Bacillus 

subtilis. An extracellular enzyme cellulase was highly upregulated 

during the stationary phase while under control of 

the cry3Aa promoter. Improvement of the cry3Aa promoter 

was obtained by modification of the promoter sequence. 

Specifically, a 5-fold increase in lacZ expression was obtained 

by changing both the -35 and -10 boxes of the cry3Aa 

promoter to the consensus sequence of the sigma(A)-dependent 

promoter of B. subtilis. The modified 

cry3Aa promoter produced a significantly higher yield of 

AprE, which suggests that the promoter may be useful for 

high-level protein expression in B. subtilis. 

PMID: 20600378 

Keywords: Bacillus subtilis; Bacillus thuringiensis cry3Aa; 

Bacterial proteins; Endotoxins; Expression system; 

Hemolysin proteins; Promoter modification; 

Promoter regions, genetic 

Article 113 

Molecular identification of mealybugs 

(Hemiptera: Pseudococcidae) found on Korean 

pears 

J Econ Entomol. 2010 Feb; 103(1):25-33. 

Park DS, Leem YJ, Hahn KW, Suh SJ, Hong KJ, Oh HW * 

* Correspondence: hwoh@kribb.re.kr 


Mealybugs are under a strict regulation at foreign trades 

of agricultural products because they are one of the most 

economically damaging groups of insects on food crops and 

ornamental plants. However, the absence of morphological 

characteristics enabling the discrimination of early life stages 

often cause a significant delay or rejection of a shipment 

when infested fruit is discovered, causing significant economic 

loss. A polymerase chain reaction-based method for species 

identification was developed for six mealybug species known 

to infest Korean pears including two regulated insects, 

Planococcus kraunhiae (Kuwana) and Crisicoccus matsumotoi 

(Siraiwa). Six sets of species-specific primers were designed 

based on the sequence comparison of the internal 

transcribed spacer 1 and 2 regions. Efficiency tests against 

29 mealybug samples showed that this method could effectively 

discriminate different mealybug species regardless of 

their developmental stages. Blind tests against 11 field collected 

mealybug nymph samples indicated that a single polymerase 

chain reaction is enough to discriminate unidentified 

mealybugs collected on Korean pears. This new method will 

facilitate trade and export requirements, as well as identify 

the species at any stage of mealybug intercepted. 

PMID: 20214364 

Keywords: DNA, ribosomal spacer; Genetic variation; 

Hemiptera; ITS; Mealybug; Molecular identification; 

Pear; Pyrus; Republic of Korea; Species-specific 

primer 


Article 114 

Tobacco seeds simultaneously over-expressing 

Cu/Zn-superoxide dismutase and ascorbate peroxidase 

display enhanced seed longevity and germination 

rates under stress conditions 

J Exp Bot. 2010 May; 61(9):2499-506. 

Lee YP, Baek KH, Lee HS, Kwak SS, Bang JW, Kwon 

SY * 

Article 115 

Potent anticariogenic activity of Aceriphyllum 

rossii and its components, aceriphyllic acid A and 

3-oxoolean-12-en-27-oic acid 

J Food Sci. 2010 Mar; 75(2):M78-82. 

Zheng CJ, Oh HW, Kim WG * 



* Correspondence: sykwon@kribb.re.kr 


Reactive oxygen species (ROS) are produced during seed 

desiccation, germination, and ageing, leading to cellular damage 

and seed deterioration and, therefore, decreased seed 

longevity. The effects of simultaneous over-expression of 

two antioxidant enzymes on seed longevity and seed germination 

under stressful conditions were investigated. Transgenic 

tobacco simultaneously over-expressing the Cu/Zn-superoxide 

dismutase (CuZnSOD) and ascorbate peroxidase (APX) 

genes in plastids showed normal growth and seed 

development. Furthermore, the transgenic seeds displayed 

increased CuZnSOD and APX enzymatic activities during 

seed development and maintained antioxidant enzymatic activity 

after two years of dried storage at room temperature. 

The two-year stored non-transgenic seeds (aged NT seeds) 

had higher levels of ion leakage than the two-year stored 

transgenic seeds (aged CA seeds), indicating membrane damage 

caused by ROS was more severe in the aged NT seeds 

than the aged CA seeds. The aged CA seeds decreased germination 

rates as compared to newly harvested transgenic and 

non-transgenic seeds. The aged CA seeds, however, significantly 

increased germination rates under various abiotic 

stress conditions as compared to aged NT seeds. These data 

strongly suggest that simultaneous over-expression of the 

CuZnSOD and APX genes in plastids improves seed longevity 

and germination under various environmental stress conditions 

by attenuating the effects of oxidative stress produced 

by elongated storage conditions and harsh environmental 

stresses. 

PMID: 20423937 

Aceriphyllum rossii Engler (Saxifragaceae) have been used 

as a nutritious food in Korea. We found that the methanol 

extract of A. rossii root and its components, aceriphyllic 

acid A and 3-oxoolean-12-en-27-oic acid, potently inhibited 

the growth of the key cariogenic bacteria, Streptococcus 

mutans, with MIC of 2 to 4 microg/mL. They also showed 

antibacterial activity against other cariogenic bacteria such 

as S. oralis, S. sobrinus, and S. salivarius with the similar 

potency. In the time-kill study, aceriphyllic acid A reduced 

the viable counts of S. mutans by 90% in 1 min at 8 microg/mL, 

indicating that aceriphyllic acid A had the fast 

bacteriostatic activity. Severe damages of the cell surface 

of S. mutans by aceriphyllic acid A were observed by transmission 

electron microscopy, suggesting with its fast antibacterial 

activity that its mechanism of action might be membrane 

disruption. These results suggest that the methanol 

extract of A. rossii root and its components, aceriphyllic 

acid A and 3-oxoolean-12-en-27-oic acid, could have the 

great potential as natural agents for preventing dental caries. 

PMID:20492245 

Keywords: 3-oxoolean-12-en-27-oic acid; Aceriphyllum 

rossii; Anti-bacterial agents; Anticariogenic activity; 

Dental pulp cavity; Food microbiology; Microbial 

sensitivity tests; Plant extracts; Saxifragaceae; 

Streptococcus mutans; Triterpenes 

Keywords: Antioxidant enzymes; Gene expression 

regulation; Germination; Oxidative stress; 

Peroxidases; Plant proteins; Seed longevity; Stress, 

physiological; Superoxide dismutase; Tobacco; 

Transgenic plants 


Article 116 

Enhancing the 1-butanol tolerance in escherichia 

coli through repetitive proton beam irradiation 

J Kor Phys Soc. 2010; 56(61):2041-5. 

Jeong H * , Han J 

* Correspondence: hyjeong@kribb.re.kr 


The low butanol tolerance of most microorganisms severely 

limits the production of 1-butanol on an economical scale 

in alternative hosts other than the natural butanol producer 

Clostridium acetobutylicum, which is not amenable for genetic 

manipulation and requires demanding culture conditions. 

To generate butanol-tolerant E. coli, we devised a cyclic 

selection strategy that consists of an iterative application 

of proton irradiation at a dose of 

∼250 Gy by using 45-MeV 

protons and selection by daily serial transfer in a minimal 

medium containing increasing concentrations of 1-butanol. 

Applying five rounds of the cyclic selection of E. coli ATCC 

8739 (a C strain) over 61 days resulted in a mutant population 

that could tolerate 1.2% 1-butanol (v/v). However, without 

proton irradiation, the cells were unable to grow at ≥0.8% 

1-butanol in a control experiment. Seven different mutations 

were identified within one clone from the endpoint population 

through 454 pyrosequencing of the genome. Tracing each 

mutation in terms of the prevalence in the population during 

the period of evolution suggested that proton beam irradiation-induced 

mutations were rapidly fixed during the early 

phase of the selection procedure. This approach, which is 

still being applied to increase butanol tolerance beyond 1.3%, 

can be considered useful for improving targeted traits whose 

corresponding genes are unknown. 

Keywords: 1-butanol; Escherichia coli; Genome 

sequencing; Mutation; Proton beam; Tolerance 

Article 117 

Ethanolic extracts of Brassica campestris spp. rapa 

roots prevent high-fat diet-induced obesity via 

β(3)-adrenergic regulation of white adipocyte lip- 

olytic activity 

J Med Food. 2010 Apr; 13(2):406-14. 

An S, Han JI, Kim MJ, Park JS, Han JM, Baek NI, Chung 

HG, Choi MS, Lee KT, Jeong TS * 

* Correspondence: tsjeong@kribb.re.kr 


The influence of ethanolic extracts of Brassica campestris 

spp. rapa roots (EBR) on obesity was examined in imprinting 

control region (ICR) mice fed a high-fat diet (HFD) and 

in 3T3-L1 adipocytes. The ICR mice used were divided 

into regular diet, HFD, EBR (50 mg/kg/day EBR administered 

orally), and orlistat (10 mg/kg/day orlistat administered 

orally) groups. The molecular mechanism of the 

anti-obesity effect of EBR was investigated in 3T3-L1 adipocytes 

as well as in HFD-fed ICR mice. In the obese mouse 

model, both weight gain and epididymal fat accumulation 

were highly suppressed by the daily oral administration of 

50 mg/kg EBR for 8 weeks, whereas the overall amount 

of food intake was not affected. EBR treatment induced 

the expression in white adipocytes of lipolysis-related genes, 

including 

β (3)-adrenergic receptor 

( β (3)-AR), hormone-sensitive 

lipase (HSL), adipose triglyceride lipase, and uncoupling 

protein 2. Furthermore, the activation of cyclic 

AMP-dependent protein kinase, HSL, and extracellular signal-regulated 

kinase was induced in EBR-treated 3T3-L1 

cells. The lipolytic effect of EBR involved 

lation, as inferred from the inhibition by the 

β(3)-AR modu- 

β(3)-AR antago - 

nist propranolol. These results suggest that EBR may have 

potential as a safe and effective anti-obesity agent via the 

inhibition of adipocyte lipid accumulation and the stimulation 

of 

β(3)-AR-dependent lipolysis. 

PMID: 20132043 

Keywords: Adipocytes; Adrenergic agents; Anti-obesity 

agents; Brassica; Dietary fats; Enzyme activation; 

Lipolysis; Mitochondrial proteins; Plant extracts; 

Propranolol; Receptors, adrenergic; Sterol esterase; 

Weight gain 


Article 118 

Investigation of possible horizontal gene transfer 

from transgenic rice to soil microorganisms in 

paddy rice field 

Article 119 

Methyl-branched fatty acids, inhibitors of enoyl-ACP 

reductase with antibacterial activity from 

Streptomyces sp. A251 

J Microbiol Biotechnol. 2010 Jan; 20(1):187-92. 

J Microbiol Biotechnol. 2010 May; 20(5):875-80. 

Kim SE, Moon JS, Kim JK, Choi WS, Lee SH, Kim SU * 

Zheng CJ, Sohn MJ, Chi SW, Kim WG * 





In order to monitor the possibility of horizontal gene transfer 

between transgenic rice and microorganisms in paddy rice 

field, the gene flow from bifunctional fusion (TPSP) rice 

containing trehalose-6-phosphate synthase and phosphatase 

to microorganisms in soils was investigated. The soil samples 

collected every month from the paddy rice field during June, 

2004 to March, 2006 were investigated by multiplex PCR, 

Southern hybridization, and amplified fragment length polymorphism 

(AFLP). The TPSP gene from soil genomics DNAs 

was not detected by PCR. Soil genomic DNAs were not 

shown its homologies on the Southern blotting data, indicating 

that gene-transfer did not occur during the last two years 

in paddy rice field. In addition, the AFLP band patterns 

produced by both soil genomic DNAs extracted from transgenic 

and non-transgenic rice field appeared similar to each 

other when analyzed by NTSYSpc program. Thus, these 

data suggest that transgenic rice does not give a significant 

impact on the communities of soil microorganisms although 

long-term observation may be needed. 

PMID:20134251 

Keywords: AFLP; Environmental risk assessment; 

Glucosyltransferases; Horizontal gene transfer; 

Oryza sativa; Plant proteins; Plants, genetically 

modified; Soil microorganisms; Transgenic TPSP 

rice 

Bacterial enoyl-ACP reductase (FabI) has been demonstrated 

to be a novel antibacterial target. In the course of our screening 

for FabI inhibitors we isolated two methyl-branched fatty 

acids from Streptomyces sp. A251. They were identified 

as 14-methyl-9(Z)-pentadecenoic acid and 

15-methyl-9(Z)-hexadecenoic acid by MS and NMR spectral 

data. These compounds inhibited Staphylococcus aureus FabI 

with IC50 of 16.0 and 16.3mu M, respectively, while didn't 

affect FabK, an enoyl-ACP reductase of Streptococcus pneumonia, 

at 100μM . Consistent with their selective inhibition 

for FabI, they blocked intracellular fatty acid synthesis as 

well as the growth of S. aureus, while didn't inhibit the 

growth of S. pneumonia. Additionally, these compounds 

showed reduced antibacterial activity against fabI-overexpressing 

S. aureus compared to the wild-type strain. These 

results demonstrate that the methyl-branched fatty acids 

showed antibacterial activity by inhibiting FabI in vivo. 

PMID: 20519910 

Keywords: Antibacterial activity; Bacterial proteins; 

Enoyl-ACP reductase; Enzyme inhibitors; Fatty 

acids; Kinetics; Methyl-branched fatty acid; 

Staphylococcus aureus; Streptomyces 


Article 120 

Monitoring of possible horizontal gene transfer 

from transgenic potatoes to soil microorganisms 

in the potato fields and the emergence of variants 

in Phytophthora infestans 

J Microbiol Biotechnol. 2010 Jun; 20(6):1027-31. 

Kim SE, Moon JS, Kim JK, Yoo RH, Choi WS, Lee EN, 

Lee SH, Kim SU * 

Article 121 

Diversity and abundance of ammonia-oxidizing 

bacteria in activated sludge treating different types 

of wastewater 

J Microbiol Biotechnol. 2010 Jul; 20(7):1128-33. 

Baek K, Park C, Oh HM, Yoon BD, Kim HS * 

* Correspondence: hkim@kribb.re.kr 




To examine the possibility of horizontal gene transfer between 

transgenic potatoes and microorganisms in potato 

fields, the gene flow from transgenic potatoes containing 

nucleoside diphosphate kinase 2 (NDPK2) gene to microorganisms 

in soils was investigated. The soil samples collected 

from the potato fields from March to October in 2007 

were examined by PCR, Southern hybridization, and AFLP 

fingerprinting. The NDPK2 gene from soil genomic DNAs 

was not detected by both PCR and Southern hybridization, 

indicating that gene-transfer did not occur in the potato fields. 

In addition, no discrepancy was found in pathogenicity and 

noticeable changes for the appearance of variants of 

Phytophthora infestans in each generation when serial inoculations 

and the analysis of genomic DNAs by AFLP 

was conducted. Thus, these data suggest that transgenic potatoes 

do not give significant impacts on the communities 

of soil microorganisms and the emergence of variants although 

continued research efforts may be necessary to make 

a decisive conclusion. 

PMID: 20622504 

Keywords: AFLP; Emerging variants; Gene transfer, 

Horizontal; Genetic variation; 

Nucleoside-diphosphate kinase; Phytophthora 

infestans; Soil microorganisms; Solanum tuberosum; 

Transgenic NDPK2 potatoes 

The diversity and abundance of ammonia-oxidizing bacteria 

(AOB) in activated sludge were compared using PCR-DGGE 

and real-time PCR assays. Activated sludge samples were 

collected from five different types of wastewater treatment 

plants (WWTPs) mainly treating textile, paper, food and 

livestock wastewater or domestic sewage. The composition 

of total bacteria determined by PCR-DGGE was highly diverse 

between the samples, whereas the community of AOB 

was similar across all the investigated activated sludge. Total 

bacterial numbers and AOB numbers in the aerated mixed 

liquor were in the range of 1.8x10(10) to 3.8x10(12) and 

1.7x10(6) to 2.7x10(10) copies/l, respectively. Activated 

sludge from livestock, textile, and sewage treating WWTPs 

contained relatively high amoA gene copies (more than 10(5) 

copies/l) whereas activated sludge from food and paper 

WWTPs revealed the low number of amoA gene (less than 

10(3) copies/L). The value of the amoA gene copy effectively 

showed the difference in composition of bacteria in different 

activated sludge samples and this was better than the measurement 

with the AOB 16S rRNA or total 16S rRNA gene. 

These results suggest that the quantification of the amoA 

gene can help monitor AOB and ammonia oxidation in 

WWTPs. 

PMID: 20668407 

Keywords: Activated sludge; Ammonia-oxidizing bacteria; 

Gene dosage; Industrial waste; PCR-DGGE; 

Real-time PCR; Sewage treatment; Species diversity; 

Textile industry; Wastewater 


Article 122 

Growth inhibition of Microcystis aeruginosa by 

a glycolipid-type compound from Bacillus subtilis 

C1 

J Microbiol Biotechnol. 2010 Aug; 20(8):1240-2. 

Kim HS, Ahn CY, Joung SH, Ahn JS, Oh HM * 



We attempted to identify the compound responsible for the 

growth inhibition of Microcystis aeruginosa occurring when 

a culture broth of Bacillus subtilis C1 was added to the 

medium. The active compound was purified from B. subtilis 

C1 culture broth by adsorption chromatography and HPLC, 

and was identified as a type of glycolipid based on 1H 

NMR and MS analyses. The purified active compound completely 

inhibited the growth of M. aeruginosa at a concentration 

of 10 microgram/ml. This is the first report of a 

glycolipid produced by a Bacillus strain that has potential 

as an agent for the selective control of bloom-forming M. 

aeruginosa. 

PMID: 20798589 

Keywords: Antibacterial activity; Bacillus subtilis; Culture 

media; Glycolipid; Growth inhibition; Lipogenesis; 

Microcystis aeruginosa 

Article 123 

Recombinant Production of an Inulinase in a 

Saccharomyces cerevisiae gal80 Strain 

J Microbiol Biotechnol. 2010 Nov; 20(11):1529-33. 

Lim SH, Lee H, Sok DE, Choi ES * 

* Correspondence: choi4162@kribb.re.kr 


The inulinase gene (INU1) from Kluyveromyces marxianus 

NCYC2887 strain was overexpressed by using GAL10 promotor 

in a 

△gal80 strain of 

Saccharomyces cerevisiae. The 

inulinase gene lacking the original signal sequence was fused 

in-frame to mating factor α signal sequence for secretory 

expression. Use of the 

△gal80 strain allowed the gal- 

actose-free induction of inulinase expression using a glucose-only 

medium. Shake flask cultivation in YPD medium 

produced 34.6 U/ml of the recombinant inulinase, which 

was approximately 13-fold higher than that produced by 

K. marxianus NCYC2887. It was found that the use of the 

△gal80 strain improved the expression of inulinase in the 

recombinant S. cerevisiae in both the aerobic and the anaerobic 

condition by about 2.9- and 1.7-fold, respectively. 5 

L fed-batch fermentation using YPD medium was performed 

under aerobic condition with glucose feeding, which resulted 

in the inulinase production of 31.7 U/ml at OD600 of 67. 

Ethanol fermentation of dried powder of Jerusalem artichoke, 

an inulin-rich biomass, was also performed using the recombinant 

S. cerevisiae expressing INU1 and K. marxianus 

NCYC2887. Fermentation in a 5L scale fermentor was carried 

out at an aeration rate of 0.2 vvm, an agitation rate of 300 

rpm, and the pH was controlled at 5.0. The temperature 

was maintained at 30degrees C and 37degrees C, respectively, 

for the recombinant S. cerevisiae and K. marxianus. The 

maximum productivities of ethanol were 59.0 and 53.5 g/L, 

respectively. 

PMID: 21124058 

Keywords: δgal80; Bioreactors; Fungal proteins; Glycoside 

hydrolases; Inulinase; Jerusalem artichoke; 

Kluyveromyces; Mutation; Recombinant; 

Saccharomyces cerevisiae 


Article 124 

Catalytic properties of a GH10 endo-β 

-1,4-xylanase from Streptomyces thermocarboxydus 

HY-15 isolated from the gut of Eisenia fetida 

Article 125 

Kinetic correlation between degradation and dechlorination 

of perchloroethylene in the Fenton reaction 

J Mol Catal B. 2010 Jan; 62(1):32-9. 

Kor J Chem Eng. 2010; 27(6):1750-4. 

Kim DY, Han MK, Oh HW, Park DS, Kim SJ, Lee SG, 

Shin DH, Son KH, Bae KS, Park HY * 

* Correspondence: hypark@kribb.re.kr 


A novel GH10 endo-β-1,4-xylanase (XylG) gene from 

Streptomyces thermocarboxydus HY-15, which was isolated 

from the gut of Eisenia fetida, was cloned, over-expressed, 

and characterized. The XylG gene (1182 bp) encoded a polypeptide 

of 393 amino acids with a deduced molecular mass 

of 43,962 Da and a calculated pI of 6.74. The primary structure 

of XylG was 69% similar to that of Thermobifida fusca 

YX endo-β-1,4-xylanase. It was most active at pH 6.0 and 

55 °C. The susceptibilities of xylans to XylG were as follows: 

oat spelt xylan > birchwood xylan > beechwood xylan. The 

XylG also showed high activity (474 IU/mg) toward 

p-nitrophenylcellobioside. Moreover, at pH 6.0 and 50 °C, 

the Vmax and Km values of the XylG were 127 IU/mg 

and 2.51 mg/ml, respectively, for oat spelt xylan and 782 

IU/mg and 5.26 μM, respectively, for 

p-nitrophenylcellobioside. A homology model indicated that 

XylG folded to form a ( β/ α)8-barrel with two catalytic resi- 

dues of an acid/base (Glu181) and a nucleophile (Glu289). 

The formation of a disulfide bond between Cys321 and 

Cys327 were predicted by homology modeling. 

Keywords: Endo-β-1,4-xylanase; Glycoside hydrolase 

family 10; p-Nitrophenylcellobioside; 

PNP-cellobioside; Streptomyces thermocarboxydus 

HY-15 

Kim HS, Lee WS, Ahn CY, Kim BH, Kim JE, Oh HM * 



In the Fenton reaction, degradation and dechlorination are 

directly affected by the concentrations of hydrogen peroxide 

and Fe3+. Although there is considerable research on the 

biodegradation of chlorinated compounds combined with the 

Fenton reaction, the kinetics of degradation and dechlorination 

of the reaction, with various concentrations of hydrogen 

peroxide and Fe3+, have been rarely investigated. Therefore, 

we investigated the degradation and dechlorination of PCE 

with various concentrations of hydrogen peroxide and Fe3+. 

The initial concentration of PCE (10 

μM) decreased from 

a value of 8.9 μM (with 0.1 μM of hydrogen peroxide and 

5 μM of Fe3+) to 1.1 μM (with 10 μM of hydrogen peroxide 

and 5 

μM of Fe3+); the respective values for chloride ions 

produced were 0.9 and 21.6 μM. Also, the initial 10 μM 

of PCE decreased from 8.9 (with 0.1 μM of Fe3+ and 5 

μM of hydrogen peroxide) to 2.2 μM (with 10μM of Fe3+ 

and 5 

μM of hydrogen peroxide); the respective chloride 

ions produced were 0.7 and 14.5 

μM. The logarithmic correla - 

tions between the degradation and dechlorination coefficients 

were 0.7682 and 0.7834 for concentrations of hydrogen peroxide 

and Fe3+, respectively. Both coefficients were used, 

from all possible cases, to derive six models which displayed 

both the ratio of degradation and dechlorination and the 

hydrogen peroxide and Fe3+ concentrations. The dechlorination 

of PCE could then be predicted with the model obtained 

by the coefficient with the concentration of hydrogen peroxide 

and Fe3+. The models could be applied to various 

Fenton reactions for optimization of degradation or dechlorination, 

such as biodegradation of PCE which is scarcely 

degraded by aerobic bacteria. 

Keywords: Dechlorination value; Degradation; Fenton 

reaction; Kinetic correlation; Perchloroethylene 

(PCE) 


Article 126 

Inhibition of primary roots and stimulation of lateral 

root development in Arabidopsis thaliana by 

the rhizobacterium Serratia marcescens 90-166 

is through both auxin-dependent and -independent 

signaling pathways 

Article 127 

Simultaneous expression of choline oxidase, 

superoxide dismutase and ascorbate peroxidase 

in potato plant chloroplasts provides 

synergistically enhanced protection against 

various abiotic stresses 

Mol Cells. 2010 Mar; 29(3):251-8. 

Physiol Plant. 2010 Apr; 138(4):520-33. 

Shi CL, Park HB, Lee JS, Ryu S, Ryu CM * 

* Correspondence: cmryu@kribb.re.kr 


The rhizobacterium Serratia marcescens strain 90-166 was 

previously reported to promote plant growth and induce resistance 

in Arabidopsis thaliana. In this study, the influence 

of strain 90-166 on root development was studied in vitro. 

We observed inhibition of primary root elongation, enhanced 

lateral root emergence, and early emergence of second order 

lateral roots after inoculation with strain 90-166 at a certain 

distance from the root. Using the DR5::GUS transgenic A. 

thaliana plant and an auxin transport inhibitor, N-1-naphthylphthalamic 

acid, the altered root development was still 

elicited by strain 90-166, indicating that this was not a result 

of changes in plant auxin levels. Intriguingly, indole-3-acetic 

acid, a major auxin chemical, was only identified just above 

the detection limit in liquid culture of strain 90-166 using 

liquid chromatography-mass spectrometry. Focusing on bacterial 

determinants of the root alterations, we found that 

primary root elongation was inhibited in seedlings treated 

with cell supernatant (secreted compounds), while lateral 

root formation was induced in seedlings treated with lysate 

supernatant (intracellular compounds). Further study revealed 

that the alteration of root development elicited by 

strain 90-166 involved the jasmonate, ethylene, and salicylic 

acid signaling pathways. Collectively, our results suggest 

that strain 90-166 can contribute to plant root development 

via multiple signaling pathways. 

PMID: 20108166 

Keywords: Arabidopsis thaliana; Auxin; Cyclopentanes; 

Indoleacetic acids; Oxylipins; Phthalimides; Plant 

growth-promoting rhizobacteria; Root development; 

Seedling; Serratia marcescens; Signal transduction 

Ahmad R, Kim YH, Kim MD, Kwon SY, Cho K, Lee HS, 

Kwak SS * 



Plants synthesize compatible solutes such as glycinebetaine 

(GB) in response to abiotic stresses. To evaluate the synergistic 

and protective effect of GB, transgenic potato plants 

expressing superoxide dismutase (SOD) and ascorbate peroxidase 

(APX) targeting to chloroplasts (referred to as SSA 

plants) were retransformed with a bacterial choline oxidase 

(codA) gene to synthesize GB in chloroplast in naturally 

occurring non-accumulator potato plants (including SSA) 

under the control of the stress-inducible SWPA2 promoter 

(referred to as SSAC plants). GB accumulation resulted in 

enhanced protection of these SSAC plants and lower levels 

of H(2)O(2) compared with SSA and non-transgenic (NT) 

plants after methyl viologen (MV)-mediated oxidative stress. 

Additionally, SSAC plants demonstrated synergistically enhanced 

tolerance to salt and drought stresses at the 

whole-plant level. GB accumulation in SSAC plants helped 

to maintain higher activities of SOD, APX and catalase following 

oxidative, salt and drought stress treatments than 

is observed in SSA and NT plants. Conclusively, GB accumulation 

in SSAC plants along with overexpression of antioxidant 

genes rendered the plants tolerant to multiple environmental 

stresses in a synergistic fashion. 

PMID: 20059737 

Keywords: Adaptation, physiological; Alcohol 

oxidoreductases; Betaine; Chloroplasts; Droughts; 

Gene expression regulation; Oxidative stress; 

Paraquat; Peroxidases; Plants, genetically modified; 

Sodium chloride; Solanum tuberosum; Superoxide 

dismutase 


Article 128 

The sweet potato IbMYB1 gene as a potential visible 

marker for sweet potato intragenic vector system 

Physiol Plant. 2010 Jul; 139(3):229-40. 

Article 129 

Enhanced tolerance to methyl viologen-induced 

oxidative stress and high temperature in transgenic 

potato plants overexpressing the CuZnSOD, APX 

and NDPK2 genes 

Kim CY, Ahn YO, Kim SH, Kim YH, Lee HS, Catanach 

AS, Jacobs JM, Conner AJ, Kwak SS * 



MYB transcription factors play important roles in transcriptional 

regulation of many secondary metabolites including 

anthocyanins. We cloned the R2R3-MYB type IbMYB1 complementary 

DNAs from the purple-fleshed sweet potato 

(Ipomoea batatas L. cv Sinzami) and investigated the expression 

patterns of IbMYB1 gene with IbMYB1a and 

IbMYB1b splice variants in leaf and root tissues of various 

sweet potato cultivars by reverse transcription-polymerase 

chain reaction. The transcripts of IbMYB1 were predominantly 

expressed in the purple-fleshed storage roots and 

they were also detectable in the leaf tissues accumulating 

anthocyanin pigments. In addition, transcript levels of 

IbMYB1 gene were up-regulated by treatment with methyl 

jasmonate or salicylic acid in leaf and root tissues of cv. 

White Star. To set up the intragenic vector system in sweet 

potato, we first evaluated the utilization of the IbMYB1 gene 

as a visible selectable marker. The IbMYB1a was transiently 

expressed in tobacco leaves under the control of a constitutive 

cauliflower mosaic virus 35S promoter, a root-specific and 

sucrose-inducible sporamin promoter, and an oxidative 

stress-inducible sweet potato anionic peroxidase2 promoter. 

We also showed that overexpression of IbMYB1a induced 

massive anthocyanin pigmentation in tobacco leaves and 

up-regulated the transcript levels of the structural genes in 

anthocyanin biosynthetic pathway. Furthermore, high-performance 

liquid chromatography analysis revealed that the 

expression of IbMYB1a led to production of cyanidin as 

a major core molecule of anthocyanidins in tobacco leaves. 

These results suggest that the IbMYB1 gene can be applicable 

to a visible marker for sweet potato transformation with 

intragenic vectors, as well as the production of anthocyanin 

as important nutritive value in other plant species. 

PMID: 20163556 

Keywords: Alternative splicing; Anthocyanin; 

Cyclopentanes; Genetic markers; Genetic vectors; 

Ipomoea batatas; Oxylipins; Protein isoforms; 

Tobacco; Transcription factors; Transformation, 

genetic 

Physiol Plant. 2010 Oct; 140(2):153-62. 

Kim MD, Kim YH, Kwon SY, Yun DJ, Kwak SS, Lee 

HS * 

* Correspondence: hslee@kribb.re.kr 


Oxidative stress is a major threat for plants exposed to various 

environmental stresses. Previous studies found that transgenic 

potato plants expressing both copper zinc superoxide 

dismutase (CuZnSOD) and ascorbate peroxidase (APX) 

(referred to as SSA plants), or nucleoside diphosphate kinase 

2 (NDPK2) (SN plants), showed enhanced tolerance to methyl 

viologen (MV)-induced oxidative stress and high 

temperature. This study aimed to develop transgenic plants 

that were more tolerant of oxidative stress by introducing 

the NDPK2 gene into SSA potato plants under the control 

of an oxidative stress-inducible peroxidase (SWPA2) promoter 

to create SSAN plants. SSAN leaf discs and whole 

plants showed enhanced tolerance to MV, as compared to 

SSA, SN or non-transgenic (NT) plants. SSAN plants sprayed 

with 400 µM MV exhibited about 53 and 83% less visible 

damage than did SSA and SN plants, respectively. The expression 

levels of the CuZnSOD, APX and NDPK2 genes 

in SSAN plants following MV treatment correlated well 

with MV tolerance. SOD, APX, NDPK and catalase antioxidant 

enzyme activities were also increased in MV-treated 

SSAN plants. In addition, SSAN plants were more tolerant 

to high temperature stress at 42°C, exhibiting a 6.2% reduction 

in photosynthetic activity as compared to plants grown 

at 25°C. In contrast, the photosynthetic activities of SN and 

SSA plants decreased by 50 and 18%, respectively. These 

results indicate that the simultaneous overexpression of 

CuZnSOD, APX and NDPK2 is more effective than single 

or double transgene expression for developing plants with 

enhanced tolerance to various environmental stresses. 

PMID: 20553417 

Keywords: Gene expression regulation; Herbicides; 

Nucleoside-diphosphate kinase; Oxidative stress; 

Paraquat; Peroxidases; Plants, genetically modified; 

Solanum tuberosum; Superoxide dismutase; 

Transgenes 


Article 130 

Rapid and simple method for DNA extraction 

from plant and algal species suitable for PCR 

amplification using a chelating resin Chelex 100 

Plant Biotech Rep. 2010 Jan; 4(1):49-52. 

HwangBo K, Son SH, Lee JS, Min SR, Ko SM, Liu JR, 

Choi D, Jeong WJ * 

* Correspondence: wonjoong@kribb.re.kr 


A DNA extraction method using Chelex 100 is widely used 

for bacteria, Chlamydomonas, and animal cell lines, but only 

rarely for plant materials due to the need for additional 

time-consuming and tedious steps. We have modified the 

Chelex 100 protocol and successfully developed a rapid and 

simple method of DNA extraction for efficient PCR-based 

detection of transgenes from a variety of transgenic plant 

and algal species. Our protocol consists of homogenizing 

plant tissue with a pestle, boiling the homogenized tissue 

in a microfuge tube with 5% Chelex 100 for 5 min, and 

centrifuging the boiled mixture. The supernatant, which is 

used for PCR analysis, was able to successfully amplify 

transgenes in transgenic tobacco, tomato, potato, 

Arabidopsis, rice, strawberry, Spirodela polyrhiza, 

Chlamydomonas, and Porphyra tenera. The entire DNA extraction 

procedure requires

Article 132 

Cucumber mosaic virus 2b protein inhibits RNA 

silencing pathways in green alga Chlamydomonas 

reinhardtii 

Article 133 

Functional domain marker (FDM): An in silico 

demonstration in solanaceae using simple sequence 

repeats (SSRs) 

Plant Cell Rep. 2010 Sep; 29(9):967-75. 

Plant Mol Biol Rep. 2010 Jun; 28(2):352-6. 

Ahn JW, Yin CJ, Liu JR, Jeong WJ * 

Yu JK, Paik H, Choi JP, Han JH, Choe JK, Hur CG * 

* Correspondence: wonjoong@kribb.re.kr 


* Correspondence: hurlee@kribb.re.kr 


The functions of RNA silencing are repression of endogenous 

gene expression and antiviral defense in plants and animals. 

Cucumber mosaic virus 2b (CMV2b) is a suppressor of RNA 

silencing in higher plants. In the present study, we evaluated 

the RNA silencing suppressor activity of CMV2b in 

Chlamydomonas reinhardtii. Before transformation, we 

modified CMV2b codons to increase the GC content for 

optimal expression in C. reinhardtii. Inhibition of Maa7 silencing 

was detected in CMV2b-expressing Maa7-IR44 

strains, indicating that CMV2b suppressed siRNA pathways 

in C. reinhardtii as in higher plants. In addition, mRNA 

expression targeted for cleavage by miRNA was significantly 

higher in CMV2b-expressing strains, but increased accumulation 

of miRNA was not detected. These results indicate 

that the suppression of miRNA pathways is mediated by 

CMV2b in C. reinhardtii. Interestingly, expression of both 

Argonaute 1 (AGO1) and Dicer-like 1 (DCL1), regulated 

by a bidirectional promoter, was reduced in CMV2b-expressing 

strains, suggesting that CMV2b may affect transcription 

factors involved in RNA silencing pathways. Furthermore, 

reduction of AGO2 and AGO3 expression was detected in 

CMV2b-expressing strains. Taken together, our results demonstrate 

that CMV2b may suppress both siRNA and miRNA 

pathways, and also impair AGOs and DCL1 expression in 

C. reinhardtii. 

PMID: 20532888 

A simple sequence repeat-functional domain marker 

(SSR-FDM) relies on development of molecular markers 

for putative functional domains using simple sequence repeats 

and in silico annotated information of those sequences 

using biological databases. A total of 148,921 tomato ESTs 

and 115,598 pepper ESTs were analyzed, resulting in the 

identification of 439 tomato SSR-FDMs and 489 pepper 

SSR-FDMs. Among them, 54 pepper SSR-FDMs were tested 

on pepper. Several genomic databases were used for the 

in silico annotation of the SSR-FDM sequences that revealed 

a wide range of candidate genes. This study demonstrates 

that SSR-FDMs provide information regarding transcribed 

genetic markers and putative function as a genomic resource 

database for Solanaceae. This system could be applied to 

the development of a functional marker database for any 

crop species. 

Keywords: Bioinformatic tool; Biological database; 

Functional marker development; Gene annotation; 

Lycopersicon esculentum; Magnoliophyta; 

Sequence; Solanaceae 

Keywords: Algal proteins; Argonaute (AGO); 

Chlamydomonas reinhardtii; Cucumber mosaic virus 

2b (CMV2b); Dicer-like (DCL); MicroRNA 

(miRNA); RNA, messenger; Small interfering RNA 

(siRNA); Viral proteins 


Article 134 

High-level expression of a human 

β-site APP 

cleaving enzyme in transgenic tobacco chloroplasts 

and its immunogenicity in mice 

Transgenic Res. 2010 Dec; 19(6):1099-108. 

Youm JW, Jeon JH, Kim H, Min SR, Kim MS, Joung H, 

Jeong WJ * , Kim HS * 

* Correspondence: wonjoong@kribb.re.kr hyuns@kribb.re.kr 


Plastid transformation has to date been applied to the expression 

of heterologous genes involved in agronomic traits 

and to the production of useful recombinant proteins. Here, 

we report a feasibility study for producing the human 

β-site 

APP cleaving enzyme (BACE) via transformation of tobacco 

chloroplasts. Stable integration of human BACE into the 

plastome was confirmed by PCR. Genomic Southern blot 

analysis detected the presence of the tobacco aadA and human 

BACE genes between trnI and trnA in the plastome. Northern 

blot analysis revealed that the aadA and BACE genes were 

both properly transcribed into a dicistronic transcriptional 

unit. Human BACE protein expression in transplastomic tobacco 

was determined by western blot analysis. ELISA analysis 

revealed that, based on a dilution series of E. coli-derived 

BACE as a standard, transplastomic lines accumulated BACE 

to levels of 2.0% of total soluble proteins. When mice were 

gavaged with the transplastomic tobacco extracts, they 

showed an immune response against the BACE antigen. The 

successful production of plastid-based BACE protein has 

the potential for developing a plant-based vaccine against 

Alzheimer disease. 

PMID: 20229285 

Keywords: β-secretase; Alzheimer disease; Amyloid 

precursor protein; Aspartic acid endopeptidases; 

Chloroplast transformation; Nicotiana tabacum L.; 

Plant-derived vaccine; Tobacco 


2010 




Division of Leading R&D 



AI Control Material Research Center 



Kinomics Based Cancer Research World Class Institute 



www.kribb.re.kr

Article 135 

SM22α-induced activation of p16INK4a/retino - 

blastoma pathway promotes cellular senescence 

caused by a subclinical dose of 

doxorubicin in HepG2 cells 

γ-radiation and 

Biochem Biophys Res Commun. 2010 Sep; 400(1):100-5. 

Kim TR, Lee HM, Lee SY, Kim EJ, Kim KC, Paik SG, 

Cho EW * , Kim IG 

* Correspondence: ewcho@kribb.re.kr 


Smooth muscle protein 22- α (SM22 α) is known as a trans- 

formation- and shape change-sensitive actin cross-linking 

protein found in smooth muscle tissue and fibroblasts; however, 

its functional role remains uncertain. We reported previously 

that SM22α 

overexpression confers resistance against 

anti-cancer drugs or radiation via induction of metallothionein 

(MT) isozymes in HepG2 cells. In this study, 

we demonstrate that SM22α 

overexpression leads cells to 

a growth arrest state and promotes cellular senescence caused 

by treatment with a subclinical dose of γ-radiation (0.05 

and 0.1 Gy) or doxorubicin (0.01 and 0.05 

μg/ml), compared 

to control cells. Senescence growth arrest is known to be 

controlled by p53 phosphorylation/p21(WAF1/Cip1) induction 

or p16(INK4a)/retinoblastoma protein (pRB) 

activation. SM22α 

overexpression in HepG2 cells elevated 

p16(INK4a) followed by pRB activation, but did not activate 

the p53/p21(WAF1/Cip1) pathway. Moreover, MT-1G, 

which is induced by SM22α 

overexpression, was involved 

in the activation of the p16(INK4a)/pRB pathway, which 

led to a growth arrest state and promoted cellular senescence 

caused by damaging agents. Our findings provide the first 

demonstration that SM22α 

modulates cellular senescence 

caused by damaging agents via regulation of the 

p16(INK4a)/pRB pathway in HepG2 cells and that these 

effects of SM22α 

are partially mediated by MT-1G. 

PMID:20705054 

Article 136 

Gerontome: a web-based database server for aging-related 

genes and analysis pipelines 

BMC Genomics. 2010 Dec; 11(Suppl 4):S20. 

Kwon J, Lee B * , Chung H 

* Correspondence: bulee@kribb.re.kr 


BACKGROUND: Aging is a complex and challenging phenomenon 

that requires interdisciplinary efforts to unravel 

its mystery. Insight into genes relevant to the aging process 

would offer the chance to delay and avoid some of deteriorative 

aspects of aging through the use of preventive methods. 

To assist basic research on aging, a comprehensive database 

and analysis platform for aging-related genes is required. 

RESULTS: We developed a web-based database server, 

called Gerontome that contains aging-related gene information 

and user-friendly analysis pipelines. To construct 

the Gerontome database, we integrated aging-related genes 

and their annotation data. The aging-related genes were categorized 

by a set of structural terms from Gene Ontology 

(GO). Analysis pipelines for promoter analysis and protein-ligand 

docking were developed. The promoter analysis pipeline 

allows users to investigate the age-dependent regulation 

of gene expression. The protein-ligand docking pipeline provides 

information on the position and orientation of a ligand 

in an age-related protein surface. 

CONCLUSION: Gerontome can be accessed through web 

interfaces for querying and browsing. The server provides 

comprehensive age-related gene information and analysis 

pipelines. Gerontome is available free at 

http://gerontome.kobic.re.kr. 

PMID: 21143804 

Keywords: Aging; Databases, factual; Gene expression 

regulation; Internet; Ligand binding; Promoter 

region; User-computer interface 

Keywords: 

γ-Radiation; Antibiotics, antineoplastic; Cell 

aging; Cell growth arrest; Doxorubicin; 

Metallothionein; Microfilament proteins; Muscle 

proteins; p16; Retinoblastoma protein; Senescence; 

SM22α 


Article 137 

Human papillomavirus type 16 E6-specific antitumor 

immunity is induced by oral administration 

of HPV16 E6-expressing Lactobacillus casei in 

C57BL/6 mice 

Cancer Immunol Immunother. 2010 Nov; 59(11):1727-37. 

Lee TY, Kim YH, Lee KS, Kim JK, Lee IH, Yang JM, 

Sung MH, Park JS, Poo H * 

* Correspondence: haryoung@kribb.re.kr 


Given that local cell-mediated immunity (CMI) against the 

human papillomavirus type 16 E6 (HPV16 E6) protein is 

important for eradication of HPV16 E6-expressing cancer 

cells in the cervical mucosa, the HPV16 E6 protein may 

be a target for the mucosal immunotherapy of cervical cancer. 

Here, we expressed the HPV16 E6 antigen on Lactobacillus 

casei (L. casei) and investigated E6-specific CMI following 

oral administration of the L. casei-PgsA-E6 to mice. Surface 

expression of HPV16 E6 antigens was confirmed and mice 

were orally inoculated with the L. casei-PgsA or the L. 

casei-PgsA-E6. Compared to the L. casei-PgsA-treated mice, 

significantly higher levels of serum IgG and mucosal IgA 

were observed in L. casei-PgsA-E6-immunized mice; these 

differences were significantly enhanced after boost. 

Consistent with this, systemic and local CMI were significantly 

increased after the boost, as shown by increased 

counts of IFN-γ-secreting cells in splenocytes, mesenteric 

lymph nodes (MLN), and vaginal samples. Furthermore, in 

the TC-1 tumor model, animals receiving the orally administered 

L. casei-PgsA-E6 showed reduced tumor size and 

increased survival rate versus mice receiving control (L. 

casei-PgsA) immunization. We also found that L. 

casei-PgsA-E6-induced antitumor effect was decreased by 

in vivo depletion of CD4(+) or CD8(+) T cells. Collectively, 

these results indicate that the oral administration of lactobacilli 

bearing the surface-displayed E6 protein induces T 

cell-mediated cellular immunity and antitumor effects in 

mice. 

PMID: 20706715 

Keywords: Antitumor effect; Cell-mediated immunity; 

Enzyme-linked immunosorbent; Flow cytometry; 

Genetic vectors; HPV16 E6; Immunotherapy; 

Interferon- γ; 

vaccines; PgsA 

Lactobacillus casei; Papillomavirus 

Article 138 

Identification of tyrosine-nitrated proteins in 

HT22 hippocampal cells during 

glutamate-induced oxidative stress 

Cell Prolif. 2010 Dec; 43(6):584-93. 

Yoon SW, Kang S, Ryu SE, Poo H * 

* Correspondence: haryoung@kribb.re.kr 


OBJECTIVES: Nitration of tyrosine residues in protein is 

a post-translational modification, which occurs under oxidative 

stress, and is associated with several neurodegenerative 

diseases. To understand the role of nitrated proteins in oxidative 

stress-induced cell death, we identified nitrated proteins 

and checked correlation of their nitration in glutamate-induced 

HT22 cell death. 

MATERIALS AND METHODS: Nitrated proteins were detected 

by western blotting using an anti-nitrotyrosine antibody, 

extracted from matching reference 2-dimensional electrophoresis 

gels, and identified with matrix-assisted laser 

desorption/ionization time-of-flight mass spectrometry. 

RESULTS: Glutamate treatment induced apoptosis in HT22 

cells, while reactive oxygen species (ROS) inhibitor or neuronal 

nitric oxide synthase (nNOS) inhibitor blocked glutamate-induced 

HT22 cell death. Nitration levels of 13 proteins 

were increased after glutamate stimulation; six of them were 

involved in regulation of energy production and two were 

related to apoptosis. The other nitrated proteins were associated 

with calcium signal modulation, ER dysfunction, or 

were of unknown function. 

CONCLUSIONS: The 13 tyrosine-nitrated proteins were detected 

in these glutamate-treated HT22 cells. Results demonstrated 

that cell death, ROS accumulation and nNOS expression 

were related to nitration of protein tyrosine in the 

glutamate-stimulated cells. 

PMID: 21039997 

Keywords: Apoptosis; Cell survival; Cells, cultured; 

Glutamic acid; Hippocampus; Nitrates; Nitro 

compounds; Oxidative stress; Tyrosine 


Article 139 

Short rare MUC6 minisatellites-5 alleles influence 

susceptibility to gastric carcinoma by regulating 

gene expression 

Article 140 

Identification of autoantibody against fatty acid 

synthase in hepatocellular carcinoma mouse model 

and its application to diagnosis of HCC 

Hum Mutat. 2010 Aug; 31(8):942-9. 

Int J Oncol. 2010 Jun; 36(6):1453-9. 

Kwon JA, Lee SY, Ahn EK, Seol SY, Kim MC, Kim SJ, 

Kim SI, Chu IS * , Leem SH 

Heo CK, Woo MK, Yu DY, Lee JY, Yoo JS, Yoo HS, 

Ko JH, Kim JM, Choi JY, Kim IG, Paik SG, Cho EW * 

* Correspondence: chu@kribb.re.kr 


* Correspondence: ewcho@kribb.re.kr 


The human MUC6 gene, which is reported to be expressed 

in the stomach and gall bladder, is clustered on chromosome 

11p15.5 with other secreted mucins. In this study, the genomic 

structure of MUC6 has been analyzed and five VNTR 

(minisatellites; MS1-MS5) were identified. These minisatellites 

were analyzed in genomic DNA extracted from 1,103 

controls, 470 gastric cancer patients, and multigenerational 

families. Five novel minisatellites were found to be polymorphic 

and transmitted through meiosis by Mendelian inheritance 

in families. We evaluated allelic variation in these 

minisatellites to determine if such variation affected the susceptibility 

to gastric cancer. A significant association (odds 

ratio [OR]=7.08) between short rare MUC6-MS5 alleles and 

relative risks were observed for gastric cancer (95% confidence 

interval [CI], 1.43-35.19; P=0.005). To investigate 

the function of minisatellite alleles of MUC6-MS5, we examined 

the effects on gene expression from luciferase reporters 

when inserted with minisatellites. Interestingly, when the 

shortest allele (7TR) was inserted in the promoter, the expression 

level decreased over 20-fold (P

Article 141 

Expression signature of E2F1 and its associated 

genes predict superficial to invasive progression 

of bladder tumors 

J Clin Oncol. 2010 Jun; 28(16):2660-7. 

Lee JS, Leem SH, Lee SY, Kim SC, Park ES, Kim SB, 

Kim SK, Kim YJ, Kim WJ, Chu IS * 

* Correspondence: chu@kribb.re.kr 


PURPOSE: In approximately 20% of patients with superficial 

bladder tumors, the tumors progress to invasive tumors after 

treatment. Current methods of predicting the clinical behavior 

of these tumors prospectively are unreliable. We aim to identify 

a molecular signature that can reliably identify patients 

with high-risk superficial tumors that are likely to progress 

to invasive tumors. 

PATIENTS AND METHODS: Gene expression data were 

collected from tumor specimens from 165 patients with bladder 

cancer. Various statistical methods, including 

leave-one-out cross-validation methods, were applied to identify 

a gene expression signature that could predict the likelihood 

of progression to invasive tumors and to test the 

robustness of the expression signature in an independent 

cohort. The robustness of the gene expression signature was 

validated in an independent (n = 353) cohort. 

RESULTS: Supervised analysis of gene expression data revealed 

a gene expression signature that is strongly associated 

with invasive bladder tumors. A molecular classifier based 

on this gene expression signature correctly predicted the 

likelihood of progression of superficial tumor to invasive 

tumor. 

CONCLUSION: We present a molecular signature that can 

predict, at diagnosis, the likelihood of bladder cancer progression 

and, possibly, lead to improvements in patient 

therapy. 

PMID:20421545 

Article 142 

Identification of novel fatty acid glucosides from 

the tropical fruit Morinda citrifolia L 

Phytochem Lett. 2010 Dec; 3(4):238-41. 

Kim HK, Kwon MK, Kim JN, Kim CK, Lee YJ, Shin HJ, 

Lee J * , Lee HS 

* Correspondence: joongku@kribb.re.kr 


Two new fatty acid glucosides, 1,6-di-O-octanoyl-β-D-glu- 

copyranose (1) and 6-O-( β-D-glucopyranosyl)-1-O-dec- 

anoyl-β 

-D-glucopyranose (2), were isolated from a methanol 

extract of the fruit of Morinda citrifolia L. along with five 

known saccharide fatty acid esters. The structures of these 

compounds were determined by combination of spectral and 

chemical analyses. These fatty acid glucosides exhibited inhibitory 

effect against copper-induced low-density lipoprotein 

oxidation. Compound 2 had the strongest effect, 

which was almost comparable to that of butylated 

hydroxytoluene. 

Keywords: Copper-induced LDL oxidation; Fatty acid 

glucoside; Lipid oxidation; Morinda citrifolia L. 

(noni); Rubiaceae 

Keywords: Biopsy, needle; Carcinoma; Cystoscopy; E2F2 

transcription factor; Immunohistochemistry; 

Neoplasm invasiveness; Neoplasm staging; 

Proportional hazards models; Risk assessment; RNA, 

neoplasm; Urinary bladder neoplasms 


Article 143 

Whole-genome sequencing and intensive analysis 

of the undomesticated soybean (Glycine soja Sieb. 

and Zucc.) genome 

Proc Natl Acad Sci U S A. 2010 Dec; 107(51):22032-7. 

Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, 

Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park 

S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim 

KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon 

JK, Schmutz J, Jackson SA, Bhak J * , Lee SH 



The genome of soybean (Glycine max), a commercially important 

crop, has recently been sequenced and is one of 

six crop species to have been sequenced. Here we report 

the genome sequence of G. soja, the undomesticated ancestor 

of G. max (in particular, G. soja var. IT182932). The 48.8-Gb 

Illumina Genome Analyzer (Illumina-GA) short DNA reads 

were aligned to the G. max reference genome and a consensus 

was determined for G. soja. This consensus sequence spanned 

915.4 Mb, representing a coverage of 97.65% of the G. 

max published genome sequence and an average mapping 

depth of 43-fold. The nucleotide sequence of the G. soja 

genome, which contains 2.5 Mb of substituted bases and 

406 kb of small insertions/deletions relative to G. max, is 

∼0.31% different from that of G. max. In addition to the 

mapped 915.4-Mb consensus sequence, 32.4 Mb of large 

deletions and 8.3 Mb of novel sequence contigs in the G. 

soja genome were also detected. Nucleotide variants of G. 

soja versus G. max confirmed by Roche Genome Sequencer 

FLX sequencing showed a 99.99% concordance in single-nucleotide 

polymorphism and a 98.82% agreement in 

insertion/deletion calls on Illumina-GA reads. Data presented 

in this study suggest that the G. soja/G. max complex may 

be at least 0.27 million y old, appearing before the relatively 

recent event of domestication (6,000∼9,000 y ago). This 

suggests that soybean domestication is complicated and that 

more in-depth study of population genetics is needed. In 

any case, genome comparison of domesticated and undomesticated 

forms of soybean can facilitate its 

improvement. 

PMID:21131573 

Keywords: Divergence; Genetic variation; Genome, plant; 

Genome duplication; Massively parallel sequencing; 

Sequence variation; Wild soybean 



2010 




Korea Biological Resource Center 


Plant Resource Center 

Human Derived Material Center 


Animal Model Resource Center 



www.kribb.re.kr

Article 144 

Role of Geobacter sulfurreducens outer surface 

c-type cytochromes in reduction of soil humic 

acid and anthraquinone-2,6-disulfonate 

Appl Environ Microbiol. 2010 Apr; 76(7):2371-5. 

Voordeckers JW, Kim BC * , Izallalen M, Lovley DR 

* Correspondence: bckim@kribb.re.kr 


Deleting individual genes for outer surface c-type cytochromes 

in Geobacter sulfurreducens partially inhibited the 

reduction of humic substances and anthraquinone-2,6,-disulfonate. 

Complete inhibition was obtained 

only when five of these genes were simultaneously 

deleted, suggesting that diverse outer surface cytochromes 

can contribute to the reduction of humic substances and 

other extracellular quinones. 

PMID:20154112 

Keywords: Anthraquinones; Bacterial proteins; 

Cytochromes; Gene deletion; Genes, bacterial; 

Geobacter; Humic substances; Oxidation-reduction; 

Soil microbiology 

Article 145 

Identification and characterization of a novel 

Terrabacter ginsenosidimutans sp. nov. β 

-glucosidase that transforms ginsenoside Rb1 into 

the rare gypenosides XVII and LXXV 

Appl Environ Microbiol. 2010 Sep; 76(17):5827-36. 

An DS, Cui CH, Lee HG, Wang L, Kim SC, Lee ST, Jin 

F, Yu H, Chin YW, Lee HK, Im WT, Kim SG * 

* Correspondence: sgkim@kribb.re.kr 


A new β-glucosidase from a novel strain of Terrabacter 

ginsenosidimutans (Gsoil 3082 T ) obtained from the soil of 

a ginseng farm was characterized, and the gene, bgpA (1,947 

bp), was cloned in Escherichia coli. The enzyme catalyzed 

the conversion of ginsenoside Rb1 {3-O-[ β-D-glucopyr- 

anosyl-(1-2)-β-D-glucopyranosyl]-20-O-[ β-D-glucopyr- 

anosyl-(1-6)-β-D-glucopyranosyl]-20(S)-protopanaxadiol} 

to the more pharmacologically active rare ginsenosides gypenoside 

XVII {3-O-β-D-glucopyranosyl-20-O-[ β-D-gluco- 

p y r a n o s y l - ( 1 - 6 ) - β - D - g l u c o p y r- 

anosyl]-20(S)-protopanaxadiol}, gypenoside LXXV {20-O- 

[ β - v - g l u c o p y r a n o s y l - ( 1 - 6 ) - β - D - g l u c o p y r- 

anosyl]-20(S)-protopanaxadiol}, and C-K [20-O-( β-D-glu- 

copyranosyl)-20(S)-protopanaxadiol]. A BLAST search of 

the bgpA sequence revealed significant homology to family 

3 glycoside hydrolases. Expressed in E. coli, β-glucosidase 

had apparent K(m) values of 4.2 +/- 0.8 and 0.14 +/- 0.05 

μM and V(max) values of 100.6 +/- 17.1 and 329 +/- 31 

micromol x min(-1) x mg of protein(-1) against p-nitrophenyl-β-D-glucopyranoside 

and Rb1, respectively. The en- 

zyme catalyzed the hydrolysis of the two glucose moieties 

attached to the C-3 position of ginsenoside Rb1, and the 

outer glucose attached to the C-20 position at pH 7.0 and 

37 degrees C. These cleavages occurred in a defined order, 

with the outer glucose of C-3 cleaved first, followed by 

the inner glucose of C-3, and finally the outer glucose of 

C-20. These results indicated that BgpA selectively and sequentially 

converts ginsenoside Rb1 to the rare ginsenosides 

gypenoside XVII, gypenoside LXXV, and then C-K. Herein 

is the first report of the cloning and characterization of a 

novel ginsenoside-transforming β-glucosidase of the glyco- 

side hydrolase family 3. 

PMID:20622122 

Keywords: Actinomycetales; Bacterial proteins; β 

-Glucosidase; Biotransformation; DNA, bacterial; 

Ginsenosides; Gynostemma; Kinetics; Membrane 

proteins; Panax; Phylogeny; Plant extracts; Soil 

microbiology; Substrate specificity; Transferases 


Article 146 

Mucilaginibacter dorajii sp. nov., isolated from 

the rhizosphere of Platycodon grandiflorum 

FEMS Microbiol Lett. 2010 Aug; 309(2):130-5. 

Kim BC, Lee KH, Kim MN, Lee J, Shin KS * 

* Correspondence: ksshin@kribb.re.kr 


Article 147 

Chestnut (Castanea crenata) inner shell extract 

inhibits development of hepatic steatosis in 

C57BL/6 mice fed a high-fat diet 

Food Chem. 2010 Jul; 121(2):437-42. 

Noh JR, Kim YH, Gang GT, Yang KJ, Lee HS, Nguyen 

PH, Oh WK, Song KS, Lee CH * 

* Correspondence: chullee@kribb.re.kr 

A Gram-negative, nonmotile and rod-shaped bacterial strain 

was isolated from the rhizosphere of Platycodon grandiflorum 

in a study of bacterial diversity, and its taxonomic 

position was investigated by a genotypic and phenotypic 

analysis. This isolate, designated as DR-f4, grew at 4-30 

degrees C (optimally at 20-25 degrees C) and in the presence 

of 0-1% (w/v) NaCl. It contained MK-7 as the predominant 

menaquinone. The isolate had activities of catalase, oxidase 

and 

β-galactosidase and hydrolyzed aesculin, casein, carbox - 

ymethyl-cellulose, starch and L-tyrosine. The major cellular 

fatty acids were summed feature 3 (C(16:1) ω7c and/or 

iso-C(15:0) 2OH) and iso-C(15:0). The DNA G+C content 

was 42.6 mol%. This isolate belonged to the genus 

Mucilaginibacter based on phylogenetic analysis using 16S 

rRNA gene sequences. The nearest phylogenetic neighbors 

of strain DR-f4 T were Mucilaginibacter lappiensis ANJL12 T 

and Mucilaginibacter rigui WPCB133 T , with 16S rRNA gene 

sequence similarity levels of 96.9% and 96.4%, respectively. 

The genotypic and phenotypic evidence suggests that strain 

DR-f4 T should be classified as a novel species, for which 

the name Mucilaginibacter dorajii sp. nov. is proposed. The 

type strain for the novel species is DR-f4 T (=KACC 

14556 T =JCM 16601 T ). 

PMID: 20572870 

Keywords: Bacteroidetes; DNA, bacterial; DNA, 

ribosomal; Doraji; Mucilaginibacter dorajii; 

Platycodon grandiflorum; Rhizosphere; RNA, 

ribosomal, 16S; Soil microbiology 


The effects of chestnut inner shell extract (CISE) on hepatic 

steatosis and lipid metabolism in mice fed high-fat diet (HFD) 

were evaluated. Hepatic triacylglycerol and plasma lipid levels 

decreased significantly in CISE-administered mice compared 

to control group. Relative mRNA expression levels 

for lipogenic genes SREBP-1c, FAS, ACCs, ACAT, and 

HMG-CoA were significantly decreased in CISE-administered 

mice (P < 0.05). CISE suppressed FAS and 

HMG-CoA reductase activity and increased CPT activity. 

To determine the active compound of CISE, the fractionation 

of CISE have conducted and resulted in the isolation of 

scoparone and scopoletin, as main compounds contained 

in CISE. Based on these results, we speculate that the inhibitory 

effect on hepatic steatosis of CISE containing scoparone 

and scopoletin may be the result of suppression of lipid 

synthesis and the acceleration of fatty acid oxidation in mice 

fed HFD, suggesting that CISE may be beneficial in preventing 

hepatic steatosis. 

Keywords: Animal model; Castanea crenata; Chestnut 

inner shell; Enzyme activity; Fatty liver; Hepatic 

lipid; Hepatic steatosis; Lipid diet; Lipid metabolism; 

Triacylglycerol blood level; Weight change 


Article 148 

Antioxidant effects of the chestnut (Castanea 

crenata) inner shell extract in t-BHP-treated 

HepG2 cells, and CCl4- and high-fat diet-treated 

mice 

Food Chem Toxicol. 2010 Nov; 48(11):3177-83. 

Noh JR, Gang GT, Kim YH, Yang KJ, Hwang JH, Lee 

HS, Oh WK, Song KS, Lee CH * 



The antioxidant effects of chestnut inner shell extract (CISE) 

were investigated in a tert-butylhydroperoxide 

(t-BHP)-treated HepG2 cells, and in mice that were administered 

carbon tetrachloride (CCl(4)) and fed a high-fat 

diet (HFD). Pre-incubation with CISE significantly blocked 

the oxidative stress induced by t-BHP treatment in HepG2 

cells (P

Article 150 

Comparative genomic analysis of the false killer 

whale (Pseudorca crassidens) LMBR1 locus 

Article 151 

The effects of various antioxidants on the development 

of parthenogenetic porcine embryos 

Genome. 2010 Sep; 53(9):658-66. 

In Vitro Cell Dev Biol Anim. 2010 Feb; 46(2):148-54. 

Kim DW, Choi SH, Kim RN, Kim SH, Paik SG, Nam SH, 

Kim DW, Kim A, Kang A, Park HS * 

* Correspondence: hspark@kribb.re.kr 


The sequencing and comparative genomic analysis of LMBR1 

loci in mammals or other species, including human, would 

be very important in understanding evolutionary genetic 

changes underlying the evolution of limb development. In 

this regard, comparative genomic annotation of the false 

killer whale LMBR1 locus could shed new light on the evolution 

of limb development. We sequenced two false killer 

whale BAC clones, corresponding to 156 kb and 144 kb, 

respectively, harboring the tightly linked RNF32, LMBR1, 

and NOM1 genes. Our annotation of the false killer whale 

LMBR1 gene showed that it consists of 17 exons (1473 

bp), in contrast to 18 exons (1596 bp) in human, and it 

displays 93.1% and 95.6% nucleotide and amino acid sequence 

similarity, respectively, compared with the human 

gene. In particular, we discovered that exon 10, deleted in 

the false killer whale LMBR1 gene, is present only in primates, 

and this fact strongly implies that exon 10 might be crucial 

in determining primate-specific limb development. ZRS and 

TFBS sequences have been well conserved across 11 species, 

suggesting that these regions could be involved in an important 

function of limb development and limb patterning. 

The neighboring gene RNF32 showed several lineage-conserved 

exons, such as exons 2 through 9 conserved in eutherian 

mammals, exons 3 through 9 conserved in mammals, 

and exons 5 through 9 conserved in vertebrates. The other 

neighboring gene, NOM1, had undergone a substitution 

(ATG→GTA) at the start codon, giving rise to a 36 

bp shorter N-terminal sequence compared with the human 

sequence. Our comparative analysis of the false killer whale 

LMBR1 genomic locus provides important clues regarding 

the genetic regions that may play crucial roles in limb development 

and patterning. 

PMID: 20924415 

Keywords: Body patterning; Comparative analysis; Exon 

deletion; Extremities; Gene organization; LMBR1; 

Molecular sequence annotation; NOM1; RNF32; 

Sequence homology; Whale genome 

Yuh HS, Yu DH, Shin MJ, Kim HJ, Bae KB, Lee DS, 

Lee HC, Chang WK, Park SB, Lee SG, Park HD, Ha JH, 

Hyun BH * , Ryoo ZY 

* Correspondence: hyunbh@kribb.re.kr 


The major objective of this study was to improve the development 

rate of parthenogenetic porcine embryos. In this study, 

the anti-oxidative and anti-apoptotic effects of three antioxidants, 

β-mercaptoethanol ( β-ME), α-tocopherol, and ex- 

tracellular superoxide dismutase (EC-SOD), were examined 

on the development of parthenogenetic porcine embryos. 

The development rate of parthenogenetic porcine embryos 

to the blastocyst stage was 8.1% for control; 19.1%, 14.6%, 

and 5.0% for 1, 3, and 5 μM β-ME; 17.2% and 17.5% 

for 50 and 100 μM α-tocopherol and 12.0% and 4.0% for 

EC-SOD transgenic mouse embryonic fibroblast (Tg-MEF) 

and EC-SOD non-transgenic mouse embryonic fibroblast 

(NTg-MEF) conditioned medium at day 3, respectively. Here, 

β-ME, 

α-tocopherol, and EC-SOD Tg-MEF conditioned me- 

dium increased the development rate of parthenogenetic porcine 

embryos to the blastocyst stage (P < 0.05). The average 

number of total cells and apoptotic cells at the blastocyst 

was analyzed at the optimal conditions of the three 

antioxidants. The three antioxidants increased the average 

number of total cells at the blastocyst, and they decreased 

apoptotic cells at the blastocyst as compared to control without 

supplementation (P < 0.05). When the reactive oxygen 

species levels in two-cell embryos after 1 μM β-ME and 

100 μM α-tocopherol treatment were examined, those were 

lower than control group (P < 0.05). In conclusion, it was 

found that the three antioxidants, 

β-mercaptoethanol, 

-tocopherol, and EC-SOD Tg-MEF, conditioned medium can 

play a role as a strong stimulator in the development of 

parthenogenetic porcine embryos. 

PMID:19915933 

Keywords: Antioxidant; Anti-apoptosis; Blastocyst stage; 

Embryo; Mus musculus; Parthenogenesis; Porcine 

α 


Article 152 

Kocuria koreensis sp. nov., isolated from 

fermented seafood 


Park EJ, Roh SW, Kim MS, Jung MJ, Shin KS, Bae JW * 



A Gram-positive, aerobic, non-motile and coccoid actinobacterium, 

designated P31 T , was isolated from a traditional, 

fermented seafood. The strain was catalase-positive and oxidase-negative. 

Cells grew in the presence of 0-15.0 % (w/v) 

NaCl, and at pH 5-10 and 15-37 degrees C. Major cellular 

fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and 

iso-C(16 : 0). Strain P31 T contained MK-7 as the predominant 

menaquinone. The DNA G+C content of the genomic DNA 

of strain P31 T was 65.2 mol%. A phylogenetic analysis based 

on the 16S rRNA gene sequence indicated that strain P31 T 

was most closely related to Kocuria kristinae DSM 20032 T , 

with 96.9 % similarity, and these two strains clustered together 

in constructed phylogenetic trees. The DNA-DNA hybridization 

value between strain P31 T and K. kristinae DSM 

20032 T was 21.1 %. On the basis of the phenotypic, chemotaxonomic 

and phylogenetic data, it is suggested that strain 

P31 T represents a novel species of the genus Kocuria, for 

which the name Kocuria koreensis sp. nov. is proposed. 

The type strain is P31 T (=KCTC 19595 T =JCM 15915 T ). 

PMID:19648328 


ribosomal; Fermentation; Micrococcaceae; 


ribosomal, 16S; Seafood 

Article 153 

Halomonas stevensii sp. nov., Halomonas hamiltonii 

sp. nov. and Halomonas johnsoniae sp. nov., 

isolated from a renal care centre 


Kim KK, Lee KC, Oh HM, Lee JS * 

* Correspondence: jslee@kribb.re.kr 


A total of 14 Halomonas strains were isolated from the 

blood of two patients and from dialysis machines of a renal 

care centre. The strains were Gram-negative, halophilic, motile 

and non-spore-forming rods. They produced cream-coloured 

colonies and contained Q-9 as the predominant ubiquinone 

and C(18 : 1) ω7c and C(16 : 0) as the major fatty 

acids. Phylogenetic analysis based on 16S rRNA gene sequencing 

showed that the 14 isolates were most closely related 

to Halomonas magadiensis 21 MI(T) with 98.1-98.9 

% sequence similarity and that they formed three separate 

lineages among themselves. Combined phenotypic and 

DNA-DNA hybridization data support the conclusion that 

they represent three novel species of the genus Halomonas, 

for which the names Halomonas stevensii sp. nov. (type 

strain S18214 T =KCTC 22148 T =DSM 21198 T ), Halomonas 

hamiltonii sp. nov. (type strain W1025 T =KCTC 

22154 T =DSM 21196 T ) and Halomonas johnsoniae sp. nov. 

(type strain T68687 T =KCTC 22157 T =DSM 21197 T ) are 

proposed. 

PMID: 19651714 

Keywords: Bacteremia; Base sequence; DNA, bacterial; 

Halomonas; Hemodialysis units, hospital; Molecular 

sequence data; Phylogeny; Renal dialysis; RNA, 

bacterial; RNA, ribosomal, 16S; Sequence homology 


Article 154 

Nocardioides panacisoli sp. nov., isolated from 

the soil of a ginseng field 


Cho CH, Lee JS, An DS, Whon TW, Kim SG * 



Article 155 

Haloechinothrix alba gen. nov., sp. nov., a 

halophilic, filamentous actinomycete of the 

suborder Pseudonocardineae 


Tang SK, Wang Y, Zhang H, Lee JC, Lou K, Kim CJ * , 

Li WJ 

* Correspondence: changjin@kribb.re.kr 

A Gram-positive, rod-shaped, non-spore-forming bacterium 

(Gsoil 346 T ) was isolated from the soil of a ginseng field 

in South Korea and was characterized in order to determine 

its taxonomic position. On the basis of 16S rRNA gene 

sequences, strain Gsoil 346 T was shown to belong to the 

genus Nocardioides in the family Nocardioidaceae, with the 

most closely related species being Nocardioides aquiterrae 

GW-9 T (96.6 % 16S rRNA gene sequence similarity); however, 

the strain clustered in a distinct branch of the phylogenetic 

tree with Nocardioides kongjuensis A2-4 T (96.2 %), 

Nocardioides aromaticivorans H-1 T (96.1 %), Nocardioides 

nitrophenolicus NSP41 T (96.1 %) and Nocardioides simplex 

ATCC 15799 T (95.9 %). Strain Gsoil 346 T was characterized 

chemotaxonomically and found to have ll-2,6-diaminopimelic 

acid in the cell-wall peptidoglycan, phosphatidylinositol 

and phosphatidylglycerol as the major polar lipids, 

MK-8(H(4)) as the predominant menaquinone and iso-C 16:0, 

C(18 : 1) ω9c and C(17 : 1) ω8c as the major fatty acids. 

The G+C content of the genomic DNA of the novel strain 

was 73.0 mol%. These chemotaxonomic properties supported 

the placement of strain Gsoil 346 T in the genus Nocardioides. 

The results of physiological and biochemical tests, along 

with the phylogenetic analysis, allowed strain Gsoil 346 T 

to be differentiated genotypically and phenotypically from 

recognized species of the genus Nocardioides. Therefore, 

strain Gsoil 346 T represents a novel species, for which the 

name Nocardioides panacisoli sp. nov. is proposed, with 

Gsoil 346 T (=KCTC 19470 T =DSM 21348 T ) as the type strain. 

PMID:19651712 

Keywords: Actinomycetales; Base sequence; DNA, 

bacterial; Molecular sequence data; Panax; 

Phylogeny; Republic of Korea; RNA, bacterial; 

RNA, ribosomal, 16S; Sequence homology, Soil 

microbiology 


A novel halophilic, filamentous actinomycete strain, designated 

YIM 93221 T , was isolated from a salt lake in Xinjiang 

province, north-west China, and subjected to a polyphasic 

taxonomic characterization. The isolate grew with 9-23 % 

(w/v) NaCl and did not grow without NaCl. The isolate 

formed spiny aerial mycelium and did not form spores at 

maturity. The isolate contained meso-diaminopimelic acid 

as the diagnostic diamino acid and glucose, glucosamine, 

mannose and an unknown sugar as the major whole-cell 

sugars. The phospholipids were diphosphatidylglycerol, 

phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, 

phosphatidylinositol mannosides and an unknown 

phospholipid. MK-8(H 4) was the predominant 

menaquinone. The major fatty acid was iso-C 16:0. The DNA 

G+C content was 68.1 mol%. Phylogenetic analysis based 

on 16S rRNA gene sequences indicated that strain YIM 

93221 T formed a distinct lineage within the suborder 

Pseudonocardineae and showed 91.9-94.8 % 16S rRNA gene 

sequence similarity with members of the suborder 

Pseudonocardineae. On the basis of the evidence from this 

polyphasic study, a novel genus and species, Haloechinothrix 

alba gen. nov., sp. nov., are proposed. The type strain of 

Haloechinothrix alba is YIM 93221 T (=DSM 45207 T 

=CCTCC AB 208140 T ). 

PMID:19880632 

Keywords: Actinobacteria; Actinomycetales; 

Bacterial 

typing techniques; China; DNA, bacterial; DNA, 

ribosomal; Fatty acids; Fresh water; Molecular 


Sodium chloride 


Article 156 

Pontibaca methylaminivorans gen. nov., sp. nov., 

a member of the family Rhodobacteraceae 

Article 157 

Alishewanella agri sp. nov., isolated from landfill 

soil 



Kim KK, Lee JS, Lee KC, Oh HM, Kim SG * 

Kim MS, Jo SK, Roh SW, Bae JW * 





The alphaproteobacterial strains GRP21 T and PH34, which 

were isolated from coastal sediment of the East Sea, Korea, 

were subjected to a polyphasic taxonomic investigation. The 

strains were Gram-negative, non-motile, non-spore-forming, 

oval-shaped rods that produced creamy-white colonies on 

tryptic soy agar, required NaCl for growth, contained Q-10 

as the predominant ubiquinone, contained 16 : 0, 18 : 1ω7c 

and 19 : 0 cyclo 

ω8c as major fatty acids and had polar 

lipid profiles consisting of phosphatidylcholine, phosphatidylglycerol, 

an unknown aminolipid, an unknown phospholipid 

and three unknown lipids. Phylogenetic analysis, based 

on 16S rRNA gene sequencing, showed that the strains were 

most closely related to Donghicola eburneus KCTC 12735 T , 

with 94.5 % sequence similarity, but formed a separate lineage 

within the family Rhodobacteraceae. The combined genotypic 

and phenotypic data supported the conclusion that 

the strains represent a novel genus and species, for which 

the name Pontibaca methylaminivorans gen. nov., sp. nov. 

is proposed. The type strain of Pontibaca methylaminivorans 

is GRP21 T (=KCTC 22497 T =DSM 21219 T ). 

PMID: 19897619 

Keywords: DNA, bacterial; DNA, ribosomal; Fatty acids; 

Geologic sediments; Molecular sequence data; 

Phylogeny; Rhodobacteraceae; RNA, ribosomal, 

16S; Sodium chloride 

Strain BL06 T was isolated from landfill soil in Pohang, Korea. 

Strain BL06 T is Gram-negative, aerobic, non-motile and 

rod-shaped. For growth, the NaCl range is 0-6 % (w/v), 

the temperature range is 10-44 degrees C and the pH range 

is 5.5-12.0. Based on the 16S rRNA gene and gyrase B 

(gyrB) gene sequences, phylogenetic analysis showed that 

strain BL06 T is associated with the genus Alishewanella and 

related closely to the type strains of Alishewanella species 

(98.8 % 16S rRNA gene sequence similarity to Alishewanella 

aestuarii, 98.7 % to Alishewanella fetalis and 98.5 % to 

Alishewanella jeotgali). Physiological and biochemical tests 

verified that strain BL06 T is genotypically and phenotypically 

different from previously described species in the genus 

Alishewanella. DNA-DNA hybridization experiments 

showed that relatedness between the genomic DNA of strain 

BL06 T and type strains of other Alishewanella species is 

Article 158 

Clostridium arbusti sp. nov., an anaerobic bacterium 

isolated from pear orchard soil 

Article 159 

Cohnella thailandensis sp. nov., a xylanolytic bacterium 

from Thai soil 


Int J Syst Evol Microbiol. 2010 Oct; 60(10):2284-7. 

Jung MY, Park IS, Kim W, Kim HL, Paek WK, Chang 

YH * 

Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, 

Lee KC, Lee JS * 

* Correspondence: yhchang@kribb.re.kr 




An obligately anaerobic, Gram-positive, spore-forming bacterial 

strain, designated SL206 T , was isolated from pear orchard 

soils. Strain SL206 T cells were straight or slightly 

curved rods, with motility by peritrichate flagella. Cell walls 

contained meso-diaminopimelic acid; wall sugars were glucose, 

rhamnose and mannose. The major fatty acids were 

C(16 : 0), C(18 : 1) ω9c and summed feature 10 (containing 

C(18 : 1) ω11c/9t/6t). API 20A reactions were negative for 

oxidase, catalase and acid production from l-rhamnose, sucrose, 

trehalose, d-xylose, melezitose, salicin and d-sorbitol, 

and positive for acid production from d-glucose, sucrose, 

maltose, d-mannose and raffinose. Glucose was fermented 

to acetate, butyrate, CO(2), H(2) and ethanol in culture. 

The G+C content of the genomic DNA was 31.1 mol%. 

Based on comparative 16S rRNA gene sequence analysis, 

the isolate belonged to the genus Clostridium and formed 

a clade with Clostridium pasteurianum. The species most 

closely related to strain SL206 T were C. pasteurianum (98.6 

% similarity) and Clostridium acidisoli (97.8 % similarity). 

In DNA-DNA relatedness studies, the isolate had 59.5 % 

relatedness with C. pasteurianum and thus represented a 

unique species. On the basis of these studies, strain SL206 T 

(=KCTC 5449 T =JCM 14858 T ) is proposed to represent the 

type strain of a novel species, Clostridium arbusti sp. nov. 

PMID: 19915114 

A xylanolytic bacterium, strain S1-3 T , was isolated from 

soil collected in Nan province, Thailand. It was characterized 

taxonomically based on phenotypic characteristics and 16S 

rRNA gene sequence comparison. The strain was a 

Gram-stain-positive, facultatively anaerobic, spore-forming, 

rod-shaped bacterium. It contained meso-diaminopimelic 

acid in the cell-wall peptidoglycan. The major menaquinone 

was MK-7. Iso-C 16:0 (39.5 %) and anteiso-C 15:0 (26.8 %) 

were predominant cellular fatty acids. 

Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine 

and lysyl-phosphatidylglycerol were the major 

polar lipids. The DNA G+C content was 53.3 mol%. 

Phylogenetic analysis using 16S rRNA gene sequences 

showed that strain S1-3 T was affiliated to the genus Cohnella, 

and was closely related to Cohnella ginsengisoli GR21-5 T 

and Cohnella thermotolerans CCUG 47242 T with 95.7 and 

95.3 % sequence similarity, respectively. Strain S1-3 T could 

be clearly distinguished from related species of the genus 

Cohnella by its physiological and biochemical characteristics 

as well as by its phylogenetic position. Therefore, the strain 

represents a novel species of the genus Cohnella, for which 

the name Cohnella thailandensis sp. nov. is proposed. The 

type strain is S1-3 T (=KCTC 22296 T =TISTR 1890 T =PCU 

306 T ). 

PMID:19915111 

Keywords: Anaerobiosis; Clostridium; DNA, bacterial; 

DNA, ribosomal; Fatty acids; Molecular sequence 

data; Phylogeny; Pyrus; RNA, ribosomal, 16S; Soil 

microbiology 

Keywords: Anaerobiosis; Bacillales; Cluster analysis; 

DNA, bacterial; Peptidoglycan; Phospholipids; 

Phylogeny; RNA, ribosomal, 16S; Sequence 

analysis, DNA; Soil microbiology; Spores, bacterial; 

Vitamin K 2; Xylans 


Article 160 

Nocardioides mesophilus sp. nov., isolated from 

soil 

Article 161 

Paenibacillus sputi sp. nov., isolated from the 

sputum of a patient with pulmonary disease 



Dastager SG, Lee JC, Pandey A, Kim CJ * 

Kim KK, Lee KC, Yu H, Ryoo S, Park Y, Lee JS * 

* Correspondence: changjin@kribb.re.kr 




A short coccoid- to rod-shaped, motile, mesophilic actinobacterium, 

strain MSL-22 T , was isolated from soil on Bigeum 

Island, Korea. A polyphasic study was undertaken to establish 

the taxonomic position of this strain. Phylogenetic analysis 

based on 16S rRNA gene sequences revealed that strain 

MSL-22 T formed an evolutionary lineage within the radiation 

of the genus Nocardioides. In particular, it formed a monophyletic 

lineage with Nocardioides jensenii KCTC 9134 T 

with which it shared the highest sequence similarity of about 

97.3%. However, DNA-DNA relatedness demonstrated that 

strain MSL-22 T was distinct from its closest phylogenetic 

neighbours. The cell-wall peptidoglycan of strain 

MSL-22 T contained LL-diaminopimelic acid. The predominant 

menaquinone was MK-8(H ₄). Strain MSL-22 

T had a cellular 

fatty acid profile containing straight-chain, branched, unsaturated 

and 10-methyl fatty acids, with iso-C 16:0 as the 

major fatty acid. The DNA G+C content of the strain was 

68.7 mol%. On the basis of phenotypic and phylogenetic 

evidence, the strain is separated from previously described 

members of the genus Nocardioides and represents a novel 

species in this genus, for which the name Nocardioides mesophilus 

sp. nov. is proposed. The type strain is MSL-22 T 

(=DSM 19432 T =KCTC 19310 T ). 

PMID:19915109 

Strain KIT 00200-70066-1 T was isolated from the sputum 

of a patient with pulmonary disease. Cells of the strain were 

Gram-variable, facultatively anaerobic, motile, spore-forming 

rods and formed colourless to white colonies on tryptic 

soy agar at 30&emsp14;°C and pH&emsp14;7. The pathogenicity 

of the strain is not known. The strain contained meso-diaminopimelic 

acid as the diagnostic diamino acid in the 

cell-wall peptidoglycan, MK-7 as the predominant menaquinone, 

anteiso-C 15:0, iso-C 16:0 and C 16:0 as the major fatty acids 

and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine 

and several unknown lipids in the polar 

lipid profile. Phylogenetic analysis based on 16S rRNA gene 

sequences showed that the isolate belongs to the genus 

Paenibacillus, sharing the highest levels of sequence similarity 

with Paenibacillus nanensis MX2-3 T , Paenibacillus 

agaridevorans DSM 1355 T and Paenibacillus alkaliterrae 

KSL-134 T (95.4, 95.2 and 94.8 %, respectively), and that 

it occupied a distinct position within this genus. Combined 

phylogenetic and phenotypic data supported the conclusion 

that strain KIT 00200-70066-1 T represents a novel species 

of the genus Paenibacillus, for which the name Paenibacillus 

sputi sp. nov. is proposed; the type strain is KIT 

00200-70066-1 T (=KCTC 13252 T =DSM 22699 T ). 

PMID: 19946060 

Keywords: Actinomycetales; Cluster analysis; DNA, 

bacterial; DNA, ribosomal; Locomotion; Molecular 

sequence data; Nucleic acid hybridization; 

Peptidoglycan; Phylogeny; RNA, ribosomal, 16S; 

Soil microbiology; Vitamin K 2 

Keywords: Aerobiosis; Anaerobiosis; Cluster analysis; 

DNA, bacterial; DNA, ribosomal; Gram-positive 

bacterial infections; Lung diseases; Molecular 

sequence data; Paenibacillus; Phospholipids; 

Phylogeny; Quinones; RNA, ribosomal, 16S; Spores, 

bacterial; Sputum 


Article 162 

Cohnella xylanilytica sp. nov. and Cohnella terrae 

sp. nov., xylanolytic bacteria from soil 

Article 163 

Genome sequence of Leuconostoc argentinum 

KCTC 3773 


J Bacteriol. 2010 Dec; 192(24):6490-1. 

Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, 

Lee KC, Lee JS * 

Nam SH, Choi SH, Kang A, Kim DW, Kim RN, Kim A, 

Park HS * 





Two xylan-degrading bacteria, strains MX15-2 T and 

MX21-2 T , were isolated from soils collected in Nan province, 

Thailand. Cells were Gram-reaction-positive, facultatively 

anaerobic, spore-forming and rod-shaped. They contained 

meso-diaminopimelic acid in the cell-wall peptidoglycan. 

The major menaquinone was MK-7. iso-C(16 : 0) and anteiso-C(15 

: 0) were the predominant cellular fatty acids. 

Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine 

and lysyl-phosphatidylglycerol were the major 

polar lipids. The genomic DNA G+C contents of strains 

MX15-2 T and MX21-2 T were 63.0 and 65.1 mol%, 

respectively. Phylogenetic analysis using 16S rRNA gene 

sequences showed that strains MX15-2 T and MX21-2 T were 

affiliated with the genus Cohnella and were closely related 

to Cohnella thermotolerans CCUG 47242 T , with 96.5 and 

95.6 % sequence similarity, respectively. The strains could 

be clearly distinguished from each other and from all known 

species of the genus Cohnella based on their physiological 

and biochemical characteristics as well as their phylogenetic 

positions and levels of DNA-DNA hybridization. Therefore, 

these two strains represent novel species of the genus 

Cohnella, for which the names Cohnella xylanilytica sp. 

nov. (type strain MX15-2 T =KCTC 22294 T =PCU 309 T 

=TISTR 1891 T ) and Cohnella terrae sp. nov. (type strain 

MX21-2 T =KCTC 22295 T =PCU 310 T =TISTR 1892 T ) are 

proposed. 

PMID:20097800 

Leuconostoc argentinum is one of the most prevalent lactic 

acid bacteria present during the manufacturing process of 

kimchi, the best-known traditional Korean dish. Here, we 

present the draft genome sequence of type strain KCTC 

3773 of Leuconostoc argentinum (1,720,683 bp, with a G+C 

content of 42.9%), which consists of 98 large contigs (>100 

bp in size). 

PMID: 20952569 

Keywords: Fermentation; Food microbiology; Gene 

expression regulation; Genome, bacterial; 

Leuconostoc; Molecular sequence data 

Keywords: Bacterial cell wall; Bacterial strain; Cohnella 

terrae; Cohnella thermotolerans; Cohnella 

xylanilytica; DNA base composition; DNA 

hybridization; Gene sequence; Gram positive 

bacterium; Nucleotide sequence; Phylogeny; 

Physiology; Thailand 


Article 164 

Effects of regulator of G protein signaling 19 

(RGS19) on heart development and function 

Article 165 

Bacillus gaemokensis sp. nov., isolated from foreshore 

tidal flat sediment from the Yellow Sea 

J Biol Chem. 2010 Sep; 285(37):28627-34. 

J Microbiol. 2010 Dec; 48(6):867-71. 

Ji YR, Kim MO, Kim SH, Yu DH, Shin MJ, Kim HJ, Yuh 

HS, Bae KB, Kim JY, Park HD, Lee SG, Hyun BH * , Ryoo 

ZY 

* Correspondence: hyunbh@kribb.re.kr 


Wnt/Wg genes play a critical role in the development of 

various organisms. For example, the Wnt/ β-catenin signal 

promotes heart formation and cardiomyocyte differentiation 

in mice. Previous studies have shown that RGS19 (regulator 

of G protein signaling 19), which has Gα 

subunits with 

GTPase activity, inhibits the Wnt/ β-catenin signal through 

inactivation of G α(o). In the present study, the effects of 

RGS19 on mouse cardiac development were observed. In 

P19 teratocarcinoma cells with RGS19 overexpression, 

RGS19 inhibited cardiomyocyte differentiation by blocking 

the Wnt signal. Additionally, several genes targeted by Wnt 

were down-regulated. For the in vivo study, we generated 

RGS19-overexpressing transgenic (RGS19 TG) mice. In 

these transgenic mice, septal defects and thin-walled ventricles 

were observed during the embryonic phase of development, 

and the expression of cardiogenesis-related genes, 

BMP4 and Mef2C, was reduced significantly. RGS19 TG 

mice showed increased expression levels of brain natriuretic 

peptide and 

β-MHC, which are markers of heart failure, 

increase of cell proliferation, and electrocardiogram analysis 

shows abnormal ventricle repolarization. These data provide 

in vitro and in vivo evidence that RGS19 influenced cardiac 

development and had negative effects on heart function. 

PMID:20562099 

Keywords: Bone morphogenetic protein 4; Cell 

differentiation; GTP-binding protein 

α 

subunits; 

Heart septal defects; Myocytes, cardiac; Myogenic 

regulatory factors; Myosin heavy dhains; Natriuretic 

peptide, brain; RGS proteins; Signal transduction; 

Wnt proteins 

Jung MY, Paek WK, Park IS, Han JR, Sin Y, Paek J, Rhee 

MS, Kim H, Song HS, Chang YH * 

* Correspondence: yhchang@kribb.re.kr 


A Gram-positive, rod-shaped, endospore-forming organism, 

strain BL3-6 T , was isolated from tidal flat sediments of the 

Yellow Sea in the region of Tae-An. A 16S rRNA gene 

sequence analysis demonstrated that this isolate belongs to 

the Bacillus cereus group, and is closely related to Bacillus 

mycoides (99.0% similarity), Bacillus thuringiensis (99.0%), 

Bacillus weihenstephanensis (99.0%), Bacillus cereus 

(98.9%), Bacillus anthracis (98.8%), and Bacillus pseudomycoides 

(98.1%). The phylogenetic distance from any validly 

described Bacillus species outside the Bacillus cereus group 

was less than 95.6%. The DNA G+C content of the strain 

was 39.4 mol% and the major respiratory quinone was menaquinone-7. 

The major cellular fatty acids were iso-C(14:0) 

(17.8%), iso-C(16:0) (15.8%), and iso-C(12:0) (11.3%). The 

diagnostic amino acid of the cell wall was meso-diaminopimelic 

acid and the major cell wall sugar was galactose. 

The results of DNA-DNA hybridization (

Article 166 

Differential modulatory effects of rosiglitazone 

and pioglitazone on white adipose tissue in db/db 

mice 

Life Sci. 2010 Sep; 87(13-14):405-10. 

Yang KJ, Noh JR, Kim YH, Gang GT, Hwang JH, Yang 

SJ, Yeom YI, Lee CH * 



AIMS: this study was performed to clarify the different action 

mechanisms through which rosiglitazone and pioglitazone 

regulate lipogenesis in white adipose tissues of db/db mice, 

an animal model of diabetes. 

MAIN METHODS: male C57BLKS/J-Lepr(db/db) (db/db) 

mice were used for all experiments. Rosiglitazone or pioglitazone 

were administered once daily by oral gavage for 4 

weeks at concentrations of 20mg/kg and 75 mg/kg, 

respectively. At 0, 3, 6, 9, 12, 15, 21, and 28 days of administration, 

body weights and blood glucose were determined. 

At the end of experiment, adiposity and gene expression 

were confirmed by perilipin A immunostaining and real-time 

PCR. 

KEY FINDINGS: pioglitazone treatment increased fat mass 

and the surface area of adipocytes more than rosiglitazone 

at dosages with equivalent effects on plasma glucose. Lipid 

parameters including plasma total cholesterol and triglycerides 

were decreased more in rosiglitazone-treated mice. 

Relative mRNA expression levels for lipid synthesis and 

transport including diacylglycerol acyltransferase 

(DGAT1/2), fatty acid translocase (CD36/FAT), fatty acid 

transport protein (FATP) were increased in pioglitazone-treated 

group compared to rosiglitazone-treated mice, 

but mRNA expression levels of β-oxidation-related genes 

acyl-Coenzyme A dehydrogenase, very long chain (Acadvl), 

acyl-Coenzyme A dehydrogenase, medium chain (Acadm), 

and the energy expenditure-related genes triosephosphate 

isomerase 1 (Tpi1) and carnitine palmitoyltransferase 1b 

(Cpt1b) were decreased. 

SIGNIFICANCE: these results suggest that pioglitazone activates 

lipid deposition by increasing lipid synthesis and transport, 

but rosiglitazone stimulates β-oxidation and energy 

expenditure in adipocytes of db/db mice. 

PMID: 20723549 

Keywords: Acyl-CoA Dehydrogenase; Blood glucose; 

Cholesterol; Db mouse; Diabetes mellitus, 

experimental; Diacylglycerol O-acyltransferase; 

Gene expression; Hypoglycemic agents; Lipid 

metabolism; Thiazolidinediones; Triglycerides; 

White adipose tissue 

Article 167 

Comparative analysis of expressed sequence tags 

from the white-rot fungi (Phanerochaete chrysosporium) 

Mol Cells. 2010 Feb; 29(2):131-44. 

Kim DW, Kim A, Kim RN, Nam SH, Kang A, Chung WT, 

Choi SH, Park HS * 



Comprehensive analysis of the transcriptome of the P. chrysosporium 

is a useful approach to improve our understanding 

of its special and unique enzyme system and fungal evolution 

in molecular and industrial aspects. In order to unveil the 

functional diversity of this white-rot fungus in gene level 

and the expression patterns of its genes, in this study we 

carried out sequencing and annotation of 4,917 P. chrysosporium 

expressed sequence tags (ESTs). Through our bioinformatic 

ESTs analysis, we elucidated that 1,751 genes 

were derived from the present dataset of 4,917 ESTs, based 

on clustering and comparative genomic analyses of the ESTs. 

Of the 1,751 unique ESTs, 1,006 (57.5%) had homologues 

and orthologues in similarity searches. Our P. chrysosporium 

ESTs showed many genes for encoding 23 secreted proteins, 

many proteins for the degradation of cellulose and hemicelluloses, 

and heat shock proteins for stress resistance, which 

explain the reason why P. chrysosporium is very important 

and unique white-rot fungus in dealing with contaminated 

resources and in degrading lignin and in applying this organism 

to several industrial aspects.In addition, comparative 

analysis has shed the fresh light on the mystery about how 

its unique enzyme system and stress resistance have been 

evolved differently from its closest relatives. 

PMID: 20069385 

Keywords: Chromosome mapping; Comparative genomics; 

Computational biology; Expressed sequence tags; 

Fungal proteins; Neurospora crassa; Phanerochaete; 

RNA, messenger; Saccharomyces cerevisiae; 

Schizosaccharomyces; Secretome; White-rot fungi 


Article 168 

High frequency plant regeneration system for 

Nymphoides coreana via somatic embryogenesis 

from zygotic embryo-derived embryogenic cell 

suspension cultures 

Plant Biotech Rep. 2010 Apr; 4(2):125-8. 

Oh MJ, Na HR, Choi HK, Liu JR, Kim SW * 

* Correspondence: kimsw@kribb.re.kr 


Culture conditions were established for high frequency plant 

regeneration via somatic embryogenesis from cell suspension 

cultures of Nymphoides coreana. Zygotic embryos formed 

pale-yellow globular structures and calluses at a frequency 

of 85.6% when cultured on half-strength Murashige and 

Skoog (MS) medium supplemented with 0.3 mg l-1 of 2,4-D. 

However, the frequency of pale-yellow globular structures 

and white callus formation decreased slightly with an increasing 

concentration of 2,4-D up to 10 mg l-1 with the frequency 

rate falling to 16.7%. Cell suspension cultures were established 

from zygotic embryo-derived calluses using 

half-strength MS medium supplemented with 0.3 mg l-1 

of 2,4-D. Upon plating onto half-strength MS basal medium, 

over 92.3% of cell aggregates gave rise to numerous somatic 

embryos and developed into plantlets. Regenerated plantlets 

were successfully transplanted into potting soil and achieved 

full growth to an adult plant in a growth chamber. The 

high frequency plant regeneration system for Nymphoides 

coreana established in this study will be useful for genetic 

manipulation and cryopreservation of this species. 

Article 169 

Identification of a novel garlic cellulase gene 

Plant Mol Biol Rep. 2010; 28(3):388-93. 

Kim A, Kim RN, Kim DW, Choi SH, Kang A, Nam SH, 

Park HS * 



Genes encoding cellulase enzymes have been investigated 

in various plants due to the importance of cellulase enzymes 

in industrial applications, especially in the conversion of 

biomass into biofuels. Although several cellulase genes have 

been cloned and characterized, little is known about cellulase 

genes from garlic or enzyme activities of their gene products. 

In this study, a cellulase gene from garlic was cloned and 

characterized in gene and protein levels for the first time. 

The DNA sequence of the garlic cellulase gene showed 81% 

identity with the sequence of the endo-β-1,4-glucanase of 

Pisum sativum. The open reading frame of this gene is 1,506 

bp, which corresponds to 501 deduced amino acids. We 

identified the novel ORF region, which was translated into 

a 55.2 kDa protein using the protein expression vector, 

pET28a, in Escherichia coli and we confirmed that this protein 

has cellulase activity in vitro. Our study demonstrates 

that garlic is very useful, not only for the culinary and pharmaceutical 

industries, but also as an excellent natural source 

of various kinds of important genes and enzymes. 

Keywords: Allium sativum; Cellulase genes; Cloning; 

Escherichia coli; Garlic; Pisum sativum; Protein 

expression 

Keywords: Cell suspension; Nymphoides coreana; Plant 

regeneration; Somatic embryogenesis; Zygotic 

embryo culture 



2010 




Bio-Therapeutics Research Institute 








www.kribb.re.kr

Article 170 

Inhibitory activity of diacylglycerol acyltransferase 

by glabrol isolated from the roots of licorice 

Article 171 

Two acetylated megastigmane glycosides from the 

leaves of Ilex paraguariensis 

Arch Pharm Res. 2010 Feb; 33(2):237-42. 

Arch Pharm Res. 2010 Mar; 33(3):369-73. 

Choi JH, Choi JN, Lee SY, Lee SJ, Kim K, Kim YK * 

* Correspondence: kimyk@kribb.re.kr 


Acyl-coenzyme A: diacylglycerol acyltransferase (DGAT, 

EC 2.3.1.20) catalyzes triglyceride synthesis in the glycerol 

phosphate pathway. It has relations with the excess supply 

and accumulation of triglycerides. Therefore, DGAT inhibitors 

may act as a potential therapy for obesity and type 

2 diabetes. Five flavonoids were isolated from the ethanol 

extracts of licorice roots, using an in vitro DGAT inhibitory 

assay. One isoprenyl flavonoid showed most potential inhibition 

of DGAT on five flavonoids (1-5). On the basis 

of spectral evidences, the compound was identified as glabrol 

(5). Compound 5 inhibited rat liver microsomal DGAT activity 

with an IC50 value of 8.0 

for four flavonoids (1-4) was more than 100 

μM , but the IC50 value 

μM . In addition, 

glabrol showed a noncompetitive type of inhibition against 

DGAT. These data suggest that potential therapy for the 

treatment in obesity and type 2 diabetes patients by licorice 

roots might be related with its DGAT inhibitory effect. 

PMID:20195824 

Xu GH, Kim YH, Choo SJ, Ryoo IJ, Yoo JK, Ahn JS, 

Yoo ID * 

* Correspondence: idyoo@kribb.re.kr 


Two acetylated megastigmane glycosides, matenosides A 

(1) and B (2), have been isolated from the MeOH extract 

of Ilex paraguariensis leaves, and their structures were elucidated 

on the basis of spectroscopic analysis. Compounds 

1 and 2 exhibited human neutrophil elastase (HNE) inhibitory 

activity with IC(50) values of 50.4 μM and 11.1 μM , 

respectively. 

PMID: 20361300 

Keywords: Acetylation; Glycosides; Ilex paraguariensis; 

Leukocyte elastase; Matenosides A and B; 

Megastigmane glycosides; Norisoprenoids; Plant 

leaves; Proteinase inhibitory proteins; 

Structure-activity relationship 

Keywords: Acyl-coenzyme A: Diacylglycerol; Enzyme 

inhibitors; Flavonoids; Glycyrrhiza; Isoprenyl 

flavonoid; Licorice; Obesity; Plant extracts; Plant 

roots; Structure-activity relationship; Type 2 diabetes 


Article 172 

6-Alkylsalicylic acid analogues inhibit in vitro 

ATPase activity of heat shock protein 90 

Arch Pharm Res. 2010 Dec; 33(12):1997-2001. 

Wu CZ, Moon AN, Choi O, Kang SY, Lee JJ, Lee D, Hwang 

BY, Kim YH, Lee HS, Hong YS * 

* Correspondence: hongsoo@kribb.re.kr 


The molecular chaperone heat shock protein 90 (Hsp90) 

is responsible for maintaining the correct folding and stability 

of many signaling proteins. It is a promising target of cancer 

therapeutics and several other diseases, including neurodegenerative 

disease, nerve injuries, inflammation, and 

infection. In an effort to identify new Hsp90 inhibitors from 

natural sources using an in vitro ATPase inhibition assay, 

two 6-alkylsalicylic acid analogues, salaceyin A and B were 

identified from the culture extract of Streptomyces. Salaceyin 

A and B exhibited moderate ATPase inhibitory activities 

with IC(50) values of 68.3 and 65.2 

μM, respectively. Binding 

of salaceyins to human Hsp90 α was examined by competition 

binding experiments with ATP-Sepharose beads. However, 

the compounds exhibited no degradation activity of Hsp90 

client proteins, Her2, c-Raf, or Akt. 

PMID: 21191765 

Keywords: Antineoplastic activity; ATPase inhibitor; Cell 

viability; Cytotoxicity; Down regulation; Enzyme 

inhibition; Hsp90 inhibitor; IC 50; Protein 

degradation; Salaceyin; Streptomyces 

Article 173 

Zinc-finger protein 91 plays a key role in 

LIGHT-induced activation of non-canonical NF-κ 

B pathway 

Biochem Biophys Res Commun. 2010 Oct; 400(4):581-6. 

Jin HR, Jin X, Lee JJ * 

* Correspondence: jjlee@kribb.re.kr 


LIGHT is a member of tumor necrosis factor (TNF) superfamily, 

and its function is mediated through lymphotoxin-β 

receptor (LTβR), which is known to play important roles 

in inflammatory and immune responses through activation 

of NF-κB signaling pathways. However, molecular mecha- 

nism of LTβR ligation-induced NF-κB signaling remains 

incompletely understood. In this report we demonstrate that 

a novel zinc-finger protein 91 (ZFP91) is a critical regulator 

in LIGHT-induced activation of non-canonical NF-κB 

pathway. ZFP91 appears to be required for NF-κB2 (p100) 

processing to p52, nuclear translocation of p52 and RelB, 

and DNA-binding activity of NF-κB in LIGHT-induced acti- 

vation of non-canonical NF-κB pathway. Furthermore, 

ZFP91 knock-down by RNA interference blocks the 

LIGHT-induced accumulation of NIK and p100 processing, 

as well as the expression of non-canonical NF-κB target 

genes. These data clearly indicate that ZFP91 is a key regulator 

in LIGHT-induced activation of non-canonical NF-κB 

pathway in LTβR signaling. 

PMID: 20804734 

Keywords: CD40 ligand; Gene knockdown techniques; 

Hela cells; LIGHT; LTβR; NF-κB; NIK; p52; Signal 

transduction; Ubiquitin-protein ligases; ZFP91 


Article 174 

Preventative effects of Platycodon grandiflorum 

treatment on hepatic steatosis in high fat diet-fed 

C57BL/6 mice 

Article 175 

Anti-Skin aging effect of syriacusins from hibiscus 

syriacus on Ultraviolet-Irradiated human 

dermal fibroblast cells 

Biol Pharm Bull. 2010; 33(3):450-4. 

Biomol Therap. 2010 Jul; 18(3):300-7. 

Noh JR, Kim YH, Gang GT, Yang KJ, Kim SK, Ryu SY, 

Kim YS, Lee CH * , Lee HS * 

Ryoo IJ, Moon EY, Kim YH, Lee IS, Choo SJ, Bae K, 

Yoo ID * 

* Correspondence: chullee@kribb.re.kr leehs@kribb.re.kr 



Platycodon grandiflorum (PG) (Korean name, Doraji; 

Chinese name, Jiegeng; and Japanese name, Kikyo) is a 

perennial plant in the Campanulaceae family that contains 

triterpenoid saponins, carbohydrates, and fibers. This study 

was carried out to investigate effects of root of PG on fatty 

liver inhibition in high fat diet (HFD)-fed C57BL/6 mice. 

C57BL/6 mice were divided into control, total extract of 

PG (T-PG, 500 mg/kg) and saponin fraction (S-PG, 50 

mg/kg)-treated groups. Significant decreases in body weight, 

associated with fat mass reduction, were observed in 

PG-treated groups (p

Article 176 

Evaluation of human neutrophil elastase inhibitory 

effect of iridoid glycosides from Hedyotis diffusa 

Bioorg Med Chem Lett. 2010 Jan; 20(2):513-5. 

Xu GH, Kim YH, Chi SW, Choo SJ, Ryoo IJ, Ahn JS, 

Yoo ID * 



Five iridoid glycosides were isolated from the MeOH extract 

of Hedyotis diffusa, and their structures were elucidated as 

E-6-O-p-methoxycinnamoyl scandoside methyl ester (1), 

Z-6-O-p-methoxycinnamoyl scandoside methyl ester (2), 

E-6-O-p-feruloyl scandoside methyl ester (3), E-6-O-p-coumaroyl 

scandoside methyl ester (4), and Z-6-O-p-coumaroyl 

scandoside methyl ester (5) by interpretation of their spectroscopic 

data. All the isolated compounds were evaluated for 

human neutrophil elastase inhibitory effect, and compound 

1 showed potent activity with an IC(50) value of 18.0μM 

. The molecular docking simulation suggested a structural 

model for the inhibition of human neutrophil elastase by 

compound 1. 

PMID: 20004577 

Keywords: Computer simulation; Hedyotis diffusa; Human 

neutrophil elastase; Iridoid glycosides; Leukocyte 

elastase; Plant extracts; Protease inhibitors 

Article 177 

Generation of donor natural killer cells from 

CD34(+) progenitor cells and subsequent infusion 

after HLA-mismatched allogeneic hematopoietic 

cell transplantation: a feasibility study 

Bone Marrow Transplant. 2010 Jun; 45(6):1038-46. 

Yoon SR, Lee YS, Yang SH, Ahn KH, Lee JH, Lee JH, 

Kim DY, Kang YA, Jeon M, Seol M, Ryu SG, Chung JW, 

Choi I * , Lee KH 

* Correspondence: ipchoi@kribb.re.kr 


Post transplant infusion of donor-type natural killer (NK) 

cells has been shown to have an anti-leukemia-enhancing 

effect without evoking GVHD in murine hematopoietic cell 

transplantation (HCT) models. Here, we tested 14 patients 

(age, 23-65 years), 12 with acute leukemia and 2 with myelodysplastic 

syndrome, who underwent HLA-mismatched HCT 

and subsequently received donor NK cell infusions. Cell 

donors (age, 16-51 years), comprising seven siblings, five 

offspring, and two mothers of the patients, underwent growth 

factor-mobilized leukapheresis for 3-5 days. Cells collected 

on the first 2-4 days were used for HCT, whereas those 

collected on the last day were CD34 selected by magnetic-activated 

cell sorting (median, 2.22 x 10(6) cells/kg; 

range, 0.29-5.66). Donor NK cells were generated from the 

CD34(+) cells by ex vivo cell culture over a 6-week period 

(median, 9.28 x 10(6) cells/kg; range, 0.33-24.50; 

CD122/CD56(+) 64%; CD3(+) 1.0%; and viability 88%). 

There were no signs of acute toxicity in patients infused 

with these cells 6-7 weeks post transplant. Overall, one and 

five patients developed acute and chronic GVHD during 

post transplant period, respectively. These results showed 

that clinical-grade donor NK cell production from CD34(+) 

cells is feasible. 

PMID: 19881555 

Keywords: Donor CD34+ cells; Donor NK cell infusion; 

GCSF; Hematopoietic stem cell; HLA antigens; 

HLA-mismatched HCT; Killer cells, natural; 

Leukemia; Lymphocyte transfusion; 

Myelodysplastic syndromes 


Article 178 

MS-1020 is a novel small molecule that selectively 

inhibits JAK3 activity 

Article 179 

Anti-inflammatory constituents from Solanum 

nigrum 

Br J Haematol. 2010 Jan; 148(1):132-43. 

Bull Kor Chem Soc. 2010 Jan; 31(1):199-201. 

Kim BH, Oh SR, Yin CH, Lee S, Kim EA, Kim MS, Sandoval 

C, Jayabose S, Bach EA, Lee HK * , Baeg GH 

* Correspondence: hykylee@kribb.re.kr 


In order to identify Janus kinase/signal transducer and activator 

of transcription (JAK/STAT) signalling inhibitors, a 

cell-based high throughput screening was performed using 

a plant extract library that identified Nb-(α 

-hydroxynaphthoyl)serotonin called MS-1020 as a novel 

JAK3 inhibitor. MS-1020 potently inhibited persistently-active 

STAT3 in a cell type-specific manner. Further 

examination showed that MS-1020 selectively blocked constitutively-active 

JAK3 and consistently suppressed interleukin-2-induced 

JAK3/STAT5 signalling but not prolactin-induced 

JAK2/STAT5 signalling. Furthermore, 

MS-1020 affected cell viability only in cancer cells harbouring 

persistently-active JAK3/STATs, and in vitro kinase assays 

showed MS-1020 binds directly with JAK3, blocking 

its catalytic activity. Therefore, the present study suggested 

that this reagent selectively inhibits JAK3 and subsequently 

leads to a block in STAT signalling. Finally, MS-1020 decreased 

cell survival by inducing apoptosis via down-regulation 

of anti-apoptotic gene expression. These results suggest 

that MS-1020 may have therapeutic potential in the treatment 

of cancers harbouring aberrant JAK3 signalling. 

PMID:19793252 

Cai XF, Chin YW, Oh SR, Kwon OK, Ahn KS, Lee HK * 

* Correspondence: hykylee@kribb.re.kr 


The whole plant of Solanum nigrum L. (Solanaceae) has 

been used as a folk medicine in Asian countries for the 

treatment of inflammation, edema, and mastitis. In the present 

study, the structure elucidation of a new compound along 

with 14 known compounds and their inhibitory activities 

on leukotriene C4 release are described. All the compounds 

obtained from the fruits of S. nigrum were evaluated for 

their inhibitory activities on LTC4 release, and the results 

were summarized. Leukotrienes including LTC4 are lipid 

mediators found elevated in various inflammatory diseases 

such as allergic rhinitis, asthma, and atopic dermitis. 

Currently, antileukotrienes are being prescribed for the treatment 

of asthma and have been approved for the treatment 

of allergic rhinitis. In the present study, compound 4 was 

found to possess the inhibitory activity and seemed to be 

a potential therapeutic effect on the aforementioned inflammatory 

diseases. 

Keywords: 12β-diol; Anti-inflammatory; Leukotriene C4; 

Nolanum nigrum; Phenylpropanoids; Solanum 

nigrum; Spirost-5-ene-3 β; 

Spirostane 

Keywords: Apoptosis; Breast neoplasms; Cancer; 

Cell-based high throughput; Drosophila; 

Interleukin-2; Janus kinase/signal transducer; Plant 

extracts; Small molecule inhibitor 


Article 180 

Cytotoxic sesquilignans from the roots of 

Saururus chinensis 

Article 181 

Bisamides from the twigs of Aglaia perviridis 

collected in Vietnam 

Bull Kor Chem Soc. 2010 Jul; 31(7):2088-90. 


Chin YW, Cai XF, Ahn KS, Lee HK, Oh SR * 

* Correspondence: seiryang@kribb.re.kr 

Chin YW, Chae HS, Lee J, 

H, Oh SR * 

TT, Ahn KS, Lee HK, Joung 


Saururus chinensis Hort. ex Loudon (Saururaceae) is a perennial 

herb distributed in China and Korea, and has been 

used as a folk medicine for the treatment of edema, gonorrhea, 

jaundice, pneumonia, and several inflammatory diseases in 

Korea. This paper reports the structures elucidation of the 

two new lignans and six known compounds, along with 

their cytotoxicity. The CD spectroscopic data exhibited the 

positive Cotton effect at 232 nm in the same manner. The 

structure of compound 1 was determined as 7''R,8''S-saucerneol, 

a diastereomer of (-)-saucerneol(3), and the structure 

of compound 2 was confirmed to be 

7'-epi-7''R,8''S-4''-demethylsaucerneol. All the compounds 

isolated were evaluated against HL-60 (human promyelocytic 

leukemia) cells. Compounds 1-8 exhibited cytotoxicity 

(IC50, 0.5, 7.1, 3.3, 5.2, 3.6, 2.3, 8.5 and 0.8 

μM, respectively) 

against HL-60 cell lines (camptothecin, IC50 0.8 

μM). 

Keywords: Cytotoxicity; Saururaceae; Saururus chinensis; 

Sesquilignans 



The genus Aglaia Lour. belongs to the Family Meliaceae 

and about 120 species is distributed in tropical and subtropical 

Asia, tropical Australia and Pacific islands. There are about 

30 Aglaia species in Vietnam. Aglaia perviridis is a tree 

about 15 m tall and has glabrous lanceolate leaves and ovoid 

fruit. Previous studies for this plant have reported the occurrence 

of dammarane-type triterpenoids and pregnane steroids. 

There has been no report regarding pharmacological evaluation 

for this plant. A chloroform-soluble extract of A. perviridis 

twigs, collected in Vietnam, was chosen for phytochemical 

studies due to its inhibitory effect of NO production 

in the initial screening test. Bioactivity-guided fractionation 

of a chloroform-soluble fraction of A. perviridis twigs led 

to the isolation of two new compounds (1 and 2) along 

with a known compound (3). Thus, the present study describes 

the isolation and structure elucidation of all isolates as well 

as evaluation of inhibitory activity against NO production 

in LPS-induced RAW 264.7 cells. The structure of compound 

1 was determined as N-(4-(2-(4-hydroxyphenyl) acetamido)butyl)cinnamamide 

and named perviridamide. The 

structure of 2 was confirmed as 4-hydroxypyramidatine. The 

compound 3 was identified as pyramidatine by comparison 

of its data to the published values. All isolates obtained 

from active fractions were evaluated for their inhibitory activity 

against NO production in LPS-induced RAW 264.7 cells, 

and compounds 1 and 2 displayed moderate inhibition of 

NO production with IC50 values of 65.3 and 83.4 

μg/mL, 

respectively, while compound 3 was found to be inactive. 

Keywords: Aglaia perviridis; Bisamde; Meliaceae; Nitric 

oxide 


Article 182 

Effect of AC-264, a novel indole derivative, on 

apoptosis in HL-60 cells 

Article 183 

CUG2, a novel oncogene confers reoviral replication 

through Ras and p38 signaling pathway 

Bull Kor Chem Soc. 2010 Dec; 31(12):3777-81. 

Cancer Gene Ther. 2010 May; 17(5):307-14. 

Lee K, Kwon OK, Xia Y, Ahn KS * 

* Correspondence: ksahn@kribb.re.kr 


The anticancer effect and apoptotic mechanism of a novel 

indole derivative AC-264, a lead derived from a chemical 

library, were investigated in human promyelocytic leukemia 

HL-60 cells. HL-60 cells treated with AC-264 at various 

concentrations showed the morphological features of apoptosis, 

such as plasma membrane blebbing and cell shrinkage. 

AC-264 exhibited cytotoxic effect in various cancer cell 

lines with different degrees of potency. Especially, AC-264 

was effective on increasing the population of apoptotic cells 

in HL-60 cells, as detected by the number of cells stained 

with Annexin V and PI. Furthermore, AC-264 activated caspase-3 

enzyme activity and induced internucleosomal DNA 

fragmentation. These results indicated that AC-264 produces 

anti-cancer effect via apoptotic cell death by activating caspase-3 

and inducing internucleosomal DNA fragmentation 

in HL-60 cells. 

Keywords: Annexins; Anticancer effects; Apoptosis; 

Cancer cell lines; Caspase-3; Cytotoxic effects; DNA 

fragmentation; HL-60 cells; Indole derivatives; 

Morphological features; Plasma membranes; 

Promyelocytic leukemia 

Park EH, Park EH, Cho IR, Srisuttee R, Min HJ, Oh MJ, 

Jeong YJ, Jhun BH, Johnston RN, Lee S, Koh SS * , Chung 

YH 

* Correspondence: sskoh@kribb.re.kr 


As we have recently found a novel oncogene, the cancer-upregulated 

gene 2 (CUG2), which was elevated in a variety 

of tumor tissues such as the ovary, liver, lung and pancreas, 

we examined whether reovirus could efficiently induce cytolysis 

in cancer cells expressing CUG2 and thus be used as 

a potential cancer therapeutic agent. In this study, we describe 

experiments in which we use reovirus to treat NIH3T3 cells 

stably expressing either CUG2 (NIH-CUG2) or vector only 

(NIH-Vec). NIH-CUG2 cells readily support reoviral proliferation 

and undergo apoptosis, whereas NIH-Vec cells 

are highly resistant to reoviral infection and virus-induced 

apoptosis. This notable result may be explained by the observation 

that CUG2 expression inhibits PKR activation, 

leading to reoviral proliferation in nonpermissive NIH3T3 

cells. Furthermore, reovirus infection results in almost complete 

regression of tumorgenic NIH-CUG2 cells in transplanted 

nude mice. As we found that CUG2 enhances activation 

of MAPK (ERK, JNK and p38), Src kinase and Ras, 

we examined whether CUG2 confers reoviral replication 

independent of the Ras or p38 MAPK signaling pathway. 

From these experiments we found that either inhibition of 

p38 MAPK or Ras blocks reoviral proliferation even in the 

presence of CUG2 but inhibition of ERK, JNK and Src 

kinase does not, indicating that activation of p38 MAPK 

and Ras has critical roles in reoviral replication in 

CUG2-expressing tumor cells. Accordingly, we propose that 

reovirus can be useful in the treatment of transformed cells 

expressing CUG2, which is commonly detected in various 

tumor tissues. 

PMID:20075984 

Keywords: Apoptosis; CUG2; Immunohistochemistry; 

NIH 3T3 cells; Nuclear proteins; p38 MAPK; ras 

Proteins; Reoviridae; Reovirus; Signal transduction 


Article 184 

TMPRSS4 induces invasion and epithelial-mesenchymal 

transition through upregulation of integrin 

α5 and its signaling pathways 

Carcinogenesis. 2010 Apr; 31(4):597-606. 

Kim S * , Kang HY, Nam EH, Choi MS, Zhao XF, Hong 

CS, Lee JW, Lee JH, Park YK. 

* Correspondence: semikim@kribb.re.kr 


Article 185 

Modulation of E-cadherin expression by K-Ras; 

involvement of DNA methyltransferase-3b 

Carcinogenesis. 2010 Jul; 31(7):1194-201. 

Kwon O, Jeong SJ, Kim SO, He L, Lee HG, Jang KL, 

Osada H, Jung M, Kim BY, Ahn JS * 

* Correspondence: jsahn@kribb.re.kr 


TMPRSS4 is a novel type II transmembrane serine protease 

that is highly expressed on the cell surface in pancreatic, 

thyroid and other cancer tissues, although its oncogenic significance 

and molecular mechanisms are unknown. 

Previously, we have shown that TMPRSS4 promotes invasion, 

migration and metastasis of human tumor cells by 

facilitating an epithelial-mesenchymal transition (EMT). In 

this study, we explored the molecular basis underlying 

TMPRSS4-mediated effects. We show that multiple downstream 

signaling pathways, including focal adhesion kinase 

(FAK), extracellular signal-regulated kinase (ERK), Akt, Src 

and Rac1, are activated by TMPRSS4 expression and that 

FAK signaling and ERK activation are required for 

TMPRSS4-induced invasiveness and EMT, including cadherin 

switch. Inhibition of PI3K or Src reduced invasiveness 

and actin rearrangement mediated by TMPRSS4 without 

restoring E-cadherin expression. Downregulation of E-cadherin 

was required for TMPRSS4-mediated effects but was 

not sufficient to induce EMT and invasion. TMPRSS4 induced 

integrin α5 expression and its signal transduction, 

leading to invasiveness and EMT accompanied by downregulation 

of E-cadherin. Functional blocking confirmed that 

integrin α5β1 is a critical signaling molecule that is sufficient 

to induce TMPRSS4-mediated effects. 

Immunohistochemical analysis showed that TMPRSS4 expression 

was significantly higher in human colorectal cancer 

tissues from advanced stages than in that of early stage. 

Furthermore, upregulation of TMPRSS4 was correlated with 

enhanced integrin α5 expression. These observations im- 

plicate integrin α5 upregulation as a molecular mechanism 

by which TMPRSS4 induces invasion and contributes to 

cancer progression. 

PMID: 20118200 

Keywords: Cadherins; Cell differentiation; Colorectal 

neoplasms; Epithelial cells; Integrin α5; Membrane 

proteins; Mesoderm; Neoplasm invasiveness; rac1 

GTP-binding protein; Serine endopeptidases; Signal 

transduction 

E-cadherin, as a tumor suppressor, plays an important role 

for intercellular adhesion involved in metastasis. Although 

K-Ras is highly expressed in a variety of cancers, the regulation 

of E-cadherin expression by K-Ras in association with 

DNA methylation and cell metastasis has not been completely 

clarified. In this study, E-cadherin expression was repressed 

in 267B1/K-Ras human epithelial prostate cancer cells stably 

overexpressing K-Ras, resulting from hypermethylation of 

E-cadherin promoter as evidenced by methylation-specific 

polymerase chain reaction (PCR), bisulfite sequencing, real-time 

reverse transcription-PCR and western blot analysis. 

The increased level of DNA methyltransferase (DNMT) 3b 

in 267B1/K-Ras cells was reduced by small interfering 

RNA-mediated knockdown of k-ras, whereas DNMT1 and 

DNMT3a did not change regardless of K-Ras or 5-aza-2'-deoxycytidine 

(5'-AzaC) treatment. Furthermore, binding of 

DNMT3b to E-cadherin promoter was increased in 

267B1/K-Ras cells but was reduced by 5'-AzaC, as revealed 

by chromatin immunoprecipitation assay, which was in agreement 

with cell aggregation and invasive mobilization of the 

cells. Hence, our data suggest that increased binding of 

DNMT3b to E-cadherin promoter region by K-Ras cause 

promoter hypermethylation for reduced expression of E-cadherin, 

leading to the decreased cell aggregation and increased 

metastasis of human prostate cancer cells overexpressing 

K-Ras. 

PMID:20375073 

Keywords: Azacitidine; Cadherins; Cell communication; 

Tumor; Cell movement; CpG islands; DNA 

methylation; Genes, ras; Promoter regions, genetic; 

Prostatic neoplasms 


Article 186 

Antiviral activity of yogurt against enterovirus 

71 in Vero cells 

Food Sci Biotech. 2010 Apr; 19(2):289-95. 

Choi HJ, Song JH, Park KS, Baek SH, Lee ES, Kwon DH * 

* Correspondence: dhkwon@kribb.re.kr 


Five yogurts were fermented with each bacteria strain. The 

viability and pH of each yogurt during fermentation or storage 

were evaluated, and then the cytotoxicity and antiviral activity 

against enterovirus (EV) 71 of cell-free supernatants (CFS) 

of the metabolites of each yogurt were compared with those 

of de Man, Rogosa, and Sharpe (MRS) broth fermented 

with the same bacteria. As the results, the number of viable 

bacteria for each yogurt after fermentation or during storage 

always remained higher than 5 log CFU/mL and the pH 

of those ranged from 4 to 6. The CFS of all yogurts showed 

antiviral activity over 45% against EV71, while it didn't 

exhibit cytotoxicity in Vero cells. Specially, the CFS of 

yogurt fermented with Lactobacillus plantarum and 

Bifidobacterium bifidum exhibited high anti-EV71 activity 

of 92.74 and 90.44%, respectively. In contrast, the CFS of 

each MRS broth fermented with the same bacteria showed 

low antiviral activity of less than 30%. 

Keywords: Antiviral activity; Bacteria strain; 

Bifidobacterium bifidum; Cell-free supernatant; 

Cytotoxicity; Enterovirus 71; Lactobacillus 

plantarum; Supernatants; Vero cells; Yogurt 

Article 187 

Total synthesis of (±)-scuteflorin A 

Heterocycles. 2010; 81(11):2593-8. 

Tan F, Shen LL, Kwak YS * , Jeong JH 

* Correspondence: yskwak@kribb.re.kr 

Bio-Therapeutics Research Institute 

Scutellaria lateriflora L. (also called "American skullcap") 

has long been used as an herbal medicine for treating 

neurological disorders such as anxiety, mervous tension, and 

convulsions in North America and Europe. The therapeutic 

benefit of S. lateriflora has been validated by demonstrating 

significant anxiolytic effects of its aqueous extracts in rodent 

models and in healthy human volunteers. Two new coumarins 

in the chemical constituents of S. lateriflora extract, 

Scuteflorin A ((+)-1) is a very close analog of decursin 

(3). We describe here the first total synthesis of 

(+-)-scuteflorin A (1), with the aim of developing efficienct 

syntheses of its analogs for biologicl evaluation. Finally, 

O-acylation of 9 with senecioyl chloride in the presence 

of pyridine provided racemic (+-)-scuteflorin A (1) were 

identical to those reported for (+)-1 from a natural source. 

In conclusion, we demonstrated the first total synthesis of 

racemic (+-)-scuteflorin A (1) in a highly efficient manner, 

attesting to the viability of our synthetic strategy for the 

future SAR study of scuteflorin and decursin derivatives. 

Asymmetric synthesis of (+-)-scuteflorin A ((+)-1) is 

currently under way. The biological activity of scuteflorin 

and its derivatives is under investigation and will be reported 

in due course. 

Keywords: American skullcap; Herbal medicine; 

Neurological disorders; Scuteflorin A; Scutellaria 

lateriflora; Synthesis 


Article 188 

TXNIP regulates germinal center generation by 

suppressing BCL-6 expression 

Article 189 

YC-1 enhances natural killer cell differentiation 

from hematopoietic stem cells 

Immunol Lett. 2010 Apr; 129(2):78-84. 

Int Immunopharmacol. 2010 Apr; 10(4):481-6. 

Shao Y, Kim SY, Shin D, Kim MS, Suh HW, Piao ZH, 

Jeong M, Lee SH, Yoon SR, Lim BH, Kim WH, Ahn JK, 

Choi I * 

Yun S, Lee SH, Kang YH, Jeong M, Kim MJ, Kim MS, 

Piao ZH, Suh HW, Kim TD, Myung PK, Yoon SR * , Choi 

I * 



* Correspondence: sryoon@kribb.re.kr ipchoi@kribb.re.kr 


The detailed mechanism driving the germinal center (GC) 

reaction to B cell lymphomagenesis has not been clarified. 

Thioredoxin interacting protein (TXNIP), also known as vitamin 

D3 up-regulated protein 1 which is an important tumor 

repressor, is involved in stress responses, redox regulation, 

and cellular proliferation. Here, we report that TXNIP has 

a potential role in the formation of GC in peripheral lymphoid 

organs where B lymphocytes divide rapidly. First, we compared 

changes in GC from wild type mice and Txnip(-/-) 

mice. After immunization, Txnip(-/-) mice exhibited higher 

expression level of BCL-6 and larger percentage of GC B 

cells with the reduction in antibody production and plasma 

cell numbers. In addition, Txnip(-/-) spleens had a much 

larger population which expressed Ki-67, a marker of cell 

proliferation, in the red pulp border than WT spleens. 

Furthermore, the expression of BCL-6 was decreased in 

TXNIP overexpressing cells and elevated in TXNIP deficient 

cells. Taken together, we conclude that TXNIP may contribute 

to the formation of GCs after immunization. During 

this process, TXNIP suppresses BCL-6 expression. 

PMID: 20156484 

Keywords: B cells; BCL-6; B-Lymphocytes; Carrier 

proteins; Cell proliferation; Flow cytometry; 

Germinal center; Immunohistochemistry; Plasmids; 

Proto-oncogene proteins c-bcl-6; TXNIP 

NK cells play crucial roles in innate immunity and adaptive 

immunity. The detailed mechanisms, however, governing 

NK cell development remains unclear. In this study, we 

report that YC-1 significantly enhances NK cell populations 

differentiated from human umbilical cord blood hematopoietic 

stem cells (HSCs). NK cells increased by YC-1 

display both phenotypic and functional features of fully mature 

NK (mNK) cells, but YC-1 does not affect the activation 

of mNK cells. YC-1 did not affect cGMP production and 

phosphorylation of STAT-5 which is essential for IL-15R 

signaling. On the other hand, YC-1 increased p38 MAPK 

phosphorylation during NK cell differentiation. Furthermore, 

p38 inhibitor SB203580 inhibited the differentiation of NK 

cells enhanced by YC-1. Taken together, these data suggest 

that YC-1 enhances NK cell differentiation through the activation 

of p38 MAPK which is involved in NK cell 

differentiation. 

PMID: 20116458 

Keywords: Cell differentiation; Cyclic GMP; Enzyme 

inhibitors; Flow cytometry; Hematopoietic stem cell; 

Imidazoles; Indazoles; NK cells; p38; 

Phosphorylation; Pyridines; Signal transduction; 

STAT5 transcription factor; YC-1 


Article 190 

The protease inhibitor, elafin, induces p53-dependent 

apoptosis in human melanoma cells 

Int J Cancer. 2010 Sep; 127(6):1308-20. 

Yu KS, Lee Y, Kim CM, Park EC, Choi J, Lim DS, Chung 

YH, Koh SS * 



Expression of the protease inhibitor elafin is deregulated 

in several human cancers. However, functions of the protein 

in cancer are yet to be established. Here, we show that elafin 

elicits pro-apoptotic effects in melanoma cells but not in 

normal melanocytes. Elafin triggered the intrinsic apoptotic 

pathway as evidenced by the increased caspase 9 activity 

and unaltered caspase 8 activity. Caspase 9-specific siRNA, 

but not caspase 8-specific siRNA, dramatically abrogated 

elafin-induced apoptosis. Elevated level of p53 was observed, 

resulting in increased transcriptional activation and consequent 

expression of downstream effector molecules (Bax, 

Puma, Noxa, p21). Moreover, the apoptotic effect of elafin 

was inhibited by p53-specific siRNA and the p53 inhibitor 

pifithrin- α. Elafin treatment of xenograft mice of melanoma 

cells led to significantly smaller tumor sizes compared with 

those of untreated control mice. Immunohistochemical analysis 

revealed decreased elafin expression in melanoma tissue 

specimens. Western blot and reverse transcription analyses 

indicated transcriptional repression of the elafin gene in melanoma 

cells. Our results collectively indicate that elafin induces 

apoptosis in melanoma cells through a p53-dependent 

intrinsic apoptotic pathway, and that repression of elafin 

expression in melanoma may contribute to disease 

progression. 

PMID: 20020498 

Keywords: Apoptosis; Elafin; Immunohistochemistry; 

Melanoma; Neoplasm transplantation; Protease 

inhibitors; Recombinant proteins; RNA, small 

interfering; Tumor suppressor protein p53; 

Therapeutics 

Article 191 

Lactariolines A and B: new guaiane sesquiterpenes 

with a modulatory effect on interferon-γ 

production from the fruiting bodies of Lactarius 

hatsudake 

J Antibiot. 2010 Jun; 63(6):335-7. 

Xu GH, Kim JW, Ryoo IJ, Choo SJ, Kim YH, Seok SJ, 

Ahn JS, Yoo ID * 



Lactarius hatsudake, belonging to the family Russulaceae 

of Basidiomycete, is a common edible mushroom widely 

distributed in Korea, China, Japan, Europe and North 

America, and biological activity of L. hatsudake has been 

reported. During the investigation of novel bioactive metabolites 

from L. hatsudake, we identified two new guaiane sesquiterpenes, 

lactariolines A (1) and B (2). The fruiting bodies 

of L. hatsudake provided by the National Agrobiodiversity 

Center (Suwon, Korea) were extracted three times with 

MeOH at room temperature over 3 days. The structure of 

1 was elucidated as 7-acetyl-4-methyl-1-methoxymethyl azulene, 

and the compound was named ‘lactariolines A’. The 

structure of 2 was elucidated as 1-formyl-4-methyl-7-(1-methoxy-1-methylethyl) 

azulene, and the compound 

was named ‘lactariolines B’. Compounds 1 and 2 were evaluated 

for their effects on the modulation of IFN-γ 

in NK92 

cells. Compound 1 inhibited IFN-γ 

production in NK92 cells 

in a dose-dependent manner, corresponding to 56.7% inhibition 

at 400 

μM and 21.4% at 100 mM, respectively. 

Compound 2 also showed a dose-dependent effect, with 

80.9% inhibition at 400 μM and 31.2% at 100 mM. The 

WST-1 cell proliferation assay showed that no cytotoxicity 

was observed in the NK92 cells with both cell density up 

to a concentration of 400 mM. 

PMID: 20448667 

Keywords: Basidiomycota; Guaiane sesquiterpene; 

Immunosuppressive agents; Interferon- γ; 

Lactariolines A and B; Lactarius hatsudake; 

Sesquiterpenes 


Article 192 

Preparative isolation and purification of deoxypodophyllotoxin 

from the rhizomes of Anthriscus 

sylvestris by high-speed counter-current chromatography 

J Appl Biol Chem. 2010; 53(1):110-3. 

Quan GH, Chin YW, Lee HK, Oh SR * 



A simple and rapid purification method of deoxypodophyllotoxin 

from the crude methanol extract of rhizomes 

of Anthriscus sylvestris was established using high-speed 

counter-current chromatography. From the crude extract 

(288.9 mg), deoxypodophyllotoxin (8.8 mg) was separated 

using a two-phase solvent system composed of n-hexane/ethyl 

acetate/methanol/water (7:3:5:5, v/v). The final purity of 

the deoxypodophyllotoxin was determined to be over 98% 

by ultra-performance liquid chromatography-UV analysis. 

Article 193 

A new phenolic glycoside from Bridelia cambodiana 

J Appl Biol Chem. 2010; 53(2):253-5. 

Khiev P, Chin YW, Cai XF, Lee HK, Joung H, Oh SR * 



A new phenolic glycoside, 5-hydroxy-3-methoxyphenyl-6-O-syringoyl-β-D-glucoside 

(1), was isolated from 

the n-BuOH-soluble fraction of Bridelia cambodiana along 

with three known phenolic glycosides. The structures of the 

isolates were determined on the basis of NMR (1H, 13C, 

HSQC, HMBC) and chemical method. All the compounds 

were tested for their antioxidant activity in a DPPH antioxidant 

assay. 

Keywords: Antioxidant activity; Bridelia cambodiana; 

Euphorbiaceae; Phenolic glycosides 

Keywords: Anthriscus sylvestris; Deoxypodophyllotoxin; 

High-speed counter-current chromatography 

(HSCCC) 


Article 194 

An atypical E3 ligase zinc finger protein 91 stabilizes 

and activates NF-κB-inducing kinase 

Lys63-linked ubiquitination 

J Biol Chem. 2010 Oct; 285(40):30539-47. 

Jin X, Jin HR, Jung HS, Lee SJ, Lee JH, Lee JJ * 



via 

Article 195 

Anti-inflammatory and anti-asthmatic effects of 

Viola mandshurica W. Becker (VM) ethanolic 

(EtOH) extract on airway inflammation in a mouse 

model of allergic asthma 

J Ethnopharmacol. 2010 Jan; 127(1):159-64. 

Lee MY, Yuk JE, Kwon OK, Kim HS, Oh SR, Lee HK, 

Ahn KS * 


The NF-κB transcription factors control many physiological 

processes, including inflammation, immunity, and apoptosis. 

Its activity contributes to the development of various cell 

malignancies. NF-κB-inducing kinase (NIK) plays a pivotal 

role in NF-κB activation. However, the molecular mechanism 

to stabilize and activate NIK remains elusive, although it 

is known that cIAP1/2 (cellular inhibitor of apoptosis 1 and 

2) ubiquitinate NIK for degradation. Here, we report a novel 

NF-κB-related zinc finger protein 91 (ZFP91) that stabilizes 

and activates NIK in a ubiquitination-dependent manner. 

We show that ZFP91 interacts with and promotes the 

Lys(63)-linked ubiquitination of NIK and subsequent processing 

of p100 to p52. The results of in vitro biochemical 

assays indicate that ZFP91 functions as an E3 ligase directly 

to NIK. Remarkably, the ubiquitination of NIK coincides 

with its Thr(559) phosphorylation. Furthermore, knockdown 

of ZFP91 expression by RNA interference inhibits the CD40 

ligation-induced activation of NIK and p100 processing as 

well as the expression of noncanonical NF-κB target genes. 

These data clearly indicate that ZFP91 is an important regulator 

of the noncanonical NF-κB pathway. 

PMID: 20682767 

Keywords: Apoptosis; Biochemical assay; Cellular 

inhibitors; E3 ligase; In-vitro; Molecular mechanism; 

Physiological process; RNA interference; Target 

genes; Ubiquitination; Zinc finger protein 


AIM OF THE STUDY: We investigated the efficacy of 

Viola mandshurica W. Becker (VM) ethanolic (EtOH) extract 

in the treatment of bronchial asthma in an ovalbumin 

(OVA)-induced asthmatic BALB/c mouse model. 

MATERIALS AND METHODS: Female BALB/c mice were 

sensitized with intraperitoneal (i.p.) ovalbumin (OVA) on 

days 0 and 14, and were next given intranasal OVA on 

days 28-30. Randomized treatment groups of sensitized mice 

received VM EtOH extract, dexamethasone, or placebo, orally, 

from days 28 to 30. 

RESULTS: VM EtOH extract significantly inhibited increases 

in total immunoglobulin E (IgE) and cytokines IL-4 

and IL-13 levels in serum and bronchoalveolar lavage fluid 

(BALF), and also effectively suppressed airway hyperresponsiveness 

(AHR), eosinophilia, and mucus hypersecretion, 

in mice with OVA-induced asthma. 

CONCLUSIONS: The results suggest that VM EtOH extract 

and allied extracts could be useful herbal medicines for asthma 

treatment, and that VM may also be a valuable lead 

material for anti-asthma drug development. 

PMID: 19786084 

Keywords: Anti-asthmatic agents; Anti-inflammatory 

agents; Bronchial hyperreactivity; Bronchoalveolar 

lavage fluid; Eosinophilia; Immunoglobulin E; 

Interleukins; Mucus; Ovalbumin; Phytotherapy; 

Plant extracts; Viola 


Article 196 

Anti-inflammatory effects of methanol extracts 

of the root of Lilium lancifolium on LPS-stimulated 

Raw264.7 cells 

Article 197 

Suppressor of cytokine signaling 2 regulates 

IL-15-primed human NK cell function via control 

of phosphorylated Pyk2 

J Ethnopharmacol. 2010 Jul; 130(1):28-34. 

J Immunol. 2010 Jul; 185(2):917-28. 

Kwon OK, Lee MY, Yuk JE, Oh SR, Chin YW, Lee HK, 

Ahn KS * 



AIM OF THE STUDY: Lilium lancifolium is commonly 

used to treat bronchitis, pneumonia, etc. In this study, we 

investigated the anti-inflammatory effects of methanol extracts 

of the root of Lilium lancifolium (LL extracts) in 

LPS-stimulated Raw264.7 cells. 

MATERIAL AND METHODS: Levels of NO, PGE(2) and 

pro-inflammatory cytokines (IL-6 and TNF- α) in the super- 

natant fraction were determined using sandwich ELISA. 

Expression of COX-2 and iNOS, phosphorylation of MAPK 

subgroups (ERK and JNK), and NF-κB activation in extracts 

were detected via Western blot and immunocytochemistry 

assays. 

RESULTS: The LL extract significantly inhibited NO, 

PGE(2), IL-6 and TNF-α 

production in LPS-stimulated cells, 

and suppressed iNOS and COX-2 expression. A mechanism-based 

study showed that phosphorylation of ERK1/2 

and JNK and translocation of the NF-κB p65 subunit into 

nuclei were inhibited by the LL extract. Furthermore, interleukin-4 

and interleukin-13 production in Con A-induced 

splenocytes was suppressed. 

CONCLUSION: These results indicate that anti-inflammatory 

effects of methanol extracts from Lilium lancifolium 

are due to downregulation of iNOS and COX-2 via 

suppression of NF-κB activation and nuclear translocation 

as well as blocking of ERK and JNK signaling in LPS-stimulated 

Raw264.7 cells. 

PMID: 20412846 

Lee SH, Yun S, Piao ZH, Jeong M, Kim DO, Jung H, Lee 

J, Kim MJ, Kim MS, Chung JW,Kim TD, Yoon SR, 

Greenberg PD, Choi I * 



NK cells are capable of killing virus-infected or tumor cells 

and producing IFN- γ. Resting NK cells, however, have only 

minimal cytolytic activity and secrete a low level of IFN- γ. 

The cytokine IL-15 can promote the expression of effector 

functions by resting NK cells. In this study, we demonstrate 

that suppressor of cytokine signaling 2 (SOCS2) has a novel 

role in IL-15-primed human NK cell function. SOCS2 expression 

was upregulated in NK cells following stimulation 

with IL-15. During IL-15-mediated NK cell priming, SOCS2 

interacted with phosphorylated proline-rich tyrosine kinase 

2 (Pyk2) at tyrosine 402 (p-Pyk2(Tyr402)) and induced the 

proteasome-mediated degradation of p-Pyk2(Tyr402) via 

ubiquitination. Knockdown of SOCS2 resulted in the accumulation 

of p-Pyk2(Tyr402) and blocked NK cell effector 

functions. In addition, NK cell cytolytic activity and IFN-γ 

production were inhibited by overexpression of the wild-type 

of Pyk2 but not by the overexpression of tyrosine 402 mutant 

of Pyk2. These results suggest that SOCS2 regulates human 

NK cell effector functions via control of phosphorylated 

Pyk2 depending on IL-15 existence. 

PMID: 20543098 

Keywords: Cytotoxicity; Focal adhesion kinase 2; 

Interferon- γ; Interleukin-15; Jurkat cells; K562 cells; 

Killer cells, natural; Mutation; Phosphorylation; 

RNA interference; Signal transduction; Tyrosine 

Keywords: Anti-inflammatory agents; COX-2; IL-13; IL-4; 

Immunohistochemistry; Inflammation; INOS; Lilium 

lancifolium; Lipopolysaccharides; NF-κB; Plant 

extracts; TNF-α 


Article 198 

Vitamin D3 upregulated protein 1 suppresses 

TNF-α-induced NF-κB activation in hep- 

atocarcinogenesis 

J Immunol. 2010 Oct; 185(7):3980-9. 

Kwon HJ, Won YS, Suh HW, Jeon JH, Shao Y, Yoon SR, 

Chung JW, Kim TD, Kim HM, Nam KH, Yoon WK, Kim 

DG, Kim JH, Kim YS, Kim DY, Kim HC * , Choi I * 

Article 199 

Secondary metabolites of Volvariella bombycina 

and their inhibitory effects on melanogenesis 

J Microbiol Biotechnol. 2010 Jan; 20(1):78-81. 

Xu GH, Choo SJ, Kim YH, Ryoo IJ, Seok SJ, Ahn JS, 

Yoo ID * 



* Correspondence: hckim@kribb.re.kr ipchoi@kribb.re.kr 



Vitamin D(3) upregulated protein 1 (VDUP1) is a candidate 

tumor suppressor, the expression of which is dramatically 

reduced in various tumor tissues. In this study, we found 

that VDUP1 expression is suppressed during human hepatic 

carcinogenesis, and mice lacking VDUP1 are much more 

susceptible to diethylnitrosamine-induced hepatocarcinogenesis 

compared with wild type mice. VDUP1-deficient 

tumors proliferated significantly more than wild type tumors 

and had corresponding changes in the expression of key 

cell cycle regulatory proteins. In addition, the hepatomitogen-induced 

response was associated with a considerable 

increase in the release of TNF-α 

and subsequent enhancement 

of NF-κB activation in VDUP1-deficient mice. When cells 

were treated with TNF- α, the VDUP1 level was markedly 

reduced, concomitant with elevated NF-κB activation. 

Furthermore, the overexpression of VDUP1 resulted in the 

robust suppression of TNF-α-activated NF-κB activity via 

association with HDAC1 and HDAC3. These results indicate 

that VDUP1 negatively regulates hepatocarcinogenesis by 

suppressing TNF-α-induced NF-κB activation. 

PMID: 20826751 

Four compounds were isolated from the broth culture of 

Volvariella bombycina and they were identified as ergosta-4,6,8(14),22-tetraene-3-one 

(1), ergosterol peroxide (2), 

indole-3-carboxaldehyde (3) and indazole (4) by interpretation 

of spectroscopic data. Among them, compound 

2 exhibited melanogenesis inhibitory effect in cultured B16 

mouse melanoma cells. 

PMID: 20134236 

Keywords: Biological factors; Cell survival; Ergosterol; 

Indazoles; Melanins; Melanogenesis; Melanoma; 

Metabolism; Structure elucidation; Volvariella 

bombycina 

Keywords: Carcinoma, hepatocellular; Electrophoretic 

mobility; 

Immunohistochemistry; 

Immunoprecipitation; Liver neoplasms; Microscopy, 

fluorescence; NF-κ 

B; Signal transduction; 

Thioredoxins; Tumor necrosis factor-α 


Article 200 

Hydoroxyhibiscone A, a novel human neutrophil 

elastase inhibitor from Hibiscus syriacus 

J Microbiol Biotechnol. 2010 Aug; 20(8):1189-91. 

Ryoo IJ, Yun BS, Lee IK, Kim YH, Lee IS, Ahn JS, Bae 

K, Yoo ID * 



In an ongoing investigation of compounds from natural products 

that exhibit anti-aging properties, hydroxyhibiscone A 

(1), a new furanosesquiterpenoid, together with hibiscone 

D (2), was isolated from the root bark of Hibiscus syriacus. 

Utilizing UV, IR, NMR, and MS spectroscopic analyses, 

these chemical structures were revealed. Compounds 1 and 

2 were found to possess significant anti-aging properties 

on the human neutrophil elastase (HNE) assay, exhibiting 

HNE inhibitory activities with IC50 values of 5.2 and 4.6 

micronM, respectively. 

PMID: 20798580 

Keywords: Hibiscus syriacus; Human neutrophil elastase; 

Hydroxyhibiscone A; Leukocyte elastase; Molecular 

structure; Plant extracts; Proteinase inhibitory 

proteins 

Article 201 

Identification of three positive regulators in the 

geldanamycin PKS gene cluster of Streptomyces 

hygroscopicus JCM4427 

J Microbiol Biotechnol. 2010 Nov; 20(11):1484-90. 

Kim W, Lee JJ, Paik SG, Hong YS * 



In the Streptomyces hygroscopicus JCM4427 geldanamycin 

biosynthetic gene cluster, Five putative regulatory genes were 

identified by protein homology searching. Among three of 

those genes, gel14, gel17, and gel19, are located downstream 

of polyketide synthase genes. Gel14 and Gel17 are members 

of the LAL family of transcriptional regulators, including 

an ATP/GTP-binding domain at the N-terminus and a DNA 

binding helix-turn-helix domain at the C-terminus. Gel19 

is a member of the TetR family transcriptional regulators, 

which generally act to repress transcription. To verify the 

biological significance of the putative regulators in geldanamycin 

production, they were individually characterized by 

gene disruption, genetic complementation and transcriptional 

analyses. All three genes were confirmed as positive regulators 

of geldanamycin production. Specifically, Gel17 and 

Gel19 are required for gel14 as well as gelA gene expression. 

PMID: 21124051 

Keywords: Amino acid sequence; Bacterial proteins; 

Benzoquinones; Biosynthesis; Geldanamycin; 

Lactams, macrocyclic; Multigene family; Regulator; 

Sequence alignment; Streptomyces 


Article 202 

Anti-human rhinovirus activity of raoulic acid 

from Raoulia australis 

J Med Food. 2010 Apr; 13(2):326-8. 

Choi HJ, Song JH, Lim CH, Baek SH, Kwon DH * 



Human rhinoviruses (HRVs), members of the Picornaviridae 

family, are composed of over 100 different virus serotypes. 

Until now there is no recorded clinically effective antiviral 

chemotherapeutic agent for treatment of diseases caused by 

HRVs. Our previous study of raoulic acid tested against 

serotype human rhinoviruses showed anti-HRV2 (species 

A) and -3 (species B) activities. In this study, raoulic acid 

was found to possess broad-spectrum antiviral activity against 

six HRVs with a 50% inhibition concentration of less than 

9.5 microg/mL through inhibition of the cellular absorption 

of the HRV particles. Furthermore, the effect of raoulic acid 

on resistance of HRV5 exhibited to pleconaril was more 

pronounced than the effect on HRV1b, -6, -14, -15, and 

-40. However, ribavirin did possess weak antiviral activity 

against HRVs. Collectively, the results demonstrate that 

raoulic acid is a novel therapeutic candidate for two different 

groups of human rhinovirus. 

PMID:20412019 

Keywords: Antiviral agents; Asteraceae; Common cold; 

Microbial sensitivity tests; Oxadiazoles; 

Phytotherapy; Picornaviridae infections; Plant 

extracts; Rhinovirus; Ribavirin; Terpenes; Virus 

internalization 

Article 203 

An isoaurone and other constituents from 

Trichosanthes kirilowii seeds inhibit hypoxia-inducible 

factor-1 and nuclear factor- κB 

J Nat Prod. 2010 Jun; 73(6):1167-9. 

Dat NT, Jin X, Hong YS, Lee JJ * 



Hypoxia-inducible factor-1 and nuclear factor-κB have be- 

come important targets in cancer treatment due to their critical 

role in the regulation of genes involved in tumorigenesis. 

Bioassay-guided fractionation of the methanol extract of 

Trichosanthes kirilowii seeds led to the isolation of a naturally 

rare isoaurone, 4',6-dihydroxy-4-methoxyisoaurone (1), together 

with three known compounds, cucurbitacin B (2), 

6-(3-hydroxy-4-methoxystyryl)-4-methoxy-2H-pyran-2-one 

(3), and blumenol A (4). All compounds inhibited HIF-1 

and NF-κB activities in reporter assays. Compounds 1-3 

potently inhibited HIF-1α 

accumulation and VEGF secretion 

under hypoxic condition. These results suggest that the tumor 

cell growth inhibitory activity of T. kirilowii is likely associated 

with the inhibition of HIF-1 and NF-κB activities. 

PMID:20469887 

Keywords: Hypoxia-inducible factor 1; Molecular 

structure; NF-κ 

B; Plants, medicinal; Sesquiterpenes; 

Trichosanthes kirilowii; Triterpenes 


Article 204 

Hepatoprotective effects of Sedum sarmentosum 

on D-galactosamine/lipopolysaccharide-induced 

murine fulminant hepatic failure 

Article 205 

Inhibitory effects of orobol 7-O-D-glucoside from 

banaba (Lagerstroemia speciosa L.) on human 

rhinoviruses replication 

J Pharmacol Sci. 2010; 114(2):147-57. 

Lett Appl Microbiol. 2010 Jul; 51(1):1-5. 

Lian LH, Jin X, Wu YL, Cai XF, Lee JJ * , Nan JX 

Choi HJ, Bae EY, Song JH, Baek SH, Kwon DH * 





The hepatoprotective effects of sarmentosin-containing extracts 

of Sedum sarmentosum (SS) in D-galactosamine 

(D-GalN) / lipopolysaccharide (LPS)-induced fulminant hepatic 

failure mouse model. Pretreatment with SS markedly 

protected mice from lethal liver injury, which has known 

to be associated with an abrupt elevation of serum tumor 

necrosis factor (TNF)-α 

level. Indeed, SS significantly 

blocked the elevation of TNF-α 

and alanine aminotransferase 

and aspartate aminotransferase as well. SS also remarkably 

reduced number of apoptotic hepatocytes and DNA fragmentation 

in the liver, which correlated with blockade of caspase-3 

activation. In addition, SS suppressed the increased 

expression of toll-like receptor 4 (TLR4). The activation 

of c-Jun NH(2)-terminal kinase, extracellular signal-regulated 

kinase, and p38 induced by D-GalN/LPS was also 

significantly suppressed by SS treatment. Furthermore, SS 

significantly inhibited the activation of nuclear factor-κB. 

In RAW 264.7 cells stimulated with LPS, TNF-α 

release 

and TLR4 expression was suppressed by SS pretreatment, 

which was in line with in vivo results. These findings suggested 

that SS prevents D-GalN/LPS-induced fulminant hepatic 

failure, and this protection is likely associated with its 

anti-apoptotic activity and the down-regulation of mitogen 

activated protein kinase activity associated at least in part 

with suppressing the transcription of LPS receptors. 

PMID:20838028 

Keywords: Caspase 3; D-galactosamine (d-GalN); Glucose; 

Hepatocytes; Lipopolysaccharide (LPS); Liver; 

Nuclear factor (NF)-κB; Plant extracts; 

Sedum 

sarmentosum; Toll-like receptor 4 (TLR4); Tumor 

necrosis factor (TNF)-α 

AIMS: The anti-human rhinovirus (HRV) activity of orobol 

7-O-d-glucoside (O7G) from Lagerstroemia speciosa L. 

(Lythraceae) was evaluated in Hela cells. 

METHODS AND RESULTS: We tested anti-HRV activity 

of O7G using a cytopathic effect (CPE) reduction method, 

which exhibited broad-spectrum anti-HRVs activity with a 

50% inhibitory concentration (IC(50)) ranging from 0.58 

to 8.80 microg ml(-1). The 50% cytotoxicity concentration 

(CC(50)) of O7G is more than 100 microg ml(-1), and the 

derived therapeutic indices are more than 12. Ribavirin didn't 

possess antiviral activity against HRV15, HRV3 and HRV5, 

but exhibited weak antiviral activity against HRV2 and 

HRV3, and showed strong anti-HRV6 and -14 activities. 

CONCLUSIONS: These results suggest that O7G is a novel 

drug class with broad spectrum antiviral activity against HRV 

species A (HRV1B, HRV2, HRV15 and HRV40) and species 

B (HRV3, HRV6 and HRV14), as well as pleconaril-resistant 

virus (HRV5). 

SIGNIFICANCE AND IMPACT OF THE STUDY: 

Therefore, these findings provide important information for 

the utilization of Q7G promising broad spectrum for human 

rhinovirus treatment. 

PMID:20497313 

Keywords: Antiviral activity; Cytopathogenic effect; 

Flavonoids; Glucosides; Hela cells; Human 

rhinoviruses; Lagerstroemia speciosa; Orobol 

7-O-d-glucoside (O7G); Ribavirin; Virus replication 


Article 206 

PAUF functions in the metastasis of human pancreatic 

cancer cells and upregulates CXCR4 expression 

Article 207 

Acanthoic acid, a diterpene in Acanthopanax koreanum, 

protects acetaminophen-induced hepatic 

toxicity in mice 

Oncogene. 2010 Jan; 29(1):56-67. 

Phytomedicine. 2010 May; 17(6):475-9. 

Lee Y, Kim SJ, Park HD, Park EH, Huang SM, Jeon SB, 

Kim JM, Lim DS, Koh SS * 

Wu YL, Jiang YZ, Jin XJ, Lian LH, Piao JY, Wan Y, Jin 

HR, Lee JJ * , Nan JX 





Pancreatic cancer is characterized by early metastatic spread, 

but the process of tumor cell dissemination is largely 

unknown. In this study we show that the soluble protein 

pancreatic adenocarcinoma upregulated factor (PAUF) has 

an important role in the metastasis and progression of the 

disease. Variations in the level of PAUF, either by overexpression 

or knockdown, resulted in altered migration, invasion 

and proliferation capacity of pancreatic cancer cells. 

Moreover, depletion of PAUF in metastatic cells dramatically 

abrogated the spread of the cells to distant organs in an 

orthotopic xenograft mouse model. PAUF elicited the activation 

of the extracellular signal-regulated kinase (ERK), c-Jun 

N-terminal kinase (JNK) and AKT intracellular signaling 

cascades and consequently their downstream transcription 

factors in an autocrine manner. Genome-wide expression 

analysis revealed that C-X-C chemokine receptor type 4 

(CXCR4) expression was induced by PAUF overexpression 

but was repressed by PAUF knockdown. The PAUF-mediated 

increase in cancer cell motility was attenuated by the 

CXCR4 inhibitor, AMD3100, or by anti-CXCR4 antibody. 

Furthermore, immunohistochemical analysis of pancreatic 

tumor tissues clearly showed a significant positive correlation 

between PAUF and CXCR4 expression. Collectively, these 

findings indicate that PAUF enhances the metastatic potential 

of pancreatic cancer cells, at least in part, by upregulating 

CXCR4 expression. 

PMID:19784070 

Keywords: Cell line, tumor; CXCR4; Heterocyclic 

compounds; Neoplasm metastasis; Pancreatic 

cancer; PAUF; RNA interference; Signaling 

The protective effect of a diterpenoid acanthoic acid (AA) 

isolated from Acanthopanax koreanum Nakai was investigated 

in acetaminophen (APAP)-induced hepatic toxicity. 

Drug-induced hepatotoxicity induced by an intraperitoneal 

(i.p.) injection of 300mg/kg (sub-lethal dose) of APAP. 

Pretreatment with AA (50 and 100mg/kg) orally 2h before 

the APAP administration attenuated the APAP-induced acute 

increase in serum aspartate aminotransferase (AST), and alanine 

aminotransferase (ALT) activites, replenished the depleted 

hepatic glutathione (GSH), superoxide dismutase 

(SOD), catalase (CAT), glutathione peroxidase (GSH-Px) 

activities, decreased malondialdehyde (MDA) level and considerably 

reduced the histopathological alterations in a manner 

similar to silymarin (Sily). Immunohistochemical analyses 

also demonstrated that AA could reduce the appearance 

of necrosis regions as well as caspase-3 and hypoxia inducible 

factor-1 α (HIF-1 α) expression in liver tissue. Our results 

indicated that AA protected liver tissue from the oxidative 

stress elicites by APAP-induced liver damage and suggestes 

that the hepatic protection mechanism of AA would relate 

to antioxidation and hypoxia factor on APAP-induced 

hepatotoxicity. 

PMID:19836221 

Keywords: Acanthoic acid; Acanthopanax koreanum; 

Acetaminophen; Antioxidation; Caspase 3; 

Diterpenes; Hepatotoxicity; Hypoxia inducible 

factor-1 α; Malondialdehyde; Oxidative Stress; Plant 

extracts 


Article 208 

Xanthone constituents of the fruits of Garcinia 

mangostana with anticomplement activity 

Phytother Res. 2010 Oct; 24(10):1575-7. 

Quan GH, Oh SR, Kim JH, Lee HK, Kinghorn AD, Chin 

YW * 



Phytochemical investigation of a chloroform-soluble fraction 

of the freeze-dried fruits of Garcinia mangostana 

(Clusiaceace) with anticomplement activity in the classical 

pathway led to the identification of five known xanthones. 

The structures of these compounds were confirmed by interpretation 

of NMR and MS spectroscopic data. Of the isolates 

obtained, 1-isomangostin and garcinone E were found to 

be active constituents in the anticomplement assay used. 

PMID: 20878711 

Keywords: 1-isomangostin; Aanticomplement activity; 

Garcinia 

mangostana; Garcinone E; Molecular 

structure; Xanthenes; Xanthones 

Article 209 

Protein tyrosine phosphatase 1B inhibitory activity 

of 24-norursane triterpenes isolated from 

Weigela subsessilis 

Phytother Res. 2010 Nov; 24(11):1716-9. 

Na M, Thuong PT, Hwang IH, Bae K, Kim BY, Osada 

H, Ahn JS * 

* Correspondence: jsahn@kribb.re.kr 


During the screening effort to discover new types of protein 

tyrosine phosphatase 1B (PTP1B) inhibitors, it was found 

that a MeOH extract of the leaves and stems of Weigela 

subsessilis (Caprifoliaceae) inhibited the enzyme activity. 

By means of an in vitro bioassay-guided fractionation on 

the MeOH extract, two 24-norursane triterpenes, ilekudinol 

A (1) and ilekudinol B (2), were isolated as active metabolites. 

Compounds 1 and 2 inhibited PTP1B with IC(50) values 

of 29.1 ± 2.8 and 5.3 ± 0.5 

μM, respectively. Kinetic studies 

suggest that both 1 and 2 are non-competitive inhibitors 

of PTP1B. The findings indicate that the free carboxyl group 

at C-28 in this type of triterpenes plays a critical role in 

the inhibition of PTP1B. 

PMID:20564495 

Keywords: Caprifoliaceae; Ilekudinol A; Ilekudinol B; 

Molecular structure; Non-competitive inhibitors; 

Plant extracts; Protein tyrosine phosphatase 1B; 

Triterpenes; Weigela subsessilis 


Article 210 

New tricyclic geldanamycin analogues from an 

engineered strain of Streptomyces hygroscopicus 

JCM4427 

Tetrahedron Letters. 2010 Jan; 51(2):351-3. 

Hong SS , Cai XF, Hwang BY, Lee HS, Su BN, Hong 

YS * , Lee D 



Two tricyclic geldanamycin analogues, DHQ5 (1) and DHQ6 

(2), were produced by a combinatorial mutant (AC15) contained 

a site-directed mutagenesis on the geldanamycin polyketide 

synthase (PKS) gene with inactivation of the post-PKS 

tailoring genes (gel7) of Streptomyces hygroscopicus 

JCM4427. The structural diversity of tricyclic geldanamycin 

analogues is due to the formation of unusual additional rings, 

which are formed by alkylation of the C-21 position by 

C-12 in DHQ5 (1) and by electrophilic addition of the C-15 

hydroxyl group to the double bond (C-8-C-9), which leads 

to the migration of the double bond (to C-7-C-8) and the 

elimination of a carbamoyloxy group in DHQ6 (2). 

Keywords: Alkylation; Bacterial gene; Bacterial strain; 

Gene inactivation; Site directed mutagenesis; 

Streptomyces hygroscopicus; Tricyclic 

geldanamycin analogues 



2010 




Division of Bio-Infra Structure 




Biotechnology Process Engineering Center 



www.kribb.re.kr

Article 211 

Processing and subcellular localization of 

ADAM2 in the Macaca fascicularis testis and 

sperm 

Anim Reprod Sci. 2010 Jan; 117(1-2):155-9. 

Kim E, Lee JW, Baek DC, Lee SR, Kim MS, Kim SH, 

Kim CS, Ryoo ZY, Kang HS, Chang KT * 

* Correspondence: changkt@kribb.re.kr 


Fertilin, a heterodimeric protein complex composed of 

ADAM1 and ADAM2 located on the sperm surface, is involved 

in sperm-egg interaction. In our study, we examined 

the physiological processing and subcellular localization of 

M. fascicularis ADAM2 during spermatogenesis in the testis 

and epididymal tract. M. fascicularis ADAM2 was initially 

synthesized as a 100 kDa precursor in testicular germ cells. 

After passing into 50 kDa intermediate form in the epididymal 

tracts, the precursor form was finally processed into a 47 

kDa protein in sperm. We found that M. fascicularis ADAM2 

is localized on the sperm surface and contributes to the 

formation of a candidate fertilin complex. In particular, 

Far-Western blot analysis revealed that M. fascicularis 

ADAM2 cystein-rich domain may be related to protein-protein 

interaction. Therefore, the cystein-rich domain of 

ADAM2 could provide a mechanism to form a fertilin 

complex. 

PMID: 19443142 

Keywords: ADAM proteins; Cell membrane; Epididymis; 

Fertilin; Fertilization; Macaca fascicularis ADAM2; 

Membrane glycoproteins; Recombinant proteins; 

Spermatogenesis; Spermatozoa; Testis 

Article 212 

Differential expression patterns of gangliosides 

in the tissues and cells of NIH-mini pig kidneys 

Animal Cell System. 2010; 14(2):83-9. 

Cho JH, Kim JS, Lee YC, Oh KB, Kwak DH, Kim WS, 

Hwang SS, Ko K, Chang KT * , Choo YK 



Gangliosides are a ubiquitous component of the membranes 

of mammalian cells that have been suggested to play important 

roles in various cell functions such as cell-cell interaction, 

adhesion, cell differentiation, growth control and 

signaling. However, the role that gangliosides play in the 

immune rejection response in xenotransplantation is not yet 

clearly understood. In this study, differential expression patterns 

of gangliosides in HEK293 (human embryonic kidney 

cells), PK15 (porcine kidney cells), NIH-kd (NIH-mini pig 

kidney cells, primary cultured) and the cortex, medulla and 

calyx of the NIH-mini pig kidney were investigated by 

high-performance thin-layer chromatography (HPTLC). The 

results revealed that HEK293, PK15 and NIH-kd contained 

GM3, GM2 and GD3 as major gangliosides. Moreover, GM3, 

which are the gangliosides of NIH-kd, were expressed at 

higher levels than HEK293 and PK15. Especially, GT1b 

were expressed in HEK293 and NIH-kd but not in PK15. 

Finally, GM1 and GD1a were expressed in NIH-kd, but 

not in HEK293 or PK15. These results suggest that differential 

expression patterns of gangliosides from HEK293, 

PK15 and NIH-kd are related to the immune rejection response 

in xenotransplantation. 

Keywords: Gangliosides xenotransplantation; HEK293; 

NIH-kd; NIH-mini pig kidney; PK15 


Article 213 

Implication of mousenVps26b-Vps29-Vps35 retromer 

complex in sortilin trafficking 

Article 214 

Property based optimization of 

inhibitors for metabolic stability 

δ-lactam HDAC 

Biochem Biophys Res Commun. 2010 Dec; 403(2):167-71. 

Bioorg Med Chem Lett. 2010 Nov; 20(22):6808-11. 

Kim E, Lee Y, Lee HJ, Kim JS, Song BS, Huh JW, Lee 

SR, Kim SU, Kim SH, Hong Y, Shim I, Chang KT * 

Yoon HC, Choi E, Park JE, Cho M, Seo JJ, Oh SJ, Kang 

JS, Kim HM, Park SK, Lee K * , Han G 



* Correspondence: kiholee@kribb.re.kr 


The retromer complex, which mediates retrograde transport 

from endosomes to the trans-Golgi network, is a heteropentameric 

complex that contains a multifunctional cargo 

recognition heterotrimer consisted of the vacuolar protein 

sorting (Vps) subunits Vps26, Vps29, and Vps35. In mammals, 

there are two different isoforms of Vps26, Vps26a 

and Vps26b, that localize to the endosome, and to the plasma 

membrane, respectively. To elucidate the biological significance 

of the Vps26b isoform, we generated Vps26b 

knockout mice and studied their molecular, histological, and 

behavioral phenotypes. We found that the loss of Vps26b 

results in no significant defects in the behavior, body size, 

and health of the mice. Vps26b-deficient mice showed a 

severe reduction of Vps35 protein at cellular level and lacked 

the Vps26b-Vps29-Vps35 retromer complex, despite the normal 

presence of the Vps26a-Vps29-Vps35 retromer complex. 

Relatively, the amount of sortilin was increased approximately 

20% in the Vps26b-deficient mice, whereas the 

sorLA was normal. These results suggest that mouse 

Vps26b-Vps29-Vps35 retromer complex is implicated in the 

transport of sortilin from endosomes to the trans-Golgi network 

(TGN). 

PMID: 21040701 

The novel δ-lactam based HDAC inhibitor, KBH-A118 (3) 

shows a good HDAC enzyme and cancer cell growth inhibitory 

activities but has undesirable pharmacokinetics profiles 

because of instability in mouse liver microsome. To 

improve metabolic stability, various analogues were prepared 

with substituents on aromatic ring of cap group and various 

chain lengths between the cap group and 

δ-lactam core. 

The newly prepared analogues showed moderate to potent 

in vitro activities. Among them six compounds (8a, 8e, 8j, 

8n, 8t, and 8v) were evaluated on mouse liver microsome 

assay and it turned out that the microsomal stabilities were 

dependent on lipophilicity and the number of the rotatable 

bonds. Finally, the animal pharmacokinetic profiles of 8e 

displayed improving oral exposure and oral bioavailability. 

PMID:20850971 

Keywords: Biological availability; Cell line, tumor; Histone 

deacetylase; In vitro ADME; Inhibitor; Lactam; 

Optimization 

Keywords: Animal cell; Cell membrane; Endosomes; 

Genetic transfection; Phenotype; Protein transport; 

Retromer complex; Trans-Golgi network (TGN); 

Vacuolar protein sorting 26b (Vps26b); 

Vps26b-deficient mice 


Article 215 

Full-length cDNA sequences from Rhesus monkey 

placenta tissue: analysis and utility for comparative 

mapping 

BMC Genomics. 2010 Jul; 11:427. 

Kim DS, Huh JW, Kim YH, Park SJ, Lee SR, Chang KT * 



BACKGROUND: Rhesus monkeys (Macaca mulatta) are 

widely-used as experimental animals in biomedical research 

and are closely related to other laboratory macaques, such 

as cynomolgus monkeys (Macaca fascicularis), and to humans, 

sharing a last common ancestor from about 25 million 

years ago. Although rhesus monkeys have been studied extensively 

under field and laboratory conditions, research has 

been limited by the lack of genetic resources. The present 

study generated placenta full-length cDNA libraries, characterized 

the resulting expressed sequence tags, and described 

their utility for comparative mapping with human RefSeq 

mRNA transcripts. 

RESULTS: From rhesus monkey placenta full-length cDNA 

libraries, 2000 full-length cDNA sequences were determined 

and 1835 rhesus placenta cDNA sequences longer than 100 

bp were collected. These sequences were annotated based 

on homology to human genes. Homology search against 

human RefSeq mRNAs revealed that our collection included 

the sequences of 1462 putative rhesus monkey genes. 

Moreover, we identified 207 genes containing exon alterations 

in the coding region and the untranslated region of 

rhesus monkey transcripts, despite the highly conserved 

structure of the coding regions. Approximately 10% (187) 

of all full-length cDNA sequences did not represent any 

public human RefSeq mRNAs. Intriguingly, two rhesus monkey 

specific exons derived from the transposable elements 

of AluYRa2 (SINE family) and MER11B (LTR family) were 

also identified. 

CONCLUSION: The 1835 rhesus monkey placenta 

full-length cDNA sequences described here could expand 

genomic resources and information of rhesus monkeys. This 

increased genomic information will greatly contribute to the 

development of evolutionary biology and biomedical 

research. 

PMID:20624290 

Article 216 

Shiga toxin A subunit mutant of Escherichia coli 

O157:H7 releases outer membrane vesicles containing 

the B-pentameric complex 

FEMS Immunol Med Microbiol. 2010 Apr; 58(3):412-20. 

Kim SH, Lee SR, Kim KS, Ko A, Kim E, Kim YH, Chang 

KT * 



Shiga toxins (STx) are secreted extracellularly through the 

outer membrane vesicles (OMVs) of Escherichia coli 

O157:H7. In an attempt to produce STxA-deficient OMVs 

from E. coli O157:H7, site-specific deletions of the stx1A 

and stx2A subunit genes were carried out. The STxA-deficient 

phenotype of the stx1A/stx2A mutant was confirmed by Vero 

cell cytotoxicity and VTEC-RPLA assay. Western blot analyses 

showed that the B (STxB) subunits were present without 

coupling to STxA in the OMVs of the STxA-deficient mutant. 

Furthermore, STxB was located in its homo-pentameric complexes, 

as revealed by immunoprecipitation and immunoblotting 

with anti-STxB antibodies. These results suggest that 

STxB alone can be oligomerized into the B pentamer in 

the periplasm, and subsequently entrapped into the OMVs. 

Determination of the median lethal dose concentration for 

the OMV preparations suggests that the STxA-deficient 

OMVs containing STxB complex could be safely used as 

vaccine delivery vehicles. 

PMID: 20199568 

Keywords: Cell membrane; Cercopithecus aethiops; 

Escherichia coli O157; Median lethal dose; 

Mutation; Outer membrane vesicle detoxification; 

Secretory vesicles; Shiga toxin A mutation; Vaccine 

vehicle 

Keywords: Animals; DNA, complementary; Gene library; 

INDEL mutation; Macaca mulatta; Placenta; 

Pregnancy; RNA, messenger; Sequence analysis, 

DNA; Sequence homology 


Article 217 

Monitoring the occurrence of genetically modified 

maize at a grain receiving port and along transportation 

routes in the Republic of Korea 

Food Control. 2010 Apr; 21(4):456-61. 

Park KW, Lee B, Kim CG, Kim DY, Park JY, Ko EM, 

Jeong SC, Choi KH, Yoon W, Kim HM * 

* Correspondence: hwanmook@kribb.re.kr 


The cultivation area of genetically modified (GM) crops 

is increasing all over the world. Though no land in the 

Republic of Korea is currently used for the cultivation of 

GM crops, GM crop imports for food and foraging purposes 

are continuously increasing. This may promote the unintentional 

escape of GM crops. This study was conducted to 

investigate whether imported GM maize is released into our 

environment during the transportation of grain in the Republic 

of Korea. Based on PCR analysis, most of the maize grains 

in the forage products were GM, and about 50% of the 

grains were germinated. Monitoring was conducted in two 

major grain receiving ports, 15 feed manufacturing plants, 

and 14 livestock barns in five provinces of the Republic 

of Korea from July to September 2007. We found many 

spilled maize grains around open storage areas of ports and 

along truck transportation routes near feed manufacturing 

plants. Established maize plants were not found at or around 

Incheon port. However, we found 18 established maize plants 

at the Gunsan port, 15 of which were GM. We also found 

eight GM maize plants around four feed manufacturing plants 

and in two livestock barns. Based on the event-specific PCR 

analysis, three maize events (NK603, Mon810, and TC1507) 

were identified. Though several GM maize plants were found 

around the port and feed manufacturing plants, most of these 

facilities were located inside the industrial park and were 

far from cultivated fields, likely rendering the impact of 

these GM maize on the natural environments negligible. 

However, most of the livestock barns were close to cultivated 

areas. Moreover, maize plants were cultivated for food or 

feed near some livestock barns. This practice may facilitate 

gene flow from GM maize to non-GM maize plants. 

Therefore, continuous monitoring is necessary to detect the 

occurrence of GM maize, and appropriate action should be 

taken to prevent genetic admixture in our environment. 

Article 218 

Four different ways of alternative transcripts 

generation mechanism in ADRA1A gene 

Genes Genet Syst. 2010 Feb; 85(1):65-73. 

Huh JW, Kim YH, Lee SR, Kim DS, Park SJ, Kim H, 

Kim JS, Song BS, Kim HS, Chang KT * 



The ADRA1A ( α-1-adrenergic receptor) gene is one of the 

members of G protein-coupled receptor superfamily. 

Alternative splicing of this gene was known to generate 

four transcript variants which code four isoforms with various 

C-terminal regions. In this study, we conducted expression 

analysis and evolutionary characterization of alternative transcripts 

of the ADRA1A gene. In total, 10 alternative transcripts 

were identified using experimental approaches and in silico 

analysis. Among them, 6 alternative transcripts (T1, T2, T3, 

T4, T4-1, and T8) were validated by RT-PCR approaches 

and sequencing procedures. From the alternative splicing 

analysis, it could be assumed that there were three different 

alternative transcripts generation mechanisms and unknown 

mechanism. First one is the integration event of three different 

TEs (AluSc, L1MC5, and MIR3) as seen on the last exons 

of T3, T4, T4-1, T5, T6, and T7 transcripts. The second 

mechanism is a differential promoter usage on T8. The third 

one is a substitution event of the 3' splicing site during 

the primate evolution on T3. The last one is an unknown 

mechanism which was identified in the T4-1 transcript. 

Therefore, alternative transcripts of human ADRA1A gene 

occurred by four different ways, such as integration of TEs, 

differential promoter usage, substitution of splicing sites, 

and unknown mechanism. 

PMID: 20410666 

Keywords: Adra1a gene; Alternative splicing; 

Computational biology; DNA transposable elements; 

Exons; Primates; Sequence homology; Substitution; 

Tes integra 

Keywords: Environmental risk; Genetically modified 

organism; Maize; Monitoring; Republic of Korea; 

Transportation route; Zea mays 


Article 219 

Bioinformatic analysis of TE-spliced new exons 

within human, mouse and zebrafish genomes 

Article 220 

Genetic analysis of genes controlling natural variation 

of seed coat and flower colors in soybean 

Genomics. 2010 Nov; 96(5):266-71. 

J Hered. 2010 Nov; 101(6):757-68. 

Kim DS, Huh JW, Kim YH, Park SJ, Kim HS, Chang KT * 



Recent studies indicate major roles for transposable elements 

(TEs) in alternative splicing. In this study, we conducted 

genome-wide alternative splicing analyses focusing on new 

internal exon birth derived from TEs in human, mouse, and 

zebrafish genomes. We identified two different exon sets, 

TE-spliced exons and non-TE-spliced exons. The proportion 

of TE-spliced exons was nearly twice as high as the proportion 

of non-TE-spliced exons in the coding sequence (CDS) 

region. Detailed analysis of various families of TEs in three 

different species of TE-spliced exons revealed a different 

pattern in zebrafish. In our analysis, we could identify the 

functional role of TE insertions in the vertebrate genome 

affecting mRNA splicing machinery. Their effects can be 

directly linked to the shift from constitutive to alternative 

splicing during primate evolution. Our results indicate that 

TEs have a significant effect on shaping new internal exons 

in human, mouse, and zebrafish transcriptomes. 

PMID: 20728532 

Keywords: Alternative splicing; Bioinformatics; 

Computational biology; DNA transposable elements; 

Genome; TE-spliced exon; Vertebrates; Zebrafish 

Yang K, Jeong N, Moon JK, Lee YH, Lee SH, Kim HM, 

Hwang CH, Back K, Palmer RG, Jeong SC * 

* Correspondence: scjeong@kribb.re.kr 


Soybean exhibits natural variation in flower and seed coat 

colors via the deposition of various anthocyanin pigments 

in the respective tissues. Although pigmentation in seeds 

or flowers has been well dissected at molecular level in 

several plant species, the genes controlling natural variation 

in anthocyanin traits in the soybean are not completely 

understood. To evaluate the genetic correlation between genetic 

loci and genes, 8 enzyme-encoding gene families and 

a transcription factor were localized in a soybean genome-wide 

genetic map. Among the seed coat color-controlling 

loci, the genetic location of the gene encoding for W1 

was substantiated in the context of the current soybean molecular 

genetic map and O was postulated to correspond to 

anthocyanidin reductase. Among the genetic loci that regulate 

flower pigmentation, the genetic locations of the genes encoding 

for W1, W4, and Wp were identified, W3 was mapped 

on soybean linkage group B2 (chromosome 14), and W2 

was postulated to correspond to an MYB transcription factor. 

Correlation studies between the developed markers and 3 

color-controlling loci provided important empirical data that 

should prove useful in the design of marker-assisted breeding 

schemes as well as future association studies involving 

soybean. 

PMID: 20584753 

Keywords: Anthocyanin; Chromosome mapping; Flower 

color; Genetic variation; Glycine max; 

Glycosyltransferases; Molecular marker; 

Oxygenases; Pigmentation; Seed coat color; 

Soybean; Transcription factors 


Article 221 

DBM1285 suppresses tumor necrosis factor α pro - 

duction by blocking p38 mitogen-activated protein 

kinase/mitogen-activated protein kinase-activated 

protein kinase 2 signaling pathway 

J Pharmacol Exp Ther. 2010 Aug; 334(2):657-64. 

Kang JS, Kim HM, Choi IY, Han SB, Yoon YD, Lee H, 

Park KH, Cho IJ, Lee CW, Lee K, Lee KH, Park SK * 

* Correspondence: spark123@kribb.re.kr 


Tumor necrosis factor α (TNF- α) is a major inflammatory 

cytokine that plays an important role in the development 

of various inflammatory diseases. TNF-α 

has been considered 

as a potential therapeutic target for the treatment of chronic 

inflammatory diseases, including rheumatoid arthritis and 

inflammatory bowel disease. In this study, we report that 

c y c l o- 

p r o p y l - { 4 - [ 4 - ( 4 - f l u o r o p h e n y l ) - 2 - p i p e r- 

idin-4-yl-thiazol-5-yl]pyrimidin-2-yl}a mine (DBM1285) is 

a novel inhibitor of TNF-α production. DBM1285 concen- 

tration-dependently inhibited lipopolysaccharide 

(LPS)-induced TNF-α secretion in various cells of macro- 

phage/monocyte lineage, including mouse bone marrow macrophages, 

THP-1 cells, and RAW 264.7 cells. However, 

LPS-induced mRNA expression of TNF-α 

was not affected 

by DBM1285 in these cells. Further studies demonstrated 

that the inhibitory effect of DBM1285 on TNF-α 

production 

might be mediated by post-transcriptional regulation through 

the modulation of the p38 mitogen-activated protein kinase 

(MAPK)/MAPK-activated protein kinase 2 (MK2) signaling 

pathway. We also confirmed that DBM1285 directly inhibits 

p38 MAPK enzymatic activity. In vivo administration of 

DBM1285 inhibited LPS-induced increase in the plasma level 

of TNF-α 

in mice. Whole-blood in vivo target inhibition 

assay also revealed that DBM1285 attenuates p38 MAPK 

activity after oral administration in mice. Moreover, 

DBM1285 suppressed zymosan-induced inflammation and 

adjuvant-induced arthritis in murine models. Collectively, 

these results suggest that DBM1285 inhibits TNF-α pro- 

duction, at least in part, by blocking the p38 MAPK/MK2 

pathway. Furthermore, in vivo results suggest that DBM1285 

might be a possible therapeutic candidate for the treatment 

of TNF-α-related chronic inflammatory diseases. 

PMID: 20427474 

Keywords: Anti-inflammatory agents; Arthritis, 

rheumatoid; Cell lineage; Inflammation; 

Lipopolysaccharides; Macrophages; p38 kinases; 

Pyrimidines; Signal transduction; Thiazoles; Tumor 

necrosis factor-α 

Article 222 

Melatonin plus exercise-based neurorehabilitative 

therapy for spinal cord injury 

J Pineal Res. 2010 Oct; 49(3):201-9. 

Hong Y, Palaksha KJ, Park K, Park S, Kim HD, Reiter 

RJ, Chang KT * 



Spinal cord injury (SCI) is damage to the spinal cord caused 

by the trauma or disease that results in compromised or 

loss of body function. Subsequent to SCI in humans, many 

individuals have residual motor and sensory deficits that 

impair functional performance and quality of life. The available 

treatments for SCI are rehabilitation therapy, activity-based 

therapies, and pharmacological treatment using antioxidants 

and their agonists. Among pharmacological treatments, 

the most efficient and commonly used antioxidant 

for experimental SCI treatment is melatonin, an indolamine 

secreted by pineal gland at night. Melatonin's receptor-independent 

free radical scavenging action and its broad-spectrum 

antioxidant activity makes it an ideal antioxidant to 

protect tissue from oxidative stress-induced secondary damage 

after SCI. Owing to the limitations of an activity-based 

therapy and antioxidant treatment singly on the functional 

recovery and oxidative stress-induced secondary damages 

after SCI, a melatonin plus exercise treatment may be a 

more effective therapy for SCI. As suggested herein, supplementation 

with melatonin in conjunction with exercise not 

only would improve the functional recovery by enhancing 

the beneficial effects of exercise but would reduce the secondary 

tissue damage simultaneously. Finally, melatonin may 

protect against exercise-induced fatigue and impairments. 

In this review, based on the documented evidence regarding 

the beneficial effects of melatonin, activity-based therapy 

and the combination of both on functional recovery, as well 

as reduction of secondary damage caused by oxidative stress 

after SCI, we suggest the melatonin combined with exercise 

would be a novel neurorehabilitative strategy for the faster 

recovery after SCI. 

PMID:20626592 

Keywords: Animal model; Central nervous system; 

Exercise therapy; Melatonin; Rehabilitation; 

Secondary/oxidative damage; Spinal cord injury 


Article 223 

Evaluating the persistence of DNA from decomposing 

transgenic watermelon tissues in the field 

Article 224 

Persistence of genetically modified potatoes in 

the field 

J Plant Biol. 2010; 53(5):338-43. 

J Plant Biol. 2010 Dec; 53(6):395-9. 

Lee B, Park JY, Park KW, Harn CH, Kim HM, Kim CG * 

* Correspondence: cgkim@kribb.re.kr 


To analyze the persistence of the 35S promoter, nos terminator, 

and hpt, we buried the leaves and rootstocks of transgenic 

watermelons (Citrullus lanatus (Thunb.) Matsum. & 

Nakai) in 10 cm of soil. Qualitative and quantitative PCR 

analyses showed that the amount of transgenes in leaf samples 

was greatly decreased, by 70%, after 1 month, and only 

2.5% remained after 2 months. No transgenes were detected 

in the leaves after 3 months. For buried rootstock samples, 

transgenes also degraded quickly, but a very small amount 

was still detectable up to 3 months later. In our investigation 

of possible gene transfer from decomposing transgenic watermelon 

to soil bacteria, only the 35S promoter was detected. 

However, further examination using colony dot hybridization 

tests indicated that such a transfer did not occur. 

Keywords: 35S promoter; Citrullus lanatus; DNA 

persistence; Gene transfer; Soil; Transgenic crop; 

Watermelon 

Kim CG, Kim DY, Moon YS, Kim HJ, Kim DI, Chun YJ, 

Park KW, Jeong SC, Kim SY, Kim HM * 

* Correspondence: hwanmook@kribb.re.kr 


Volunteers from genetically modified (GM) potatoes may 

pose an environmental problem if allowed to grow in the 

field after the annual crop is harvested. We tested whether 

they are more likely to produce volunteers than non-GM 

potatoes. Specifically, we compared the number of volunteers, 

number of tubers per plant, tuber size, and their vertical 

distribution in the soil. More volunteer plants came from 

non-GM potatoes than from GM potatoes, but the number 

and size of tubers were similar between the two. Vertical 

distribution of the tubers differed significantly, with most 

non-GM tubers being found in shallower soil (

Article 225 

Functional impact of transposable elements using 

bioinformatic analysis and a comparative genomic 

approach 

Mol Cells. 2010 Jul; 30(1):77-87. 

Kim DS, Huh JW, Kim YH, Park SJ, Chang KT * 



A dual coding event, which is the translation of different 

isoforms from a single gene, is one of the special patterns 

among the alternative splicing events. This is an important 

mechanism for the regulation of protein diversity in human 

and mouse genomes. Although the regulation for dual coding 

events has been characterized in a few genes, the individual 

mechanism remains unclear. Numerous studies have described 

the exonization of transposable elements, which is 

the splicing mediated insertion of transposable element sequence 

fragments into mature mRNAs. Therefore, in this 

study, we investigated the number of transposable element 

(TE)-derived dual coding genes in human, chimpanzee and 

mouse genomes. TE fusion exons appeared in the dual coding 

regions of 309 human genes. Functional protein domain alterations 

by TE-derived dual coding events were observed in 

129 human genes. Comparative TE-derived dual coding 

events were also analyzed in chimpanzee and mouse 

orthologs. Seventy chimpanzee orthologs had TE-derived 

dual coding events, but mouse orthologs did not have any 

TE-derived dual coding events. Taken together, our analyses 

listed the number of TE-derived dual coding genes which 

could be investigated by experimental analysis and suggested 

that TE-derived dual coding events were major sources for 

the functional diversity of human genes, but not mouse genes. 

PMID: 20652499 

Keywords: Alternative RNA splicing; Bioinformatics; 

Chimpanzee; Exon; Genomics; Nucleotide sequence; 

Species comparison; TE-derived dual coding genes; 

Transposable element; Transposon 

Article 226 

Alu-derived old world monkeys exonization event 

and experimental validation of the LEPR gene 

Mol Cells. 2010 Sep; 30(3):201-7. 

Huh JW, Kim YH, Kim DS, Park SJ, Lee SR, Kim SH, 

Kim E, Kim SU, Kim MS, Kim HS, Chang KT * 



The leptin receptor (LEPR) is a crucial regulatory protein 

that interacts with Leptin. In our analysis of LEPR, novel 

AluJb-derived alternative transcripts were identified in the 

genome of the rhesus monkey. In order to investigate the 

occurrence of AluJb-derived alternative transcripts and the 

mechanism underlying exonization events, we conducted 

analyses using a number of primate genomic DNAs and 

adipose RNAs of tissue and primary cells derived from the 

crab-eating monkey. Our results demonstrate that the AluJb 

element has been integrated into our common ancestor genome 

prior to the divergence of simians and prosimians. 

The lineage-specific exonization event of the LEPR gene 

in chimpanzees, orangutans, and Old World monkeys appear 

to have been accomplished via transition mutations of the 

5' splicing site (second position of C to T). However, in 

New World monkeys and prosimians, the AluJb-related LEPR 

transcript should be silenced by the additional transversion 

mutation (fourth position of T to G). The AluJb-related transcript 

of human LEPR should also be silenced by a mutation 

of 

the 5' splicing site (first position of G to A) and the 

insertion of one nucleotide sequence (minus fourth position 

of A). Our data suggests that lineage-specific exonization 

events should be determined by the combination event of 

the formation of splicing sites and protection against site-specific 

mutation pressures. These evolutionary mechanisms 

could be major sources for primate diversification. 

PMID: 20803091 

Keywords: Adipose tissue; Alternative RNA splicing; 

Alternative transcript; AluJb; Alu gene; Exonization 

event; Gene mutation; LEPR gene; Leptin receptor; 

Species comparison; Transposable elements 


Article 227 

Extracellular domain of V-set and immunoglobulin 

domain containing 1 (VSIG1) interacts 

with sertoli cell membrane protein, while its 

PDZ-binding motif forms a complex with ZO-1 

Mol Cells. 2010 Nov; 30(5):443-8. 

Kim E, Lee Y, Kim JS, Song BS, Kim SU, Huh JW, Lee 

SR, Kim SH, Hong Y, Chang KT * 



V-set and immunoglobulin domain containing 1 (VSIG1) 

is a newly discovered member of the junctional adhesion 

molecule (JAM) family; it is encoded by a gene located 

on human chromosome X and preferentially expressed in 

a variety of cancers in humans. Little is known about its 

physiological function. To determine the role(s) of VSIG1 

in mammalian spermatogenesis, we first generated a specific 

antibody against mouse VSIG1 and examined the presence 

and localization of the protein in tissues. RTRCR and Western 

blot analysis of the mouse tissues indicated that VSIG1 was 

specifically expressed in the testis. Furthermore, the results 

of our trypsinization and biotinylation assays strongly support 

the assumption that VSIG1 is localized on the testicular 

germ cell surface. In order to determine whether VSIG1 

is capable of participation in homotypic interactions, we 

performed a GST-pull down assay by using recombinant 

GST-fusion and Histagging proteins. The pull-down assay 

revealed that each GST-fusion Ig-like domain shows homotypic 

binding. We further show that mVSIG1 can adhere 

to the Sertoli cells through its first Ig-like domain. To identify 

the protein that interacted with cytoplasmic domain, we next 

performed co-immunoprecipitation analysis. This analysis 

showed that ZO-1, which is the central structural protein 

of the tight junction, is the binding partner of the cytoplasmic 

domain of mouse VSIG1. Our findings suggest that mouse 

VSIG1 interacts with Sertoli cells by heterophilic adhesion 

via its first Ig-like domain. In addition, its cytoplasmic domain 

is critical for binding to ZO-1. 

PMID:20957455 

Keywords: Adhesion molecules; Antigens, neoplasm; Cell 

Communication; Germ cells; JAM family; 

Membrane glycoproteins; Phosphoproteins; 

Sequence homology; Spermatogenesis; Tight 

junction; VSIG1 

Article 228 

KBH-A42, a histone deacetylase inhibitor, inhibits 

the growth of doxorubicin-resistant leukemia cells 

expressing P-glycoprotein 

Oncol Rep. 2010 Mar; 23(3):801-9. 

Kang MR, Lee K, Kang JS, Lee CW, Lee KH, Kim JH, 

Yang JW, Kim BG, Han G, Kang JS, Park SK * , Kim HM * 

* Correspondence: spark123@kribb.re.kr hwanmook@kribb.re.kr 


Multidrug resistance mediated by the drug efflux protein, 

P-glycoprotein (P-gp), is one of the principal mechanisms 

by which tumor cells escape the cell death induced by chemotherapeutic 

agents. In our previous study, we demonstrated 

that KBH-A42 [N-hydroxy-3-(2-oxo-1-(3-phenylpropyl)-1,2,5,6-tetrahydropyridin-3-yl)propanamide 

], a synthetic 

histone deacetylase inhibitor, effectively inhibited the 

growth of several human cancer cell lines. In this study, 

we attempted to determine whether KBH-A42 was also capable 

of inhibiting the growth of multidrug-resistant cells. 

Doxorubicin dose-dependently inhibited the growth of 

P-gp-negative K562 human leukemia cells, but did not show 

substantial inhibition on the growth of P-gp-positive 

K562/ADR cells even at 10 μM , the highest concentration 

of KBH-A42 used, which increased the acetylation of histones 

in these leukemia cells, dose-dependently and effectively 

inhibited the cell growth, regardless of the presence of P-gp 

in the cells. KBH-A42 mediated G0/G1 cell cycle arrest, 

probably as the result of the down-regulation of CDK2, CDK4 

and CDK6 and the up-regulation of p21WAF1. When the 

expression of p21WAF1 was ablated by a specific siRNA, 

the inhibition of cell growth by KBH-A42 was partly reduced 

in both cell lines. In addition to the cell cycle arrest, KBH-A42 

also induced apoptosis in these cells, which was accompanied 

by the activation of caspases, including caspase-9, caspase-8 

and caspase-3. The pan-caspase inhibitor, Z-VAD-fmk, partially 

blocked the cell death induced by KBH-A42. These 

results indicate that KBH-A42 induces cell cycle arrest and 

apoptosis via the up-regulation of p21WAF1 and caspase 

activation, respectively, regardless of the presence of P-gp 

in the leukemia cells. 

PMID: 20127023 

Keywords: Apoptosis; Caspase; Cell cycle arrest; Cell 

proliferation; Doxorubicin; Histone deacetylase 

inhibitor; K562 cells; p21 WAF1; P-Glycoprotein; 

Piperidones 


Article 229 

Glabridin inhibits lipopolysaccharide-induced activation 

of a microglial cell line, BV-2, by blocking 

NF-κB and AP-1 

Article 230 

The role of osteopontin in d-galactosamine-induced 

liver injury in genetically obese 

mice 

Phytother Res. 2010 Jan; 24(S1):S29-34. 

Toxicol Appl Pharmacol. 2010 Feb; 242(3):344-51. 

Park SH, Kang JS, Yoon YD, Lee K, Kim KJ, Lee KH, 

Lee CW, Moon EY, Han SB, Kim BH, Kim HM, Park 

SK * 

* Correspondence: spark123@kribb.re.kr 


Glabridin, a flavonoid present in licorice root, is known 

to have antiinflammatory and cardiovascular protective 

activities. The present study reports an inhibitory effect of 

glabridin on microglial activation. Glabridin dose-dependently 

attenuated lipopolysaccharide (LPS)-induced production 

of inflammatory mediators, including nitric oxide, 

tumor necrosis factor-α 

and interleukin-1 β, in BV-2 cells, 

a murine microglia cell line. Moreover, mRNA expression 

of these inflammatory mediators was also suppressed by 

glabridin in LPS-stimulated BV-2 cells. Further study demonstrated 

that glabridin inhibited LPS-induced DNA binding 

activity of NF-κB and AP-1 in BV-2 cells. Collectively, 

the results presented in this report demonstrate that glabridin 

inhibits the production of inflammatory mediators in BV-2 

cells and this is mediated, at least in part, by blocking NF-κ 

B 

and AP-1 activation. The results suggest that glabridin might 

be a potential therapeutic agent for the treatment of neuroinflammatory 

and neurodegenerative diseases. 

PMID:19455572 

Keywords: Glabridin; Interleukin-1 β; Isoflavones; 

Lipopolysaccharide; Microglia; NF-κ 

B; Nitric 

oxide; Transcription factor AP-1; Tumor necrosis 

factor-α 

Kwon HJ, Won YS, Yoon WK, Nam KH, Kim DY, Kim 

HC * 

* Correspondence: hckim@kribb.re.kr 


Various epidemiological studies have shown that obesity 

increases the risk of liver disease, but the precise mechanisms 

through which this occurs are poorly understood. In the present 

study, we hypothesized that osteopontin (OPN), an extracellular 

matrix and proinflammatory cytokine, has an important 

role in making obese mice more susceptible to inflammatory 

liver injury. After exposure of genetically obese 

ob/ob and db/db mice to a single dose of d-galactosamine 

(GalN), the plasma liver enzyme levels, histology and expression 

levels of cytokines and OPN were evaluated. The 

ob/ob and db/db mice, which were more sensitive to GalN-induced 

inflammatory liver injury compared with wild-type 

mice, had significantly higher plasma and hepatic OPN expression 

levels. Increased OPN expression was mainly found 

in hepatocytes and inflammatory cells and was correlated 

with markedly up-regulated interleukin (IL)-12 and IL-18 

levels. Furthermore, pretreatment with a neutralizing OPN 

(nOPN) antibody attenuated the GalN-induced inflammatory 

liver injury in ob/ob and db/db mice, which was accompanied 

by significantly reduced macrophages recruitment and IL-12 

and IL-18 productions. Taken together, these results suggest 

that up-regulated OPN expression is a contributing factor 

to increased susceptibility of genetically obese mice to 

GalN-induced liver injury by promoting inflammation and 

modulating immune response. 

PMID: 19913045 

Keywords: Cytokines; d-Galactosamine; Hepatocytes; 

Inflammation; Interleukin-12; Interleukin-18; Liver; 

Obese mice; Obesity; Osteopontin 


Article 231 

The role of vitamin D3 upregulated protein 1 in 

thioacetamide-induced mouse hepatotoxicity 

Toxicol Appl Pharmacol. 2010 Nov; 248(3):277-84. 

Kwon HJ, Lim JH, Han JT, Lee SB, Yoon WK, Nam KH, 

Choi IP, Kim DY, Won YS * , Kim HC * 

* Correspondence: yswon@kribb.re.kr hckim@kribb.re.kr 


Thioacetamide (TA) is a commonly used drug that can trigger 

acute hepatic failure (AHF) through generation of oxidative 

stress. Vitamin D3 upregulated protein 1 (VDUP1) is an 

endogenous inhibitor of thioredoxin, a ubiquitous thiol oxidoreductase, 

that regulates cellular redox status. In this study, 

we investigated the role of VDUP1 in AHF using a TA-induced 

liver injury model. VDUP1 knockout (KO) and 

wild-type (WT) mice were subjected to a single intraperitoneal 

TA injection, and various parameters of hepatic 

injury were assessed. VDUP1 KO mice displayed a significantly 

higher survival rate, lower serum alanine aminotransferase 

and aspartate aminotransferase levels, and less 

hepatic damage, compared to WT mice. In addition, induction 

of apoptosis was decreased in VDUP1 KO mice, with the 

alteration of caspase-3 and -9 activities, Bax-to-Bcl-2 expression 

ratios, and mitogen activated protein kinase (MAPK) 

signaling pathway. Importantly, analysis of TA bioactivation 

revealed lower plasma clearance of TA and covalent binding 

of [¹ ⁴C]TA to liver macromolecules in VDUP1 KO mice. 

Furthermore, the level of oxidative stress was significantly 

less in VDUP1 KO mice than in their WT counterparts, 

as evident from lipid peroxidation assay. These results collectively 

indicate that VDUP1 deficiency protects against TA-induced 

acute liver injury via lower bioactivation of TA and 

antioxidant effects. 

PMID: 20713078 

Keywords: Apoptosis; Carrier proteins; Hepatotoxicity; 

Oxidative stress; Thioacetamide; Thioredoxins; 

Vitamin D3 upregulated protein 1 



2010 




Jeonbuk Branch Institute 






www.kribb.re.kr

Article 232 

Activity assay for nisin-like acidic pacteriocins 

using an optimal pH-conditioned gel matrix 

Anal Biochem. 2010 Feb; 397(2):259-61. 

Choi NS, Jeong SY, Yang HJ, Ahn KH, Park CS, Kim 

CY, Kim JS, Yoon BD, Kim MS * 

* Correspondence: ms5732@kribb.re.kr 


A new zymography for detecting nisin-like acidic bacteriocins 

was developed using a tricine-sodium dodecyl sulfate 

(SDS) gel and an acidic gel matrix (pH 4.0). After electrophoresis, 

proteins in the tricine gel were electrotransferred 

to an optimal pH-conditioned gel matrix (OP-CGM). The 

OP-CGM was overlaid with indicator cells (Bacillus cereus) 

embedded in nutrient broth soft agar (0.8%, w/v). 

Antibacterial activity shown as a growth inhibition using 

B. cereus was detected at approximately 3.8kDa. Because 

nisin is unstable in buffers at pH values over 6.0, the common 

electrophoretic systems, SDS-polyacrylamide gel electrophoresis 

and tricine gel, are not suitable for detection of 

nisin-like acidic bacteriocins. 

PMID: 19799850 

Keywords: Bacillus cereus; Bacteriocins; Electrophoresis, 

polyacrylamide; Hydrogen-ion concentration; Nisin; 

Zymography 

Article 233 

Identification and utilization of a 1,3-propanediol 

oxidoreductase isoenzyme for production of 

1,3-propanediol from glycerol in Klebsiella pneumoniae 

Appl Microbiol Biotechnol. 2010 Jan; 85(3):659-66. 

Seo JW, Seo MY, Oh BR, Heo SY, Baek JO, Rairakhwada 

D, Luo LH, Hong WK, Kim CH * 

* Correspondence: kim3641@kribb.re.kr 


In a previous study, we showed that 1,3-propanediol (1,3-PD) 

was still produced from glycerol by the Klebsiella pneumoniae 

mutant strain defective in 1,3-PD oxidoreductase 

(DhaT), although the production level was lower compared 

to the parent strain. As a potential candidate for another 

putative 1,3-PD oxidoreductase, we identified and characterized 

a homolog of Escherichia coli yqhD (88% homology 

in amino acid sequence), which encodes an alcohol dehydrogenase 

and is well known to replace the function of 

DhaT in E. coli. Introduction of multiple copies of the yqhD 

homolog restored 1,3-PD production in the mutant K. pneumoniae 

strain defective in DhaT. In addition, by-product 

formation was still eliminated in the recombinant strain due 

to the elimination of the glycerol oxidative pathway. An 

increase in NADP-dependent 1,3-PD oxidoreductase activity 

was observed in the recombinant strain harboring multiple 

copies of the yqhD homolog. The level of 1,3-PD production 

during batch fermentation in the recombinant strain was comparable 

to that of the parent strain; further engineering can 

generate an industrial strain producing 1,3-propanediol. 

PMID: 19626321 

Keywords: 1,3-Propanediol oxidoreductase; Alcohol 

oxidoreductases; Biosynthetic pathways; 

Escherichia coli; Gene deletion; Glycerol 

metabolism; Klebsiella pneumoniae; Sequence 

homology 


Article 234 

Detection and molecular characterization of porcine 

toroviruses in Korea 

Article 235 

Xanthones with neuraminidase inhibitory activity 

from the seedcases of Garcinia mangostana 

Arch Virol. 2010 Mar; 155(3):417-22. 

Bioorg Med Chem. 2010 Sep; 18(17):6258-64. 

Shin DJ, Park SI, Jeong YJ, Hosmillo M, Kim HH, Kim 

HJ, Kwon HJ, Kang MI, Park SJ * , Cho KO 

Ryu HW, Curtis-Long MJ, Jung S, Jin YM, Cho JK, Ryu 

YB, Lee WS * , Park KH 

* Correspondence: sjpark@kribb.re.kr 


* Correspondence: wslee@kribb.re.kr 


This study examined the prevalence and genetic diversity 

of the porcine torovirus (PToV) in Korea. Of 295 samples, 

19 (6.4%) samples tested positive for PToVs by RT-PCR. 

A low nucleotide sequence identity of the partial S gene 

was detected among the Korean PToVs (73.5%) and between 

the Korean and European PToVs (74.0%). Phylogenetic analysis 

of the spike and nucleocapsid genes showed that the 

Korean PToVs form distinct branches with clusters corresponding 

to the farm of origin, which were separate from 

the other known foreign PToVs. These findings suggest that 

genetically diverse Korean PToV strains cause sporadic infections 

in Korea. 

PMID:20127374 

Keywords: Cluster analysis; Korea; Phylogeny; Prevalence; 

RNA, viral; Sequence analysis, DNA; Sequence 

homology, Swine diseases; Torovirus infections 

This study was designed to gain deeper insights into the 

molecular properties of natural xanthones as neuraminidase 

inhibitors. A series of xanthones 1-12 was isolated from 

the seedcases of Garcinia mangostana and evaluated for 

bacteria neuraminidase inhibitory activity. Compounds 11 

and 12 emerged to be new xanthones (mangostenone F, 

mangostenone G) which we fully spectroscopically 

characterized. The IC(50) values of compounds 1-12 were 

determined to range between 0.27-65.7 

μM . The most potent 

neuraminidase inhibitor 10 which has an IC(50) of 270 nM 

features a 5,8-diol moiety on the B ring. Interestingly, structure-activity 

studies reveal that these xanthones show different 

kinetic inhibition mechanisms depending upon the arrangement 

of hydroxyl groups in the B ring. Compound 

6 possessing a 6,7-diol motif on the B-ring operated under 

the enzyme isomerization model (k(5)=0.1144 

k(6)=0.001105 s(-1), and K(i)(app)=7.41 

μM (-1) s(-1), 

μM ), whereas com- 

pound 10 possessing a 5,8-diol unit displayed simple reversible 

slow-binding inhibition (k(3)=0.02294 

μM (-1) s(-1), 

k(4)=0.001025 s(-1), and K(i)(app)=0.04468 μM ). 

PMID:20696581 

Keywords: Enzyme inhibitors; Garcinia mangostana; 

Kinetics; Neuraminidase; Plant extracts; Seeds; 

Time-dependent; Xanthone 


Article 236 

In vitro anti-rotavirus activity of polyphenol compounds 

isolated from the roots of Glycyrrhiza uralensis 

Bioorg Med Chem. 2010 Nov; 18(21):7668-74. 

Kwon HJ, Kim HH, Ryu YB, Kim JH, Jeong HJ, Lee SW, 

Chang JS, Cho KO, Rho MC, Park SJ * , Lee WS * 

* Correspondence: sjpark@kribb.re.kr wslee@kribb.re.kr 


We evaluated the ability of six polyphenols isolated from 

the roots of Glycyrrhiza uralensis to inactivate rotaviruses, 

specially G5P[7] and G8P[7]. Upon finding that all polyphenols 

possessed anti-rotavirus activity, we evaluated 

whether these properties were attributable to direct inhibition 

of the binding of rotavirus to cells and/or to inhibition of 

viral replication. Using the virucidal assay, we found that 

all six compounds directly inhibited rotavirus binding, with 

activity being dependent on the type of virus. The 50% 

effective inhibitory concentrations (EC(50)) of the six compounds 

were 18.7-69.5 μM against G5P[7] and 14.7-88.1 

μM against G8P[7], respectively. Five of the six compounds 

inhibited hemagglutination activity. Moreover, the CPE inhibition 

assay showed that five compounds inhibited viral 

replication with EC(50) values of 12.1-24.0 

G5P[7] and 12.0-42.0 

μM against 

μM against G8P[7], respectively. 

RT-PCR showed that the compounds suppressed viral RNA 

synthesis in TF-104 cells. Interestingly, the anti-rotavirus 

activities of four compounds were attributable to inhibition 

of both viral absorption and viral replication. These results 

suggest that compounds isolated from the roots of G. uralensis 

may be potent anti-rotavirus agents in vivo, acting 

by inhibiting both viral absorption and viral replication. 

PMID: 20850329 

Keywords: Anti-rotavirus; Antiviral agents; Cattle; 

Flavonoids; Glycyrrhiza uralensis; Hemagglutinin; 

Macaca mulatta; Plant roots; Viral absorption; Viral 

replication 

Article 237 

Biflavonoids from Torreya nucifera displaying 

SARS-CoV 3CL(pro) inhibition 

Bioorg Med Chem. 2010 Nov; 18(22):7940-7. 

Ryu YB, Jeong HJ, Kim JH, Kim YM, Park JY, Kim D, 

Nguyen TT, Park SJ, Chang JS, Park KH, Rho MC * , Lee 

WS * 

* Correspondence: rho-m@kribb.re.kr wslee@kribb.re.kr 


As part of our search for botanical sources of SARS-CoV 

3CL(pro) inhibitors, we selected Torreya nucifera, which 

is traditionally used as a medicinal plant in Asia. The ethanol 

extract of T. nucifera leaves exhibited good SARS-CoV 

3CL(pro) inhibitory activity (62% at 100μg/mL). Following 

bioactivity-guided fractionation, eight diterpenoids (1-8) and 

four biflavonoids (9-12) were isolated and evaluated for 

SARS-CoV 3CL(pro) inhibition using fluorescence resonance 

energy transfer analysis. Of these compounds, the 

biflavone amentoflavone (9) (IC(50)=8.3μM) showed most 

potent 3CL(pro) inhibitory effect. Three additional authentic 

flavones (apigenin, luteolin and quercetin) were tested to 

establish the basic structure-activity relationship of 

biflavones. Apigenin, luteolin, and quercetin inhibited 

3CL(pro) activity with IC(50) values of 280.8, 20.2, and 

23.8μM, respectively. Values of binding energy obtained 

in a molecular docking study supported the results of enzymatic 

assays. More potent activity appeared to be associated 

with the presence of an apigenin moiety at position C-3' 

of flavones, as biflavone had an effect on 3CL(pro) inhibitory 

activity. 

PMID: 20934345 

Keywords: Amentoflavone; Apigenin; Biflavonoid; 

Cysteine endopeptidases; Luteolin; Plant leaves; 

Protease inhibitors; Quercetin; SARS-CoV 3CLpro; 

SARS virus; Taxaceae; Torreya nucif; Viral proteins 


Article 238 

Inhibition of neuraminidase activity by polyphenol 

compounds isolated from the roots of 

Glycyrrhiza uralensis 

Article 239 

SARS-CoV 3CLpro inhibitory effects of quinone-methide 

triterpenes from Tripterygium regelii 

Bioorg Med Chem Lett. 2010 Feb; 20(3):971-4. 

Bioorg Med Chem Lett. 2010 Mar; 20(6):1873-6. 

Ryu YB, Kim JH, Park SJ, Chang JS, Rho MC, Bae KH, 

Park KH, Lee WS * 

Ryu YB, Park SJ, Kim YM, Lee JY, Seo WD, Chang JS, 

Park KH, Rho MC * , Lee WS * 

* Correspondence: wslee@kribb.re.kr 


* Correspondence: rho-m@kribb.re.kr wslee@kribb.re.kr 


We isolated 18 polyphenols with neuraminidase inhibitory 

activity from methanol extracts of the roots of Glycyrrhiza 

uralensis. These polyphenols consisted of four chalcones 

(1-4), nine flavonoids (5-13), four coumarins (14-17), and 

one phenylbenzofuran (18). When we tested the effects of 

these individual compounds and analogs thereof on neuraminidase 

activation, we found that isoliquiritigenin (1, 

IC(50)=9.0 μM ) and glycyrol (14, IC(50)=3.1 μM ) had 

strong inhibitory activity. Structure-activity analysis showed 

that the furan rings of the polyphenols were essential for 

neuraminidase inhibitory activity, and that this activity was 

enhanced by the apioside group on the chalcone and flavanone 

backbone. In addition, the presence of a five-membered 

ring between C-4 and C-2' in coumestan was critical for 

neuraminidase inhibition. All neuraminidase inhibitors 

screened were found to be reversible noncompetitive 

inhibitors. 

PMID: 20064716 

Keywords: Anti-influenza; Coumestan; Enzyme activation; 

Flavonoids; Glycyrrhiza uralensis; Neuraminidase; 

Plant extracts; Plant roots 

Quinone-methide triterpenes, celastrol (1), pristimerin (2), 

tingenone (3), and iguesterin (4) were isolated from 

Triterygium regelii and dihydrocelastrol (5) was synthesized 

by hydrogenation under palladium catalyst. Isolated quinone-methide 

triterpenes (1-4) and 5 were evaluated for 

SARS-CoV 3CL(pro) inhibitory activities and showed potent 

inhibitory activities with IC(50) values of 10.3, 5.5, 9.9, 

and 2.6 

μM , respectively, whereas the corresponding 5 hav- 

ing phenol moiety was observed in low activity (IC(50)=21.7 

μM ). As a result, quinone-methide moiety in A-ring and 

more hydrophobic E-ring assist to exhibit potent activity. 

Also, all quinone-methide triterpenes 1-4 have proven to 

be competitive by the kinetic analysis. 

PMID: 20167482 

Keywords: 3CLpro; Antiviral agents; Benzoquinones; 

Celastrol; Iguesterin; Plant extracts; 

Quinone-methide; SARS-CoV; SARS virus; 

Tripterygium regelii; Triterpenes 


Article 240 

Production of pure 

β-glucan by 

Aureobasidium 

pullulans after pullulan synthetase gene disruption 

Biotechnol Lett. 2010 Jan; 32(1):137-42. 

Kang BK, Yang HJ, Choi NS, Ahn KH, Park CS, Yoon 

BD, Kim MS * 

* Correspondence: ms5732@kribb.re.kr 


By disruption of the pullulan synthetase gene (pul) of 

Aureobasidium pullulans IMS822 KCTC11179BP, we constructed 

a mutant strain, A. pullulans NP1221, which produced 

a pure 

β-glucan exopolysaccharide. The mutant 

NP1221 was white, whereas the wild-type strain produced 

a black dye. When we compared fermentation kinetics between 

wide-type and mutant strains, the mutant NP1221 

did not produce pullulan. Substrate uptake rate and 

β-glucan 

production were similar in both strains. However, the biomass 

yield of mutant NP1221 was 2.3-fold (9.2 g l(-1)) greater 

than that of wild-type. 

PMID: 19760116 

Keywords: β-Glucan; Ascomycota; 

Aureobasidium 

pullulans; Fermentation; Fungal proteins; Glucans; 

Homologous recombination; Kinetics; Pullulan 

Article 241 

Enhanced production of ethanol from glycerol by 

engineered Hansenula polymorpha expressing 

pyruvate decarboxylase and aldehyde dehydrogenase 

genes from Zymomonas mobilis 

Biotechnol Lett. 2010 Aug; 32(8):1077-82. 

Hong WK, Kim CH, Heo SY, Luo LH, Oh BR, Seo JW * 

* Correspondence: jwseo@kribb.re.kr 


To improve production of ethanol from glycerol, the methylotrophic 

yeast Hansenula polymorpha was engineered to express 

the pdc and adhB genes encoding pyruvate decarboxylase 

and aldehyde dehydrogenase II from Zymomonas 

mobilis, respectively, under the control of the glyceraldehyde-3-phosphate 

dehydrogenase (GAPDH) promoter. 

The ethanol yield was 3.3-fold higher (2.74 g l(-1)) in the 

engineered yeast compared with the parent strain (0.83 g 

l(-1)). Further engineering to stimulate glycerol utilization 

in the recombinant strain via expression of dhaD and dhaKLM 

genes from Klebsiella pneumoniae encoding glycerol dehydrogenase 

and dehydroxyacetone kinase, respectively, resulted 

in a 3.7-fold increase (3.1 g l(-1)) in ethanol yield. 

PMID: 20354759 

Keywords: Aldehyde dehydrogenase II; Ethanol 

production; Glycerol; Hansenula polymorpha; 

Pichia; Plasmids; Pyruvate decarboxylase; 

Zymomonas mobilis 


Article 242 

Quinolone alkaloids from Evodiae fructus inhibit 

LFA-1/ICAM-1-mediated cell adhesion 

Article 243 

Alkamides from Piper longum and Piper nigrum 

as inhibitors of IL-6 action 

Bull Kor Chem Soc. 2010 Jan; 31(1):64-8. 

Bull Kor Chem Soc. 2010 Apr; 31(4):921-4. 

Lee SW, Chang JS, Lim JH, Kim MS, Park SJ, Jeong HJ, 

Kim MS, Lee WS * , Rho MC * 

Lee SW, Kim MS, Park MH, Park SJ, Lee WS, Chang 

JS * , Rho MC * 

* Correspondence: wslee@kribb.re.kr rho-m@kribb.re.kr 


* Correspondence: rho-m@kribb.re.kr 


Four quinolone alkaloids were isolated by bioactivity-guided 

fractionation from the methanol extracts of Evodiae fructus 

fruits. Structures of compounds were elucidated by spectroscopic 

analysis (1H-, 13C-NMR and MS), as follows: 1-methyl-2-undecyl-4(1H)-quinolone 

(1), evocarpine (2), dihydroevocarpine 

(3) and mixture of [1-methyl-2-[(Z)-10- pentadecenyl]-4(1H)- 

quinolone and 1-methyl-2-[(Z)-6-pentadecenyl]-4(1H)-quinolone] 

(4). They inhibited 

the interaction of sICAM-1 and LFA-1 in THP-1 

cells at IC50 values of >150 (1), 109.8 (2), >150 (3) and 

40.9 μM (4), respectively. 

Keywords: Cell adhesion molecules; Evodiae fructus; 

Methanol extract; Quinolone alkaloid; Rutaceae; 

THP-1 cells 

Blocking of IL-6 has been postulated to be an effective 

therapy in the pathogenesis of several inflammatory diseases. 

The current study was performed to examine the potential 

effects of alkamides isolated from P. longum and P. nigrum 

on IL-6 induced Stat3 activation and identify the structure-activity 

relationship of these alkamides in human hepatoma 

cells. Among 10 alkamides isolated from P. longum and 

P. nigrum, compounds 6, 7 and 9 were identified as strong 

inhibitors of IL-6 action, which inhibit IL-6 induced 

Stat3-dependent luciferase activities. These inhibitory activities 

were positively influenced by the presence of piperidine 

moiety. 

Keywords: Alkamides; Human hepatoma cells; 

Inflammatory disease; Inhibitory activity; 

Interleukin-6; Luciferase activities; Piper longum; 

Piper nigrum; Stat3 


Article 244 

Inhibition of VLA-4/VCAM-1-mediated cell adhesion 

by triterpenoid saponins from Bupleurum 

falcatum L 

Article 245 

Jeongeupia naejangsanensis gen. nov., sp. nov., 

a cellulose-degrading bacterium isolated from forest 

soil from Naejang Mountain in Korea 


Int J Syst Evol Microbiol. 2010 Mar; 60(3):615-9. 

Lee SW, Kim MS, Lim JH , Chang JS, Ling J, Bae KH, 

Lee WS * , Rho MC * 



Discovery and isolation of compounds capable of blocking 

the interactions between VCAM-1 and VLA-4, a major pair 

of adhesion molecules contributing to the different steps 

of leukocyte migration across the endothelium in inflammatory 

responses, has been a major goal of this lab. 

Through bioactivity-guided fractionation, five saikosaponins 

were subsequently isolated from the methanol extracts of 

the roots of Bupleurum falcatum L. Their structures were 

elucidated by spectroscopic analysis (1H-, 13C-NMR and 

2D-NMR), as follows, saikosaponins: A (1); D (2); C (3); 

B3 (4); B4 (5). Compounds 1 and 2 inhibited interaction 

of sVCAM-1 and VLA-4 of THP-1 cells with respective 

IC50 values of 7.8 and 1.7 

μM. The aglycone structure of 

2 also showed cell adhesion inhibitory activity with an IC50 

value of 21.1 

μM. With these results, we suspect these two 

saikosaponins from the Bupleurum falcatum L. roots to be 

prime candidates for therapeutic strategies towards 

inflammation. 

Keywords: Adhesion molecules; Bupleurum falcatum L; 

Inflammatory response; Saikosaponins; Triterpenoid 

saponins; Vascular cell adhesion molecule-1 

(VCAM-1); Very late antigen-4 (VLA-4); 

Umbelliferae 

Yoon JH, Choi JH, Kang SJ, Choi NS, Lee JS, Song JJ * 

* Correspondence: jjsong@kribb.re.kr 


A Gram-stain-negative, motile, rod-shaped, cellulose-degrading 

bacterial strain, BIO-TAS4-2 T , which belongs to 

the Betaproteobacteria, was isolated from forest soil from 

Naejang Mountain, Korea, and its taxonomic position was 

investigated by using a polyphasic study. Strain 

BIO-TAS4-2 T grew optimally at pH 7.0-8.0, at 30 degrees 

C and in the presence of 0-1.0 % (w/v) NaCl. Phylogenetic 

trees based on 16S rRNA gene sequences showed that strain 

BIO-TAS4-2 T clustered with members of the genera 

Andreprevotia, Silvimonas and Deefgea of the family 

Neisseriaceae, with which it exhibited 16S rRNA gene sequence 

similarities of 93.5-94.2 %. Strain BIO-TAS4-2 T contained 

Q-8 as the predominant ubiquinone and summed feature 

3 (C(16 : 1) ω7c and/or iso-C(15 : 0) 2-OH) and C(16 

: 0) as the major fatty acids. The DNA G+C content was 

63.8 mol%. Strain BIO-TAS4-2 T could be differentiated from 

members of phylogenetically related genera by differences 

in fatty acid composition, DNA G+C content and some phenotypic 

properties. On the basis of phenotypic, chemotaxonomic 

and phylogenetic data, strain BIO-TAS4-2 T is 

considered to represent a novel species in a new genus, 

for which the name Jeongeupia naejangsanensis gen. nov., 

sp. nov. is proposed, with BIO-TAS4-2 T (=KCTC 

22633 T =CCUG 57610 T ) as the type strain. 

PMID: 19654346 

Keywords: Betaproteobacteria; Cellulose; DNA, bacterial; 

DNA, ribosomal; Fatty acids; Korea; Molecular 


Soil microbiology 


Article 246 

Gene cloning, characterization, and heterologous 

expression of levansucrase from Bacillus amyloliquefaciens 

Article 247 

Expression and characterization of a novel deoxyribose 

5-phosphate aldolase from Paenibacillus 

sp. EA001 

J Ind Microbiol Biotechnol. 2010 Feb; 37(2):195-204. 

J Microbiol Biotechnol. 2010 Jun; 20(6):995-1000. 

Rairakhwada D, Seo JW, Seo MY, Kwon O, Rhee SK, Kim 

CH * 

Kim YM, Choi NS, Kim YO, Son DH, Chang YH, Song 

JJ, Kim JS * 



* Correspondence: joongsu@kribb.re.kr 


Although levan produced by Bacillus amyloliquefaciens is 

known to have efficient immunostimulant property which 

gives 100% survival of common carp when infected with 

Aeromonas hydrophila, no detailed reports are available describing 

kinetic studies of D: -glucose production and levan 

formation. In this study, we cloned and characterized the 

enzymatic kinetics using levansucrase expressed in 

Escherichia coli. Optimum pH for D: -glucose production 

and levan formation was 6.0 and 8.0, respectively, whereas 

optimum temperature was 30 degrees C and 4 degrees C, 

respectively. The K (m) and V (max) values for levansucrase 

were calculated to be 47.81 

μM sucrose and 57.47 1mole/min 

mg protein, respectively. Prominent expression of levansucrase 

was obtained through xylose induction in Bacillus megaterium, 

where most of the His(6)-tagged protein was secreted 

into the culture broth, giving levansucrase activity 

of 12,906 U/l. Response-surface methodology (RSM) was 

further employed to optimize the fermentation conditions 

and improve the level of levansucrase production. Maximum 

levansucrase activity of 20,251 U/l was obtained in 12 h 

of fermentation carried out at 28 degrees C, starting induction 

with 0.735% xylose when A (600) was 1.2, which was 1.6- 

and 62-fold higher than those obtained in the nonoptimized 

conditions for the recombinant strain and the native strain, 

respectively. 

PMID: 19916084 

A novel deoC gene was identified from Paenibacillus sp. 

EA001 isolated from soil. The gene had an open reading 

frame (ORF) of 663 base pairs encoding 220 amino acids 

with a molecular mass of 24.5 kDa. The amino acid sequence 

was 79 % identical to that of deoxyribose 5-phosphate aldolase 

(DERA) from Geobacillus sp. Y412MC10. The deoC 

gene encoding DERA was cloned into expression vector 

and the protein was expressed in Escherichia coli. The recombinant 

DERA was purified by using Ni-NTA affinity 

chromatography and characterized. The optimum temperature 

and pH for DERA were 50 degrees C and 6.0, 

respectively. The specific activity for deoxyribose 5-phosphate 

(DR5P), substrate, was 62 micronmol/min/mg. The 

Km value for DR5P was determined to be 145 

μM with 

the Kcat value of 3.2 times 10(2 /sec) from Lineweaver-Burk 

plots. The EA001 DERA showed stability toward a high 

concentration of acetaldehyde (100 mM). 

PMID: 20622498 

Keywords: Acetaldehyde; Aldehyde-lyases; Bacterial 

proteins; Deoxyribose 5-phosphate aldolase; 

Kinetics; Paenibacillus sp.; Phylogeny; Sequence 

homology, Soil microbiology 

Keywords: Bacillus amyloliquefaciens type 1; Bacillus 

megaterium; Bacterial proteins; Escherichia coli; 

Fructans; Gene expression; Hexosyltransferases; 

Levansucrase; Response-surface methodology 


Article 248 

Melanogenesis inhibitory effect of dehydroevodiamine 

isolated from fruits of Evodia rutaecarpa 

Article 249 

Purification and characterization of a novel glucansucrase 

from Leuconostoc lactis EG001 

Kor J Chem Eng. 2010; 27(3):915-8. 

Microbiol Res. 2010 Jul; 165(5):384-91. 

Luo LH, Seo JW, Nguyen DH, Kim EK, Kang SA, Kim 

DH, Kim CH * 

Kim YM, Yeon MJ, Choi NS, Chang YH, Jung MY, Song 

JJ, Kim JS * 



* Correspondence: joongsu@kribb.re.kr 


Dehydroevodiamine, an alkaloid, was isolated from the fruit 

of Evodia rutaecarpa and melanin production, and tyrosinase 

inhibition in B16F10 melanoma cells treated with the isolated 

dehydroevodiamine was investigated. The compound decreased 

melanin synthesis significantly without promoting 

cytotoxicity. The IC50 value of dehydroevodiamine for melanogenesis 

and cell viability were 59.8 μM and 90.0 μM, 

respectively. The L-dopa oxidase activity of mushroom tyrosinase 

was reduced after dehydroevodiamine treatment by 

about 22.4% at a concentration of 33.2 

μM. However, there 

was no effect on cellular tyrosinase activity. These results 

indicate that the observed decrease in melanin content after 

treatment with dehydroevodiamine was attributed to the direct 

inhibition of tyrosinase activity, rather than the suppression 

of tyrosinase gene expression. Dehydroevodiamine 

may be a promising new agent for use in cosmeceutical 

application. 

Keywords: Cosmeceutical; Dehydroevodiamine; Evodia 

rutaecarpa; Melanogenesis; Skin whitening; 

Tyrosinase 

A gene encoding glucansucrase was identified in Leuconostoc 

lactis EG001 isolated from lactic acid bacteria (LAB) in 

Kimchi, a traditional Korean fermented food. The L. lactis 

EG001 glucansucrase gene consists of 4503 bp open reading 

frame (ORF) and encodes an enzyme of 1500 amino acids 

with an apparent molecular mass of 165 kDa. The deduced 

amino-acid sequence showed the highest amino-acid sequence 

identity (75%) to that of dextransucrase of L. 

mesenteroides. The gene was cloned and over-expressed in 

Escherichia coli strain. The recombinant enzyme was purified 

via Ni-NTA affinity chromatography and its enzymatic properties 

were characterized. The enzyme exhibited optimum 

activity at 30 degrees C and pH 5.0. In addition, the enzyme 

was able to catalyze the glycosylation of l-ascorbic acid 

to l-ascorbic acid 2-glucoside. The glycosylated product via 

EG001 glucansucrase has the potential as an antioxidant 

in industrial applications. 

PMID: 19853426 

Keywords: Glucansucrase; Glycosylation; 

Glycosyltransferases; L-ascorbic acid 2-glucoside; 

Leuconostoc; Phylogeny 


Article 250 

Kansuinine A and Kansuinine B from Euphorbia 

kansui L. inhibit IL-6-induced Stat3 activation 

Article 251 

Detection and genotyping of Korean porcine rotaviruses 

Planta Med. 2010 Oct; 76(14):1544-9. 

Vet Microbiol. 2010 Aug; 144(3-4):274-86. 

Chang JS, Lee SW, Park MH, Kim MS, Hudson BI, Park 

SJ, Lee WS * , Rho MC * 

Kim HJ, Park SI, Ha TP, Jeong YJ, Kim HH, Kwon HJ, 

Kang MI, Cho KO, Park SJ * 



* Correspondence: sjpark@kribb.re.kr 


The current study was performed to examine the mechanisms 

underlying the potential effects of E. kansui on IL-6-induced 

cellular signaling in human hepatoma cells. We found that 

two diterpenoids, kansuinine A and B, from E. kansui have 

an inhibitory effect on IL-6-induced Stat3 activation by activating 

ERK1/2. Inhibition of MEK significantly blocked the 

effects of kansuinine A and B on IL-6-induced Stat3 activation 

and tyrosine phosphorylation. These results suggest that 

blocking of IL-6-induced signal transduction is partially due 

to the sustained activation of ERK1/2 by kansuinine A and 

B, which in turn results in an increase of Stat3 serine phosphorylation 

and SOCS-3 expression. Treatment with kansuinine 

A and B represents a novel method to block these 

IL-6-induced effects. 

PMID: 20379953 

Keywords: Diterpenes; ERK1/2; Euphorbia kansui Liou; 

Euphorbiaceae; IL6; Kansuinine A; Kansuinine B; 

Phosphorylation; Signal transduction; Stat3 

transcription factor 

Porcine group A rotavirus (GARV) is considered to be an 

important animal pathogen due to their economic impact 

in the swine industry and its potential to cause heterologous 

infections in humans. This study examined 475 fecal samples 

from 143 farms located in 6 provinces across South Korea. 

RT-PCR and nested PCR utilizing primer pairs specific for 

the GARV VP6 gene detected GARV-positive reactions in 

182 (38.3%) diarrheic fecal samples. A total of 98 porcine 

GARV strains isolated from the GARV-positive feces were 

analyzed for G and P genotyping. Based on the sequence 

and phylogenetic analyses, the most predominant combination 

of G and P genotypes was G5P[7], found in 63 GARV 

strains (64.3%). The other combinations of G and P genotypes 

were G8P[7] (16 strains [16.3%]), G9P[7] (7 strains [7.1%]), 

G9P[23] (2 strains [2.0%]), and G8P[1] (1 strain [1.0%]). 

The counterparts of G or P genotypes were not determined 

in three G5, five P[7], and one P[1] strains. Interestingly, 

phylogenetic analysis indicated that all Korean G9 strains 

were more closely related to lineage VI porcine and human 

viruses than to other lineages (I-V) of GARVs and to Korean 

human G9 strains (lineage III). These results show that porcine 

GARV infections are common in diarrheic piglets in 

South Korea. The infecting strains are genetically diverse, 

and include homologous (G5P[7]), heterologous (G8P[1]), 

and reassortant (G8P[7]), as well as emerging G9 GARV 

strains. 

PMID:20359834 

Keywords: Antigens, viral; Capsid proteins; Feces; Genetic 

diversity; Genotype; Korea; Phylogeny; Prevalence; 

Reassortant; Rotavirus infections; Swine diseases 


Article 252 

In vitro inhibitory activity of Alpinia katsumadai 

extracts against influenza virus infection and hemagglutination 

Virol J. 2010 Nov; 7:307. 

Kwon HJ, Kim HH, Yoon SY, Ryu YB, Chang JS, Cho 

KO, Rho MC, Park SJ * , Lee WS * 

* Correspondence: sjpark@kribb.re.kr wslee@kribb.re.kr 


BACKGROUND: Alpinia katsumadai (AK) extracts and 

fractions were tested for in vitro antiviral activities against 

influenza virus type A, specially human A/PR/8/34 (H1N1) 

and avian A/Chicken/Korea/MS96/96 (H9N2), by means of 

time-of-addition experiments; pre-treatment, simultaneous 

treatment, and post treatment. 

RESULTS: In pre-treatment assay, the AK extracts and AK 

fractions did not show significant antiviral activity. During 

the simultaneous treatment assay, one AK extract and five 

AK fractions designated as AK-1 to AK-3, AK-5, AK-10, 

and AK-11 showed complete inhibition of virus infectivity 

against A/PR/8/34 (H1N1) and A/Chicken/Korea/MS96/96 

(H9N2). The 50% effective inhibitory concentrations (EC ₅₀) 

of these one AK extracts and five AK fractions with exception 

of the AK-9 were from 0.8 ± 1.4 to 16.4 ± 4.5 μg/mL 

against A/PR/8/34 (H1N1). The two AK extracts and three 

AK fractions had EC₅₀ 

values ranging from


2010 




Indexes 


Journal Index 

Keyword Index 



www.kribb.re.kr


Author 

Article No 

Ahn JS (Jong Seog Ahn) 185, 209 

Ahn KS (Kyung Seop Ahn) 182, 195, 196 

Bae JW (Jin-Woo Bae) 152, 157 

Bae KH (Kwang-Hee Bae) 24, 48, 58, 61 

Bhak J (Jong Bhak) 143 

Chang KT (Kyu Tae Chang) 211-213, 215, 216, 

218, 219, 222, 

225-227 

Chang YH (Young-Hyo Chang) 158, 165 

Chi SW (Seung-Wook Chi) 37 

Chin YW (Young-Won Chin) 208 

Cho EW (Eun Wie Cho) 135, 140 

Cho HS (Hye Sun Cho) 81 

Cho YS (Yeesook Cho) 67 

Choi ES (Eui Sung Choi) 123 

Choi I (Inpyo Choi) 177, 188, 189, 197, 

198 

Choi SK (Soo Keun Choi) 112 

Chu IS (In-Sun Chu) 139, 141 

Chung BH (Bong Hyun Chung) 1, 5, 6, 10, 16, 19, 25, 

28, 29 

Chung IS (Im Sik Chung) 23 

Chung KS (Kyung Sook Chung) 35 

Chung SJ (Sang Jeon Chung) 11, 22, 24 

Ha TH (Tai-Hwan Ha) 9 

Han DC (Dong Cho Han) 44 

Hoe KL (Kwang Lae Hoe) 21 

Hong YS (Young-Soo Hong) 172, 201, 210 

Hur CG (Cheol-Goo Hur) 133 

Hyun BH (Byung Hwa Hyun) 151, 164 

Im DS (Dong Soo Im) 59 

Jeong H (Haeyoung Jeong) 116 

Jeong SC (Soon Chun Jeong) 220 

Jeong TS (Tae Sook Jeong) 72, 117 

Jeong WJ (Won Joong Chung) 130, 132, 134 

Jung Y (Yongwon Jung) 2 

Kang YK (Yong Kook Kang) 54, 56, 57 

Kim BC (Byoung Chan Kim) 144 

Kim CG (Chang-Gi Kim) 223 

Kim CH (Chul Ho Kim) 233, 246, 248 

Kim CJ (Chang-Jin Kim) 155, 160 

Kim HC (Hyoung-Chin Kim) 198, 230, 231 

Kim HM (Hwan Mook Kim) 217, 224, 228 

Kim HS (Hee Sik Kim) 80, 121 

Kim HS (Hyun Soon Kim) 84, 134 

Kim JF (Jihyun F Kim) 69, 70, 110 

Kim JS (Joong Su Kim) 247, 249 

Kim JW (Jae Wha Kim) 38 

Kim M ((Moonil Kim) 1, 26 

Kim MG (Min-Gon Kim) 7, 20, 22 

Kim MH (Myung Hee Kim) 111 

Kim MS (Min Soo Kim) 232, 240 

Kim S (Semi Kim) 184 

Kim SG (Song-Gun Kim ) 145, 154, 156 

Kim SH (Seung Ho Kim) 52, 60 

Kim SJ (Seung Jun Kim) 50 

Kim SU (Sung Uk Kim) 74, 106, 118, 120 

Kim SW (Suk Weon Kim) 168 

Kim SY (Seon-Young Kim) 55 

Kim WG (Won Gon Kim) 78, 86, 115, 119 

Kim YK (Young Kook Kim) 170 

Kim YS (Yong Sung Kim) 42, 45, 47, 55 

Koh SS (Sang Seok Koh) 183, 190, 206 

Koo DB (Deog Bon Koo) 66 

Kwak SS (Sang Soo Kwak) 83, 127, 128 

Kwak YS (Young Shin Kwak) 187 

Kwon BM (Byoung-Mog Kwon) 33, 43 

Kwon DH (Dur Han Kwon) 186, 202, 205 

Kwon KS (Ki Sun Kwon) 12 

Kwon O (Ohsuk Kwon) 3, 4, 14 

Kwon SY (Suk Yoon Kwon) 71, 114 

Lee B (ByungUk Lee) 136 

Lee CH (Chul Ho Lee) 147, 148, 166, 174 

Lee DS (Dae Sil Lee) 87 

Lee HG (Hee Gu Lee) 41, 46, 51 

Lee HK (Hyeong Kyu Lee) 178, 179 

Lee HS (Heang Soon Lee) 82, 129 


Lee HS (Hyun Sun Lee) 174 

Lee J (Joongku Lee) 142 

Lee JJ (Jung Joon Lee) 173, 194, 203, 204, 

207 

Lee JS (Jung-Sook Lee) 153, 159, 161, 162 

Lee K (Kiho Lee) 214 

Lee S (Sangku Lee) 44 

Lee SC (Sang Chul Lee) 63 

Lee WS (Woo Song Lee) 235-239, 242, 244, 

250, 252 

Lee YI (Young Ik Lee) 73 

Oh HM (Hee-Mock Oh) 76, 77, 79, 85, 108, 

122, 125 

Oh HW (Hyun Woo Oh) 113 

Oh SR (Sei Ryang Oh) 180, 181, 192, 193 

Pan JG (Jae Gu Pan) 107 

Park BC (Byoung Chul Park) 36, 49 

Park HS (Hong-Seog Park) 81, 149, 150, 163, 167, 

169 

Park HY (Ho Yong Park) 75, 124 

Park JM (Jeong Mee Park) 131 

Park KC (Kyung Chan Park) 34 

Park SG (Sung Goo Park) 37, 48 

Park SH (Seung Hwan Park) 109 

Park SJ (Su-Jin Park) 234, 236, 251, 252 

Park SK (Song Kyu Park) 221, 228, 229 

Park SS (Sung Sup Park) 8, 12 

Park YW (Young Woo Park) 15 

Poo H (Haryoung Poo) 137, 138 

Rho MC (Mun Chual Rho) 237, 239, 242-244, 250 

Ryu CM (Choong-Min Ryu) 101, 126 

Seo JW (Jeong-Woo Seo) 241 

Shin KS (Kee Sun Shin) 146 

Shin YB (Yong Beom Shin) 7, 17, 27 

Sohn JH (Jung Hoon Sohn) 68 

Son KH (Kwang Hee Son) 75 

Song EY (Eun Young Song) 46 

Song JJ (Jae Jun Song) 245 

Won M (Misun Won) 39, 41 

Won YS (Young Suk Won) 231 

Woo EJ (Eui-Jeon Woo) 32, 62, 64, 65 

Yeom YI (Young Il Yeom) 34, 40, 53 

Yoo ID (Ick Dong Yoo) 171, 175, 176, 191, 

199, 200 

Yoon JH (Jung-Hoon Yoon) 88-100, 102-105 

Yoon SR (Suk Ran Yoon) 189 

Yu DY (Dae Yeul Yu) 18, 30, 31 

Yu K (Kweon Yu) 13 


Journal Index 

Journal 

Article No 

Anal Biochem 68, 232 

Anal Chim Acta 1 

Analyst 32 

Angew Chem Int Ed Engl 2 

Anim Reprod Sci 211 

Animal Cell System 212 

Appl Environ Microbiol 69, 144, 145 

Appl Microbiol Biotechnol 3, 4, 70, 233 

Arch Pharm Res 33, 170-172 

Arch Virol 234 

Biochem Biophys Res Commun 34-38, 71, 135, 173, 

213 

Biochem Pharmacol 39 

Biol Pharm Bull 72, 174 

Biomaterials 5, 40 

Biomed Pharmacother 73 

Biomol Therap 175 

Bioorg Med Chem 235-237 

Bioorg Med Chem Lett 74, 176, 214, 238, 239 

Bioprocess Biosyst Eng 6 

Bioresour Technol 75-77 

Biosci Biotechnol Biochem 78 

Biosens Bioelectron 7 

Biotechnol Lett 79, 80, 240, 241 

BMB Rep 41, 42 

BMC Genomics 136, 215 

BMC Plant Biol 81 

Bone Marrow Transplant 177 

Br J Haematol 178 

Br J Pharmacol 43 

Brain Res 8 

Bull Kor Chem Soc 44, 179-182, 242-244 

Cancer Gene Ther 183 

Cancer Immunol Immunother 137 

Cancer Sci 45, 46 

Carbohydr Res 82 

Carcinogenesis 47, 184, 185 

Cell Mol Life Sci 48 

Cell Prolif 138 

Chem Commun (Camb) 9, 10 

Chemistry 11 

Chemosphere 83 

Clin Vaccine Immunol 84 

Exp Cell Res 12 

Exp Mol Med 49 

FASEB J 50 

FEBS Lett 13 

FEMS Immunol Med Microbiol 216 

FEMS Microbiol Ecol 85 

FEMS Microbiol Lett 146 

Food Chem 86, 147 

Food Chem Toxicol 51, 148 

Food Control 217 

Food Sci Biotech 52, 186 

Gastroenterology 53 

Genes Cells 54 

Genes Genet Syst 218 

Genome 149, 150 

Genomics 219 

Heterocycles 187 

Hum Mol Genet 55 

Hum Mutat 139 

Immunol Lett 188 

In Vitro Cell Dev Biol Anim 151 

Insect Mol Biol 56 

Int Immunopharmacol 189 

Int J Cancer 190 

Int J Mol Med 58 

Int J Mol Sci 87 

Int J Oncol 140 

Int J Syst Evol Microbiol 88-105, 152-162, 245 

J Agric Food Chem 106 

J Antibiot 191 

J Antimicrob Chemother 107 

J Appl Biol Chem 192, 193 

J Appl Phycol 108 

J Bacteriol 109, 110, 163 


J Biochem 14 

J Biol Chem 111, 164, 194 

J Biotechnol 112 

J Clin Invest 59 

J Clin Oncol 141 

J Econ Entomol 113 

J Ethnopharmacol 195, 196 

J Exp Bot 114 

J Food Sci 115 

J Hered 220 

J Immunol 15, 197, 198 

J Ind Microbiol Biotechnol 246 

J Kor Phys Soc 116 

J Med Food 60, 117, 202 

J Microbiol 165 

J Microbiol Biotechnol 61, 118-123, 199-201, 

247 

J Mol Biol 62 

J Mol Catal B 124 

J Nanosci Nanotechnol 16, 17 

J Nat Prod 203 

J Neurochem 18 

J Pharmacol Exp Ther 221 

J Pharmacol Sci 204 

J Phys Chem C 19 

J Pineal Res 222 

J Plant Biol 223, 224 

Kor J Chem Eng 125, 248 

Langmuir 20 

Lett Appl Microbiol 205 

Life Sci 166 

Microbiol Res 249 

Mol Cells 63, 126, 167, 225-227 

Nat Biotechnol 21 

Oncogene 206 

Oncol Rep 228 

Peptides 22 

Physiol Plant 127-129 

Phytochem Lett 142 

Phytomedicine 207 

Phytother Res 208, 209, 229 

Plant Biotech Rep 130, 131, 168 

Plant Cell Rep 132 

Plant Mol Biol Rep 133, 169 

Planta Med 250 

Polymer 23 

Proc Natl Acad Sci U S A 143 

Protein Expr Purif 24 

Proteins 64, 65 

Reprod Fertil Dev 66 

Sensor Actuator B 25 

Sensor Lett 26 

Sensors 27, 28 

Small 29 

Stem Cells Dev 67 

Tetrahedron Letters 210 

Toxicol Appl Pharmacol 230, 231 

Transgenic Res 134 

Vet Microbiol 251 

Virol J 252 

World J Gastroenterol 30, 31 


Keyword 

Keyword Index 

Article No 

(aryloxyacetylamino)Benzoic acid 39 

1,3-dihydroisobenzofuran 78 

1,3-Propanediol oxidoreductase 233 

10% CO2 76 

12β-diol 

179 

13-(4-Isopropylbenzyl)berberine 74 

1-butanol 116 

1-isomangostin 208 

35S promoter 223 

3CLpro 239 

3-oxoolean-12-en-27-oic acid 115 

A549 51 

Aanticomplement activity 208 

Abscisic acid 131 

Acanthoic acid 207 

Acanthopanax koreanum 207 

Aceriphyllum rossii 115 

Acetaldehyde 3, 247 

Acetaminophen 207 

Acetate metabolism 70 

Acetylation 54, 171 

acillaceae 102 

Actinobacteria 155 

Actinomycetales 100, 145, 154, 155, 160 

Activated sludge 121 

Acyl-CoA Dehydrogenase 166 

Acyl-coenzyme A: Diacylglycerol 170 

ADAM proteins 211 

Adaptation, physiological 127 

Adenylate cyclase 70 

ADH1 3 

Adhesion molecules 227, 244 

Adipocytes 117 

Adipose tissue 174 

Adipose tissue 226 

Adolescent 49, 55 

Adra1a gene 218 

Adrenergic agents 117 

Aerobiosis 161 

AFLP 118, 120 

Aging 136 

Aglaia perviridis 181 

Agricultural microorganism 106 

Akt 30 

Alcohol dehydrogenase 3 

Alcohol oxidoreductases 127, 233 

Alcohol 31 

Aldehyde dehydrogenase II 241 

Aldehyde-lyases 247 

Algae 76, 77, 108, 130 

Algal proteins 132 

Algicide 79 

Alkamides 243 

Alkylation 210 

Alleles 139 

Allium sativum 169 

Allium tuberosum 52 

Alpinia 252 

Alternative RNA splicing 225, 226 

Alternative splicing 128, 218, 219 

Alternative transcript 226 

Alteromonadaceae 157 

Alu gene 226 

AluJb 226 

Alzheimer disease 134 

Amentoflavone 237 

American skullcap 187 

Amidohydrolases 78 

Amino acid sequence 50, 65, 201 

Amino acid substitution 62 

Ammonia-oxidizing bacteria 121 

Amyloid precursor protein 134 

Amylopectin 82 

Amylose 82 

Anabaena variabilis 79 

Anaerobic bacterium 104 

Anaerobic microbial enrichment 80 

Anaerobiosis 80, 158, 159, 161 

Anaphase 54 

Animal cell 213 

Animal model 147, 222 

Animalia 130 

Animals 215 

Anisotropy 16 

Annexin A4 48 

Annexins 182 

Antennapedia peptide (Antp) 40 

Anthocyanin 128, 220 

Anthraquinones 33, 144 

Anthriscus sylvestris 192 

Anti-apoptosis 151 

Anti-asthmatic agents 195 

Antibacterial activity 86, 119, 122 

Anti-bacterial agents 79, 101, 115 

Antibacterial 78 

Antibiosis 79 

Antibiotics, antineoplastic 135 

Anticancer effects 182 

Anticarcinogenic agents 51 

Anticariogenic activity 115 

Antifungal activity 74 

Antigen-antibody binding 26 

Antigen-antibody interaction 26 

Antigens, neoplasm 227 

Antigens, viral 251 

Anti-infective agents 107 


Anti-inflammatory agents 195, 196, 221 

Anti-inflammatory 179 

Anti-influenza 238 

Anti-mitotic 44 

Antineoplastic activity 172 

Antineoplastic agents 33, 45 

Anti-obesity agents 117 

Antioxidant activity 193 

Antioxidant effect 148 

Antioxidant enzyme 13, 114 

Antioxidant 31, 73, 151 

Antioxidation 207 

Anti-rotavirus 236 

Anti-solvents 19 

Antitumor effect 137 

Antiviral activity 186, 205 

Antiviral agents 202, 236, 239, 252 

Apigenin 237 

Apoptosis 35, 37, 41, 47, 51, 59, 

66, 73, 138, 178, 182, 

183, 190, 194, 228, 231 

Arabidopsis thaliana 126 

Arabidopsis 130 

Arg-gingipain 87 

Argonaute (AGO) 132 

Arthritis, rheumatoid 15, 221 

Ascomycota 240 

Asialoglycoproteins 4 

ASK1 36 

Aspartic acid endopeptidases 134 

Aspergillus flavipes 78 

Aspergillus 74 

Asteraceae 202 

Ataxin-1 36 

ATPase inhibitor 172 

Aureobasidium pullulans 240 

AU-rich element 34 

Autoantibodies 140 

Autoantigens 140 

Auxin 126 

Azacitidine 57, 185 

B cells 188 

B. cereus 165, 232 

B. gaemokensis sp. nov. 165 

Bacillaceae 92, 93, 94 

Bacillales 88, 96, 159 

Bacillus amyloliquefaciens type 1 246 

Bacillus cereus 165, 232 

Bacillus megaterium 246 

Bacillus subtilis 86, 112, 122 

Bacillus thuringiensis cry3Aa 112 

Bacillus 104, 165 

Bacteremia 153 

Bacteria strain 186 

Bacteria 80, 130 

Bacterial cell wall 104, 162 

Bacterial gene 210 

Bacterial proteins 14, 64, 70, 111, 112, 

119, 144, 145, 157, 

201, 246, 247 

Bacterial strain 104, 105, 162, 210 

Bacterial typing techniques 103, 155 

Bacteriocins 232 

Bacteriostatic 86 

Bacterium isolation 105 

Bacteroidetes 91, 146 

Base composition 88, 89, 90, 92, 93, 94, 

96, 98, 99, 103, 152 

Base sequence 92, 93, 153, 154 

Basidiomycota 191 

BCL-6 188 

Benzofurans 78 

Benzoquinones 201, 239 

Berberine derivatives 74 

Betaine 127 

Betaproteobacteria 245 

Bifidobacterium bifidum 186 

Biflavonoid 237 

Bilirubin 55 

Binding sites 32 

Biocatalysis 24 

Biochemical assay 194 

Biodegradation, environmental 83 

Biodiesel 77 

Biodiversity 85 

Bio-indicator 83 

Bioinformatic tool 133 

Bioinformatics 219, 225 

Biological availability 214 

Biological database 133 

Biological factors 199 

Biological markers 45, 49 

Biomass 76, 77 

Biomolecular interactions 25 

Biopolymers 17 

Biopsy, needle 141 

Bioreactors 76, 77, 123 

Biosensing techniques 7, 17 

Biosensor 1, 2, 25, 26 

Biosynthesis 201 

Biosynthetic pathways 69, 110, 233 

Biotransformation 145 

Biphenyl compounds 43 

Bisamde 181 

Bisphenols 23 

Blastocyst development 66 

Blastocyst stage 151 

Blood glucose 166 

Bloom 79 

Blotting, caspase 7 24 

B-Lymphocytes 188 

Body patterning 150 


Bone morphogenetic protein 4 164 

Branchio-oto-renal syndrome 50 

Brassica napus 131 

Brassica 117 

Breast neoplasms 178 

Bridelia cambodiana 193 

Bronchial hyperreactivity 195 

Bronchoalveolar lavage fluid 195 

Bupleurum falcatum L 244 

Ca2+ 48 

Cadherins 184, 185 

CAMP 70 

Cancer cell lines 182 

Cancer 178 

Candida 74 

Caprifoliaceae 209 

Capsid proteins 251 

Carbon dioxide 76 

Carbon tetrachloride 148 

Carcinoma 31, 34, 53, 140, 141, 

198 

Carrier proteins 188, 231 

Case-control studies 139 

Caspase 3 37, 182, 204, 207 

Caspase 8 51 

Caspase 228 

Cassette ligation-mediated PCR 68 

Castanea crenata 147 

Catalysis 6 

Catalytic domain 50, 62, 65 

Catalytic subunit 71 

Cattle 236 

CCl4 148 

CD40 ligand 173 

Celastrol 239 

Cell adhesion 47, 242 

Cell aging 135 

Cell communication 185, 227 

Cell cycle 21, 51, 54, 228 

Cell death 58 

Cell differentiation 15, 42, 164, 184, 189 

Cell disruption 77 

Cell growth arrest 135 

Cell hypoxia 34 

Cell imaging 5 

Cell line 33, 36, 37, 48, 206, 214 

Cell lineage 221 

Cell membrane 211, 213, 216 

Cell movement 185 

Cell nucleus 81 

Cell proliferation 33, 47, 188, 228 

Cell separation 140 

Cell surface display 4 

Cell survival 138, 199 

Cell suspension 168 

Cell viability 172, 175 

Cell-based high throughput 178 

Cell-cell communications 20 

Cell-free supernatant 186 

Cell-mediated immunity 137 

Cells, cultured 138 

Cellular inhibitors 194 

Cellulase genes 169 

Cellulase 68 

Cellulose 245 

Central nervous system 222 

Cercopithecus aethiops 216 

Cerebral cortex 12 

Cetrimonium compounds 9 

Charge effect 26 

Chelex 100 130 

Chemical fractionation 77 

Chemical precipitation 9 

Chemotherapy 45 

Chestnut inner shell 147, 148 

Chickens 252 

Chimpanzee 225 

China 155 

Chlamydomonas 130, 132 

Chlorella vulgaris 79, 108 

Chlorine 80 

Chloroform 77 

Chlorophyceae 108 

Chloroplast transformation 134 

Chloroplasts 127 

Cholesterol 166 

Chromosomal proteins 41 

Chromosome mapping 149, 167, 220 

Chromosome walking 68 

Chromosomes, bacterial 110 

Chronic exposure 12 

Chronic liver disease 31 

Citrullus lanatus 223 

C-jun N-terminal kinase 18 

Clay 108 

Cloning 70, 169 

Clostridium 158 

Cluster analysis 159, 160, 161, 165, 234 

CMOS image sensor 25 

CMV2b 132 

Coculture techniques 43 

Cohnella laeviribosi HY-21 75 

Cohnella terrae 162 

Cohnella thermotolerans 162 

Cohnella xylanilytica 162 

Cohort studies 55 

Colonic Neoplasms 39 

Colorectal cancer 41 

Colorectal neoplasms 45, 46, 59, 184 

Common cold 202 

Comparative analysis 150 

Comparative genomics 167 


Computational biology 167, 218, 219 

Computer simulation 176 

Concanavalin A 73 

Copper-induced LDL oxidation 142 

Corynebacterium diphtheriae 4, 14 

Corynebacterium glutamicum 70 

Cosmeceutical 248 

Coumarins 11, 148 

Coumestan 238 

COX-2 196 

CpG islands 42, 53, 185 

C-reactive protein 26, 49 

Cryptococcus neoformans 74 

Crystal structure 64 

Crystalline structure 19 

Crystallization 50 

Crystallography, X-ray 111 

CTAB micelles 9 

Cucumber mosaic virus 2b 132 

CUG2 183 

Culture media 122 

CXCR4 206 

CyaB 70 

Cyanobacteria 79, 85, 108 

Cyclic AMP 70 

Cyclic GMP 189 

Cyclization 11 

Cyclodextrin/pullulan-hydrolyzing 64 

Cyclooxygenase 2 66 

Cyclopentanes 126, 128 

Cyclophilins 81 

Cysteine endopeptidases 60, 237 

Cysteine proteinase inhibitors 60 

Cystoscopy 141 

Cytochromes 144 

Cytokines 15, 230 

Cytopathogenic effect 205 

Cytoplasm 81 

Cytoprotective effect 73 

Cytoskeletal proteins 58 

Cytotoxic effects 182 

Cytotoxicity 172, 180, 186, 197 

Databases, factual 136 

Db mouse 166 

DC differentiation 38 

Debranching enzyme 64 

Dechlorination 80, 125 

Defense response 71 

Degradation 125 

Dehydroevodiamine 248 

Deletion mutants 21 

Denaturing gradient gel 85 

Dental pulp cavity 115 

Deoxypodophyllotoxin 192 

Deoxyribose 5-phosphate aldolase 247 

dG9a 56 

D-galactosamine (d-GalN) 204, 230 

Diabetes mellitus 61, 166 

Diacylglycerol O-acyltransferase 166 

Dicer-like (DCL) 132 

Dideoxynucleosides 68 

Dietary fats 117, 174 

Differentiation 63 

Dimerization 64 

Diode lasers 25 

Disease-free survival 45 

Displacement reactions 23 

Diterpenes 207, 250 

Divergence 143 

DMR 57 

DNA base composition 104, 162 

DNA extraction method 130 

DNA fragmentation 182 

DNA gyrase 99, 157 

DNA hybridization 162 

DNA methylation 42, 47, 53, 185 

DNA microarray 107 

DNA persistence 223 

DNA primers 12, 66 

DNA sequence 105 

DNA stretch 16 

DNA transposable elements 218, 219 

DNA, complementary 215 

DNA, ribosomal spacer 113 

DNA 10 

DNA-binding domain 1 

Donor CD34+ cells 177 

Donor NK cell infusion 177 

Doraji 146 

Down regulation 172 

Doxorubicin 135, 228 

Drosophila 13, 56, 178 

Droughts 127 

Drug determination 175 

Drug protein binding 87 

Drug resistance, bacterial 107 

Dual specificity 11 

E2F2 transcription factor 141 

E3 ligase 194 

Elafin 190 

Electrochemical biosensor 28 

Electron spin resonance 2 

Electrophoresis, gel 58, 61 

Electrophoresis, polyacrylamide 232 

Electrophoretic mobility 198 

Ellagic acid 73 

Embryo, Mammalian 57 

Embryo 151 

Embryonic development 66 

Embryonic stem cells 67 

Emerging variants 120 

Endo-1,4-β Xylanases 

75 


Endosomes 213 

Endotoxins 112 

Endo-β-1,4-xylanase 

124 

Energy metabolism 174 

Enoyl-ACP reductase 119 

Enterovirus 71 186 

Environmental risk assessment 118 

Environmental risk 217 

Enzyme activation 8, 24, 117, 238 

Enzyme activity 6, 147 

Enzyme immobilization 6 

Enzyme inhibition 172, 175 

Enzyme inhibitors 57, 67, 119, 170, 189, 

235 

Enzyme 28 

Enzyme-catalyzed precipitation 17, 27 

Enzyme-linked immunosorbent 15, 137, 140 

Enzymes 101 

Eosinophilia 195 

Epididymis 211 

Epigenetic modification 42 

Epigenetics 54, 57 

Epithelial cells 184 

Equipment design 17 

Ergosterol 199 

Erk activation 8 

ERK1/2 250 

ERK 63 

Escherichia coli O157 216 

Escherichia coli proteins 65 

Escherichia coli 22, 24, 69, 107, 116, 

169, 233, 246 

Essential gene 21 

Esterases 6 

Estrogen receptor α 32 

Ethanol production 3, 241 

Etoposide 48 

Eukaryota 131 

Eukaryotic cells 21 

Euphorbia kansui Liou 250 

Euphorbiaceae 193, 250 

Eutrophication 85 

Evodia rutaecarpa 248 

Evodiae fructus 242 

Exercise therapy 222 

Exon deletion 150 

Exon 225 

Exonization event 226 

Exons 149, 218 

Expressed sequence tags 167 

Expression system 112 

Extracellular matrix 63 

Extracellular protein 14 

Extracellular space 8 

Extremities 150 

Eyes absent phosphatase 50 

FabI 107 

Facile fabrication 20 

Fagaceae 148 

Fas ligand protein 51 

Fatty acid glucoside 142 

Fatty acid synthase 140 

Fatty acids 76, 88, 89, 90, 91, 95, 

101, 102, 119, 155, 

156, 158, 245 

Fatty liver 147, 174 

Feces 251 

Fenton reaction 125 

Fermentation 152, 163, 240 

Ferrous compounds 60 

Fertilin 211 

Fertilization in vitro 66 

Fertilization 211 

FET-type biosensors 26 

Fibrin zymography 52 

Fibrinogen 60 

Fibrinolytic enzyme 52 

Fission yeast 21 

Fistularia commersonii 105 

Flavobacteriaceae 95, 97 

Flavonoids 170, 205, 236, 238 

Flexible films 23 

Flow cytometry 30, 51, 137, 140, 188, 

189 

Flow injection analysis 7 

Flower color 220 

Flue gas 76 

Fluorescence resonance energy 32 

Fluorescence signals 29 

Fluorescent dyes 32 

Fluorescent probes 11 

Fluorine 5 

Fluorocarbons 5 

Fluorouracil 45 

Focal adhesion kinase 2 197 

Food microbiology 115, 163 

Forkhead box O 13 

Formation mechanism 19 

Fragaria x ananassa 130 

Free energy 87 

Fresh water 155 

FRET 29 

Fructans 246 

Fullerene structure 19 

Functional marker development 133 

Fungal proteins 123, 167, 240 

Fusogenic peptide 40 

Fusome 56 

Galactose 165 

Gamma rays 35 

Gammaproteobacteria 69 

Gangliosides xenotransplantation 212 


Garcinia mangostana 208, 235 

Garcinone E 208 

Garlic 169 

Gastric cancer 41, 139 

GCSF 177 

Geldanamycin 201 

Gene annotation 133 

Gene deletion 21, 144, 233 

Gene delivery 40 

Gene dosage 121 

Gene expression profiling 41 

Gene expression regulation 82, 114, 127, 129, 136, 

163 

Gene expression 42, 166, 246 

Gene frequency 45 

Gene inactivation 210 

Gene knockdown techniques 173 

Gene library 69, 215 

Gene mutation 226 

Gene organization 150 

Gene sequence 104, 162 

Gene silencing 47 

Gene transfer 120, 223 

Genes, bacterial 69, 144 

Genes, ras 185 

Genes, rRNA 96, 97, 98, 99 

Genetic diversity 251 

Genetic markers 128 

Genetic predisposition to disease 139 

Genetic transfection 213 

Genetic variation 55, 113, 120, 143, 220 

Genetic vectors 4, 128, 137 

Genetically modified (GM) crop 224 

Genetically modified organism 106, 217 

Genistein 32 

Genome duplication 143 

Genome sequencing 116 

Genome walking 68 

Genome, bacterial 109, 110, 163 

Genome, human 149 

Genome, plant 143 

Genome 219 

Genomics 68, 149, 225 

Genotype 85, 97, 99, 251 

Geobacter 144 

Geologic sediments 85, 88, 89, 90, 91, 95, 

96, 98, 99, 102, 103, 

156, 165 

Germ cells 227 

Germinal center 188 

Germination 114 

Germline cell 56 

Ginsenosides 145 

Glabridin 229 

Glucans 240 

Glucansucrase 249 

Glucose 204 

Glucosides 33, 205 

Glucosyltransferases 118 

Glucuronosyltransferase 55 

Glutamate toxicity 12 

Glutamic acid 138 

Glutathione 73 

Glycerol fermentation 3 

Glycerol metabolism 233 

Glycerol 241 

Glycine max 220 

Glycogen debranching enzyme 65 

Glycolipid 122 

Glycoside hydrolase family 10 124 

Glycoside hydrolases 123 

Glycosides 171 

Glycosylation 14, 249 

Glycosyltransferase 62, 220, 249 

Glycyrrhiza uralensis 236, 238 

Glycyrrhiza 170 

Goats 22, 57 

Gold film 28 

Gold nano-island 27 

Gold nanoparticles 6, 9, 29 

Gold 7, 10 

Gram positive bacterium 162 

Gram staining 104 

Gram-positive bacterial infections 161 

Green fluorescent proteins 22 

Growth inhibition 122 

GTP-binding protein α subunits 164 

Guaiane sesquiterpene 191 

Gynostemma 145 

H2O2 12 

Halo-acid dehalogenase 50 

Halomonas 153 

Halophilic bacterium 104 

Handheld 25 

Hansenula polymorpha 3, 241 

Haptoglobin 49 

HAX-1 37 

HCC 53 

HCT-116 colorectal cancer cells 44 

Heart septal defects 164 

Heavy metal stress 83 

Hedyotis diffusa 176 

HEK293 212 

Hela cells 48, 173, 205 

Hemagglutination 252 

Hemagglutinin 236 

Hematopoietic stem cell 49, 177, 189 

Hemiptera 113 

Hemodialysis units, hospital 153 

Hemolysin proteins 112 

Hep G2 cells 30, 148 

Hepatic lipid 147 


Hepatic steatosis 147 

Hepatitis B antibodies 84 

Hepatitis B surface antigens 84 

Hepatitis B vaccines 84 

Hepatitis B virus X protein 30, 31 

Hepatitis B virus 31 

Hepatocellular carcinoma 30, 140 

Hepatocytes 73, 148, 204, 230 

Hepatotoxicity 207, 231 

Herbal medicine 187 

Herbicides 129 

Heterocyclic compounds 206 

Heteroduplex 29 

Hexoses 101 

Hexosyltransferases 246 

Hibiscus syriacus 175, 200 

HIF-1α 34, 39 

High-throughput screening assays 149 

Hippocampus 58, 138 

Histone deacetylase inhibitors 47, 228 

Histone deacetylase 214 

Histone methylation 56, 57 

HL-60 cells 24, 182 

HLA antigens 177 

HLA-mismatched HCT 177 

Homologous recombination 240 

Hordeum 109 

Horizontal gene transfer 106, 118 

HPV16 E6 137 

H-ras12V mouse 140 

HSCCC 192 

Hsp90 inhibitor 172 

HT22 58 

Human dermal fibroblast 175 

Human embryonic stem cell 42 

Human hepatoma cells 243 

Human neutrophil elastase 176, 200 

Human pathogenic fungi 74 

Human rhinoviruses 205 

Humic substances 144 

Hydrogen peroxide 8, 12, 83 

Hydrogen-ion concentration 60, 232 

Hydrolases 109 

Hydrolysis 65 

Hydrolytic cleavage 29 

Hydrophilicity 87 

Hydroxyhibiscone A 200 

Hypoglycemic agents 166 

Hypoxia inducible factor-1α 207 

Hypoxia 39 

Hypoxia-inducible factor 1 203 

IC 50 172, 175 

Iguesterin 239 

IL-10 38 

IL-13 196 

IL-4 196 

IL-6 250 

Ilekudinol A 209 

Ilekudinol B 209 

Ilex paraguariensis 171 

Iloprost 66 

Imidazoles 189 

Immune cell 5 

Immunoassay 7, 17 

Immunoblotting 22 

Immunocytochemistry 54 

Immuno-FET 26 

Immunoglobulin A 84 

Immunoglobulin E 195 

Immunoglobulin Fc fragments 22 

Immunoglobulin G 22, 84 

Immunohistochemistry 57, 141, 183, 188, 190, 

196, 198 

Immunophilins 81 

Immunoprecipitation 198 

Immunosensor 27, 28 

Immunosuppressive agents 67, 191 

Immunotherapy 137 

In situ hybridization 10 

In vitro ADME 214 

In vitro trans-sialylation 4 

Indazoles 189, 199 

INDEL mutation 215 

Indole derivatives 182 

Indole-3-carbinol 51 

Indoleacetic acids 126 

Industrial waste 121 

Inflammation 15, 196, 221, 230 

Inflammatory disease 243 

Inflammatory response 244 

Influenza A virus, H1N1 subtype 252 

Influenza A virus, H9N2 subtype 252 

Inhibition 44 

Inhibitor 214 

Inhibitory activity 243 

Inhibitory concentration 50 78, 252 

INOS 196 

Integrin α5 

184 

Interferon-γ 137, 191, 197 

Interleukin-12 230 



Interleukin-1β 229 



Interleukins 195 

Internet 136 

Intestinal mucosa 84 

Intracellular delivery 5 

Intracellular GH10 xylanase 75 

Intracellular signaling 59 

Intramolecular cyclizations 11 


Inulinase 123 

In-vitro 194 

Ipomoea batatas 82, 83, 128 

Iridoid glycosides 176 

ISFET 26 

Isoelectric point 60 

Isoenzymes 60 

Isoflavones 32, 229 

Isoprenyl flavonoid 170 

Isoxazole 44 

ITS 113 

Iturin 106 

JAM family 227 

Janus kinase/signal transducer 178 

Jerusalem artichoke 123 

JNK 35, 36 

Jurkat cells 197 

Jurkat 35 

K562 cells 197, 228 

KALA 40 

KALA-Antp (K-Antp) 40 

Kansuinine A 250 

Kansuinine B 250 

Killer cells, natural 177, 197 

Kinetic correlation 125 

Kinetics 14, 24, 119, 145, 235, 

240, 247 

Klebsiella pneumoniae 233 

Kluyveromyces 123 

KRIBB3 44 

Lactam 214 

Lactams, macrocyclic 201 

Lactariolines A and B 191 

Lactarius hatsudake 191 

Lactobacillus casei 137 

Lactobacillus plantarum 186 

Lagerstroemia speciosa 205 

LAR tyrosine phosphatase 63 

L-ascorbic acid 2-glucoside 249 

Lateral flow assay 7 

Lavandulyl flavonoid 72 

LEPR gene 226 

Leptin receptor 226 

Lesion mimics 71 

Leuconostoc 163, 249 

Leukemia 177 

Leukocyte elastase 171, 176, 200 

Leukotriene C4 179 

Leupeptins 60 

Levansucrase 246 

Licorice 170 

Lifespan 13 

Ligand binding 136 

Ligands 32 

LIGHT 173 

Lilium lancifolium 196 

Limit of detection 29 

Linkage disequilibrium 45 

LINT-25 41 

Lipid diet 147 

Lipid extraction 77 

Lipid metabolism 76, 147, 166 

Lipid oxidation 142 

Lipid peroxidation 148 

Lipid regulating enzyme activity 174 

Lipogenesis 122, 174 

Lipolysis 117 

Lipopolysaccharide 18, 196, 204, 221, 229, 

Liver neoplasms 30, 31, 34, 53, 140, 198 

Liver 2, 148, 204, 230 

LMBR1 150 

Locomotion 160 

Longevity 13 

LSPR 27 

LTβR 

173 

Luciferase activities 243 

Luciferases 139 

Lung cancer 51 

Lung diseases 161 

Luteolin 237 

Lycopersicon esculentum 130, 131, 133 

Lymphocyte transfusion 177 

Lysine 57 

Macaca fascicularis ADAM2 211 

Macaca mulatta 215, 236 

Macrophages 5, 221 

Magnetic nanoparticles 29 

Magnoliophyta 133 

Maize 217 

Malondialdehyde 207 

Marine bacterium 104 

Mass spectrometry 86 

Massively parallel sequencing 143 

Matenosides A and B 171 

Mealybug 113 

Median lethal dose 216 

Megastigmane glycosides 171 

Meiosis 66 

Melanins 199 

Melanogenesis 199, 248 

Melanoma 190, 199 

Melatonin 222 

Meliaceae 181 

Membrane glycoproteins 15, 211, 227 

Membrane proteins 47, 145, 184 

Mesoderm 184 

Meta positions 23 

Metabolism 199 

Metal nanoparticles 9, 10 

Metal oxide semiconductor 1 

Metalloproteins 17 

Metallothionein 135 


Methanol extract 242 

Methionine sulfoxide reductase A 13 

Methyl methacrylates 20 

Methylation 53 

Methyl-branched fatty acid 119 

Micro patterning 20 

Microalgae 76, 77 

Microarrays 2 

Microbial community analysis 80 

Microbial sensitivity tests 74, 78, 107, 115, 202 

Microbial viability 79 

Micrococcaceae 152 

Microcystis aeruginosa 122 

Microcystis genotype 85 

Microcystis 79 

Microfilament proteins 135 

Microglia 18, 43, 229 

MicroRNA 2, 132 

Microscopy, fluorescence 16, 81, 198 

Microtechnology 16 

Mini-pig 61 

Minisatellite 139 

Mitochondrial depolarization 73 

Mitochondrial proteins 117 

Mitogen-acti-vated protein kinase 72 

Mitosis 54 

Mixed self-assembled monolayer 6 

MMP-1 175 

Modulation by rotating mirror 25 

Molecular dynamics 87 

Molecular identification 113 

Molecular imaging 5 

Molecular marker 220 

Molecular mechanism 194 

Molecular sequence annotation 150 

Molecular structure 200, 203, 208, 209 

Monitoring 217 

Monocytes 15 

Mop cyclase 106 

Morinda citrifolia L. (noni) 142 

Morpholines 67 

Morphological features 182 

mRNA differential display 131 

mRNAs 149 

MUC6 139 

Mucilaginibacter dorajii 146 

Mucin-6 139 

Mucus 195 

Multigene family 69, 201 

Mus musculus 151 

Muscle proteins 47, 135 

Mutagenesis 111, 107 

Mutagens 107 

Mutant p53 1 

Mutant proteins 24, 62, 107 

Mutation 1, 18, 56, 116, 123, 

197, 216 

Myelodysplastic syndromes 177 

Myeloid cell 38 

Myocardial infarction 7 

Myocardium 2 

Myocytes, cardiac 164 

Myogenic regulatory factors 164 

Myosin heavy dhains 164 

NADPH oxidase 8, 12, 18 

NanH 4 

Nanochannel 16 

Nanodot 17 

Nanoimprint lithography (NIL) 17 

Nanoparticle 5, 7, 32 

Nanostructures 16 

Nanotechnology 7, 16 

Nanotubes 17 

Natriuretic peptide, brain 164 

Nb2O5 28 

NDRG2 38 

Neoplasm invasiveness 141, 184 

Neoplasm metastasis 206 

Neoplasm proteins 33, 46 

Neoplasm staging 141 

Neoplasm transplantation 190 

Neoplasms 59 

Neopullulanase 64 

Nerve tissue proteins 36 

Neuraminidase 4, 14, 235, 238 

Neuroinflammation 43 

Neurological disorders 187 

Neurons 12, 58 

Neuroprotection 43 

Neurospora crassa 167 

Neurotransmitter agents 8 

New species 165 

NF-κB 

48, 173, 196, 198, 203, 

229 

Nicotiana tabacum L. 134 

Nicotiana tabacum 130, 131 

NIH 3T3 cells 183 

NIH-kd 212 

NIH-mini pig kidney 212 

NIK 173 

Niobium oxide 28 

Nisin 232 

Nitrates 138 

Nitric oxide 18, 72, 181, 229 

Nitro compounds 138 

Nitroreductases 148 

NK cells 189 

Nolanum nigrum 179 

NOM1 150 

Non-competitive inhibitors 209 

Non-GM tuber 224 

Norisoprenoids 171 


Nox4 12 

Nuclear factor-κB 

72, 204 

Nuclear proteins 183 

Nucleic acid hybridization 96, 97, 99, 160 

Nucleoside-diphosphate kinase 120, 129 

Nucleotide sequence 105, 162, 225 

Nymphoides coreana 168 

Obese mice 230 

Obesity 170, 230 

Obovatol 43 

Oceanobacillus locisalsi 104 

Oceanobacillus oncorhynchi 104 

Octamer transcription factor-3 67 

OIP5 41 

Oligonucleotide array sequence 149 

Oligonucleotide duplexes 29 

Oligonucleotides 2 

Oligopeptides 22, 60 

Oocytes 56, 66 

Oogenesis 56 

Optical and electrical properties 19 

Optimization 214 

Organ specificity 82 

Organic anion transporters 55 

Ornithinibacillus 104 

Orobol 7-O-d-glucoside (O7G) 205 

Orthologs 21 

Oryza sativa 81, 118 

Osteoblast 63, 67 

Osteogenesis 67 

Osteopontin 230 

Outer membrane vesicle 216 

Ovalbumin 195 

Ovary 56 

Oxadiazoles 202 

Oxidants 148 

Oxidation-reduction 3, 80, 144 

Oxidative glutamate toxicity 8 

Oxidative stress 8, 13, 31, 36, 58, 83, 

114, 127, 129, 138, 

148, 207, 231 

Oxygenases 220 

Oxylipins 126, 128 

p16 135 

p21 WAF1 228 

p21 59 

p38 kinases 221 

p38 MAPK 38, 183 

p38 189 

p52 173 

p53 59 

Paenibacillus 75, 109, 161, 247 

Panax 145, 154 

Pancreas 61 

Pancreatic cancer 206 

Papillomavirus vaccines 137 

Paracoccus fistulariae 105 

Paracoccus zeaxanthinifaciens 105 

Paracoccus 105 

Paraquat 127, 129 

Parthenogenesis 151 

Particle size 10 

Paucisalibacillus 104 

PAUF 206 

PCR-DGGE 121 

Pear 113 

Penta-O-galloylglucose 86 

Peptide deformylase 78 

Peptide elongation factors 58 

Peptide mapping 14 

Peptide nucleic acids 10 

Peptides 6 

Peptidoglycan 159, 160 

Perchloroethylene (PCE) 125 

Perfluorocarbon 5 

Periplasm 14 

Peroxidase 83, 114, 127, 129 

Peroxiredoxin 2 43 

Peroxiredoxin V 18 

Persistence 224 

P-Glycoprotein 228 

PGPR 106 

PgsA 137 

Phanerochaete 167 

Phenolic glycosides 193 

Phenotype 96, 97, 98, 99, 100, 

104, 105, 213 

Phenylmethylsulfonyl fluoride 52 

Phenylpropanoids 179 

Phormidium parchydematicum 108 

Phosphatase and tensin homolog 30 

Phosphoglycerate kinase 68 

Phospholipids 159, 161 

Phosphoproteins 227 

Phosphorylation 63, 189, 97, 250 

Photobacterium 103 

Phthalimides 126 

Phylogenetic tree 104 

Phylogenetic 165 

Physiological process 194 

Physiology 162 

Phytoestrogens 32 

Phytophthora infestans 120 

Phytoremediation 83 

Phytotherapy 174, 195, 202 

Pichia 3, 241 

Picornaviridae infections 202 

Pigmentation 220 

Piper longum 243 

Piper nigrum 243 

Piperidones 228 

Pisum sativum 169 


PK15 212 

Placenta 215 

Plant growth regulators 109 

Plant growth-promoting 126 

Plant leaves 171, 237 

Plant proteins 114, 118 

Plant regeneration 168 

Plant roots 33, 109, 170, 174, 236, 

238 

Plant-derived vaccine 134 

Plants, genetically modified 118, 127, 129 

Plants, medicinal 203 

Plasma membranes 182 

Plasmids 69, 110, 188, 241 

Platycodon grandiflorum 146, 174 

p-Nitrophenylcellobioside 124 

PNP-cellobioside 124 

Poly(ADP-ribose) polymerases 24 

Poly(arylene ether)s 23 

Poly(ethylene glycol) methacrylate 20 

Polyglutamine diseases 36 

Polymorphism, Single nucleotide 45, 55, 149 

Polymorphism 139 

Polymyxins 109 

POPDC3 47 

Population diversity 85 

Porcine 151 

Porphyra tenera 130 

Porphyromonas gingivalis 87 

Potato 224 

Potential applications 19 

Pregnancy 215 

Preimplantation development 57 

Prevalence 234, 251 

Primates 218 

Pro-collagen 175 

Prodigiosin 69 

Projection lithography 20 

Proliferation 44 

Prolyl hydroxylation 39 

Prometaphase 54 

Promoter modification 112 

Promoter region 136 

Promoter regions, genetic 112, 185 

Promyelocytic leukemia 182 

Proportional hazards models 46, 141 

Propranolol 117 

Prostatic neoplasms 185 

Protease assay 29 

Protease inhibitors 176, 190, 237 

Protein adsorption 20 

Protein arrays 20 

Protein binding 22 

Protein chip 20 

Protein conformation 64 

Protein degradation 172 

Protein depletion 54 

Protein design 2 

Protein expression 54, 169 

Protein folding 111 

Protein interaction 37 

Protein isoforms 81, 128 

Protein kinase B 35 

Protein multimerization 64 

Protein phosphorylation 54 

Protein precursors 24 

Protein stability 54 

Protein structure, specificity 24 

Protein structure, tertiary 48 

Protein structure 65, 111 

Protein transduction domain (PTD)40 

Protein transport 213 

Protein tyrosine phosphatase 1B 209 

Protein tyrosine phosphatases 11, 33, 63 

Proteinase inhibitory proteins 171, 200 

Proteoglycans 46 

Proteolytic activities 52 

Proteomics 37, 49, 58, 61 

Proton beam 116 

Proto-oncogene proteins c-akt 67 

Proto-oncogene proteins c-bcl-6 188 

Proto-oncogene proteins c-mdm2 59 

Pseudomonas aeruginosa 86 

PTEN Phosphohydrolase 30 

Pullulan 240 

Pyridines 189 

Pyrimidines 221 

Pyrococcus horikoshii 62 

Pyrus 113, 158 

Pyruvate decarboxylase 241 

Quantum dot 5, 29 

Quantum-mechanical calculation 23 

Quercetin 237 

Quinolone alkaloid 242 

Quinone-methide 239 

Quinones 161, 165 

Quorum sensing 111 

rac1 GTP-binding protein 184 

ras Proteins 183 

Reactive oxygen species 12, 18, 30, 58, 72, 73, 

83, 148 

Real-time PCR 106, 121 

Reassortant 251 

Receptors, adrenergic 117 

Recombinant fusion proteins 22 

Recombinant proteins 190, 211 

Recombinant 123 

Recurrence 49 

Regulator 201 

Rehabilitation 222 

Renal dialysis 153 

Reoviridae 183 


Reovirus 183 

Repressor proteins 111 

Reprogramming 57 

Response elements 34 

Response-surface methodology 246 

Retinoblastoma protein 135 

Retinoic acid 42 

Retromer complex 213 

RGS proteins 164 

Rhinovirus 202 

Rhizobium 101 

Rhizosphere 146 

RhoB 35 

Rhodobacteraceae 89, 90, 98, 99, 156 

Rhodococcus 79 

Rhus trichocarpa 86 

Ribavirin 202, 205 

Ribosomal proteins 21 

Risk assessment 141 

Risk factors 31 

RNA interference 48, 194, 197, 206 

RNA polymerase 21 

RNA probes 2 

RNA recognition 2 

RNA stability 34 

RNA, bacterial 92, 93, 94, 100, 153, 

54 

RNA, messenger 132, 167, 174, 215 

RNA, neoplasm 141 

RNA, small interfering 190 

RNA, viral 234 

RNF32 150 

Root development 126 

Rotavirus infections 251 

Rubia akane, rubiaceae 33 

Rubiaceae 142 

Rutaceae 242 

Saccharomyces cerevisiae 4, 123, 167 

Saikosaponins 244 

Salaceyin 172 

Salmonella typhimurium 86 

Salt responsive WD40 1 gene 131 

Salt stress 131 

Saponins 174 

SAR 44 

SARS virus 237, 239 

SARS-CoV 3CLpro 237 

SARS-CoV 239 

Saururaceae 180 

Saururus chinensis 180 

Saxifragaceae 115 

Scenedesmus 79 

Schizosaccharomyces pombe 21 

Schizosaccharomyces 167 

Scopoletin 148 

Scuteflorin A 187 

Scutellaria lateriflora 187 

Seafood 152 

Seawater 88, 89, 90, 91, 93, 94, 

95, 96, 97, 98, 99, 102, 

103 

Secondary/oxidative damage 222 

Secretome 167 

Secretory vesicles 216 

Sedum sarmentosum 204 

Seed coat color 220 

Seed longevity 114 

Seedling 126 

Seeds 235 

Selective detection 11 

Senescence 135 

Sensitivity and specificity 32, 46 

Sequence alignment 65, 201 

Sequence analysis, DNA 110, 149, 159, 215, 234 

Sequence homology 92, 93, 94, 105, 150, 

153, 154, 215, 218, 

227, 233, 234, 247 

Sequence variation 143 

Sequence 133 

Serine endopeptidases 184 

Serine protease 52 

Serratia marcescens 126 

Sesquilignans 180 

Sesquiterpenes 191, 203 

Sewage treatment 121 

Shiga toxin A mutation 216 

Sialic acid 14 

Sialidase 4, 14 

Sialoglycoconjugate 4, 14 

Signal transduction 8, 18, 30, 59, 66, 126, 

164, 173, 183, 184, 

189, 197, 198, 221, 250 

Signaling 206 

SiliconSOI wafer 16 

Sirolimus 67 

Site directed mutagenesis 75, 210 

Skin fibroblast 175 

Skin whitening 248 

SM22α 135 

Smad proteins 67 

Small interfering RNA (siRNA) 132 

Small interfering 35, 59 

Small molecule inhibitor 178 

SNAr reaction 23 

Sodium chloride 81, 94, 103, 127, 155, 

156 

Soil microbiology 92, 100, 101, 109, 144, 

145, 146, 157, 158, 

159, 160, 245 

Soil microorganisms 118, 120 

Soil 223 

Soil-core device 106 


Solanaceae 133 

Solanum lycopersicum 71 

Solanum nigrum 179 

Solanum tuberosum 84, 120, 127, 129, 130, 

224 

Somatic embryogenesis 168 

Sophora flavescens 72 

Soybean 220 

Species 96 

Species comparison 225, 226 

Species diversity 121 

Species specificity 97, 98, 99 

Species-specific primer 113 

Spectrometry 58 

Spectrosome 56 

Spermatogenesis 211, 227 

Spermatozoa 211 

Spinal cord injury 222 

Spirodela polyrrhiza 130 

Spirost-5-ene-3β 179 

Spirostane 179 

Spores, bacterial 159, 161, 165 

SPR biosensor 25 

Sputum 161 

Standard CMOS process 26 

Staphylococcus aureus 78, 86, 119 

Starch biosynthesis 82 

Starch 82 

Stat3 transcription factor 250 

Stat3 243 

STAT5 transcription factor 189 

Static electricity 10, 87 

Sterol esterase 117 

Stilbenes 32 

Stomach neoplasms 47, 59, 139 

Streptococcus mutans 86, 115 

Streptomyces hygroscopicus 210 

Streptomyces thermocarboxydus 124 

Streptomyces 110, 119, 172, 201 

Streptozocin 61 

Stress, physiological 114 

Structural homology 87 

Structure elucidation 199 

Structure-activity relationship 170, 171 

Substitution 218 

Substrate specificity 3, 65, 145 

Subtilisin-like 52 

Sucrose feeding 82 

Sucrose 82 

SUMO-1 36 

Supernatants 186 

Superoxide dismutase 114, 127, 129 

Surface plasmon resonance (SPR) 1, 17, 22, 25 

Surface properties 10, 65 

Sus scrofa 66 

Sweetpotato 82, 83 

Swine diseases 251 

Swine 61 

Synovial fluid 15 

Synthesis 187 

Synthesized polymers 23 

Synthetic methods 19 

Syriacusin 175 

T1DM 61 

Tacrolimus binding proteins 81 

Tacrolimus 67 

Target genes 194 

Taxaceae 237 

T-BHP 148 

TE-derived dual coding genes 225 

Template-blocking PCR 68 

Terpenes 202 

Tes integra 218 

TE-spliced exon 219 

Testis 211 

Tetrachloroethene 80 

Textile industry 121 

TGF-β1 

53 

Thailand 162 

Therapeutic target 29, 41 

Therapeutics 190 

Thiazoles 221 

Thiazolidinediones 166 

Thioacetamide 231 

Thioredoxins 198, 231 

THP-1 cells 242 

Three-dimensional structure 19 

Thrombin 24 

Thrombolytic therapy 60 

Thrombosis 60 

Tight junction 227 

Time-dependent 235 

T-Lymphocytes 35 

TNF-α 196 

Tobacco 81, 114, 128, 134 

Tolerance 116 

Toll-like receptor 4 (TLR4) 204 

Toll-like receptors 15 

Torovirus infections 234 

Torreya nucif 237 

Total lipid 76 

Toxicity 85 

Trans-activators 31, 111 

Transcription factor AP-1 229 

Transcription factors 128, 220 

Transcription 13, 111 

Transcriptional activation 48 

Transfection 53 

Transferases 145 

Transformation, genetic 128 

Transgenes 129, 130 

Transgenic crop 223 


Transgenic NDPK2 potatoes 120 

Transgenic plants 114 

Transgenic TPSP rice 118 

Trans-Golgi network (TGN) 213 

Translocation 13 

Transplantation conditioning 49 

Transplantation, homologous 49 

Transportation route 217 

Transposable element 225, 226 

Transposon 225 

Transxylosylation 75 

Trees 92 

Trehalose synthase 62 

TreT 62 

Triacylglycerol blood level 147 

Trichosanthes kirilowii 203 

Triclosan MIC 107 

Tricyclic geldanamycin analogues 210 

Trifluoromethyl group 23 

Triglycerides 166 

Tripterygium regelii 239 

Tristetraprolin 34 

Triterpenes 115, 203, 209, 239 

Triterpenoid saponins 244 

Troponin I 7 

TTP 34, 53 

Tuber 224 

Tumor markers 46 

Tumor necrosis factor-α 48, 198, 204, 221, 229 

Tumor suppressor protein 1, 190 

Tumor 185 

Tumor-associated autoantibody 140 

Turbid material 108 

TXNIP 188 

Type 2 diabetes 170 

Tyrosinase 248 

Tyrosine 138, 197 

U937 cell line 38 

Ubiquitination 37, 59, 194 

Ubiquitin-protein ligases 173 

Ultraviolet B radiation 175 

Ultraviolet irradiation 175 

Umbelliferae 244 

Urinary bladder neoplasms 141 

USB interface 25 

User-computer interface 136 

UTR 34 

UV exposure 20 

Vaccine vehicle 216 

Vaccines, synthetic 84 

Vacuolar protein sorting 26b 213 

Vascular cell adhesion molecule-1 244 

VCAM-1 244 

Vero cells 186 

Vertebrates 219 

Very late antigen-4 (VLA-4) 244 

Vibrio vulnificus 111 

VIGS 71 

Viola 195 

Viral absorption 236 

Viral proteins 132, 237 

Viral replication 236 

Virus attachment 252 

Virus internalization 202 

Virus replication 205, 252 

Virus-induced gene silencing 71 

Vitamin D3 upregulated protein 1 231 

Vitamin K 2 159, 160 

Volunteer 224 

Volvariella bombycina 199 

Von-Hippel-Lindau 39 

Vps26b 213 

Vps26b-deficient mice 213 

VSIG1 227 

Wastewater 121 

Water microbiology 93, 94 

Water 9 

Watermelon 223 

Weigela subsessilis 209 

Weight change 147 

Weight gain 117 

Whale genome 150 

White adipose tissue 166 

White-rot fungi 167 

Wild soybean 143 

Wnt proteins 164 

Xanthenes 208 

Xanthone 208, 235 

XIAP 37 

X-ray structure 62 

Xylans 92, 159 

Xylooligosaccharides 75 

YC-1 189 

Yogurt 186 

Zea mays 217 

Zebrafish 219 

ZFP91 173 

Zinc finger protein 194 

Zygote 57 

Zygotic embryo culture 168 

Zymography 52, 232 

Zymomonas mobilis 241 

β-Glucan 

240 

β-Glucosidase 

145 

β-Secretase 

134 

γ-Radiation 

35, 135 

δgal80 

123

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