Summary of HIR Equipment (2012-2013) - High Impact Research

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HIR-MOHE EQUIPMENT 2012 - 2013 (CHANCELLORY)No PI's Name Title Equipment1 Dr. Chan Kok Gan Bacteria QuorumQuenchingEstimated budgetYear 2 & 3(2012 & 2013 )Approved Budget (After VM Lab)2012 (RM) 2013 (RM) Total (RM)1 LCMS 450,000 450,000 - 450,000 1 USA LCMS is an analytical chemistry technique that is used todetermine the mass of a molecule and quantify trace levels ofsuch compound. LCMS is particularly useful to study knowncompounds.Quantity/unitCountry oforiginDetailsJustification ofpurchaseThis LCMS is needed by by my group which routinely study theproduction and degradation of bacterial cell-to-cell signallingmolecules. LCMS can determine the degraded compounds, withoutthis instrument, we will not be able to identify the moleculeturnover, and hinder the elucidation of encymatic degradationpathway by the bacteria. LCMS offers rapid and efficient detectionthat other methods (e.g. biosensor) cannot compete with.Additional information(space/utilities eg electric, software etc)Lab space is available in my lab.Molecule mass identification and database softwares areincluded. Without this instrument, it is impossible to doresearch on identification of degraded quorum sensingcompounds particularly those present in trace amount.Many work reported in reputable journals including J.Bacteriology, Environmnetal Microbiology, AppliedEnviromental Microbiology.Potential users/research groupsPotential users typically involve chemist,phytochemist, natural products scientists andpharmacist.At least 2 PhD and 10 MSc students will be trainedusing this instrument.Frequency and intensity of usageUse on daily basis (6 days per week, whole day), forroutine screening of quorum sensing and quorumquenching studies.2 MultimodeLuminometer180,000 180,000 - 180,000 1 USA/GermanyIt is a 96-well microplate luminometer with high sensitivity Since we have constructed our lux based biosensor that emits This is a small instrument and table-top size. Analysisand broad dynamic range for chemiluminescent and bioluminescence, or quorum sensing and quorum quenching and softwares are included. This instrument generates databioluminescent applications. It measures bioluminescence, natrual products projects rely heavily on this automatedthat can be published in Microbial Ecology, J.fluorescence, visible or UV-visible absorbance in 96 and 384- instrument. We also use this for high throughput drug discovery Bacteriology, BMC Microbiology, PLoS ONE.well plate formats.screening. Unlike other multimode systems, readings taken withthismultimode luminometer is not degraded by indirect fiber-optictransmission or crowded optical channels. Dedicated opticalchanneling ensures that this unit provides sensitivity and dynamicrange on par with the highest performing single-mode instruments.Target users including microbiologist or scientists Use on daily basis (6 days per week, whole day), forwho require automated detection and data routine screening of quorum sensing and naturalgeneration of bioluminescence, andproducts studies.cehmiluminosence work.At least 1 PhD or 5 MSc students will be trained perPI using this instrument.3 qPCR thermocycler 180,000 180,000 - 180,000 1 USA/Korea4 Rotary evaporator 40,000 40,000 - 40,000 1 USA/GermanyqPCR (polymerase chain reaction, PCR) is which data are A full operation of this instrument will run for 6 hr to 1 day. Our lab Lab space is available in my lab. This is a small instrument. Target users including bioinformaticians, systemcollected in real-time as the reaction proceeds. Continuous will use this for twice a day for 5 days per week. It is anticipated qPCR is the only method for DNA amplication in vitro. biologist, bacteriologist, virologits, moleculardata collection enables one of the principal applications of that this instrument will be heavily used by my group members Most Tier 1 journals such as PNAS, J. Bacteriology, BMC biologist, medical scientists that requires genesreal-time PCR, target quantitation. Because we are doing tens working on GWAS and genomic work.Genomics, PLoS ONE requires qPCR as the PCR method. expression quantitation.or hundreds of novel, de novo , bacteria genomes analysis,Nearly most molecular biology research requireshence quantitation or genes expression is the only way toqPCR for PhD and MSc students work.verify genes activity in a given genome. And qPCR is one suchinstrument that provides quatitation data.This is also become one of the routine facility in molecularbiology lab.A rotary evaporator is required for the efficient and gentle The natural products and quorum sensing projects typically requires No special electricity and software needed. This is a small Natural products and quorum sensing projectsremoval of solvents from samples by evaporation. This is a isolation and concentration of small molecules. This instrument instrument. Most Tier 1 journals such as J. Nat. Products, reserchers.modular system that comes with water bath, organic solvent provides rapid, non high heat drying of compounds which is an PLoS ONE requires this instrument as part of theresistant vacuum pump.cheaper alternative as compared to freeze dryer. Hence, this is a methodology.money worth, and essential item for the projects aforesaid.Use on daily basis (6 days per week, whole day), forGWAS, gene expression and quantitation, and wholegenome work.Frequently used by natural product groups (5 daysper week, 5-6 hr per run)5 Autoclave 18,000 18,000 - 18,000 1 Japan A high volume, programmeable moisture heat sterilisinginstruments. An essential unit for all microbiology lab.We work on bacteria on a daily basis and needs this unit forsterilisation and killing of microbes.3-phase plug point needed, which has beencommunicated to Estate Office (JPPHB) in UM. We needthis instrument to comply with Biosafety requirement asstipulated by Biosafety Act 2007 and IBC ruling.All microbiologists.Very frequently used by all groups (5 days per week,6 hr per run)6 Nanodrop 50,000 50,000 - 50,000 1 USA NanoDrop is a spectrophotometers and fluorospectrometerused to quantitatemicro-volumes of sample.NanoDrop instrument is needed for diverse fields such as genomics, This instrument is required for NGS work for nucleic acids All genomic works requires this instrumentsproteomics, drug discovery, molecular diagnostics and biomanufacturing.It is based upon the patented sample retentionmy group.(DNA, RNA) intergrity prior to NGS work.involving molecular biologist and bacteriologist insystem that allows scientists to quickly and easily quantify andassess purity of samples such as proteins and nucleic acids.Very frequently used by all groups (5 days per week,1 hr per run)7 Qubit 12,000 12,000 - 12,000 1 USA Qubit quantitates DNA, RNA, and protein with unprecedented It is designed for precious samples that are rare or difficult toaccuracy, sensitivity,process, and applications requiring precise measurement such asand simplicity. It is designed for molecular biology labs that qPCRwork on genomic work.8 Table Top centrifuge 86,000 86,000 - 86,000 1 USA This is an essential instrument for correct speed control Our team needs to centrifuge bacteria cells that must rely on thiscentrifugation that is needed to spin down small particles instrument.including proteins and viruses. It will have a temperaturecontrolledchamber for heat sensitive samples.This instrument requires no special electricity and space All molecular biologists in my group.requirement. It is a small instrument. It is needed for NGSand qPCR work.This instrument requires no special electricity and space All microbiologists.requirement. It is a small instrument.Very frequently used by all groups (5 days per week,1 hr per run)Very frequently used by all groups (5 days per week,mins - 0.5 hr per run)9 Termomixer 48,000 48,000 - 48,000 2 USA It simultaneous mixing and temperature control. its countercoolingability provides efficient cooling thereby greatly small volume enzymatic reaction involving restriction enzymes, requirement. It is a small instrument.We do gene cloning work that needs special temperature control of This instrument requires no special electricity and spaceexpanding both Its temperature control functions and range ligases, and DNase and RNases. We need this accurate temperatureof applications.control heat block that fits small eppendorf tubes for ligation,inactivation of enzymes and heat inactivation of quorum quenchingassay.10 Lab freezers and12,000 12,000 - 12,000 2 USA/Malaysia Upright Freezers and fridges, 4 degree Celcius to -20 degree To store our valuable, hundreds of bacteria stocks and heat This instrument requires no special electricity and spacefridges/Japan Celcius, respectively. These instruments come with anti-frost sensitive chemicals notable quorum sensing and natural products requirement. It is a small instrument.and and auto-defrost functions.molecules.11 Workstation 140,000 140,000 - 140,000 2 USA This workstation is a computing solution for genome analyzer We have tens to hundreds of bacteria genomes to be analysed and This instrument requires no special electricity and spacesequencing platforms. It bundles with sequencing software without this workstion; analysis of these tera bases of DNA will requirement. It is a table-top size instrument. Thewith high-performance workstation to perform gene virtually impossible.softwares bundled with is one-off payment, and noannotation and genome data analysis.renewal needed.All bacteriologists.Very frequently used by all groups (5 days per week,1 - 24 hr per run)All users in the lab.Use daily (24 hr / week) non stop.Bioinformatics and GWAS researchers in my group. Use daily, data analysis can run up to 24 hr/week) forfew days for complex data.12 Ice maker 11,000 11,000 - 11,000 1 USA It is a stand-alone appliance to make ice that the size is We have no ice maker currently and unable to control the heatgraded and suitable for molecular work. We routinely needs senstive experiments.these special shape ice to cool molecular grade reagents andexzymes including the PCR reagents.This instrument requires no special electricity and spacerequirement. It is a small instrument and need a watersupply.All users in the lab.Use daily (24 hr / week) non stop.13 Optical Mappingsystem14 Essential molecularlab equipments(hotplate, magneticstirer, microfuge,microwave,electrophoresis tanketc)270,000 270,000 - 270,000 1 USA This instrument enables the user to generate the optical We have tens to hundreds of bacteria genomes to be analysed. In This instrument requires no special electricity and space Bioinformatics and GWAS researchers in my group. Frequently use (5 day per week) for genome analysis,maps in the labs, generate microbial whole genome maps addition to NGS analysis, we attempt to study the optical consensus requirement. It is a small instrument .9 hr-24 per analysisfrom single DNA molecules. It is a non gel-based, PCR-based, map that accurately show relatedness, chromasomal genomic mapon-the-chipand automated in silico genomic map. This is one of theor sequencing based methodology. It provides strain typing,comparative genomics, whole genome sequence assembly latest technology to study bacterial genomes.with user friendly built-in software.10,000 10,000 - 10,000 5 USA/Germany/ These are small but essential instruments for daily operation These items are typically available in all modern lab, and we need These instruments require no special electricity and space All users in the lab.Use daily (8 hr/day). Application usually from few minJapan/Malaysia of the labs. We need to acquire these to cope with the these to support our work or other major instruments. Some items requirement. It is a small instrument .to hours.increased demand to fulfil our KPI and to provide support for in my lab are too old and inaccurate to operate.the big instruments.15 Microfluidicbioanalyser120,000 120,000 - 120,000 1 USA Small instrument for sizing, quantification and quality control This unit can shorten biosamples (DNA, RNA, proteins) analysisof DNA, RNA, proteins and cells. This instrument is the lab-onthe-chipthat uses microfluidics technology for the analysis of confirmation that is recommended for personlaised genomefrom hours to miins. Also, it is an essential for sample integritybiological samples.analyser that we had bought.This unit can provide improved data precision and All users in the lab.reproducibility, short analysis times,minimal sample consumption, improved automation andintegration of complex workflows.Use frequently (5 days per week, 1-2 hr per run).1,627,000.00 1,627,000.00 0.00 1,627,000.00- updated on 2nd March 2012 -
HIR-MOHE EQUIPMENT 2012 - 2013 (CHANCELLORY)No PI's Name Title EquipmentEstimated budgetYear 2 & 3(2012 & 2013 )Approved Budget (After VM Lab)2012 (RM) 2013 (RM) Total (RM)Quantity/unitCountry oforiginDetailsJustification ofpurchaseAdditional information(space/utilities eg electric, software etc)Potential users/research groupsFrequency and intensity of usage2 Prof. Dr. Jamuna Molecular Genetics 1 3500xl de novoVaddiveluGenetic Analyzer1,600,000 1,600,000 - 1,600,000 1 USA 3500xl de novo genetic analyzer is a medium-to-highthroughput Sanger sequencer for sequencing, resequencing,mutation detection, AFLP analysis, SNPgenotyping, relative fluorescent quantitation,microsatellite analysis and other genetic applications.3500xl de novo genetic analyzer is one of the most versatile Lab space (13'x13' with air-con) has been allocated Potential users including geneticists, molecular Frequently used (6 days per week) and eachsequencer in the market. This equipment is not available in in the HIR Building and approved by the civil, biologists and microbiologists involved in run will take at least 1 hour.UM despite the high demand for such 24-capillarymechanical & electrical departments. Genome sequencing, re-sequencing, mutation detectionsequencing facility. For instance, the Molecular Genetics sequences and gene annotation analysis softwares and other genetic applications. At least 10 PhDteam will be embarking on a large-scale sequencing study on are included. Without this instrument, large scale and MSc students will be trained using therespiratory, gastrointestinal, central nervous system, and genome sequencing projects will be negetively instrument, producing results that could beblood-borne pathogens. Availability of 3500xl is essential and affected.published in Tier-1 journals including Nature,timely to produce tier-1 publications (Proc Natl Acad Sci U SScience, Lancet, PLoS, PNAS, Journal ofA. 2010 Dec 21;107(51):22032-7, Proc Natl Acad Sci U S A.Virology, Emerging Infectious Diseases and2010 Jul 13;107(28):12629-33).others.2 Multiplex, BeadbasedFluoroanalyzer400,000 400,000 - 400,000 1 USA A multiplex, bead-based fluoroanalyzer is a platform Fluoroanalyzer that operates on the xMAP technology Lab space (13'x13' with air-con) has been allocated Broad users including molecular biologists,Frequently used (3 days per week) and each run willthat simultaneously measures multiple analytes by enables bead-based multiplexing of up to 500 analytes per in the HIR Building and approved by the civil, immunologists and geneticists involved in varioustake at least 2 hours.exciting a sample with a laser, and subsequently specimen. Together with the Luminex 100/200 analyzer that mechanical & electrical departments. xMAPapplications in enzyme, nucleic acid and proteinanalyzing the wavelength of emitted light using protocolbaseddata acquisition with robust data regression fast and cost-effective bioassay results on many assay software are included in the platform for operation. trained using the instrument, producing results thatruns on the principles of flow cytometry, the system delivers technology, MAGPIX imaging system and xPONENT studies. At least 10 PhD and MSc students will beanalysis. A fluoroanalyzer combines advanced fluidics, formats including nucleic acid assays, receptor-ligand Without this instrument, studies using large-scale could be published in Tier-1 journals includingoptics, and high-speed digital signal processing with assays, immunoassays and enzymatic assays. The bead-based bioassays will be negetively affected.Nature, Science, Lancet, PLoS, PNAS, Journal ofcolor-coded microsphere technology to deliver Molecular Genetics team will be embarking on a large-scaleVirology, Emerging Infectious Diseases and others.multiplexed assay capabilities.surveillance study on respiratory and gastrointestinalpathogens using the xTAG RVP and GPP assays,respectively. Availability of bead-based multiplexingfluoroanalyzer is therefore essential and timely to producetier-1 publications (PLoS One. 2011;6(9):e24734, J ClinMicrobiol. 2011 May;49(5):1738-44).3 High-resolutionProteomics andMetabolomicsAnalyzer withmicrofluidicseparationcapability4 Epifluorescenceinvertedmicroscopeequiped with CCDcamera.1,800,000 1,800,000 - 1,800,000 1 USA The 6000 series Proteomics and Metabolomics Proteomics and metabolomics forms the core technological Lab space available in HIR Building. Meeting withAnalyzer has become the choice of analytical tool for backbone of our Helicobacter pylori research at UM. Only architect, mechanical & electrical engineer done tothe study of proteins and their associated posttranslationalmodifications as well as cellularwhich is not upgradable to fulfil current proteomics andone older model is currently available in UM (Chemistry) make avaiable a22'x22' room with air-conditioning.metabolites. The high sensitivity and resolution of the metabolomics research needs. The resolution of thisanalyzer enables it to be applied to meta-analysis of proposed unit is 10 times higher than the older unit. Othercomplex clinical and environmental samples. It is widely MS instruments in UM do not meet requirement in terms ofapplied to drug discovery, biomarker discovery, cancer sensitivity and resolution. Without this, it is unable toresearch, environmental research, etc.determine the accurate mass of unknown compounds(especially that of larger molecular weight compounds likeproteins which falls outside the detection range ofconventional quadrupole mass spec analyzers). Also, theexisting older unit is already heavily utilized and long queuetime will delay progression in research work. The proposednew unit will cut short the waiting time, reduce cost,increasing resolution and accuracy of molecular massmeasurement. In addition to that, the proposed unit will beequipped with state-of-the-art proprietary softwares toanalyze complex data, predict molecular functions andbiological pathways. Similar work has been performed by ourcollaborative partners at A*STAR Singapore andMetabolomics Network Australia reulting in high impactpublications. It would therefore be ideal to mirror this work inour facility so that our human resource capacity can be builtup and we can reduce time of obtaining resutls and notdepened on international sources. This instrument isimportant for publication in Tier-1 journals e.g. J. BiologicalChemistry, Cell, Science, Nature, Nature Biotech, NatureGenetics, Nature Materials, PNAS, etc. (Nature Protocols2011 vol. 6, 1060–1083; PNAS March 10, 2009 vol. 106 no.10 3698-3703)300,000 300,000 - 300,000 1 Japan / USA For study of tissue samples, living cells and its To give a better view of biological function through the study Lab space available in HIR Building.components. Specific fluorochrome staining or of cellular dynamics. As fluorescence fades, it is essential torecombineering with GFP allows investigation into have the epifluorescence microscope nearby for immediatemolecular physiology and activity.viewing.2 HIR-funded projects:Estimated usage: heavily utilized;(1) Interspecies molecular crosstalk in H. pylori average of twice or 2 weeks of 24 hrs continuousinfections;running per month (exclude possible usage by other(2) Antimicrobial susceptibility of H. pylori isolates; research groups in UM)At least 4 PhD students in our research group.Allows students to be trained in proteomics andmetabolomics.Also can be used by other UM research groups indrug discovery, biomarkers cancer research andenvironmental research.Expected no. of Tier-1 papers from 2 projects: 19Potential users including geneticists, molecular Heavily used (5 days per week) and each usebiologists and microbiologists involved in will take about 30 min to a few hours.animal, plant, bacterial and viral work. At least3 PhD student and 4 M Sc students will betrained using the instrument, producing resultsthat could be published in Tier-1 journalsincludingImmunity, Molecular Cell, Genes &Development,Proceedings of the National Academy ofSciences of the United States of America(PNAS) and others.5 Cryopreservation180,000 180,000 - 180,000 1 USA For cryopreservation of biopsy samples, cell lines,The aim of cryopreservation is to enable stocks of cells to be Lab space available in HIR Building.2 HIR-funded projects: (7); Regulation ofDaily used ( 7 days per week)system for biopsytissues and stock culture. For long term storage ofstored to prevent the need to have all cell lines in culture atImmune Response by Epigenetics and (8)samples, cell lines,RNA and protein samples.all times. It is invaluable when dealing with cells of limited lifeGenome Organization in Diseases: fromtissues and stockspan. The other main advantages of cryopreservation are:Mutations to Structural Variations andculture* Reduced risk of microbial contaminationEpigenetics* Reduced risk of cross contamination with other cell lines* Reduced risk of genetic drift and morphological changes* Work conducted using cells at a consistent passagenumber* Reduced costs (consumables and staff time)6 Thermal cycler (9690,000 90,000 - 90,000 3 USA For amplifying segments of DNA via the polymeraseTo conduct research studies in gene expression, mutation,Lab space available in HIR Building.Potential users including geneticists, molecular Heavily used (6 days per week) and each runwells)chain reaction (PCR) process.sequencing and cloning. Current units (2) in the lab is fullyMinor renovation, furnishing & maintenance.biologists and microbiologists involved inwill take at least 2-3 hours.utilized and not sufficient to meet requirement of project. Theanimal, plant and bacteria work. Results couldamount of research work involving a lot of genotypingbe published in Tier-1 journals includingdemands additional 3 units.Immunity, Molecular Cell, Genes &Development,Proceedings of the National Academy ofSciences of the United States of America(PNAS), PLoS Genetics, Medical Genetics andothers.7 Bioinformatics80,000 80,000 - 80,000 1 USA /To facilitate storage and rapidly process huge amountLarge amount of data expected from this project due to the2 HIR-funded projects: (7); Regulation ofFrequently used and complete data analysissoftware forDenmarkof genetic datahigh throughput approach.Immune Response by Epigenetics and (8)require days to weeks run on a workstation.GWAS, ChIPGenome Organization in Diseases: fromsequences andMutations to Structural Variations andgenome wide geneEpigenetics. Results could be published in Tier-expression analysis1 journals includingetc, data storageImmunity, Molecular Cell, Genes &and processingDevelopment,Proceedings of the National Academy ofSciences of the United States of America(PNAS), PLoS Genetics, Medical Genetics andothers. Other potential users includebioinformaticians and biologists.- updated on 2nd March 2012 -
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