Vol 9 No1 - Journal of Cell and Molecular Biology - Haliç Üniversitesi

More documents

Recommendations

Info

are indistinguishable in the region selected for analyses. The newly identified transcript failed to show significant similarity to any of the so far functionally characterized proteins. It is to be noted that plant specific nucleotide blast in NCBI database shows significant similarity to a hypothetical Poplus trichocarpa protein (XM_002337327.1) and other plant transcripts. Paralogues of the gene were found to be present in all tested Corchorus species. Phylogenetic analysis of drp gene and its homologues suggests that C. capsularis is the closest neighbour of C. olitorius in terms of drp. It is to be noted that all considered dicots grouped into same clade in the tree (Figure 6). Multiple sequence alignment of protein sequences from different Corchorus spp. identified a highly conserved segment of 32 amino acid residues. Secondary structure prediction at NPS@ webserver (Combet et al. 2000) suggested these amino acids are most likely to form random coils (Figure 5b and Table 2). Random coils or more specifically coils add flexibility to the protein structure (Buxbaum, 2007). Our literature survey revealed an interesting relationship between random coils and their possible role in dehydration response. It has been long known that different organisms release osmolytes when subjected to water stresses (Yancey et al. 1982). Study by Qu and co-workers (1998) identified that osmolytes cause contraction of random coils leading to decrease of conformational entropy and subsequent stabilization of protein folding. The present study has identified a novel dehydration responsive transcript from different jute (Corchorus) species. Further studies are required to elucidate the detailed mechanism of action of this transcript. Acknowledgement This research was supported by the United States Department of Agriculture (USDA). We are thankful to Bangladesh Jute Research Institute (BJRI) for providing seeds of different jute species. References Agarwal P and Jha B. Transcription factors in plants and ABA dependent and independent abiotic stress signalling. Biol Plant. 54:201-212, 2010. Novel dehydration responsive transcript from jute 27 Ahmed S, Nabi MZ, Alam MM, Islam MS, Samira R, Moosa MM and Khan H. A computational and experimental approach for developing jute ESTs from genomic clones. Aust J Crop Sci. 3:322-328, 2009. Alam M, Sharmin S, Nabi Z, Mondal S, Islam M, Nayeem S, Shoyaib M and Khan H. A Putative Leucine-Rich Repeat Receptor-Like Kinase of Jute Involved in Stress Response. Plant Mol Biol Rep. 28:394-402, 2010. Basu A, Ghosh M, Meyer R, Powell W, Basak SL and Sen SK. Analysis of genetic diversity in cultivated jute determined by means of SSR markers and AFLP profiling. Crop Science. 44:678-685, 2004. Buxbaum E. Protein structure. Fundamentals of protein structure and function. Springer ScienceBusiness Media, LLC, New York. 12- 37, 2007. BBS. Statistical pocket book of Bangladesh statistics division, Bangladesh Bureau of Statistics, Ministry of Planning, the People's Republic of Bangladesh. 2004. Bray EA. Molecular responses to water deficit. Plant Physiol. 103:1035-1040, 1993. Bray EA. Genes commonly regulated by waterdeficit stress in Arabidopsis thaliana. J Exp Bot. 55:2331-2341, 2004. Combet C, Blanchet C, Geourjon C, and Deléage G. NPS@: Network Protein Sequence Analysis. Trends in Biochemical Science. 25:147-150, 2000. Deléage G and Roux B. An algorithm for protein secondary structure prediction based on class prediction. Protein Eng. 1:289-294, 1987. Frishman D and Argos P. Incorporation of nonlocal interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng. 9:133-142, 1996. Garnier J, Osguthorpe DJ and Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 120:97-120, 1978. Geourjon C and Deléage G. SOPM: a selfoptimized method for protein secondary
28 Sazia SHARMIN et al. structure prediction. Protein Eng. 7:157-164, 1994. Ghosh T. Hand book on jute. Food and Agriculture Organization of the United Nations (FAO):115- 116, 1983. Gibrat JF, Garnier J and Robson B. Further developments of protein secondary structure prediction using information theory: New parameters and consideration of residue pairs. J Mol Biol. 198:425-443, 1987. Guermeur Y. Combinaison de classifieurs statistiques, Application a la prediction de structure secondaire des proteines., p 169, Paris: University of Paris 06, 1997. Guermeur Y, Geourjon C, Gallinari P and Deléage G. Improved performance in protein secondary structure prediction by inhomogeneous score combination. Bioinformatics. 15:413-421, 1999. Hannah MA, Heyer AG and Hincha DK. A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana. PLoS Genetics. 1:e26, 2005. Holappa LD and Walker-Simmons MK. The Wheat Abscisic Acid-Responsive Protein Kinase mRNA, PKABA1, Is Up-Regulated by Dehydration, Cold Temperature, and Osmotic Stress. Plant Physiol. 108:1203-1210, 1995. Hossain MB, Awal A, Rahman MA, Haque S and Khan H. Distinction between cold-sensitive and -tolerant Jute by DNA polymorphism. Journal of Biochemistry and Molecular Biology. 36:427-432, 2003. Huang X and Madan A. CAP3: A DNA Sequence Assembly Program. Genome Research. 9:868- 877, 1999. Ingram J and Bartels D. The molecular basis of dehydration tolerance in plants. Annual Review of Plant Physiol and Plant Molecular Biology. 47:377-403, 1996. Iseli C, Jongeneel CV and Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: Proceedings / International Conference on Intelligent Systems for Molecular Biology pp 138-148, 1999. Islam AS, Taliaferro M, Lee CT, Ingram C, Montalvo RJ, Ende Gvd, Alam S, Siddiqui J and Sathasivan K. Preliminary progress in Jute, Corchorus species. genome analysis. Plant Tissue Cult Biotechnol. 15:145-156, 2005. Keka SI, Shamsuzzaman M, Pahloan MU, Pervin S, Rahman MM and Khan H. Identifying simple sequence repeat (SSR) marker linked to mite tolerance in jute species. Bangladesh Journal of Botany. 37:161-171, 2008. King RD and Sternberg MJE. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci. 5:2298-2310, 1996. Kulheim C, Agren J and Jansson S. Rapid Regulation of Light Harvesting and Plant Fitness in the Field. Science, 297:91-93, 2002. Kundu B. Jute — world’s foremost bast fibre, II. Technology, marketing, production and utilization. Economic Botany. 10:203-240, 1956. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ and Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics. 23:2947- 2948, 2007. Mahmood N, Azam MS, Islam MS, Sharmin S, Moosa MM, Hossain MA and Khan H. Differentially expressed transcripts of wild and cultivated jute (Corchorus spp.) varieties upon fungal, Macrophomina phaseolina. infection. Annals of Biological Research. 1:120-127, 2010. Murray MG and Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8:4321-4326, 1980. Nakashima K, Ito Y and Yamaguchi-Shinozaki K. Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses. Plant Physiol. 149:88-95, 2009. Perriere G, Combet C, Penel S, Blanchet C, Thioulouse J, Geourjon C, Grassot J, Charavay C, Gouy M, Duret L and Deleage G. Integrated databanks access and sequence/structure analysis services at the PBIL. Nucleic Acids Res. 31:3393-3399, 2003. Qu Y, Bolen CL, and Bolen DW. Osmolyte-driven contraction of a random coil protein. Proceedings of the National Academy of Sciences of the United States of America. 95:9268-9273,1998.
Page 1 and 2: Journal of Cell and •Notch in apo
Page 3 and 4: Haliç University Faculty of Arts a
Page 6 and 7: Journal of Cell and Molecular Biolo
Page 8 and 9: The aforesaid, thus, strongly sugge
Page 12 and 13: factors accounts for the different
Page 14 and 15: compromise nearly 5-10% of the Cauc
Page 16 and 17: Genetic susceptibility to bladder c
Page 18 and 19: Cunningham JM. SJ Hebbring SJ, McDo
Page 22 and 23: Identification of silencing suppres
Page 24 and 25: AAUAGAAAAUGA preceding the 12K AUG
Page 28 and 29: Semiquantitative RT-PCR Total RNA w
Page 30 and 31: A Corchorus_olitorius SAPKARQRCVADG
Page 34: Rabbani MA, Maruyama K, Abe H, Khan
Page 37 and 38: 32 Preeti SINGH et al. Introduction
Page 39 and 40: 34 Preeti SINGH et al. Discussion C
Page 41 and 42: 36 Preeti SINGH et al. Mukhopadhyay
Page 43 and 44: 38 Jeyaraj ANBURAJ et al. Introduct
Page 45 and 46: 40 Jeyaraj ANBURAJ et al. Surface o
Page 47 and 48: 42 Jeyaraj ANBURAJ et al. Table 3.
Page 49 and 50: 44 Jeyaraj ANBURAJ et al. Gokhale M
Page 51 and 52: 46 Arumugam KUNTHAVAI and Somasunda
Page 59 and 60: 54 Sabira TAIPAKOVA et al. crystall
Page 61 and 62: 56 Sabira TAIPAKOVA et al. Results
Page 63 and 64: 58 Sabira TAIPAKOVA et al. Synthesi
Page 65 and 66: 60 Sabira TAIPAKOVA et al. Discussi
Page 70 and 71: µl containing 50-100 ng DNA templa
Page 72 and 73: There are number of factors which a
Page 76 and 77: Data regarding changes in hemoglobi
Page 78 and 79: elated to major structural and func
Page 82 and 83:
C: C1 & C2 and D: D1 & D2. Animals
Page 84 and 85:
Effects of Vernonia amygdalina extr
Page 86 and 87:
histological evidences from our stu
Page 88 and 89:
Journal of Cell and Molecular Biolo
Page 90 and 91:
EGFR variations in bladder cancer 8
Page 92 and 93:
Journal of Cell and Molecular Biolo
Page 94 and 95:
Submission Policies and Authorship
Page 96:
Journal of Cell and Volume 9 · No
show all

Vol 9 No1 - Journal of Cell and Molecular Biology - Haliç Üniversitesi

Create successful ePaper yourself

Delete template?

Save as template?