Publications - 2007
1.Ajay, S.M. and Bhalla, U.S. (2007). A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity. HFSP Journal, 1, 49-66.
2. Altman, D., Goswami, D., Hasson, T., Spudich, J.A. and Mayor, S. (2007). Precise positioning of myosin VI on endocytic vesicles in vivo. PLoS Biology, 5, e210.
3.Anil, V., Krishnamurthy, H. and Mathew, M.K. (2007). Limiting cytosolic Na+ confers salt tolerance to rice cells in culture: A two-photon microscopy study of SBFI loaded cells. Physiologia Plantarum,129, 607-50.
4.Anil, V., Krishnamurthy, H. and Mathew, M.K. (2007). Na+ Efflux across the plasma membrane contributes to salt tolerance of rice cells in culture: Proceedings of the Indian National Science Academy, 73, 43-50.
5.Benjamin Franklin, S. Fernando, A., Chalke, B.A. and Krishnan, K.S. (2007). Radular morphology of conus (gastropoda: caenogastropoda: conidae) from India. Molluscan Research, 27, 111-122.
6.+Bhaduri, A., and Sowdhamini, R. (2007). O-protein phosphatases in signal transduction pathways. In New Trends in Bioinformatics, P. Shanmugavel (ed), 40-58.
7.Cannon, R.C., Gewaltig, M.O., Bhalla, U.S., Cornelis, H., Gleeson, P., Hines, M.L., Howell, F.W., Muller, E., Stiles, J.R. Wils, S. and De Schutter, E. (2007). Interoperability of neuroscience modeling software: Current status and future directions. Neuroinformatics, 5.
8.Chakraborty, D., Ramakrishnan, U., Panor, J., Mishra, C. and Sinha, A. (2007). Phylogenetic relationships and morphometric affinities of the Arunachal macaque Macaca munzala, a newly described primate from Arunachal Pradesh, Northeastern India. Molecular Phylogenetics and Evolution, 44, 838-849.
9.Chaudhry, A., Das, S.R., Jameel, S., George, A., Bal, V., Mayor, S. and Rath, S. (2007). HIV-1 Nef protein triggers endocytosis of immune costimulatory proteins CD80 and CD86. Cell Host and Microbe, 1, 37-49.
10.Chadda, R., Howes, M.T., Plowman, S.J., Hancock, J.F., Parton, R.G. and Mayor, S. (2007). Cholesterol-sensitive Cdc42 activation regulates actin polymerization for endocytosis via the GEEC pathway. Traffic, 8, 702-717.
11. Dixit R., VijayRaghavan, K. and Bate, M. (2007). Hox genes and the regulation of movement in Drosophila. Develompental Neurobiology, 68, 309-331.
12.Dolen G., Osterweil E., Rao, B.S.S., Smith, G.B., Auerbach B.D., Chattarji, S. and Bear, M.F. (2007). Correction of fragile X syndrome in mice. Neuron, 56, 955-962.
13.Gadkari, R., Sandhya, S., Sowdhamini, R. and Dighe, R.R. (2007). The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor. Molecular and Cellular Endocrinology, 260, 23-32.
14. Gowd, K.H., Krishnan, K.S. and Balaram, P. (2007). Identification of conus amadis disulfide isomerase: Minimum sequence length of peptide fragment necessary for protein annotation. Molecular BioSystems, 3, 554-566.
15.Ghodke, H.B., Krishnan, R., Vignesh, K., Kumar, G.V.P., Narayana, C. and Krishnan, Y. (2007). The I-Tetraplex building block: Rational design and controlled fabrication of robust 1D DNA scaffolds through non-watson-crick interactions. Angewandte Chemie International Edition, 46, 2646-2649.
16.Goyal, G., Fell, B., Sarin, A., Youle, R.J. and Sriram, V. (2007). Role of mitochondrial remodeling in programmed cell death in Drosophila melanogaster. Developmental Cell, 12, 807-816.
17. Gupta, Y. K., Nair, D. T., Wharton, R. P. and Aggarwal, A. K. (2008) Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity. Structure. 16:549.
18.Hatton-Ellis, E.,Ainsworth, C., Sushama, Y., Wan, S., VijayRaghavan, K. and Skaer, H. (2007). Genetic regulation of patterned tubular branching in Drosophila. Proceedings of the National Academy of Sciences of USA, 104, 169-174.
19.Hayashi, M.L., Rao, B.S.S., Seo J-S., Choi H-S., Dolan, B.M., Choi S-Y., Chattarji, S. and Tonegawa, S. (2007). Inhibition of p21-activated kinase rescues symptoms of fragile X syndrome in mice. Proceedings of the National Academy of Sciences of USA, 104, 11489-494.
20.Hellman, A.N., Rau, K.R., You, H.H., S. Bae, S., Palmer, J.F., Phillips, K.S., Allbritton, N.L. and V. Venugopalan, V. (2007). Laser-induced mixing in microfluidic channels. Analytical Chemistry, 79, 4484-4492.
21.@Hellman, A.N., Rau, K.R., You, H.H. and Venugopalan, V. (2007). Biophysical response to pulsed laser microbeam-induced cell lysis and molecular delivery. Journal of Biophotonics, DOI:10.1002/jbio.200710010.
22.James, J., Ramakrishnan, U. and Datta, A. (2007). Molecular evidence for the occurrence of the leaf deer Muntiacus putaoensis in Arunachal Pradesh, north-east India. Conservation Genetics (In press).
23. Jha, S.K. and Udgaonkar, J.B. (2007). Exploring the cooperativity of the fast folding reaction of a small protein using pulsed thiol labeling and mass spectrometry. Journal of Biological Chemistry, 282, 37479-37491.
24. Khader, S. and Sowdhamini, R. (2007). IWS: Integrated Web Server for protein sequence and structure analysis. Bioinformation, 2, 86-90.
25.Kumar, S., Mohanty, S.K. and Udgaonkar, J.B. (2007). Mechanism of formation of amyloid protofibrils of barstar from soluble oligomers: Evidence for multiple steps and lateral association coupled to conformational conversion Journal of Molecular Biology, 367, 1186-1204.
26. Mandal, A., Ramakrishnan, M., Ramasamy, S., Sabareesh, V., Openshaw, M.E., Krishnan, K.S. and Balaram, P. (2007). De novo sequencing of T-superfamily conotoxins from conus virgo: Pyroglutamic acid identification, leucine/isoleucine discrimination and disulfide arrangement by MALDI mass spectrometry. Journal of American Society for Mass spectrometry, 18, 1396-404.
27.Mondal, K., Dastidar, A.G., Singh, G., Madhusudhanan, S., Gande, S.L., VijayRaghavan, K. and Varadarajan, R. (2007). Design and isolation of temperature-sensitive mutants of Gal4 in yeast and Drosophila. Journal of Molecular Biology, 370, 939-950.
28.Mondal, K., VijayRaghavan, K. and Varadarajan, R. (2007). Design and utility of temperature-aensitive Gal4 mutants for conditional gene expression in Drosophila. Fly, 1, 282-286.
29. Mayor, S. and R.E. Pagano, R.E. (2007). Pathways of clathrin-independent endocytosis. Nature Reviews in Molecular and Cellular Biology, 8, 603-612.
30. +McEwen, B.S. and Chattarji, S. (2007). Neuroendocrinology of stress. In: Handbook of Neurochemistry and Molecular Neurobiology (3rd Ed.), A. Lajtha and J.D. Blaustein (eds.), 571-594, Springer Verlag.
31. Metpally, R.R., Vigneshwar, R., Sowdhamini, R. (2007). Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigriviridis. Journal of Biological Sciences, 32, 43-50.
32. Mazumder, A. and Shivashankar, G.V. (2007). Gold-nanoparticle-assisted laser perturbation of chromatin assembly reveals unusual aspects of nuclear architecture within living cells. Biophysical Journal, 93, 2209-2216.
33. Mukherjee, N., Mondol, S., Andheria., A. and Ramakrishnan, U. (2007). Rapid multiplex PCR based species identification of wild tigers using non-invasive samples, Conservation Genetics, 8, 1465-1470.
34.Nagapriya, K.S., Raychaudhuri, A.K. and Shivashankar, G.V. (2007). Thermal fluctuations in histone during denaturation. Journal of Nanoscience Nanotechnology, 7, 2125-2128.
35. Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S. and Aggarwal, A. K. (2008) Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase. Structure. 16:239.
36. Parikh, N., Koshy, C., Dhayabharan, V., Perumalsamy, L.R., Sowdhamini, R. and Sarin, A. (2007). The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL BMC Cell Biology, 8, 16.
37.Pugalenthi, G., Suganthan, P.N., Sowdhamini, R. and Chakrabarti, S. (2007). SMotif: A server for structural motifs in proteins, Bioinformatics, 23, 637-638.
38. Pugalenthi, G., Ke Tang, Suganthan, P.N., Archunan, G. and R. Sowdhamini, R. (2007). A machine learning approach for the identification of odorant binding proteins from sequence-derived properties. BMC Bioinformatics, 8, 351.
39.Ramdass, B., Maliekal, T,T., Lakshmi, S., Rehman, M., T. T, Rema, P., Nair, P., Mukherjee, G., Reddy, B.K.M., Krishna, S. and Pillai, M.R. (2007). Co-expression of Notch1 and NF-KappaB signaling pathway components in human cervical cancer progression. Gyneiology Oncology, 104, 352-361.
40. Rao, J., Bhattacharya, D., Banerjee, B., Sarin, A. and Shivashankar, G.V. (2007). Trichostatin-A induces differential changes in histone dynamics and expression in HeLa cells. Biochemical and Biophysical Research Communications, 363, 263-268.
41. Raote, I., Bhattacharya, A. and Panicker, M.M. (2007). Serotonin 2A (5-HT2A) receptor function: Ligand-dependent mechanisms and pathways. In: Serotonin Receptors in Neurobiology, Frontiers in Neuroscience Vol 35 Edited by A. Chattopadhyay (Taylor and Francis, CRC Press).
42. Rikhy, R., Kamat, S., Ramagiri, S., Sriram, V. and Krishnan, K.S. (2007). Mutations in dynamin-related protein result in gross changes in mitochondrial morphology and affect synaptic vesicle recycling at the Drosophila neuromuscular junction. Genes Brain and Behaviour, 6, 42-53.
43. Roy, B., Singh, A.P., Shetty, C., V. Chaudhary, V., North, A., Landraf, M., VijayRaghavan, K. and Rodrigues, V. (2007). Metamorphosis of an identified serotonergic neuron in the Drosophila olfactory system. Neural Development, 2, 20.
44. Sarasij, R.C., Mayor, S. and Rao, M. (2007). Chirality-induced budding: A raft-mediated mechanism for endocytosis and morphology of caveolae? Biophysical Journal, 92, 3140-3158.
45. Srivastava, S., Banerjee, H., Chaudhry, A., Khare, A., Sarin, A., George, A., Bal, V., Durdik, J.M. and Rath, S. (2007). Apoptosis-inducing factor (Aif) regulates death in peripheral T cells. Journal of Immunology, 179, 797-803.
46. Patra, A.K. and Udgaonkar, J.B. (2007). Characterization of the folding and unfolding reactions of single-chain monellin: evidence for multiple intermediates and competing pathways. Biochemistry, 46, 11727-11743.
47. Saxena, A.M., Krishnamoorthy, G., Udgaonkar, J.B. and Periasamy, N. (2007). Identification of intermediate species in protein-folding by quantitative analysis of amplitudes in time-domain fluorescence spectroscopy. Journal of Chemical Sciences, 119, 61-69.
48. Sinha, K.K. and Udgaonkar, J.B. (2007). Dissecting the non-specific and specific components of the initial folding reacting of barstar by multi-site FRET measurements. Journal of Molecular Biology, 370, 385-405.
49. Soni, G.V., Brar, L., Meeran, F., Raychaudhuri, A.K. and Shivashankar, G.V. (2007). Distinct levels in the nanoscale organization of DNA-histone complex revealed by its mechanical unfolding. Appied Physics Letters, 90, 163904-3.
50. Dabholkar, S., and Thattai, M. (2007). Brainstorming Biology. IET Synthetic Biology, 1, 17-20.
51. Thattai, M., Burak, Y. and Shraiman, B.I. (2007). The origins of specificity in polyketide synthase protein interactions. PloS Computational Biology, 3, e186.
52.Nair, S., Agrawal, N. and Hasan, G. (2007). Homeostasis of glutamate neurotransmission is altered in Drosophila Inositol 1,4,5-trisphosphate receptor mutants. Invert Neuroscience, 7, 137-147.
53. @Reddy, C.C.S., Shameer, K., Bernard, O. and Sowdhamini, S. (2007). PURE: A web server for querying the relationship between Pre-existing domains and Unassigned Regions in proteins Nature Protocols, DOI: 10.1038/nprot. 486.
54. Sabareesh.V, Gowd, K.H., Ramasamy, P., Sudarslal, S., Krishnan, K.S., Sikdar, S.K. and Balaram, P. (2007). Characterization of contryphans from conus loroisii and conus amadis that target calcium channels. Peptides, 27, 2647-2654.
55. Shameer K and Sowdhamini R. (2007) IWS: Integrated web server for protein sequence and structure analysis.Bioinformation. 2, 86-90.
56.Tishkoff, S.A., Gonder, M.K., Henn., B.M., Mortensen, H., Fernandopulle, F., Gignoux, C., Godfrey, L., Nyambo, T.B., Underhill, P.A., Ramakrishnan, U., Reed, F.A. and Mountain, J.L. (2007). History of click-speaking populations of Africa inferred from mtDNA and Y chromosome variation. Molecular Biology and Evolution, 24, 2180-2195.
57.Titus, A.D., Rao, B.S.S., Harsha, H.N., Ramkumar, K., Srikumar, B.N., Singh, S.B., Chattarji, S. and Raju, T.R. (2007). Hypobaric hypoxia-induced dendritic atrophy of hippocampal neurons is associated with cognitive impairment in adult rats. Neuroscience, 145, 265-78.
58. Tripathi, L.P. and Sowdhamini, R. (2007). Genome-wide survey of protein families and superfamilies. Biobytes (In press).
59. van Tuinen, M., O’Keefe, K., Ramakrishnan, U. and Hadly, E. (2007). Fire and ice: Genetic structure of the uinta fround squirrel (Spermophilus armatus) across the yellowstone hotspot. Molecular Ecology (In press).
60.Vijayalakshmi, M., Shivashankar, G.V. and Sowdhamini, R. (2007). Simulations of SIN mutations and histone variants in human nucleosomes reveal altered protein-DNA and core histone interactions. Journal of Biomolecular Structure and Dynamics, 25, 207-218.
61. Rajendiran V, Karthik R, Palaniandavar M, Stoeckli-Evans H, Periasamy VS, Akbarsha MA, Srinag BS, Krishnamurthy H (2007). Mixed-Ligand Copper(II)-phenolate Complexes: Effect of Coligand on Enhanced DNA and Protein Binding, DNA Cleavage, and Anticancer Activity. Inorg Chem. 46: 8208-8221.