2009

1. Agrawal, N., Padmanabhan, N. and Hasan, G. (2009). Inositol 1,4,5 – trisphosphate receptor function in Drosophila insulin producing cells. PLOS One, 4, e6652. 2. Beena, K., Kulothungan, R., Patra, A.K., Udgaonkar, J.B. and Varadarajan, R. (2009). SecB mediated protein export need not occur via kinetic partitioning. Journal of Molecular Biology, 385, 1243–1256.   

3. Bhaduri, A., Kalaimathy, S. and Sowdhamini, R. (2009). Conservation and Divergence among Salmonella enterica subspecies . Infectious Disorders-Drug Targets special in silico. 9, 248–256.    

4. +Bhalla, U.S. (2009). Molecules, networks and memory. In: Systems Biology: The Challenge of Complexity. Ed. S. Nakanishi, R. Kageyama and D. Watanabe. Springer, Tokyo, 2009.  

5. Bhatia, D., Mehtab, S., Krishnan, R., Indi, S.S., Basu, A. and Krishnan, Y. (2009).  Icosahedral DNA nanocapsules via modular assembly. Angewandte Chemie International Edition, 48, 4134 – 4137.   

6. Bhattacharya. A., Sankar, S. and Panicker, M.M (2009). Differences in the C-terminal tail contribute to the variation in trafficking between the Rat and Human 5-HT2A receptor isoforms: Identification of a primate-specific tripeptide ASK motif that confers GRK-2 and β2-Arrestin interaction. Journal of Neurochemistry,112, 732-732.  

7. Bhattacharya, D., Talwar, S.,  Mazumder, M. and Shivashankar, G.V. (2009). Spatio-temporal plasticity in chromatin organization in mouse cell differentiation and during Drosophila embryogenesis  Biophysical Journal, 96, 3832–3839.  

8. Bonzón-Kulichenko, E., Schwudke, D., Gallardo, N., Moltó, E., Fernández-Agulló, T., Shevchenko,
A. and Andrés, A. (2009). Central leptin regulates total ceramide content and SREBP-1C proteolytic maturation in rat white adipose tissue. Endocrinology. 150, 167–178. 

9. Brierley, D.J., Blanc, E.,  Reddy, O.V.,  VijayRaghavan, K. and  Williams, D.W. (2009).   Dendritic targeting in the leg neuropil of Drosophila: the role of midline signalling molecules in generating a myotopic map. PLoS Biology, 7, e1000199.

10. Callahan, B., Thattai, M. and Shraiman, B.I. (2009). Emergent gene order in a model of modular polyketide synthases. Proceedings of the National Academy of Science of USA, 106 , 19410–19415.  

11. Cardinale, B.J., Srivastava, D.S., Duffy,J.E., Wright, J.P., Downing,A.L., Sankaran, M., Jouseau, C.,   Cadotte, M.W., Carroll, I.T., Weis, J.J., Hector, A. and Loreau, M. (2009). Effects of biodiversity on the functioning of ecosystems: A summary of 164 experimental manipulations of species richness. Ecology, 90, 854 (data paper).

12. Chakraborty, S., Sharma, S., Maiti, P.K. and Krishnan, Y. (2009). The poly dA helix: A new structural motif for high-performance DNA-based molecular switches.  Nucleic Acids Research  37, 2810–2817.  

13. Chakraborty, T.S., Goswami, S.P. and Siddiqi, O. (2009). Sensory correlates of imaginal conditioning in Drosophila melanogaster. Journal of  Neurogenetics,  23, 210–219.

14. Chaudhry, A.,  Verghese, D.A.,  Das, S.R.,  Jameel, S.,  George, A.,  Bal, V.,  Mayor, S. and Rath, S.  (2009). HIV-1 Nef Promotes Endocytosis of Cell Surface MHC Class II Molecules via a Constitutive Pathway. Journal of Immunology, 183, 2415–2424.  

15. Chiang, A., Rashi Priya., Ramaswami, M., VijayRaghavan, K. and Rodrigues, V. (2009). Neuronal activity and Wnt signaling act through GSK-3b to regulate axonal integrity in mature Drosophila olfactory sensory neurons. Development, 136, 1273–1282.  

16. Demaegdt, H., Lukaszuk, A., De Buyser, E., De Backer, J.P., Szemenyei, E., Tóth, G., Chakravarthy, S., Panicker, M.M., Michotte, Y., Tourwé, D. and Vauquelin, G. (2009). Selective labeling of IRAP by the tritiated AT(4) receptor ligand [(3)H]Angiotensin IV and its stable analog [(3)H]AL–11. Molecular Cell Endocrinology 311, 77–86. 

17. Doodhi, H.,  Ghosal, D.,  Krishnamurthy, M., Jana, S.C.,  Shamala, D., Bhaduri, A., Sowdhamini, R. and Ray, K (2009). KAP, the Accessory Subunit of Kinesin-2, Binds the Predicted Coiled-Coil Stalk of the Motor Subunits. Biochemistry, 48, 2248–2260.   

18. +Duffy, J. E., Srivastava, D. S., McLaren, J., Sankaran, M., Solan, M., Griffin, J., Emmerson, M. and Jones, K. E. (2009). Forecasting decline in ecosystem services under realistic scenarios of extinction. In Biodiversity, Ecosystem Functioning, and Human Wellbeing: An Ecological and Economic Perspective. Shahid Naeem, Daniel E. Bunker, Andy Hector, Michel Loreau and Charles Perrings (eds). Oxford University Press, 60-77.

19. Franklin, B.J., Subramanian, K.A.,  Fernando, A.S. and Krishnan, K. S. ( 2009). Diversity and distribution of conidae from TamilNadu Coast of India (Mollusca: Caenogastropoda: conidae) Zootaxa, 2250, 1– 63.  

20. Gogia, S.,  Jain, A. and  Puranik, M. (2009). Structures, ionization equilibria and tautomerism of 6-oxopurines in solution.  Journal of Physical Chemistry B, 113, 15101–15118.

21. Graessler, J., Schwudke, D., Schwarz, PEH., Herzog, R. and Shevchenko, A. (2009). Top-Down Lipidomics Reveals Ether Lipid Deficiency in Blood Plasma of Hypertensive Patients. PLoS ONE  4, e6261.

22. Gupta, G.D.,  Swetha, M.G., Kumari, S., Lakshminarayan, R., Dey, G. and Mayor, S.  (2009). Analysis of endocytic pathways in Drosophila cells reveals a conserved role for GBF1 in internalization via GEECs. PLoS One, 4, e6768.  

23. Guruharsha,  K.G., Ruiz-Gomez, M., Ranganath, H.A., Siddharthan, R. and VijayRaghavan, K. (2009). The complex spatio‐temporal regulation of the Drosophila myoblast attractant gene duf/kirre. PLoS ONE, 4, E6960.

24. Hameed, F.M., Soni, G.V., Krishnamurthy, H.  and Shivashankar G.V. (2009). Probing structural stability of chromatin assembly sorted from living cells,  Biochemical and Biophysical Research Communication, 385, 518–522. 

25. Inamdar, M., Venu, P., Srinivas, M.S., Rao, K.A. and VijayRaghavan, K. (2009). Derivation and characterization of two sibling human embryonic stem cell lines from discarded Grade III embryos. Stem Cells and Development, 18, 37‐48. 

26. Jain, P. and Bhalla, U.S. (2009). Signaling logic of activity–triggered dendritic protein synthesis: an mTOR gate but not a feedback switch. PLoS: Computational Biology, 5, e1000287.   

27. Jain, R., Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2009). Replication across template T/U by human DNA polymerase-iota. Structure, 17, 974.  

28. Jayanth, N.,  Ramachandran, S. and Puranik, M (2009).  Solution Structure of the DNA damage lesion 8-Oxoguanosine from ultraviolet resonance Raman Spectroscopy.  Journal of Physical Chemistry A, V 113, 1459–1471.

29. Jayshree, R.S., Adurthi, S., Maliekal, T. and Krishna, S. (2009) Cell intrinsic and extrinsic factors in cervical carcinogenesis. Indian Journal of Medical Research, 130, 286-295.  

30. Jayasree, K., Ranjith, P., Rao, M. and Sunil Kumar, P.B. (2009). Equilibrium properties of a grafted polyelectrolyte with explicit counter ions. Journal of Chemical Physics, 130, 094901. 

31. Jha, S.K., Dhar, D., Krishnamoorthy, G. and Udgaonkar, J.B.(2009).  Continuous dissolution of structure during the unfolding of a small protein. Proceedings of the National Academy of Science of USA, 106, 11113–11118.

32. Jha, S.K. and Udgaonkar, J.B. (2009)  Direct evidence for a dry molten globule intermediate during the unfolding of a small protein. Proceedings of the National Academy of Science of USA, 106, 12289–12294. 

33. Jha, A., Udgaonkar, J.B. and Krishnamoorthy, G. (2009). Characterization of the heterogeneity and specificity of inter-polypeptide interactions in amyloid protofibrils by measurement of site-specific fluorescence anisotropy decay kinetics. Journal of Molecular Biology, 393, 735–752.

34. Kanagarajadurai. K., Manoharan M., Bhattacharya A.,  Panicker, M.M. and Sowdhamini, R. (2009). Molecular Modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding. Molecular Biosystems, 5, 1877–1888. 

35. @Kanagarajadurai, K., Kalaimathy, S., Nagarajan, P. and Sowdhamini, R. (2009). A bioinformatics protocol for rigorous structure-based sequence alignment of distantly related proteins. Nature Protocols Network.  

36. Kavitha, S., Usman, H. and Mathew, M.K. (2009). Fast inactivation in potassium channels – interplay of multiple cytoplasmic domains. Biochem Biophys Research Communication, 388, 490–495. 

37. Khurana, S., Abu Baker, M.B. and Siddiqi, O. (2009). Odour avoidance learning in the larva of Drosophila melanogaster. Journal of  Bioscience, 34, 621–631. 

38. Kikuchi, N., Ehrlicher, A., Koch, D., Kas, J.A., Ramaswamy, S. and Rao, M. (2009).  Filament in an active medium: buckling, stiening and negative dissipation. Proceeding of the National Academy of Sciences of USA, 106, 19776–19779.

39. *Krishnan, K.S. (2009).  Scientoonic tell-tale of genome and DNA. Current Science, 96, 593.  

40. Krishnamurthy, P., Ranathunge, K., Franke, R., Prakash, H.S., Schreiber, L. and Mathew, M.K. (2009) Salt tolerance in rice (Oryza sativa L.): Role of apoplast forming barriers in the roots. Planta, 230, 119–134.

41. Kumar, V., Alla, S.R., Krishnan, K.S. and Ramaswami, M. (2009). Syndapin is dispensable for synaptic vesicle endocytosis at the Drosophila larval neuromuscular junction. Molecular Cell Neuroscience, 40, 234–241.

42. Kumar, V., Fricke, R., Bhar, D., Reddy-Alla, S., Krishnan, K.S., Bogdan, S. and Ramaswami, M. (2009). Syndapin promotes formation of a postsynaptic membrane system in Drosophila. Molecular  Biolology Cell,  20, 2254–2264.

43. Kumar, S. and Udgaonkar, J.B. (2009)  Structurally distinct amyloid protofibrils form on separate pathways of aggregation of a small protein. Biochemistry, 48, 6441–6449. 

44. Kumar, S. and Udgaonkar, J.B. (2009). Conformational conversion may precede or follow aggregate elongation on alternative pathways of amyloid protofibril formation.  Journal of Molecular Biology, 385, 1266–1276.   

45. Marudachalam, Shanmugasundaram. and Mrinalini, Puranik. (2009).  Computational prediction of vibrational spectra of normal and modified DNA Nucleobases. Journal of Raman Spectroscopy,   40, 1726–1748.

46. Mendiratta, U., Kumar, A.,  Mishra, C.,  and  Sinha, A.  (2009). Winter ecology of the Arunachal macaque macaca munzala in Pangchen Valley, Western Arunachal Pradesh, Northeastern India. American Journal of Primatology, 71, 939–947.

47. McEwen, B.S., Chattarji, S., Diamond, D.M., Jay, T.M., Reagan, L.P., Svenningsson, P. and Fuchs, E. (2009). The neurobiological properties of tianeptine (Stablon): from monoamine hypothesis to glutamatergic modulation. Molecular Psychiatry, 15, 237–249.  

48. Modi, S., Swetha, M. G., Goswami, D., Gupta, G. D., Mayor, S. and Krishnan, Y. (2009). A DNA nanomachine that maps spatial and temporal pH changes in living cells.  Nature Nanotechnology,    4, 325–330.   

49. Mondol, S., Karanth, K.U., Kumar, S., Gopalswamy, A., Andheria, A. and Ramakrishnan, U. Evaluation of non-invasive genetic sampling methods for estimating tiger population size. Biological Conservation, 142, 2350–2360.

50. Mondol, S., Karanth, K.U. and Ramakrishnan, U. (2009b). Why the Indian subcontinent holds the key to global tiger recovery. PLoS Genetics, 5, e1000603. 

51. Mondol, S., Navya, R., Athreya, V., Velu Mani, S., Sunagar, K. and Ramakrishnan, U. (2009). A panel of microsatellites to identify leopards (Panthera pardus) individually from non-invasive samples, BMC Genetics. 10:79. 

52. Muhuri, S. and  Rao, M. (2009). `Sequence dependent elasticity and local stiness of a DNA heteropolymer.  Journal of Statistical Mechanics,  6. 

53. Mysore, K., Subramanian, K.A., Sarasij, R.C., Suresh, A., Shyamala, B.V., VijayRaghavan, K. and Rodrigues, V. (2009). Caste and sex specific olfactory glomerular organization and brain architecture in two sympatric antspecies Camponotus sericeus and Camponotus compressus (Fabricius, 1798). Arthropod Structure and Development, 38, 485–497.  

54. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2009). DNA synthesis across an abasic lesion by human DNA polymerase iota. Structure, 17, 530.

55. O’Keefe, K., Ramakrishnan, U., van Tuinen, M. and Hadly, E.A. (2009). Source-sink dynamics in a common montane mammal. Molecular Ecology. 18(23):4775-89.

56. Patra, A.K. and Udgaonkar, J. B. (2009).  GroEL can unfold late intermediates populated on the folding pathways of monellin. Journal of Molecular Biology, 389, 759–775.  

57. Perumalsamy, L.R., Nagala, M., Bannerjee, P. and Sarin, A. (2009). A hierarchical cascade activated by non-canonical Notch signaling and the mTOR - Rictor complex regulates neglect-induced death in mammalian cells. Cell Death and Differentiation, 16, 879–889.

58. Purushothanam, D. and Sarin, A. (2009). Cytokine-dependent regulation of NADPH oxidase activity and the consequences for activated T cell homeostasis Journal of Experimental Medicine 206, 1515–1523.

59. Raa, H., Grimmer, S., Schwudke, D., Bergan, J., Wälchli, S., Skotland, T., Shevchenko, A. and Sandvig, K. (2009).  Glycosphingolipid Requirements for Endosome-to-Golgi Transport of Shiga Toxin. Traffic, 10, 868–82.

60. Ramadas, R. and Thattai, M. (2009). Flipping DNA to generate and regulate microbial consortia. Genetics, 184 , 285–293. 

61. Ramakrishnan, N., Bhalla, U.S. and Tyson, J.J. (2009). Computing with proteins. Computer, 42, 47–56.  

62. Ramakrishnan, U. and Hadly, E.A.H. (2009). Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions? Molecular Ecology (In press). 

63. Ramakrishnan, U. and Hadly, E.A. (2009). Using phylochronology to reveal cryptic population
histories. Molecular Ecology, 18, 1310–1330. 

64. Ramakrishnan, S., Rajendiran, V., Palaniandavar, M., Periasamy, V.S,, Srinag, B.S., Krishnamurthy, H and Akbarsha, M.A. (2009). Induction of cell death by ternary copper(II) complexes of l-Tyrosine and diimines: Role of coligands on DNA binding and cleavage and anticancer activity. Inorganic Chemistry, 48, 1309–1322.  

65. Rao, R., Suvrathan, A., Miller, M.M., McEwen, B.S. and Chattarji, S. (2009). PTSD: from Neurons to Networks. Neurobiology of PTSD, Shiromani P., Keane T., LeDoux J., Editors. Humana Press, Inc., NJ. 

66. Reich, A., Schwudke, D., Meurer, M., Lehmann, B. and Shevchenko, A. (2009). Lipidome of narrow-band ultraviolet B irradiated keratinocytes shows apoptotic hallmarks. Experimental  Dermatology (Epub ahead of print).

67. Rekha, J., Sridhara Chakravarthy., Veena, L.R., Kalai Vani, P., Rupam Choudhary., Harsha, N. Halahalli., Nirmala, M., Anandh Dhanushkodi., Phalguni Anand Alladi., Geetha M. Swamilingiah., Maulishree Agrahari., Raju, T.R., Panicker, M.M. and Bindu M. Kutty (2009). Transplantation of hippocampal cell lines improves spatial learning in rats with ventral subicular lesions. Behavioural Neuroscience,  123, 1197-1217.   

68. Roozendaal, B., McEwen, B.S. and Chattarji, S. (2009). Stress, memory and the amygdala. Nature Reviews Neuroscience, 10, 423–433.  

69. Saito, K., Dubreuil, V., Arai, Y., Wilsch-Bräuninger, M., Schwudke, D., Saher, G., Miyata, T., Breier, G., Thiele, C., Shevchenko, A., Klaus-Armin., Nave, K.A. and Huttner, W.B. (2009). Ablation of cholesterol biosynthesis in neural stem cells increases their VEGF expression and angiogenesis but causes neuron apoptosis. Proceedings of the National Academy of Science of USA, 106, 8350–8355.

70. Sankaran, S.,  Rani,S.S.,  Pankaj, B.,  Govind, M.K.,  Offman, B., Narayanaswamy Srinivasan, B. and  Sowdhamini, R (2009). Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One, 4, e4981 

71. Shameer, K., Nagarajan, P., Gaurav, K. and Sowdhamini, R. (2009). 3PFDB – A database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach.  BioData Mining, 2, 8

72. Shameer, K., Ambika, S.,  Varghese, S.M., Karaba, N., Udayakumar, M. and Sowdhamini, R. (2009). STIFDB – Arabidopsis stress responsive transcription factor database. International Journal of Plant Genomics, 2009, 583429. 
Sane, S.P. and McHenry, M.J. (2009). The biomechanics of sensory organs, Integrative and Comparative Biology, 49, i8–i23. 

73. Sankaran, M. (2009). Diversity patterns in savanna grassland communities: implications for conservation strategies in a biodiversity hotspot. Biodiversity and Conservation, 18, 1099 – 1115. 

74. Sankaran, M. and Anderson, T.M. (2009). Management and restoration in African Savannas: Interactions and feedbacks. In New Models for Ecosystem Dynamics and Restoration, Richard Hobbs and Kate Suding (eds). Island Press, 136 – 155.

75. Sinha, K.K. and Udgaonkar, J.B. (2009). Early events in protein folding. Current Science,  96,  1053–1070.  

76. Srivastava, D.S., Cardinale B.J., Downing A.L., Duffy J.E., Jouseau, C., Sankaran, M.and Wright, J.P. (2009). Diversity has stronger top-down than bottom-up effects on decomposition. Ecology, 90, 1073 – 1083.

77. Srivastava, S. and Krishna, S. (2009) Cancer stem cells: An approach to identify newer therapeutic targets.   Journal of Stem Cells, 4, 123-131.   

78. Sundaramurthy, P.,  Gakkhar, S. and Sowdhamini, R. (2009). Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each ther: A systems approach . Bioinformation, 3, 244-249.  

79. Sundaramurthy, P.,  Gakkhar, S. and Sowdhamini, R. (2009). Computational prediction and analysis of impact of the cross-talks between JNK and P38 kinase cascades . Bioinformation, 3, 250-254.   

80. Venkiteswaran, G. and Hasan, G. (2009). Intracellular calcium signaling and store operated Ca2+ entry are required in Drosophila neurons for flight. Proceedings of the National Academy of Sciences of USA, 106, 10326–10331. 

81. Upadhyay, S.K., Nagarajan, P. and Mathew, M.K. (2009). Potassium channel opening: A subtle two step. Journal of  Physiology, 587, 3851–3868.    

82. Wani, A.H. and Udgaonkar, J.B. (2009). Revealing a concealed intermediate that forms after the rate-limiting step of refolding of the SH3 domain of PI3 kinase. Journal of Molecular Biology, 387, 348–362.   

83. Wani, A.H. and Udgaonkar, J.B. (2009). Native state dynamics drive the unfolding of the SH3 domain of PI3 kinase at high denaturant concentration. Proceedings of the  National Academy of Science of USA, 106, 20711–20716.

84. Sane S.P.* and McHenry M.J. (2009) The biomechanics of sensory organs. Integrative and Comparative Biology, 49(6):i8-i23. | PMID

85. P. Kain, Chandrashekaran, S., V. Rodrigues and G. Hasan (2009). Drosophila mutants in phospholipid signaling have reduced olfactory responses as adults and larvae. J. Neurogenetics. 23(3):303-12

86. Holford M, Zhang MM, Gowd KH, Azam L, Green BR, Watkins M, Ownby JP, Yoshikami D, Bulaj G, Olivera BM. 2009. Pruning Nature: Biodiversity-Derived Discovery of Novel Sodium Channel Blocking Conotoxins from Conus bullatus. Toxicon; 53(1):90-8