Publications - 2014
2014
1. Srinivasan, Umesh; Tamma, Krishnapriya; Ramakrishnan, Uma (2014) Past climate and species ecology drive nested species richness patterns along an east-west axis in the Himalaya. Global Ecology and Biogeography, 23, 1, 52-60
2. Modi, Souvik; Halder, Saheli; Nizak, Clement; et al. (2014) Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways. Nanoscale, 6, 2, 1144-1152
3. Tri Quang Truong; Vu Hoang Phan; Sane, Sanjay P.; et al. (2014) Pitching Moment Generation in an Insect-Mimicking Flapping-Wing System. Journal of Bionic Engineering, 11, 1, 36-51
4. Yadav, Mahipal; Raghupathy, Riya; Saikam, Varma; et al. (2014) Synthesis of non-hydrolysable mimics of glycosylphosphatidylinositol (GPI) anchors. Organic and Biomolecular Chemistry, 12, 7, 1163-1172
5. Mutt, Eshita; Mathew, Oommen K.; Sowdhamini, Ramanathan (2014) LenVarDB: database of length-variant protein domains. Nucleic Acid Research, 42, Issue D1, D246-D250
6. Roy, T.; Sane, S. P. (2014) The antennal positioning response of flying honeybees. Integrative and Comparative Biology, 54, Supplement: 1, E179-E179
7. Saxena, N.; Natesan, D.; Sane, S. P. (2014) Odor tracking behavior of fruit flies in the presence of landmark cues. Integrative and Comparative Biology, 54, Supplement: 1, E184-E184 Published: 2014
8. Bhalla, Upinder S. (2014) Multiscale Modeling and Synaptic Plasticity. In Computational Neuroscience, Book Series: Progress in Molecular Biology and Translational Science, Edited by: Blackwell, KT, 123, 351-386
9. Dharmaprakash, Akhilandeswarre; Mutt, Eshita; Jaleel, Abdul; et al. (2014) Proteome profile of a pandemic Vibrio parahaemolyticus SC192 strain in the planktonic and biofilm condition. Biofouling, 30, 6, 729-739
10. Manoharan, Malini; Fuchs, Patrick F. J.; Sowdhamini, Ramanathan; et al. (2014) Insights on pH-dependent conformational changes of mosquito odorant binding proteins by molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 32, 11, 1742-1751
11. Vaigundan, D.; Kalmankar, Neha V.; Krishnappa, J.; et al. (2014) A Novel Mutation in the Transglutaminase-1 Gene in an Autosomal Recessive Congenital Ichthyosis Patient. Biomed Research International, Article Number: 706827
12. Gogia, Spriha; Puranik, Mrinalini (2014) Solution structures of purine base analogues 6-chloroguanine, 8-azaguanine and allopurinol. Journal of Biomolecular Structure & Dynamics, 32, 1, 27-35
13. Suvrathan, Aparna; Bennur, Sharath; Ghosh, Supriya; et al. (2014) Stress enhances fear by forming new synapses with greater capacity for long-term potentiation in the amygdale. Philosophical Transactions of the Royal Society B- Biological Sciences, 369, 1633, Article Number:
14. Sudhakaran, Indulekha P.; Hillebrand, Jens; Dervan, Adrian; et al. (2014) FMRP and Ataxin-2 function together in long-term olfactory habituation and neuronal translational control. Proceeding the of the National Academy of Sciences of the United States of America, 111, 1, E99-E108
15. Paul, Arya; Sengupta, Surajit; Rao, Madan (2014) Non-affine fields in solid-solid transformations: the structure and stability of a product droplet. Journal of Physics-Condensed Matter, 26, 1, Article Number: 015007
16. Moulick, Roumita; Udgaonkar, Jayant B.(2014) Thermodynamic Characterization of the Unfolding of the Prion Protein. Biophysical Journal, 106, 2, 410-420
17. Koester, Darius V.; Husain, Kabir; Iljazi, Elda; et al (2014) In Vitro Reconstitution of Remodeling Actin Asters - Steps towards a Minimal Active Actomyosin Cortex. Biophysical Journal, 106, 2, Supplement: 1, 170A-170A
18. Saha, Suvrajit; Das, Amit; Polley, Anirban; et al. (2014) Active Patterning of Cell Surface Molecules from Nanoscale Clusters to Mesoscale Membrane Mosaics Dictated by Dynamic Actin. Biophysical Journal, 106, 2, Supplement: 1, 521A-521A
19. Sarkar, Saswata; Udgaonkar, Jayant B.; Krishnamoorthy, Guruswamy (2014) Evidence for the Formation of Dry and Wet Molten Globules During Unfolding Process of a Small Protein. Biophysical Journal, 106, 2, Supplement: 1, 671A-671A
20. Lehmann, Caroline E. R.; Anderson, T. Michael; Sankaran, Mahesh; et al. (2014) Savanna Vegetation-Fire-Climate Relationships Differ Among Continents. Science, 343, 6170, 548-552
21. Pillay, Rajeev; Miller, David A. W.; Hines, James E.; et al. (2014) Accounting for false positives improves estimates of occupancy from key informant interviews. Diversity and Distributions, 20, 2, 223-235
22. Lakshmi, B.; Ramakrishnan, C.; Archunan, G.; et al. (2014) Investigations of Ramachandran disallowed conformations in protein domain families. International Journal of Biological Macromolecules, 63, 119-125.
23. Surana, Parag; Satchidanandam, Vijaya; Nair, Deepak T. (2014) RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state. Nucleic Acid Research, 42, 4, 2758-2773
24. Garg, M.; Ramdas, N.; Vijayalakshmi, M.; et al (2014) The C-terminal domain (CTD) in linker histones antagonizes anti-apoptotic proteins to modulate apoptotic outcomes at the mitochondrion. Cell Death and Disease, 5, Article Number: e1058
25. Mirza, Zeeshan Ayaz; Sanap, Rajesh V.; Upadhye, Raman (2014) A new species of scorpion of the genus Neoscorpiops Vachon, 1980 (Scorpiones: Euscorpiidae) from India. Comptes Rendus Biologies, 337, 2, 143-149
26. Malhotra, Sony; Sankar, Kannan; Sowdhamini, Ramanathan (2014) Structural Interface Parameters Are Discriminatory in Recognising Near-Native Poses of Protein-Protein Interactions. PLOS ONE, 9, 2, Article Number: e80255
27. Mirza, Zeeshan A.; Sanap, Rajesh V.; Bhosale, Harshal (2014) Preliminary Review of Indian Eumenophorinae (Araneae: Theraphosidae) with Description of a New Genus and Five New Species from the Western Ghats. PLOS ONE, 9, 2, Article Number: e87928
28. Ting, Chun-Yuan; McQueen, Philip G.; Pandya, Nishith; et al. (2014) Photoreceptor-Derived Activin Promotes Dendritic Termination and Restricts the Receptive Fields of First-Order Interneurons in Drosophila. Neuron, 81, 4, 830-846
29. Mudgal, Richa; Sowdhamini, Ramanathan; Chandra, Nagasuma; et al. (2014) Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability. Journal of Molecular Biology, 426, 4, 962-979
30. Sabareesan, A. T.; Udgaonkar, Jayant B. (2014) Amyloid Fibril Formation by the Chain B Subunit of Monellin Occurs by a Nucleation-Dependent Polymerization Mechanism. Biochemistry, 53, 7, 1206-1217
31. Yadahalli, Shilpa; Gosavi, Shachi (2014) Designing cooperativity into the designed protein Top7. Proteins-Structure Function and Bioinformatics, 82, 3, 364-374
32. Kim, So-Yeon; Burris, Jessica; Bassal, Frederick; et al. (2014) Fear-Specific Amygdala Function in Children and Adolescents on the Fragile X Spectrum: A Dosage Response of the FMR1 Gene. Cerebral Cortex, 24, 3, 600-613
33. Chandraprakash, Deepti; Seshasayee, Aswin Sai Narain (2014) Inhibition of factor-dependent transcription termination in Escherichia coli might relieve xenogene silencing by abrogating H-NS-DNA interactions in vivo. Journal of Biosciences, 39, 1, 53-61 Published: MAR 2014
34. Krishnan, Anand; Sane, Sanjay P. (2014) Visual feedback influences antennal positioning in flying hawk moths. Journal of Experimental Biology, 217, 6, 908-917
35. Dey, Gautam; Gupta, Gagan D.; Ramalingam, Balaji; et al. (2014) Exploiting Cell-To-Cell Variability To Detect Cellular Perturbations. PLOS ONE, 9, 3, Article Number: e90540
36. Joseph, Agnel P.; Shingate, Prashant; Upadhyay, Atul K.; et al. (2014) 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. Database-The Journal of Biological Database and Curation, Article Number: bau026
37. Manzo, Carlo; van Zanten, Thomas S.; Saha, Suvrajit; et al. (2014) PSF decomposition of nanoscopy images via Bayesian analysis unravels distinct molecular organization of the cell membrane. Scientific Reports, 4, Article Number: 4354
38. Modi, Mehrab N.; Dhawale, Ashesh K.; Bhalla, Upinder S. (2014) CA1 cell activity sequences emerge after reorganization of network correlation structure during associative learning. Elife, 3, Article Number: e01982
39. Savory, Fiona R.; Benton, Timothy G.; Varma, Varun; et al. (2014) Stressful environments can indirectly select for increased longevity. Ecology and Evolution, 4, 7, 1176-1185
40. Bhalla, Upinder S. (2014) Molecular computation in neurons: a modeling perspective. Current Opinion in Neurobiology, 25, 31-37
41. Hautier, Yann; Seabloom, Eric W.; Borer, Elizabeth T.; et al. (2014) Eutrophication weakens stabilizing effects of diversity in natural grasslands. Nature, 508, 7497, 521
42. Ray, A.; Quader, S. (2014) Genetic diversity and population structure of Lantana camara in India indicates multiple introductions and gene flow. Plant Biology, 16, 3, 651-658
43. Bay, Rachael A.; Ramakrishnan, Uma; Hadly, Elizabeth A. (2014) A Call for Tiger Management Using Reserves of Genetic Diversity. JOURNAL OF HEREDITY, 105, 3, 295-302
44. Jain, Pragati; Bhalla, Upinder S (2014) Transcription Control Pathways Decode Patterned Synaptic Inputs into Diverse mRNA Expression Profiles. PLOS ONE, 9, 5, Article Number: e95154
45. Savory, Fiona R.; Varma, Varun; Ramakrishnan, Uma (2014) Identifying geographic hot spots of reassortment in a multipartite plant virus. Evolutionary Applications, 7, 5, 569-579
46. Savory, F. R.; Ramakrishnan, U. (2014) Asymmetric patterns of reassortment and concerted evolution in Cardamom bushy dwarf virus. Infection Genetics and Evolution, 24, 15-24
47. Chakraborty, Saikat; Mehtab, Shabana; Krishnan, Yamuna (2014) The Predictive Power of Synthetic Nucleic Acid Technologies in RNA Biology. Accounts of Chemical Research, 47, 6, 1710-1719
48. Kohli, Mayank; Sankaran, Mahesh; Suryawanshi, Kulbhushansingh R.; et al. (2014). A penny saved is a penny earned: lean season foraging strategy of an alpine ungulate. Animal Behaviour, 92, 93-100
49. Wordley, Claire F. R.; Foui, Eleni K.; Mudappa, Divya; et al. (2014) Acoustic identification of bats in the southern Western Ghats, India . ACTA Chiropterologica, 16, 1, 213-222
50. Hebbar, Santa; Schulz, Wolf Dieter; Sauer, Ulrich; et al. (2014) Laser Capture Microdissection Coupled with On-Column Extraction LC-MSn Enables Lipidomics of Fluorescently Labeled Drosophila Neurons. Analytical Chemistry, 86, 11, 5345-5352
51. Srivathsa, Arjun; Karanth, Krithi K.; Jathanna, Devcharan; et al. (2014) On a Dhole Trail: Examining Ecological and Anthropogenic Correlates of Dhole Habitat Occupancy in the Western Ghats of India . PLOS ONE, 9, 6, Article Number: e98803
52. Joseph, Agnel Praveen; de Brevern, Alexandre G. (2014) From local structure to a global framework: recognition of protein folds. Journal of the Royal Society Interface, 11, 95, Article Number: 20131147
53. Malhotra, Poop; Udgaonkar, Jayant B. (2014) High-Energy Intermediates in Protein Unfolding Characterized by Thiol Labeling under Nativelike Conditions. Biochemistry, 53, 22, 3608-3620
54. Bhardwaj, Vishal; Panicker, Mitradas M.; Udgaonkar, Jayant B. (2014) Fluorescence Anisotropy Uncovers Changes in Protein Packing with Inclusion Growth in a Cellular Model of Polyglutamine Aggregation. Biochemistry, 53, 22, 3621-3636
55. Ramaswami, Mani (2014) Network Plasticity in Adaptive Filtering and Behavioral Habituation. Neuron, 82, 6, 1216-1229
56. Dasgupta, Amrita; Udgaonkar, Jayant B.; Das, Payel (2014) Multistage Unfolding of an SH3 Domain: An Initial Urea-Filled Dry Molten Globule Precedes a Wet Molten Globule with Non-Native Structure. Journal of Physical Chemistry B, 118, 24, Special Issue: SI, 6380-6392
57. Maitra, Ananyo; Srivastava, Pragya; Rao, Madan; et al.(2014) Activating Membranes. Physical Review Letters, 112, 25, Article Number: 258101
58. Gupta, Gagan D.; Dey, Gautam; Swetha, M. G.; et al. (2014) Population Distribution Analyses Reveal a Hierarchy of Molecular Players Underlying Parallel Endocytic Pathways. PLOS ONE, 9, 6, Article Number: e100554
59. Kalmankar, Neha V.; Ramakrishnan, C.; Balaram, P. (2014) Sparsely populated residue conformations in protein structures: Revisiting "experimental" Ramachandran maps. Proteins-Structure Function and Bioinformatics, 82, 7, 1101-1112
60. Kaushik, Swati; Etchebest, Catherine; Sowdhamini, Ramanathan (2014) Decoding the structural events in substrate-gating mechanism of eukaryotic prolyl oligopeptidase using normal mode analysis and molecular dynamics simulations. Proteins-Structure Function and Bioinformatics, 82, 7, 1428-1443
61. Kumar, Dayanidhi; Salian, Sujith Raj; Kalthur, Guruprasad; et al. (2014) Association between sperm DNA integrity and seminal plasma antioxidant levels in health workers occupationally exposed to ionizing radiation. Environmental Research, 132, 297-304
62. Ghosh, Arindam; Krishnan, Yamuna (2014) At a long-awaited turning point. Nature Nanotechnology, 9, 7, 491-494
63. Krishnan, Yamuna (2014) Molecular DNA Devices in Living Systems. Protein Science, 23, Supplement: 1, 64-64, Meeting Abstract: 07-12
64. Moulick, Roumita; Udgaonkar, Jayant B. (2014) Native State Dynamics of The Prion Protein Probed By Hydrogen Exchange And Mass Spectrometry. Protein Science, 23, Supplement: 1, 241-241, Meeting Abstract: 07-378
65. Sanap, Rajesh V.; Mirza, Zeeshan A. (2014) A new iridescent tarantula of the genus Thrigmopoeus Pocock, 1899 from Western Ghats, India. Comptes Rendus Biologies, 337, 7-8, 480-486
66. Muthusamy, Thangaselvam; Mukherjee, Odity; Menon, Radhika; et al. (2014) A Method to Identify and Isolate Pluripotent Human Stem Cells and Mouse Epiblast Stem Cells Using Lipid Body-Associated Retinyl Ester Fluorescence. Stem Cell Reports, 3, 1
67. Chakraborty, Debapriyo; Sinha, Anindya; Ramakrishnan, Uma (2014) Mixed Fortunes: Ancient Expansion and Recent Decline in Population Size of a Subtropical Montane Primate, the Arunachal Macaque Macaca munzala. PLOS ONE, 9, 7, Article Number: e97061
68. Polley, Anirban; Mayor, Satyajit; Rao, Madan (2014) Bilayer registry in a multicomponent asymmetric membrane: Dependence on lipid composition and chain length. Journal of Chemical Physics, 141, 6, Article Number: 064903
69. Kedia, Sonal; Chattarji, Sumantra (2014) Marble burying as a test of the delayed anxiogenic effects of acute immobilisation stress in mice. Journal of Neuroscience Methods, 233, 150-154
70. Srivathsa, Arjun; Karanth, Krithi K.; Jathanna, Devcharan; et al. (2014) On a Dhole Trail: Examining Ecological and Anthropogenic Correlates of Dhole Habitat Occupancy in the Western Ghats of India (vol 9, e98803, 2014). PLOS ONE, 9, 8, Article Number: e106213
71. Gunage, Rajesh D.; Reichert, Heinrich; Raghavan, K. Vijay (2014) Identification of a new stem cell population, which generates Drosophila flight muscles. ELIFE, 3
72. Velho, Nandini; Agarwala, Meghna; Srinivasan, Umesh; et al. (2014) Collateral damage: impacts of ethno-civil strife on biodiversity and natural resource use near Indian nature reserves. Biodiversity and Conservation, 23, 10, 2515-2527
73. Jameel, Shahid; Banerjee, Utpal; VijayRaghavan, K. (2014) Remembering Obaid - One Year Later. Journal of Biosciences, 39, 4, 543-544
74. Sadaf, Sufia; Hasan, Gaiti (2014) Serotonergic neurons of the Drosophila air-puff-stimulated flight circuit. Journal of Biosciences, 39, 4, 575-583
75. Chib, Savita (2014) Continuous evolution of laboratory strains of bacteria and yeast. Journal of Biosciences, 39, 4, 605-607
76. Lucek, Kay; Sivasundar, Arjun; Seehausen, Ole (2014) Disentangling the role of phenotypic plasticity and genetic divergence in contemporary ecotype formation during a biological invasion. Evolution, 68, 9, 2619-2632
77. Milan-Garces, Erix A.; Mondal, Sayan; Udgaonkar, Jayant B.; et al. (2014) Intricate packing in the hydrophobic core of barstar through a CH-pi interaction . Journal of Raman Spectroscopy, 45, 9, 814-821
78. Banerjee, Shamik; Chinthapalli, Balaji (2014) A proteomic screen with Drosophila Opa1-like identifies Hsc70-5/Mortalin as a regulator of mitochondrial morphology and cellular homeostasis. International Journal of Biochemistry & Cell Biology. 54, 36-48
79. Chattarji, Sumantra; Rao, Rajnish P. (2014) Blood-brain biomarkers for stress susceptibility. PNAS, 111, 37, 13253-13254
80. Rahman, Mohammed Mostafizur; Kerskens, Christian M.; Chattarji, Sumantra; et al. (2014) Chronic immobilization stress occludes in vivo cortical activation in an animal model of panic induced by carbon dioxide inhalation. Frontiers in Behavioral Neuroscience, 8, Article Number: 311
81. Shingate, Prashant; Manoharan, Malini; Sukhwal, Anshul; et al. (2014) ECMIS: computational approach for the identification of hotspots at protein-protein interfaces. BMC Bioinformatics, 15, Article Number: UNSP 303
82. Osuri, Anand M.; Kumar, Vijay S.; Sankaran, Mahesh (2014) Altered stand structure and tree allometry reduce carbon storage in evergreen forest fragments in India's Western Ghats. Forest Ecology and Management, 329, 375-383
83. Sampath, Dayalan; Sabitha, K. R.; Hegde, Preethi; et al. (2014) A study on fear memory retrieval and REM sleep in maternal separation and isolation stressed rats. Behavioral Brain Research, 273, 144-154
84. Singh, Sandeep Kumar; Gaur, Ruchi; Kumar, Akhil; et al. (2014) The Flavonoid Derivative 2-(4' Benzyloxyphenyl)-3-hydroxy-chromen-4-one Protects Against A beta (42)-Induced Neurodegeneration in Transgenic Drosophila: Insights from In Silico and In Vivo Studies. Neurotoxicity Research, 26, 4, 331-350
85. B. Nagarathnam, Snehal D. Karpe, K. Harini, Kannan Sankar, Mohammed Iftekar, D. Rajesh, S. Giji, G. Archunan, V. Balakrishnan, M. Gromiha, W. Nemoto, K. Fukui and R. Sowdhamini. (2014) DOR- A Database of Olfactory Receptors- integrated repository for sequence and secondary structural information of olfactory receptors in selected eukaryotic genomes. Bioinformatics and Biology Insights, 12;8:147-58.
86. Sondhi, S., and K. Kunte. (2014). Butterflies and Moths of Pakke Tiger Reserve. Titli Trust (Dehradun) and Indian Foundation for Butterflies (Bengaluru). vi+202pp.
87. Kunte, K., W. Zhang, A. Tenger-Trolander, D. H. Palmer, A. Martin, R. D. Reed, S. P. Mullen, and M. R. Kronforst. (2014). Doublesex is a mimicry supergene. Nature Vol 507 (7491), 1-14.
89. Garg M, Perumalsamy LR, Shivashankar GV, Sarin A (2014) The linker histone H1.2 is an intermediate in the apoptotic response to cytokine deprivation in T-effectors. Int. J. Cell Biol. 2014, 674753.
90. Anita Rachel Chacko, Oommen K. Mathew, Adwait Joshi, Upadhyayula Surya Raghavender and R. Sowdhamini. (2014) SMOS.2: Update of database of structural motifs in superfamilies. Nucleic Acids Research, Database Issue, Jan. 2014.
91. Thattai, Mukund, and Sergio G. Peisajovich. (2014) Current approaches in evolution: From molecules to cells and organisms. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322.7: 465-467.
92. Parent CE*, Agashe D* and Bolnick DI (2014). Intraspecific competition reduces niche width in experimental populations. Ecology and Evolution 4(20): 3878-3990
93. Agashe D and Shankar N (2014). The evolution of bacterial DNA base composition. Journal of Experimental Zoology B 322(7): 517-528
94. Soham Jagtap and P.V. Shivaprasad. (2014). Diversity, expression and mRNA targeting abilities of argonaute targeting miRNAs in plants. BMC Genomics. 15:1409.
95. Garg M, Perumalsamy LR, Shivashankar GV, Sarin A. (2014) The linker histone h1.2 is an intermediate in the apoptotic response to cytokine deprivation in T-effectors. Int J Cell Biol. 2014;2014:674753.
96. Garg M, Ramdas N, Vijayalakshmi M, Shivashankar GV, Sarin A. (2014) The C-terminal domain (CTD) in linker histones antagonizes anti-apoptotic proteins to modulate apoptotic outcomes at the mitochondrion. Cell Death Dis. 2014 Feb 13;5:e1058.
97. Dieudonne, A, Daniel, TL and Sane, SP* (2014) Encoding properties of the mechanosensory neurons in the Johnston's organ of the hawk moth, Manduca sexta. Journal of Experimental Biology 217, 3045-3056
98. Parween, R*; Pratap, R.; Deora, T. and Sane, S.P. (2014).Modeling strain sensing by the gyroscopic halteres in the Dipteran soldier fly, Hermetia illucens. Mechanics Based Design of Structures and Machines 42 (3), 371-385
99. Kumaran, D., Balagopal, K., Tharmaraj, R. G. A., Aaron, S., Kuriyan, G., Muliyil, J., Sivadasan, A., Danda, S., Alexander, M. and Hasan, G. (2014) Genetic characterization of Spinocerebellar Ataxia 1 in a South Indian cohort. BMC Med Genetics 15, 114-121.