PUBLICATIONS DURING 2008

• Saluja, P. and Prasad, G.S.
  Candida ruelliae sp. nov., a novel yeast species isolated from flowers of Ruellia sp. (Acanthaceae). FEMS Yeast Res., 8, 660-666, 2008.



• Thakur, A.; Kaur, J. and Bachhawat, A.K.
  Pgt1, a glutathione transporter from the fission yeast Schizosaccharomyces pombe. FEMS Yeast Res., 8, 916-929, 2008.



• Kaur, R.; Ahuja, S.; Anand, A.; Singh, B.; Stark, B.C.; Webster, D.A. and Dikshit, K.L.
  Functional implications of the proximal site hydrogen bonding network in Vitreoscilla hemoglobin (VHb): role of Tyr95 (G5) and Tyr126 (H12). FEBS Lett., 582, 3494-3500, 2008.



• Sharm, M.K.; Jani, D.; Thungapathra, M.; Gautam, J.K.; Meena, L.S.; Singh, Y.; Ghosh, A.; Tyagi, A.K. and Sharma, A.K.
  Expression of accessory colonization factor subunit A (ACFA) of Vibrio cholerae and ACFA fused to cholera toxin B subunit in transgenic tomato (Solanum lycopersicum). J. Biotechnol., 135, 22-27, 2008.



• Kumar, M.; Gromiha, A.M. and Raghava, G.P.S.
  Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins-Structure Function And Bioinformatics, 71, 189-194, 2008.



• Sharma, M.K.; Singh, N.K.; Jani, D.; Sisodia, R.; Thungapathra, M.; Gautam, J.K.; Meena, L.S.; Singh, Y.; Ghosh, A.; Tyagi, A.K. and Sharma, A.K.
  Expression of toxin co-regulated pilus subunit A (TCPA) of Vibrio cholerae and its immunogenic epitopes fused to cholera toxin B subunit in transgenic tomato (Solanum lycopersicum). Plant Cell Rep., 27, 307-318, 2008.



• Cameotra, S.S. and Singh, P.
  Bioremediation of oil sludge using crude biosurfactants. Int. Biodeterioration & Biodegradation., 62, 274-280, 2008.



• Jhamb, K.; Jawed, A. and Sahoo, D.K.
  Immobilized chaperones: A productive alternative to refolding of bacterial inclusion body proteins. Process Biochem., 43, 587-597,2008.



• Guptasarma, P.
  Solution-state characteristics of the ultraviolet A-induced visible fluorescence from proteins. Arch Biochem Biophys., 478, 127-129, 2008.



• Kapoor, D.; Kumar, V.; Chandrayan, S.K.; Ahmed, S.; Sharma, S.; Datt, M.; Singh, B.; Karthikeyan, S. and Guptasarma, P.
  Replacement of the active surface of a thermophile protein by that of a homologous mesophile protein through structure-guided 'protein surface grafting' Biochim. Biophys. Acta., 1784, 1771-1776, 2008. .



• Gandhi, S.; Sharma, P.; Capalash, N.; Verma, R.S. and Suri, C.R.
  Group-selective antibodies based fluorescence immunoassay for monitoring opiate drug heroin and its metabolites. Anal. Bioanal. Chem., 392, 215-222, 2008.



• Aggarwal, M.; Radha Kishan, K.V.and Mondal, A.K.
  Creation of salt-insensitive 3'(2'), 5'-bisphosphate nucleotidase by modelling and mutagenesis approach. Arch. Biochem. Biophys., 469, 174-183, 2008.



• Kush, A. and Raghava, G.P.S.
  AC2Dgel: Analysis and Comparison of 2D gels. Journal of Proteomics & Bioinformatics, 1, 43-46, 2008.



• Shanmugam, V.; Sharma, V. and Ananthapadmanaban
  Genetic relatedness of trichoderma isolates antagonistic against fusarium oxysporum f.sp. dianthi Folia Microbial., 53, 130-138, 2008. inflicting carnation wilt.



• Krishnamurthi, S. and Chakrabarti, T.
  Proposal for transfer of Pelagibacillus goriensis Kim et al. 2007 to the genus Terribacillus as Terribacillus goriensis comb. nov. Int. J. Syst. Evol. Microbiol. 58, 2287-2291, 2008.



• Sethi, D.; Garg, A. and Raghava, G.P.S.
  DPROT: prediction of disordered proteins using evolutionary information. Amino Acids. 35, 599-605, 2008.



• Kapoor, D.; Kumar, V.; Chandrayan, S.K.; Ahmed, S.; Sharma, S.; Datt, M.; Singh, B.; Karthikeyan, S. and Guptasarma, P.
  Replacement of the active surface of a thermophile protein by that of a homologous mesophile protein through structure-guided 'protein surface grafting' Biochim. Biophys. Acta. 1784, 1771-1776, 2008.



• Gandhi, S.; Sharma, P.; Capalash, N.; Verma, R.S. and Suri, C.R.
  Group-selective antibodies based fluorescence immunoassay for monitoring opiate drug heroin and its metabolites. Anal. Bioanal. Chem. 392, 215-222, 2008.



• Saxena, R.; Karthikeyan, S.; Datt, M.; Singh, B. and Chakraborti, P. K.
  Three consecutive arginines are important for the mycobacterial peptide deformylase enzyme activity. J. Biol. Chem. 283, 23754-23764, 2008.



• Thakur, M. and Chakraborti, P.K.
  Ability of PknA, a mycobacterial eukaryotic-type serine/threonine kinase to transphosphorylate MurD, a ligase involved in the process of peptidoglycan biosynthesis. Biochem. J. 415, 27-33, 2008.



• Alam, M. S. and Agrawal, P.
  Matrix-assisted refolding and redox properties of WhiB3/Rv3416 of Mycobacterium tuberculosis H37Rv. Protein Expr. Purif. 61, 83-91, 2008.



• Kumar, M.; Thakur, V. and Raghava, G.P.S.
  COPid: composition based protein identification. In Silico Biol. 8, 121-128, 2008.



• Dhiman, R.; Kathania, M.; Raje, M. and Majumdar, S.
  Inhibition of bfl-1/A1 by siRNA inhibits mycobacterial growth in THP-1 cells by enhancing phagosomal acidification. Biochim Biophys Acta. 1780, 733-42, 2008.



• Aggarwal, M.; Radha Kishan, K.V.and Mondal, A.K.
  Creation of salt-insensitive 3'(2'), 5'-bisphosphate nucleotidase by modelling and mutagenesis approach. Arch. Biochem. Biophy. 469, 174-83, 2008.



• Sharma, S. and Guptasarma, P.
  Evidence of Native-like Substructure(s) in Polypeptide Chain of Carbonic Anhydrase Deposited into Insoluble Aggregates During Thermal Unfolding. Protein J. 27, 50-58.



• Garg, A. and Raghava, G.P.S.
  ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins. BMC Bioinformatics, 9, 503, 2008.



• *Cameotra, Swaranjit Singh and Singh, Pooja
  Bioremediation of oil sludge using biosurfactants. Int. Biodeterio. Biodegradation 62: 274-280, 2008



• Swaranjit Singh Cameotra
  Biosurfactant-enhanced bioremediation of hydrophobic pollutants. J. Biotechnol. 136, 678, 2008



• Pawaria, S.; Lama, A.; Raje, M. and Dikshit, K.L.
  Responses of Mycobacterium tuberculosis hemoglobin promoters to in vitro and in vivo growth conditions. Appl. Environ. Microbiol.,74, 3512-3522, 2008.



• Patnaik, P.R.
  Response coefficient analysis of a fed-batch bioreactor to dissolved oxygen perturbation in complementary cultures during PHB production. J. Biol. Eng., 2, 4, 2008.



• Bisht, K. K.; Arora, S.; Ahmed, S. and Singh, Jagmohan
  Role of heterochromatin in suppressing subtelomeric recombination in Fission yeast. Yeast, 25, 537-548, 2008.



• Yadav, S.; Datt, M.; Singh, B.; and Sahni, G. Role of the 88-97 loop in plasminogen activation by streptokinase probed through site-specific mutagenesis. Biochim. Biophys. Acta., 1784, 1310-1318, 2008.



• Sharma, S. and Guptasarma, P.
  Evidence of Native-like Substructure(s) in Polypeptide Chain of Carbonic Anhydrase Deposited into Insoluble Aggregates During Thermal Unfolding. Protein J. 27, 50-58, 2008.



• Dongre M, Tripathi R, Jain V, Raychaudhuri S.
  Functional independence of a variant LuxOPL91 from a non-O1 non-O139 Vibrio cholerae over the activity of CsrA and Fis. J. Med. Microbiol. 57, 1041-1045, 2008



• Verma, R.; Tiwari, A.; Kaur, S.; Varshney, G.C. and Raghava, G.P.S.
  Identification of proteins secreted by malaria parasite into erythrocyte using SVM and PSSM profiles. BMC Bioinformatics. 16, 9:201, 2008.



• Garg, A. and Raghava, G.P.S
  A machine learning based method for the prediction of secretory proteins using amino acid composition, their order and similarity-search. In Silico Biol., 8, 12, 2008.



• Shukla, A. ; Raje, M. and Guptasarma, P..
  Coalescence of spherical beads of retro-HSP12.6 into linear and ring-shaped amyloid nanofibers. Biochemistry (Moscow) 73, 681-685, 2008.



• Kalita, M.K.; Nandal, U.K.; Pattnaik, A.; Sivalingam, A,; Ramasamy, G.; Kumar, M.; Raghava, G.P.S. and Gupta, D.
  CyclinPred: a SVM-based method for predicting cyclin protein sequences. PLoS ONE, 3, e2605, 2008.



• Sharma, S. and Guptasarma, P.
  Dimorphic aggregation behavior of a fusion polypeptide incorporating a stable protein domain (EGFP) with an amyloidogenic sequence (retroCspA). FEBS Lett., 582, 2203-2211, 2008.



• Mir, M.A. and Agrewala, J.N.
  Signaling through CD80: an approach for treating lymphomas. Expert Opin. Ther. Targets. 12, 969-979, 2008.



• Thakur, M.; Chaba, R.; Mondal, A.K. and Chakraborti, P.K.
  Inter-domain interaction reconstitutes the functionality of PknA, a eukaryotic-type Ser/Thr kinase from Mycobacterium tuberculosis. J. Biol. Chem., 283, 8023-8033, 2008.



• Chandrayan, S.K. & Guptasarma, P.
  Partial destabilization of native structure by a combination of heat and denaturant facilitates cold denaturation in a hyperthermophile protein. Proteins : Structure, Function & Bioinformatics, 72, 539-546, 2008.



• Ahmed, S.; Kapoor, D.; Singh, B. and Guptasarma, P.
  Conformational behavior of polypeptides derived through simultaneous global conservative site-directed mutagenesis of chymotrypsin inhibitor 2. Biochim. Biophys. Acta : Proteins and Proteomics, 1784, 796-805, 2008.



• Ahmed, S.; Shukla, A. and Guptasarma, P.
  Folding behavior of a backbone reversed protein : Reversible polyproline type II to beta-sheet thermal transitions in retro-GroES multimers with GroES-like features. Biochim. Biophys. Acta : Proteins and Proteomics, 1784, 916-923, 2008.



• Dhiman, R.; Kathania, M.; Raje, M. and Majumdar, S.
  Inhibition of bfl-1/A1 by siRNA inhibits mycobacterial growth in THP-1 cells by enhancing phagosomal acidification. Biochim. Biophys. Acta., 1780, 733-742, 2008.



• Ahmed, S. and Guptasarma, P.
  Design of a soluble mini-protein through tandem duplication of the minimally-engineered beta hairpin 'tongue' motif of alpha hemolysin. Biochimie, 90, 957-967, 2008.



• Lata, S. and Raghava, G.P.S.
  PRRDB: a comprehensive database of pattern-recognition receptors and their ligands. BMC Genomics, 2008, 9, 180, 2008.



• Kumar, R, and Rajagopal, K.
  Single-step overlap-primer-walk polymerase chain reaction for multiple mutagenesis without overlap extension. Anal. Biochem., 377, 105-107, 2008.



• Manickam, N.; Ghosh, A.,Jain, R.K. and Mayilraj, S.
  Description of a novel indole oxidizing bacterium Pseudomonas indoloxydans sp. nov., isolated from a pesticide contaminated site. Syst. Appl. Microbiol., 31, 101-107, 2008.



• Chandrayan, S.K.; Dhaunta, N. and Guptasarma, P.
  Expression, purification, refolding and characterization of a putative lysophospholipase from Pyrococcus furiosus : Retention of structure and lipase/esterase activity in the presence of water-miscible organic solvents at high temperatures. Protein Expr. Purif., 59, 327-333, 2008.



• Wangoo, N.; Bhasin, K.K.; Mehta, S.K. and Suri, C.R.
  Synthesis and capping of water-dispersed gold nanoparticles by an amino acid: Bioconjugation and binding studies. J. Colloid Interface Sci. 323, 247-254, 2008.



• Kaur, J.; Boro, R.C.; Wangoo, N.; Singh, K.R. and Suri, C.R.
  Direct hapten coated immunoassay format for the detection of atrazine and 2,4-dichlorophenoxyacetic acid herbicides. Anal. Chim. Acta. 607,92-99, 2008.



• Wangoo, N.; Bhasin, K.K.; Boro, R. and Suri, C.R.
  Facile synthesis and functionalization of water-soluble gold nanoparticles for a bioprobe. Anal. Chim. Acta. 610, 142-148, 2008.



• Wangoo, N.; Shekhawat, G.S. and Suri, C.R.
  Interaction of gold nanoparticles with protein: A spectroscopic study to monitor protein conformational change. Appl. Phys. Lett. 92, 133104, 2008.



• Suri, C.R.; Kaur J.; Gandi, S. and Shekhawat, G.S.
  Lable-free ultra-sensitive detection of atrazine based on nanomechanics. Nanotechnology, 19, 235502, 2008.



• Verma, A., Sharma, S., Ganguly, N.K., Majumdar, S., Guptasarma, P., and Luthra-Guptasarma, M.
  Identification and characterization of a spontaneously aggregating amyloid-forming variant of human PrP((90-231)) through phage-display screening of variants randomized between residues 101 and 112. Int. J. Biochem. Cell Biol., 40, 663-676, 2008.



• Vyas, R.; Kumar, V.; Panjikar, S.; Karthikeyan, S.; Kishan, K.V.; Tewari, R. and Weiss, M.S.
  Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis. Acta. Crystallogr. Sect F Struct. Biol. Cryst. Commun., 64, 167-170, 2008.



• Wangoo, N.; Bhasin, K.K.; Boro, R. and Suri, C.R.
  Facile synthesis and functionalization of water-soluble gold nanoparticles for a bioprobe. Anal. Chim. Acta., 610, 142-148, 2008.



• Sharma, S. and Guptasarma, P.
  Evidence of Native-like Substructure(s) in Polypeptide Chain of Carbonic Anhydrase Deposited into Insoluble Aggregates During Thermal Unfolding. Protein J., 27, 50-58, 2008.



• Wallet, M.A.; Sen, Pradip; Flores, R.R.; Wang, Y.; Yi, Zuoan; Huang, Y.; Mathews, C.E.; Earp, H.S.; Matsushima, G.; Wang, Bo and Roland T.
  MerTK is required for apoptotic cell induced T cell tolerance. J. Exp. Med., 205, 219-232, 2008.



• Sinha, A.; Gupta, S.; Bhutani, S.; Pathak, A. and Sarkar, D.
  PhoP-PhoP interaction at adjacent PhoP binding sites is influenced by protein phosphorylation. J. Bacteriol., 190, 1317-1328, 2008.



• Ahmed, S. and Singh Jagmohan
  RT-PCR method for selective detection of silent gene transcripts in silencing mutants in hemothallic strains of Schizosaccharomyces pombe. Biotechniques, 44, 54-58, 2008.



• Gowthaman, U. and Agrewala, J.N.
  In silico tools for predicting peptides binding to HLA-class II molecules: more confusion than conclusion. J. Proteome. Res. 7, 154-163, 2008.



• Kaur, J.; Boro, R.C.; Wangoo, N.; Singh, K.R. and Suri, C.R.
  Direct hapten coated immunoassay format for the detection of atrazine and 2,4-di chlorophenoxyacetic acid herbicides. Anal. Chim. Acta., 607, 92-99, 2008.



• Chakraborti, D; Basu, J.M.; Sen, Pradip; Sundar, S. and Roy, S.
  Human placental extract offers protection against pentavalent antimonial-sensitive and resistant experimental visceral leishmaniasis: a pilot study for phase I clinical trial. Ann. Trop. Med. Parasitol., 102, 21-38, 2008.



• Aggarwal, M.; Radha Kishan, K.V.and Mondal, A.K.
  Creation of salt-insensitive 3'(2'), 5'-bisphosphate nucleotidase by modelling and mutagenesis approach. Arch. Biochem. Biophys., 469, 174-183, 2008.