open: No conditions. Results ordered Creators, Title. 2024-03-29T04:30:21ZEPrintshttp://crdd.osdd.net/images/sitelogo.gifhttp://crdd.osdd.net/open/2012-09-03T09:33:23Z2015-08-03T10:59:03Zhttp://crdd.osdd.net/open/id/eprint/1153This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11532012-09-03T09:33:23ZCostimulatory molecules mediated regulation of the activation and differentiation of antigen presenting cells. "SUMMARY OF THE THESIS IS ATTACHED"Manzoor Ahmad Mir 2011-12-08T19:35:09Z2011-12-08T19:35:09Zhttp://crdd.osdd.net/open/id/eprint/562This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5622011-12-08T19:35:09ZPrediction of guide strand of microRNAs from its sequence and secondary structure.In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex. This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their nucleotide sequence and secondary structure. This method will be useful in understanding microRNA processing and can be implemented in RNA silencing technology to improve the biological and clinical research. A web server has been developed based on SVM models described in this study (http://crdd.osdd.net:8081/RISCbinder/).Firoz AhmedHifzur Rahman AnsariG.P.S. Raghava2011-12-08T19:33:10Z2011-12-08T19:33:10Zhttp://crdd.osdd.net/open/id/eprint/547This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5472011-12-08T19:33:10ZPrediction of polyadenylation signals in human DNA sequences using nucleotide frequencies.The polyadenylation signal plays a key role in determining the site for addition of a polyadenylated tail to nascent mRNA and its mutation(s) are reported in many diseases. Thus, identifying poly(A) sites is important for understanding the regulation and stability of mRNA. In this study, Support Vector Machine (SVM) models have been developed for predicting poly(A) signals in a DNA sequence using 100 nucleotides, each upstream and downstream of this signal. Here, we introduced a novel split nucleotide frequency technique, and the models thus developed achieved maximum Matthews correlation coefficients (MCC) of 0.58, 0.69, 0.70 and 0.69 using mononucleotide, dinucleotide, trinucleotide, and tetranucleotide frequencies, respectively. Finally, a hybrid model developed using a combination of dinucleotide, 2nd order dinucleotide and tetranucleotide frequencies, achieved a maximum MCC of 0.72. Moreover, for independent datasets this model achieved a precision ranging from 75.8-95.7% with a sensitivity of 57%, which is better than any other known methods.Firoz AhmedManish KumarG.P.S. Raghava2011-12-08T19:36:42Z2011-12-08T19:36:42Zhttp://crdd.osdd.net/open/id/eprint/574This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5742011-12-08T19:36:42ZStudies on structural and functional divergence among seven WhiB proteins of Mycobacterium tuberculosis H37Rv.The whiB-like genes (1-7) of Mycobacterium tuberculosis are involved in cell division, nutrient starvation, pathogenesis, antibiotic resistance and stress sensing. Although the biochemical properties of WhiB1, WhiB3 and WhiB4 are known, there is no information about the other proteins. Here, we elucidate in detail the biochemical and biophysical properties of WhiB2, WhiB5, WhiB6 and WhiB7 of M. tuberculosis and present a comprehensive comparative study on the molecular properties of all WhiB proteins. UV-Vis spectroscopy has suggested the presence of a redox-sensitive [2Fe-2S] cluster in each of the WhiB proteins, which remains stably bound to the proteins in the presence of 8 m urea. The [2Fe-2S] cluster of each protein was oxidation labile but the rate of cluster loss decreased under reducing environments. The [2Fe-2S] cluster of each WhiB protein responded differently to the oxidative effect of air and oxidized glutathione. In all cases, disassembly of the [2Fe-2S] cluster was coupled with the oxidation of cysteine-thiols and the formation of two intramolecular disulfide bonds. Both CD and fluorescence spectroscopy revealed that WhiB proteins are structurally divergent members of the same family. Similar to WhiB1, WhiB3 and WhiB4, apo WhiB5, WhiB6 and WhiB7 also reduced the disulfide of insulin, a model substrate. However, the reduction efficiency varied significantly. Surprisingly, WhiB2 did not reduce the insulin disulfide, even though its basic properties were similar to those of others. The structural and functional divergence among WhiB proteins indicated that each WhiB protein is a distinguished member of the same family and together they may represent a novel redox system for M. tuberculosis.Md Suhail AlamSaurabh K GargPushpa Agrawal2011-12-08T19:35:27Z2011-12-08T19:35:27Zhttp://crdd.osdd.net/open/id/eprint/565This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5652011-12-08T19:35:27ZTotal RNA isolation from recalcitrant yeast cells.Conventional methods of RNA isolation are not suitable for yeast cells from stationary phase and fermentation broth. Methods specially reported for such cells are cumbersome and do not lend themselves for use with large number of samples. Here we report a facile method of RNA isolation from such recalcitrant yeast cells. The entire procedure is performed in microcentrifuge tubes and, thus, is ideal for faster processing of multiple samples. The method consistently gives high quality and quantity of RNA, which was found to be suitable for downstream applications such as quantitative real-time polymerase chain reaction. Besides Saccharomyces cerevisiae, the method was found to work equally well with other yeast species; thus, it is likely to have wider applicability.M Amin-ul MannanSushma SharmaK Ganesan2012-09-06T07:08:20Z2012-09-06T07:08:20Zhttp://crdd.osdd.net/open/id/eprint/1168This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11682012-09-06T07:08:20ZIdentification of cellular partner of VHb and studies on protein-protein interactions to explore novel function(s) of vitreoscilla hemoglobin.Arvind Anand2011-12-08T19:32:59Z2015-01-07T08:33:25Zhttp://crdd.osdd.net/open/id/eprint/546This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5462011-12-08T19:32:59ZIdentification of a new exosite involved in catalytic turnover by the streptokinase-plasmin activator complex during human plasminogen activation.With the goal of identifying hitherto unknown surface exosites of streptokinase involved in substrate human plasminogen recognition and catalytic turnover, synthetic peptides encompassing the 170 loop (CQFTPLNPDDDFRPGLKDTKLLC) in the beta-domain were tested for selective inhibition of substrate human plasminogen activation by the streptokinase-plasmin activator complex. Although a disulfide-constrained peptide exhibited strong inhibition, a linear peptide with the same sequence, or a disulfide-constrained variant with a single lysine to alanine mutation showed significantly reduced capabilities of inhibition. Alanine-scanning mutagenesis of the 170 loop of the beta-domain of streptokinase was then performed to elucidate its importance in streptokinase-mediated plasminogen activation. Some of the 170 loop mutants showed a remarkable decline in k(cat) without any alteration in apparent substrate affinity (K(m)) as compared with wild-type streptokinase and identified the importance of Lys(180) as well as Pro(177) in the functioning of this loop. Remarkably, these mutants were able to generate amidolytic activity and non-proteolytic activation in "partner" plasminogen as wild-type streptokinase. Moreover, cofactor activities of the 170 loop mutants, pre-complexed with plasmin, against microplasminogen as the substrate showed a similar pattern of decline in k(cat) as that observed in the case of full-length plasminogen, with no concomitant change in K(m). These results strongly suggest that the 170 loop of the beta-domain of streptokinase is important for catalysis by the streptokinase-plasmin(ogen) activator complex, particularly in catalytic processing/turnover of substrate, although it does not seem to contribute significantly toward enzyme-substrate affinity per se.Rachna AnejaManish DattBalvinder SinghShekhar KumarGirish Sahni2012-01-10T08:05:07Z2012-04-03T07:08:30Zhttp://crdd.osdd.net/open/id/eprint/31This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/312012-01-10T08:05:07ZOxDBase: a database of oxygenases involved in biodegradation.OxDBase is the first database that is dedicated only to oxygenases and provides comprehensive information about them. Due to the importance of the oxygenases in chemical synthesis of drug intermediates and oxidation of xenobiotic compounds, OxDBase database would be very useful tool in the field of synthetic chemistry as well as bioremediation.Pankaj Kumar AroraManish KumarArchana ChauhanG.P.S. RaghavaR K Jain2012-09-06T06:26:12Z2012-09-06T06:26:12Zhttp://crdd.osdd.net/open/id/eprint/1165This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11652012-09-06T06:26:12ZMolecular and functional analysis of integrase gene of bacteriphase PIS 136.Richa Bajpai2012-09-06T07:16:43Z2015-01-07T10:06:59Zhttp://crdd.osdd.net/open/id/eprint/1170This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11702012-09-06T07:16:43ZStudy of prokaryotic diversity fromn selected niches of western ghats of IndiaA Bhattacharya2011-12-08T19:31:29Z2011-12-09T06:30:29Zhttp://crdd.osdd.net/open/id/eprint/533This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5332011-12-08T19:31:29ZCharacterization of hapten-protein conjugates: antibody generation and immunoassay development for chlorophenoxyacetic acid pesticides.The generation of specific and sensitive antibodies against small molecules is greatly dependent upon the characteristics of the hapten-protein conjugates. In this study, we report a new fluorescence-based method for the characterization of hapten-protein conjugates. The method is based on an effect promoted by hapten-protein conjugation density upon the fluorescence intensity of the intrinsic tryptophan chromophore molecules of the protein. The proposed methodology is applied to quantify the hapten-protein conjugation density for two different chlorophenoxyacetic acid pesticides, 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4-dichlorophenoxybutyric acid (2,4-DB), coupled to carrier protein. Highly sensitive anti-2,4-D and anti-2,4-DB antibodies were obtained using these well-characterized hapten-protein conjugates. The generated antibodies were used in an immunoassay format demonstrating inhibitory concentration (IC50) values equal to 30 and 7 ng/mL for 2,4-D and 2,4-DB, respectively. Linearity was observed in the concentration range between 0.1-500 nglmL with LODs around 4 and 3 ng/mL for 2,4-D and 2,4-DB, respectively, in standard water samples. The proposed method was successfully applied for the determination of the extent of hapten-protein conjugation to produce specific antibodies for immunoassay development against pesticides.Robin C BoroK Vikas SinghC Raman Suri2011-12-08T19:35:37Z2011-12-08T19:35:37Zhttp://crdd.osdd.net/open/id/eprint/566This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5662011-12-08T19:35:37ZSynthesis of rhamnolipid biosurfactant and mode of hexadecane uptake by Pseudomonas species.This study throws more light on the uptake mechanism of hydrocarbon by Pseudomonas aeruginosa. We report here a new and exciting line of research for hydrocarbon uptake involving internalization of biosurfactant covered hydrocarbon inside cell for subsequent breakdown.Swaranjit Singh CameotraPooja Singh2012-02-28T16:12:05Z2012-02-28T16:12:05Zhttp://crdd.osdd.net/open/id/eprint/1085This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10852012-02-28T16:12:05ZAttenuation of ionic interactions profoundly lowers the kinetic thermal stability of Pyrococcus furiosus triosephosphate isomerase.We investigate here the high structural stability of Pyrococcus furiosus triosephosphate isomerase (PfuTIM) by exploring the effects - upon the protein's structure and kinetic thermal stability - of modulation of its ionic interactions through pH variations, and mutations. PfuTIM shows comparable structural contents at pH 3.0, 7.0 and 10.0. However, at pH 3.0, subtle changes are seen in the protein's surface hydrophobicity and association status, and its kinetic thermal stability is profoundly reduced (as evidenced by its facile heat- and cold-mediated denaturation, characterized by a high degree of hysteresis and irreversibility). Increase in ionic strength through addition of salt counters the reduction of stability, and reversal of pH facilitates partial refolding. Further, a mutated form of PfuTIM (mPfuTIM) lacking 4 key charged residues involved in ionic interactions displays a structural content identical to PfuTIM but profound reduction in kinetic stability to thermal and chemical denaturation, as well as evidence of partial unfolding at temperatures between 90 degrees C and 100 degrees C, unlike PfuTIM. We conclude, therefore, that ionic interactions (which are known to determine protein thermodynamic stability) can also contribute significantly to protein kinetic thermal stability.Sanjeev Kumar ChandrayanPurnananda Guptasarma2012-02-28T16:10:32Z2012-02-28T16:10:32Zhttp://crdd.osdd.net/open/id/eprint/1094This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10942012-02-28T16:10:32ZSilk-fiber immobilized lipase-catalyzed hydrolysis of emulsified sunflower oil.Lipase was immobilized in silk fibers through glutaraldehyde cross-linking to a maximum loading of 59 U/g silk-fiber and the immobilized lipase was utilized for the hydrolysis of sunflower oil (Helianthus annuus). The hydrolytic activity of the lipase, which was poor in biphasic oil in water system, was increased significantly when the sunflower oil was emulsified in aqueous medium. The hydrolytic activities of the immobilized lipase were 48.73 +/- 1.26 U, 36.11 +/- 0.96 U, and nil when the substrate sunflower oil was used as emulsion created by a rhamnolipid biosurfactant, Triton X100, and ultrasonication, respectively. Although the efficiency of the immobilized lipase was less than 12% than the corresponding free lipase, the immobilized lipase could be reused for the biosurfactant-mediated hydrolysis of sunflower oil up to third cycle of the reaction. The yield of the fatty acids in the second, third, and fourth cycles were 49.45%, 22.91%, and 5.09%, respectively, of the yield obtained in the first cycle.Sushovan ChatterjeeLepakshi BarboraSwaranjit Singh CameotraPinakeswar MahantaPranab Goswami2012-01-10T08:04:50Z2012-01-10T08:04:50Zhttp://crdd.osdd.net/open/id/eprint/27This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/272012-01-10T08:04:50ZProphylactic and Therapeutic Potential of Asp f1 Epitopes in Naïve and Sensitized BALB/c Mice.Asp f1-derived peptide P1, prophylactically and therapeutically administered to Balb/c mice, is effective in regulating allergic response to allergens/antigens of Afu, and may be explored for immunotherapy of allergic aspergillosis in humans.Neelkamal ChaudharyLakshna MahajanTaruna MadanAnil KumarG.P.S. RaghavaSeturam Bandacharya KattiWahajul HaqPuranam Usha Sarma2011-12-08T19:32:07Z2012-04-03T06:51:21Zhttp://crdd.osdd.net/open/id/eprint/538This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5382011-12-08T19:32:07ZExpression, purification, crystallization and preliminary X-ray analysis of maleylacetate reductase from Burkholderia sp. strain SJ98.Maleylacetate reductase (EC 1.3.1.32) is an important enzyme that is involved in the degradation pathway of aromatic compounds and catalyzes the reduction of maleylacetate to 3-oxoadipate. The gene pnpD encoding maleylacetate reductase in Burkholderia sp. strain SJ98 was cloned, expressed in Escherichia coli and purified by affinity chromatography. The enzyme was crystallized in both native and SeMet-derivative forms by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant at 293 K. The crystals belonged to space group P2(1)2(1)2, with unit-cell parameters a = 72.91, b = 85.94, c = 53.07 A. X-ray diffraction data for the native and SeMet-derivative crystal were collected to 2.7 and 2.9 A resolution, respectively.Archana ChauhanZeyaul IslamR K JainSubramanian Karthikeyan2011-12-08T19:32:26Z2011-12-08T19:32:26Zhttp://crdd.osdd.net/open/id/eprint/540This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5402011-12-08T19:32:26ZIdentification of ATP binding residues of a protein from its primary sequence.This study demonstrates that it is possible to predict 'ATP interacting residues' in a protein with moderate accuracy using its sequence. The evolutionary information is important for the identification of 'ATP interacting residues', as it provides more information compared to the primary sequence. This method will be useful for researchers studying ATP-binding proteins. Based on this study, a web server has been developed for predicting 'ATP interacting residues' in a protein http://www.imtech.res.in/raghava/atpint/.Jagat S ChauhanNitish K MishraG.P.S. Raghava2012-09-06T07:01:04Z2012-09-06T07:01:04Zhttp://crdd.osdd.net/open/id/eprint/1167This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11672012-09-06T07:01:04ZStudies on the mechanism of protease negative phenotype of vibrio cholerae non-01,non-0139 strain.Mitesh Dongre2012-02-28T16:10:40Z2012-02-28T16:10:40Zhttp://crdd.osdd.net/open/id/eprint/1093This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10932012-02-28T16:10:40ZInteraction of APC/C-E3 ligase with Swi6/HP1 and Clr4/Suv39 in heterochromatin assembly in fission yeast.Heterochromatin assembly in fission yeast is initiated by binding of Swi6/HP1 to the Lys-9-dimethylated H3 followed by spreading via cooperative recruitment of Swi6/HP1. Recruitment of Cohesin by Swi6/HP1 further stabilizes the heterochromatin structure and integrity. Subsequently, polyubiquitylation of Cut2 by anaphase-promoting complex-cyclosome (APC/C)-ubiquitin-protein isopeptide ligase (E3 ligase) followed by degradation of Cut2 releases Cut1, which cleaves the Rad21 subunit of Cohesin, facilitating sister chromatid separation during mitosis. Here, we demonstrate a surprising role of APC/C in assembly of heterochromatin and silencing at mating type, centromere, and ribosomal DNA loci. Coincidentally with the loss of silencing, recruitment of Swi6, H3-Lys-9-Me2, and Clr4 at dg-dh repeats at cen1 and the K region of mat locus is abrogated in mutants cut4, cut9, and nuc2. Surprisingly, both Cut4 and Cut9 are also highly enriched at these regions in wild type and depleted in swi6Delta mutant. Cut4 and Cut9 interact directly with Swi6/HP1 and Clr4, whereas the mutant Cut4 does not, suggesting that a direct physical interaction of APC subunits Cut4 and Cut9 with Swi6 and Clr4 is instrumental in heterochromatin assembly. The silencing defect in APC mutants is causally related to ubiquitylation activity of APC-E3 ligase. Like swi6 mutant, APC mutants are also defective in Cohesin recruitment and exhibit defects like lagging chromosomes, chromosome loss, and aberrant recombination in the mat region. In addition, APC mutants exhibit a bidirectional expression of dh repeats, suggesting a role in the RNA interference pathway. Thus, APC and heterochromatin proteins Swi6 and Clr4 play a mutually cooperative role in heterochromatin assembly, thereby ensuring chromosomal integrity, inheritance, and segregation during mitosis and meiosis.Rudra Narayan DubeyNandni NakwalKamlesh Kumar BishtAshok SainiSwati HaldarJagmohan Singh2011-12-08T19:33:29Z2015-07-22T05:34:02Zhttp://crdd.osdd.net/open/id/eprint/549This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5492011-12-08T19:33:29ZStrip-based immunochromatographic assay using specific egg yolk antibodies for rapid detection of morphine in urine samples.Using specific egg yolk antibodies (IgY), a strip-based immunochromatographic assay was developed for rapid detection of morphine in urine samples. IgY type antibody against morphine was generated by immunizing chickens with well-characterized monoacetyl morphine-protein conjugate. The antibody was labeled with gold nanoparticles and used as an immunoprobe in the dipstick format for the visual detection of morphine in urine samples. The dipstick was developed using three membranes: an application pad made of glass fiber membrane to hold the tracer, a signal generation test line on nitrocellulose membrane (detection zone) and a cellulose membrane used as an absorption pad. Analytes of interest (morphine and its analogues) added to the sample well, dissolved the labeled antibody (tracer), and the antigen-antibody complex formed was transported by the flow caused by capillary action to the test line. The color signal of test line in proportion to the morphine concentration in urine samples was measured using a detector. The developed dipstick assay format was optimized, showing the average IC(50) values of morphine as low as 9.45 ng/mL, the detection range of 1-1000 ng/mL and the lowest detection limit 2.5 ng/mL under optimal conditions of analysis. The correlation between the developed dipstick and ELISA was 0.948 in the analysis of urine samples spiked with morphine. The developed dipstick could be a highly sensitive and convenient tool for rapid detection of opiate drugs in samples with high degree of stability.Sonu GandhiNeena CaplashPrince SharmaC Raman Suri2011-12-08T19:36:17Z2015-01-08T09:39:19Zhttp://crdd.osdd.net/open/id/eprint/571This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5712011-12-08T19:36:17ZRedox biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide.We conclude that M. tuberculosis GlgB has one intra-molecular disulfide bond which is formed between C193 and C617. WhiB1, a thioredoxin like protein interacts with GlgB and transfers its electrons to the disulfide thus reduces the intra-molecular disulfide bond of GlgB. For the first time, we report that GlgB is one of the in vivo substrate of M. tuberculosis WhiB1.Saurabh K GargMd Suhail AlamRicha BajpaiK V Radha KishanPushpa Agrawal2011-12-08T19:32:53Z2015-01-07T04:58:36Zhttp://crdd.osdd.net/open/id/eprint/545This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5452011-12-08T19:32:53ZIn silico methods for predicting T-cell epitopes: Dr Jekyll or Mr Hyde?In silico tools offer an attractive alternative strategy to the cumbersome experimental approaches to identify T-cell epitopes. These computational tools have metamorphosed over the years into complex algorithms that attempt to efficiently predict the binding of a plethora of peptides to HLA alleles. In recent years, the scientific community has embraced these techniques to reduce the burden of wet-laboratory experimentation. Although there are some splendid examples of the utility of these methods, there are also evidences where they fall short and remain inconsistent. Hence, are these computational tools 'Dr Jekyll' or 'Mr Hyde' to the researcher, who wishes to utilize them intrepidly? This article reviews the progress and pitfalls of the in silico tools that identify T-cell epitopes.Uthaman GowthamanJ N Agrewala2011-12-08T19:34:52Z2011-12-08T19:34:52Zhttp://crdd.osdd.net/open/id/eprint/559This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5592011-12-08T19:34:52ZEnhanced production of recombinant streptokinase in Escherichia coli using fed-batch culture.Fed-batch culture strategy is often used for increasing production of heterologous recombinant proteins in Escherichia coli. This study was initiated to investigate the effects of dissolved oxygen concentration (DOC), complex nitrogen sources and pH control agents on cell growth and intracellular expression of streptokinase (SK) in recombinant E. coli BL21(DE3). Increase in DOC set point from 30% to 50% did not affect SK expression in batch culture where as similar increase in fed-batch cultivation led to a significant improvement in SK expression (from 188 to 720 mg l(-1)). This increase in SK could be correlated with increase in plasmid segregational stability. Supplementation of production medium with yeast extract and tryptone and replacement of liquid ammonia with NaOH as pH control agent further enhanced SK expression without affecting cell growth. Overall, SK concentration of 1120 mg l(-1) representing 14-fold increase in SK production on process scale-up from flask to bioreactor scale fed-batch culture is the highest reported concentration of SK to date.Deepika GoyalGirish SahniDebendra K Sahoo2011-12-08T19:35:53Z2011-12-08T19:35:53Zhttp://crdd.osdd.net/open/id/eprint/568This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5682011-12-08T19:35:53ZHDAC3 as a molecular chaperone for shuttling phosphorylated TR2 to PML: a novel deacetylase activity-independent function of HDAC3.TR2 is an orphan nuclear receptor specifically expressed in early embryos (Wei and Hsu, 1994), and a transcription factor for transcriptional regulation of important genes in stem cells including the gate keeper Oct4 (Park et al. 2007). TR2 is known to function as an activator (Wei et al. 2000), or a repressor (Chinpaisal et al., 1998, Gupta et al. 2007). Due to the lack of specific ligands, mechanisms triggering its activator or repressor function have remained puzzling for decades. Recently, we found that all-trans retinoic acid (atRA) triggers the activation of extracellular-signal-regulated kinase 2 (ERK2), which phosphorylates TR2 and stimulates its partitioning to promyelocytic leukemia (PML) nuclear bodies, thereby converting the activator function of TR2 into repression (Gupta et al. 2008; Park et al. 2007). Recruitment of TR2 to PML is a crucial step in the conversion of TR2 from an activator to a repressor. However, it is unclear how phosphorylated TR2 is recruited to PML, an essential step in converting TR2 from an activator to a repressor. In the present study, we use both in vitro and in vivo systems to address the problem of recruiting TR2 to PML nuclear bodies. First, we identify histone deacetylase 3 (HDAC3) as an effector molecule. HDAC3 is known to interact with TR2 (Franco et al. 2001) and this interaction is enhanced by the atRA-stimulated phosphorylation of TR2 at Thr-210 (Gupta et al. 2008). Secondly, in this study, we also find that the carrier function of HDAC3 is independent of its deacetylase activity. Thirdly, we find another novel activity of atRA that stimulates nuclear enrichment of HDAC3 to form nuclear complex with PML, which is ERK2 independent. This is the first report identifying a deacetylase-independent function for HDAC3, which serves as a specific carrier molecule that targets a specifically phosphorylated protein to PML NBs. This is also the first study delineating how protein recruitment to PML nuclear bodies occurs, which can be stimulated by atRA in an ERK2-independent manner. These findings could provide new insights into the development of potential therapeutics and in understanding how orphan nuclear receptor activities can be regulated without ligands.Pawan GuptaPing-Chih HoSung Gil HaYi-Wei LinLi-Na Wei2012-02-28T16:11:58Z2012-02-28T16:11:58Zhttp://crdd.osdd.net/open/id/eprint/1086This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10862012-02-28T16:11:58ZMycobacterium tuberculosis PhoP recognizes two adjacent direct-repeat sequences to form head-to-head dimers.Mycobacterium tuberculosis PhoP of the PhoP-PhoR two-component signaling system orchestrates a complex transcription program and is essential for the growth and virulence of the tubercle bacillus. PhoP comprises a phosphorylation domain at the amino-terminal half and a DNA-binding domain in the carboxy-terminal half of the protein. We show here that the protein recognizes a 23-bp sequence of the phoP upstream region comprising two adjacent direct repeat motifs believed to promote transcription regulation. DNA binding, which involves the recruitment of two monomeric PhoP molecules, was dependent on conserved adenines of the repeat sequences and the orientation of the repeat motifs relative to each other. Although response regulators such as PhoB and FixJ dimerize upon phosphorylation, we demonstrate here that PhoP dimerization can also be stimulated by DNA binding. Using the established asymmetric tandem binding model by members of the OmpR/PhoB protein family as a guide, we set out to examine intermolecular interactions between PhoP dimers by protein cross-linking. Our results are consistent with a model in which two PhoP protomers bind the duplex DNA with a symmetric head-to-head orientation to project their N termini toward one another, arguing against previously proposed head-to-tail tandem dimer formation for members of the OmpR/PhoB protein subfamily.Sankalp GuptaAnuj PathakAkesh SinhaDibyendu Sarkar2012-02-28T16:11:51Z2012-02-28T16:11:51Zhttp://crdd.osdd.net/open/id/eprint/1087This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10872012-02-28T16:11:51ZA negative regulatory pathway of GLUT4 trafficking in adipocyte: new function of RIP140 in the cytoplasm via AS160.Receptor-interacting protein 140 (RIP140), a nuclear receptor corepressor, is important for lipid and glucose metabolism. In adipocytes, RIP140 can be phosphorylated by protein kinase C epsilon (PKCvarepsilon), followed by arginine methylation, and exported to the cytoplasm. This study demonstrates for the first time a cytoplasmic function for RIP140: to counteract insulin-stimulated glucose transporter 4 (GLUT4) membrane partitioning and glucose uptake in adipocytes. Cytoplasmic RIP140 interacts with the Akt substrate AS160, thereby impeding AS160 phosphorylation by Akt; this in turn reduces GLUT4 trafficking. This signal transduction pathway can be recapitulated in the epididymal adipocytes of diet-induced obese mice: nuclear PKCvarepsilon is activated, cytoplasmic RIP140 increases, and GLUT4 trafficking and glucose uptake are reduced. The data reveal a new, cytoplasmic function for RIP140 as a negative regulator of GLUT4 trafficking and glucose uptake, and shed insight into the regulation of basal and insulin-stimulated glucose disposal by a nuclear-initiated counteracting mechanism.Ping-Chih HoYi-Wei LinYao-Chen TsuiPawan GuptaLi-Na Wei2012-09-06T04:43:55Z2012-09-06T04:43:55Zhttp://crdd.osdd.net/open/id/eprint/1160This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11602012-09-06T04:43:55ZMechanistic insight into substrate- assisted catalysis by streptokinase.Kishore K. Joshi2012-02-28T16:11:30Z2016-03-01T06:28:28Zhttp://crdd.osdd.net/open/id/eprint/1089This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10892012-02-28T16:11:30ZAntimicrobial and toxicological studies of some metal complexes of 4- methylpiperazine-1-carbodithioate and phenanthroline mixed ligandsA few mixed ligand transition metal carbodithioate complexes of the general formula [M(4-
MPipzcdt)x(phen)y]Y (M = Mn(II), Co(II), Zn(II); 4-MPipzcdt = 4-methylpiperazine-1-carbodithioate;
phen = 1,10-phenanthroline; x = 1 and y = 2 when Y = Cl; x = 2 and y = 1 when Y = nil) were synthesized
and screened for their antimicrobial activity against Candida albicans, Escherichia coli, Pseudomonas
aeruginosa, Staphylococcus aureus and Enterococcus faecalis by disk diffusion method. All the
complexes exhibited prominent antimicrobial activity against tested pathogenic strains with the MIC
values in the range <8-512 �gmL-1. The complexes [Mn(4-MPipzcdt)2(phen)] and [Co(4-
MPipzcdt)(phen)2]Cl inhibited the growth of Candida albicans at a concentration as low as 8 μgmL-1. The
complexes were also evaluated for their toxicity towards human transformed rhabdomyosarcoma cells
(RD cells). Moderate cell viability of the RD cells was exhibited against the metal complexes.S.B. KaliaG. KaushalManoj Kumar(1)Swaranjit Singh CameotraA. SharmaM.L. Verma S.S. Kanwar2012-09-03T09:40:05Z2012-09-03T09:40:05Zhttp://crdd.osdd.net/open/id/eprint/1154This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11542012-09-03T09:40:05ZShort-circuiting natural evolution through selected transplantations of residues to engineer the physical behaviour of protein surface. "SUMMARY OF THE THSIS IS ATTACHED"Divya Kapoor2011-12-08T19:34:45Z2011-12-08T19:34:45Zhttp://crdd.osdd.net/open/id/eprint/558This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5582011-12-08T19:34:45ZCreation of a new eye lens crystallin (Gambeta) through structure-guided mutagenic grafting of the surface of betaB2 crystallin onto the hydrophobic core of gammaB crystallin.The degree of conservation of three-dimensional folds in protein superfamilies is greater than that of amino acid sequences. Therefore, very different groups of residues (and schemes of residue packing) can be found displayed upon similar structural scaffolds. We have previously demonstrated the workability of a protein engineering-based method for rational mixing of the interior features of an all-beta enzyme with the substrate-binding and catalytic (surface) features of another enzyme whose sequence is not similar but which is structurally homologous to the first enzyme. Here, we extend this method to whole-protein surfaces and interiors. We show how two all-beta Greek key proteins, betaB2 crystallin and gammaB crystallin, can be recombined to produce a new protein through rational transplantation of the entire surface of betaB2 crystallin upon the structure of gammaB crystallin, without altering the latter's interior. This new protein, Gambeta, consists of 61 residues possessing the same identity at structurally equivalent positions in betaB2- and gammaB crystallin, 91 surface residues unique to betaB2 crystallin, and 27 interior residues unique to gammaB crystallin. Gambeta displays a mixture of the structural/biochemical characteristics, surface features and colligative properties of its progenitor crystallins. It also displays optical properties common to both progenitor crystallins (i.e. retention of transparency at high concentrations, as well as high refractivity). The folding of a protein with such a 'patchwork' residue ancestry suggests that interior/surface transplants involving all-beta proteins are a feasible engineering strategy.Divya KapoorBalvinder SinghKarthikeyan SubramanianPurnananda Guptasarma2012-09-06T04:32:50Z2012-09-06T04:32:50Zhttp://crdd.osdd.net/open/id/eprint/1159This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11592012-09-06T04:32:50ZGenetic studies on the glutamylcysteine synthetase enzyme involved in glutathione biosynthesis in the yeast S. cerevisae.Neha Kastuia2012-01-10T08:05:00Z2012-01-10T08:05:00Zhttp://crdd.osdd.net/open/id/eprint/30This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/302012-01-10T08:05:00ZRSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information.The attainment of complete map-based sequence for rice (Oryza sativa) is clearly a major milestone for the research community. Identifying the localization of encoded proteins is the key to understanding their functional characteristics and facilitating their purification. Our proposed method, RSLpred, is an effort in this direction for genome-scale subcellular prediction of encoded rice proteins. First, the support vector machine (SVM)-based modules have been developed using traditional amino acid-, dipeptide- (i+1) and four parts-amino acid composition and achieved an overall accuracy of 81.43, 80.88 and 81.10%, respectively. Secondly, a similarity search-based module has been developed using position-specific iterated-basic local alignment search tool and achieved 68.35% accuracy. Another module developed using evolutionary information of a protein sequence extracted from position-specific scoring matrix achieved an accuracy of 87.10%. In this study, a large number of modules have been developed using various encoding schemes like higher-order dipeptide composition, N- and C-terminal, splitted amino acid composition and the hybrid information. In order to benchmark RSLpred, it was tested on an independent set of rice proteins where it outperformed widely used prediction methods such as TargetP, Wolf-PSORT, PA-SUB, Plant-Ploc and ESLpred. To assist the plant research community, an online web tool 'RSLpred' has been developed for subcellular prediction of query rice proteins, which is freely accessible at http://www.imtech.res.in/raghava/rslpred.Rakesh KaundalG.P.S. Raghava2011-12-08T19:35:16Z2011-12-08T19:35:16Zhttp://crdd.osdd.net/open/id/eprint/563This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5632011-12-08T19:35:16ZDug1p Is a Cys-Gly peptidase of the gamma-glutamyl cycle of Saccharomyces cerevisiae and represents a novel family of Cys-Gly peptidases.GSH metabolism in yeast is carried out by the gamma-glutamyl cycle as well as by the DUG complex. One of the last steps in the gamma-glutamyl cycle is the cleavage of Cys-Gly by a peptidase to the constitutent amino acids. Saccharomyces cerevisiae extracts carry Cys-Gly dipeptidase activity, but the corresponding gene has not yet been identified. We describe the isolation and characterization of a novel Cys-Gly dipeptidase, encoded by the DUG1 gene. Dug1p had previously been identified as part of the Dug1p-Dug2p-Dug3p complex that operates as an alternate GSH degradation pathway and has also been suggested to function as a possible di- or tripeptidase based on genetic studies. We show here that Dug1p is a homodimer that can also function in a Dug2-Dug3-independent manner as a dipeptidase with high specificity for Cys-Gly and no activity toward tri- or tetrapeptides in vitro. This activity requires zinc or manganese ions. Yeast cells lacking Dug1p (dug1Delta) accumulate Cys-Gly. Unlike all other Cys-Gly peptidases, which are members of the metallopeptidase M17, M19, or M1 families, Dug1p is the first to belong to the M20A family. We also show that the Dug1p Schizosaccharomyces pombe orthologue functions as the exclusive Cys-Gly peptidase in this organism. The human orthologue CNDP2 also displays Cys-Gly peptidase activity, as seen by complementation of the dug1Delta mutant and by biochemical characterization, which revealed a high substrate specificity and affinity for Cys-Gly. The results indicate that the Dug1p family represents a novel class of Cys-Gly dipeptidases.Hardeep KaurChitranshu KumarChristophe JunotMichel B ToledanoAnand K Bachhawat2011-12-08T19:34:04Z2011-12-08T19:34:04Zhttp://crdd.osdd.net/open/id/eprint/553This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5532011-12-08T19:34:04ZGln-222 in transmembrane domain 4 and Gln-526 in transmembrane domain 9 are critical for substrate recognition in the yeast high affinity glutathione transporter, Hgt1p.Hgt1p, a member of the oligopeptide transporter family, is a high affinity glutathione transporter from the yeast Saccharomyces cerevisiae. We have explored the role of polar or charged residues in the putative transmembrane domains of Hgt1p to obtain insights into the structural features of Hgt1p that govern its substrate specificity. A total of 22 charged and polar residues in the predicted transmembrane domains and other conserved regions were subjected to alanine mutagenesis. Functional characterization of these 22 mutants identified 11 mutants which exhibited significant loss in functional activity. All 11 mutants except T114A had protein expression levels comparable with wild type, and all except E744A were proficient in trafficking to the cell surface. Kinetic analyses revealed differential contributions toward the functional activity of Hgt1p by these residues and identified Asn-124 in transmembrane domain 1 (TMD1), Gln-222 in TMD4, Gln-526 in TMD9, and Glu-544, Arg-554, and Lys-562 in the intracellular loop region 537-568 containing the highly conserved proline-rich motif to be essential for the transport activity of the protein. Furthermore, mutants Q222A and Q526A exhibited a nearly 4- and 8-fold increase in the K(m) for glutathione. Interestingly, although Gln-222 is widely conserved among other functionally characterized oligopeptide transporter family members including those having a different substrate specificity, Gln-526 is present only in Hgt1p and Pgt1, the only two known high affinity glutathione transporters. These results provide the first insights into the substrate recognition residues of a high affinity glutathione transporter and on residues/helices involved in substrate translocation in the structurally uncharacterized oligopeptide transporter family.Jaspreet KaurAnand K Bachhawat2011-12-08T19:37:04Z2011-12-08T19:37:04Zhttp://crdd.osdd.net/open/id/eprint/577This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5772011-12-08T19:37:04ZA modified Western blot protocol for enhanced sensitivity in the detection of a membrane protein.Membrane proteins, owing to their highly hydrophobic nature, have always posed a daunting challenge to biochemists and structural biologists working on the characterization of these "naughty" proteins. Here we describe a problem that we encountered in the immunodetection of a hemagglutinin (HA) epitope-tagged membrane protein, Hgt1p (high-affinity glutathione transporter from the yeast Saccharomyces cerevisiae), for which little or no signal was observed on the blots with monoclonal antibody, on following the standard Western blot protocol. The introduction of a single step that involved posttransfer incubation of the blots with sodium dodecyl sulfate (SDS)/beta-mercaptoethanol solution at 55 degrees C for 15 min enabled us to detect a strong, stable, and reproducible signal for the membrane protein.Jaspreet KaurAnand K Bachhawat2011-12-08T19:34:29Z2011-12-08T19:34:29Zhttp://crdd.osdd.net/open/id/eprint/556This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5562011-12-08T19:34:29ZDifferential roles played by the native cysteine residues of the yeast glutathione transporter, Hgt1p.Hgt1p, a high-affinity glutathione transporter from the yeast Saccharomyces cerevisiae, belongs to the structurally uncharacterized oligopeptide transporter (OPT) family. To initiate structural studies on Hgt1p, a cysteine-free (cys-free) Hgt1p was generated. This cys-free Hgt1p was nonfunctional and pointed to a critical role being played by the native cysteine residues of Hgt1p. To investigate their role, genetic and biochemical approaches were undertaken. Functional suppressors of the cys-free Hgt1p were isolated, and yielded double revertants bearing C622 and C632. Subsequent biochemical characterization of the individual C622S/A or C632S/A mutations revealed that both these cysteine residues were, in fact, individually indispensable for Hgt1p function and were required for trafficking to the plasma membrane. However, despite their essentiality, the presence of only these two native cysteines in Hgt1p generated a very weak glutathione transporter with minimal functional activity. Hence, the remaining 10 cysteines were also contributing towards Hgt1p activity, although they were not found to be singly responsible or crucial for Hgt1p functional activity. These residues, however, contributed cumulatively towards the stability and the functionality of Hgt1p, without affecting the trafficking to the cell surface. The study reveals differential roles for the cysteines of Hgt1p and provides first insights into the structural features of an OPT family member.Jaspreet KaurChittur V SrikanthAnand K Bachhawat2011-12-08T19:34:23Z2015-01-09T11:33:36Zhttp://crdd.osdd.net/open/id/eprint/555This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5552011-12-08T19:34:23ZDescription of Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al. 2003 as Paenisporosarcina macmurdoensis comb. nov.In the course of a study of the prokaryotic diversity of a landfill site in Chandigarh, India, a strain designated SK 55(T) was isolated and characterized using a polyphasic approach. Its 16S rRNA gene sequence showed closest similarity (98.3 %) to that of Sporosarcina macmurdoensis CMS 21w(T). The sequence similarity to strains of other hitherto described species of Sporosarcina was less than 95.5 %. Strain SK 55(T) contains peptidoglycan of the A4alpha type (l-Lys-d-Asp), MK-8 and MK-7 as the major menaquinones and iso-C(15 : 0) as the major fatty acid. Strain SK 55(T), Sporosarcina macmurdoensis and Sporosarcina ureae, the type species of the genus, had some polar lipids in common (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and an unknown lipid). However, an aminolipid, an aminophospholipid and an unknown lipid found in the former two organisms are similar, though not identical, but quite different from the profile of S. ureae. The genomic DNA G+C contents of strain SK 55(T) (46.0 mol%) and S. macmurdoensis CMS 21w(T) (44.0 mol%) are higher than those reported for the majority of species of Sporosarcina (36-42 mol%). As revealed by 16S rRNA gene sequence analysis, strain SK 55(T) and S. macmurdoensis CMS 21w(T) form a clade which is distinct from the clade occupied by other species of Sporosarcina. On the basis of phenotypic characteristics including chemotaxonomic data and analysis of the 16S rRNA gene sequence, we conclude that strain SK 55(T) should be considered as a member of a novel genus and species, for which the name Paenisporosarcina quisquiliarum gen. nov., sp. nov. is proposed. The type strain of Paenisporosarcina quisquiliarum is SK 55(T) (=MTCC7604(T) =JCM 14041(T)). S. macmurdoensis CMS 21w(T) shows more similarity in its 16S rRNA gene sequence (98.3 %), DNA G+C content and polar lipid profile to strain SK 55(T) than to S. ureae DSM 2281(T). Phylogenetically, it forms a coherent cluster with strain SK 55(T) which is separate from the Sporosarcina cluster. Moreover, iso-C(15 : 0), anteiso-C(15 : 0) and C(16 : 1)omega7c alcohol are the three major fatty acids in both S. macmurdoensis CMS 21w(T) and SK 55(T). All these data suggest that S. macmurdoensis should be a member of the genus Paenisporosarcina. However, S. macmurdoensis can be differentiated from SK 55(T) in several physiological and biochemical characteristics, especially in the patterns of oxidation and acid production from carbohydrates. The genomic relatedness of S. macmurdoensis CMS 21w(T) and strain SK 55(T) was also very low (18.0 %). It is therefore logical to transfer Sporosarcina macmurdoensis to the newly created genus as Paenisporosarcina macmurdoensis comb. nov. The type strain is CMS 21w(T) (=MTCC4670(T) =DSM 15428(T)).S KrishnamurthiA BhattacharyaShanmugam MayilrajSudipto SahaPeter SchumannT Chakrabarti2011-12-08T19:34:58Z2012-03-29T07:08:41Zhttp://crdd.osdd.net/open/id/eprint/560This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5602011-12-08T19:34:58ZRe-examination of the taxonomic position of Bacillus silvestris Rheims et al. 1999 and proposal to transfer it to Solibacillus gen. nov. as Solibacillus silvestris comb. nov.Following the transfer of three of the six species enclosed in the original definition of rRNA group 2 of Bacillus to the genus Sporosarcina and two to Lysinibacillus, other species of this group, some of which were added later, still await taxonomic revision. In a recent publication, a set of 'core' characteristics was proposed for species to be included in the genus Bacillus (Kämpfer et al., 2006). Except for Bacillus silvestris, however, several or none of these properties are available for members of rRNA group 2. According to our analysis of data including the 'core' characteristics, Bacillus silvestris should not be a member of the genus Bacillus. We therefore propose the establishment of a new genus, Solibacillus gen. nov., and transfer Bacillus silvestris to this genus as Solibacillus silvestris comb. nov., with the type strain HR3-23(T) (=DSM 12223(T)=ATCC BAA-269(T)=CIP 106059(T)).S KrishnamurthiT ChakrabartiErko Stackebrandt2012-09-06T06:21:07Z2012-09-06T06:21:07Zhttp://crdd.osdd.net/open/id/eprint/1164This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11642012-09-06T06:21:07ZRole of chromatin assembly factor-1 and Pap 1 in gene silencing in schizasachharomyces pombe.Ashok Kumar2011-12-08T19:36:10Z2011-12-08T19:36:10Zhttp://crdd.osdd.net/open/id/eprint/570This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5702011-12-08T19:36:10ZPrediction of nuclear proteins using SVM and HMM models.This study describes a highly accurate method for predicting nuclear proteins. SVM module has been developed for the first time using SAAC for predicting nuclear proteins, where amino acid composition of N-terminus and the remaining protein were computed separately. In addition, our study is a first documentation where exclusively nuclear and non-nuclear domains have been identified and used for predicting nuclear proteins. The performance of the method improved further by combining both approaches together.Manish KumarG.P.S. Raghava2012-09-06T04:51:43Z2012-09-06T04:51:43Zhttp://crdd.osdd.net/open/id/eprint/1162This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11622012-09-06T04:51:43ZStudies on concerted structural transitions and protein- protein interactions in plasminogen activation by bacterial plasminogen activator. Shekhar Kumar2012-02-28T16:10:50Z2012-02-28T16:10:50Zhttp://crdd.osdd.net/open/id/eprint/1092This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10922012-02-28T16:10:50ZAssembly of the cysteine synthase complex and the regulatory role of protein-protein interactions.Macromolecular assemblies play critical roles in regulating cellular functions. The cysteine synthase complex (CSC), which is formed by association of serine O-acetyltransferase (SAT) and O-acetylserine sulfhydrylase (OASS), acts as a sensor and modulator of thiol metabolism by responding to changes in nutrient conditions. Here we examine the oligomerization and energetics of formation of the soybean CSC. Biophysical examination of the CSC by size exclusion chromatography and sedimentation ultracentrifugation indicates that this assembly (complex M(r) approximately 330,000) consists of a single SAT trimer (trimer M(r) approximately 110,000) and three OASS dimers (dimer M(r) approximately 70,000). Analysis of the SAT-OASS interaction by isothermal titration calorimetry reveals negative cooperativity with three distinct binding events during CSC formation with K(d) values of 0.3, 7.5, and 78 nm. The three binding events are also observed using surface plasmon resonance with comparable affinities. The stability of the CSC derives from rapid association and extremely slow dissociation of OASS with SAT and requires the C terminus of SAT for the interaction. Steady-state kinetic analysis shows that CSC formation enhances SAT activity and releases SAT from substrate inhibition and feedback inhibition by cysteine, the final product of the biosynthesis pathway. Cysteine inhibits SAT and the CSC with K(i) values of 2 and 70 microm, respectively. These results suggest a new model for the architecture of this regulatory complex and additional control mechanisms for biochemically controlling plant cysteine biosynthesis. Based on previous work and our results, we suggest that OASS acts as an enzyme chaperone of SAT in the CSC.Sangaralingam KumaranHankuil YiHari B KrishnanJoseph M Jez2011-12-08T19:35:22Z2011-12-08T19:35:23Zhttp://crdd.osdd.net/open/id/eprint/564This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5642011-12-08T19:35:22ZRole of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis.Mycobacterium tuberculosis truncated hemoglobin, HbN, is endowed with a potent nitric-oxide dioxygenase activity and has been found to relieve nitrosative stress and enhance in vivo survival of a heterologous host, Salmonella enterica Typhimurium, within the macrophages. These findings implicate involvement of HbN in the defense of M. tuberculosis against nitrosative stress. The protein carries a tunnel system composed of a short and a long tunnel branch that has been proposed to facilitate diatomic ligand migration to the heme and an unusual Pre-A motif at the N terminus, which does not contribute significantly to the structural integrity of the protein, as it protrudes out of the compact globin fold. Strikingly, deletion of Pre-A region from the M. tuberculosis HbN drastically reduces its ability to scavenge nitric oxide (NO), whereas its insertion at the N terminus of Pre-A lacking HbN of Mycobacterium smegmatis improved its nitric-oxide dioxygenase activity. Titration of the oxygenated adduct of HbN and its mutants with NO indicated that the stoichiometric oxidation of protein is severalfold slower when the Pre-A region is deleted in HbN. Molecular dynamics simulations show that the excision of Pre-A motif results in distinct changes in the protein dynamics, which cause the gate of the tunnel long branch to be trapped into a closed conformation, thus impeding migration of diatomic ligands toward the heme active site. The present study, thus, unequivocally demonstrates vital function of Pre-A region in NO scavenging and unravels its unique role by which HbN might attain its efficient NO-detoxification ability.Amrita LamaSudesh PawariaAxel Bidon-ChanalArvind AnandJosé Luis GelpíSwati AryaMarcelo MartíDario A EstrinF Javier LuqueKanak L Dikshit2012-02-28T16:10:58Z2012-02-28T16:10:58Zhttp://crdd.osdd.net/open/id/eprint/1091This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10912012-02-28T16:10:58ZComplete genome sequence of Actinosynnema mirum type strain (101).Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO(2) atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.Miriam LandAlla LapidusShanmugam MayilrajFeng ChenAlex CopelandTijana Glavina Del RioMatt NolanSusan LucasHope TiceJan-Fang ChengOlga ChertkovDavid BruceLynne GoodwinSam PitluckManfred RohdeMarkus GökerAmrita PatiNatalia IvanovaKonstantinos MavromatisAmy ChenKrishna PalaniappanLoren HauserYun-Juan ChangCynthia C JeffriesThomas BrettinJohn C DetterCliff HanPatrick ChainBrian J TindallJim BristowJonathan A EisenVictor MarkowitzPhilip HugenholtzNikos C KyrpidesHans-Peter Klenk2012-07-05T09:21:10Z2012-07-05T09:21:10Zhttp://crdd.osdd.net/open/id/eprint/1152This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11522012-07-05T09:21:10ZBioinformatics approach for searching subunit vaccine candidates and adjuvants."SUMMARY OF THE THISIS IS ATTACHED"Sneh Lata2011-12-08T19:35:03Z2011-12-08T19:35:03Zhttp://crdd.osdd.net/open/id/eprint/561This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5612011-12-08T19:35:03ZMHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes.MHCBN database updating is meant to facilitate immunologist in understanding the immune system and provide them the latest information. We feel that our database will complement the existing databases in serving scientific community.Sneh LataManoj BhasinG.P.S. Raghava2011-12-08T19:34:36Z2011-12-09T09:42:21Zhttp://crdd.osdd.net/open/id/eprint/557This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5572011-12-08T19:34:36ZPrediction and classification of chemokines and their receptors.Chemokines are low molecular mass cytokine-like proteins that orchestrate myriads of immune functions like leukocyte trafficking, T cell differentiation, angiogenesis, hematopeosis and mast cell degranulation. Chemokines also play a role as HIV-1 inhibitor and act as potent natural adjuvant in antitumor immunotherapy. Receptors for these molecules are all seven-pass transmembrane G-protein-coupled receptors that are intimately involved with chemokines in a wide array of physiological and pathological conditions. These receptors also have a major role as co-receptors for HIV-1 entry into target cells. Therefore, chemokine receptors have proven to be excellent targets for small molecule in pharmaceutical industry. The immense importance of chemokines and their receptors motivated us to develop a support vector machine-based method ChemoPred to predict this important class of proteins and further classify them into subfamilies. ChemoPred is capable of predicting chemokines and chemokine receptors with an accuracy of 95.08% and 92.19%, respectively. The overall accuracy of classification of chemokines into three subfamilies was 96.00% and that of chemokine receptors into three families was 92.87%. The server ChemoPred is freely available at www.imtech.res.in/raghava/chemopred.Sneh LataG.P.S. Raghava2012-09-06T04:55:54Z2012-09-06T04:55:54Zhttp://crdd.osdd.net/open/id/eprint/1163This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11632012-09-06T04:55:54Ztudies towards understanding the molecular mechanism of stress tolerance mediated by RPI 1 yeast.M Amin-ul Mannan2011-12-08T19:36:28Z2011-12-08T19:36:28Zhttp://crdd.osdd.net/open/id/eprint/573This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5732011-12-08T19:36:28ZDesulfonauticus autotrophicus sp. nov., a novel thermophilic sulfate-reducing bacterium isolated from oil-production water and emended description of the genus Desulfonauticus.A novel moderately thermophilic and halophilic sulfate-reducing bacterium, strain TeSt(T), was isolated from production water of an oil field in Northern Germany near Hamburg. The cells were Gram-negative, straight to slightly curved rods and motile by a single polar flagellum. Only hydrogen and formate served as electron donors, whereas a wide variety of organic substrates and CO(2) could be used as carbon sources. Sulfate, sulfite, thiosulfate and sulfur were used as electron acceptors, but not nitrate or ferric iron. The novel isolate was negative for oxidase, catalase and desulfoviridin enzyme activity. Cytochromes were present and predominantly of the c-type. Whole-cells fatty acid patterns were dominated by the branched-chain fatty acids anteiso-C(15:0), iso-C(15:0), iso-C(17:0) and anteiso-C(17:0). As major respiratory lipoquinones partially saturated derivates of menaquinone 6 [MK-6(H(2)) and probably MK-6(H(4))] were identified. The G + C content of the genomic DNA was 41.3 mol% (HPLC method). An analysis of the 16S rRNA gene sequence indicated that strain TeSt(T) belongs to the family Desulfohalobiaceae within the class Deltaproteobacteria. The most closely related species with a sequence similarity of 95.0% was Desulfonauticus submarinus suggesting an affiliation of TeSt(T) to the genus Desulfonauticus. The novel isolate could be clearly distinguished from Desulfonauticus submarinus by its ability to grow chemolithoautotrophically and hence should be assigned to a novel species for which the name Desulfonauticus autotrophicus sp. nov. is proposed. The type strain is TeSt(T) (=DSM 4206(T)=JCM 13028(T)).Shanmugam MayilrajAnna H KaksonenRalf Cord-RuwischPeter SchumannCathrin SpröerBrian J TindallStefan Spring2012-09-06T06:30:16Z2012-09-06T06:30:16Zhttp://crdd.osdd.net/open/id/eprint/1166This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11662012-09-06T06:30:16ZMolecular characterization of the putative osmosensors in debaryomyces hansenil.Netrapal Meena2011-12-08T19:36:35Z2011-12-08T19:36:35Zhttp://crdd.osdd.net/open/id/eprint/572This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5722011-12-08T19:36:35ZDevelopment of host and vector for high-efficiency transformation and gene disruption in Debaryomyces hansenii.Debaryomyces hansenii is one of the most osmotolerant and halotolerant yeasts. The molecular mechanisms underlying its extreme osmotolerance and halotolerance have drawn considerable attention in the recent past. However, progress in this regard has been limited due to lack of availability of a transformation system and molecular tools to study the functions of the genes in D. hansenii. Here, we have described the development of an efficient transformation system for D. hansenii that is based on a histidine auxotrophic recipient strain and the DhHIS4 gene as the selectable marker. By screening the D. hansenii genomic library, we have isolated several autonomous replication sequences that can be used for constructing a replicating vector. Moreover, our study is the first to demonstrate gene disruption in D. hansenii by homologous recombination.Anupriya MinhasDipanwita BiswasAlok K Mondal2012-09-06T07:20:36Z2012-09-06T07:20:36Zhttp://crdd.osdd.net/open/id/eprint/1171This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11712012-09-06T07:20:36ZNew biocatalyst for nitrile hydrolysis and novel chiral solvating agents for NMR enantiodiscrimination of cyanohydrins. Lomary S Moon2011-12-08T19:35:45Z2012-04-02T09:48:35Zhttp://crdd.osdd.net/open/id/eprint/567This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5672011-12-08T19:35:45ZA new chiral shift reagent for the determination of enantiomeric excess and absolute configuration in cyanohydrins.Optically active mandelic acid in the presence of dimethylaminopyridine is an excellent chiral shift reagent for the determination of enantiomeric excess and absolute configuration in cyanohydrins.Lomary S MoonR S JollyYoganjaneyulu KasettiPrasad V Bharatam2011-12-08T19:33:58Z2011-12-08T19:33:58Zhttp://crdd.osdd.net/open/id/eprint/552This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5522011-12-08T19:33:58ZA novel bacterial isolate Stenotrophomonas maltophilia as living factory for synthesis of gold nanoparticles.The process of synthesis of well-dispersed nanoparticles using a novel microorganism isolated from the gold enriched soil sample has been reported in this study, leading to the development of an easy bioprocess for synthesis of GNPs. This is the first study in which an extensive characterization of the indigenous bacterium isolated from the actual gold enriched soil was conducted. Promising mechanism for the biosynthesis of GNPs by the strain and their stabilization via charge capping is suggested, which involves an NADPH-dependent reductase enzyme that reduces Au3+ to Au0 through electron shuttle enzymatic metal reduction process.Yogesh NangiaNishima WangooNisha GoyalG ShekhawatC Raman Suri2012-02-28T16:11:20Z2012-02-28T16:11:20Zhttp://crdd.osdd.net/open/id/eprint/1090This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10902012-02-28T16:11:20ZBacillus canaveralius sp. nov., an alkali-tolerant bacterium isolated from a spacecraft assembly facility.Two Gram-positive, rod-shaped, alkali-tolerant (pH 10.5), endospore-forming bacteria (strains KSC SF8bT and KSC SF10a) were isolated from surfaces within the Payload Hazardous Servicing Facility, where robotic spacecraft are assembled and tested before launch, at the Kennedy Space Center at Cape Canaveral. Based on 16S rRNA gene sequence similarities, these strains were shown to belong to the family Bacillaceae and the genus Bacillus. The highest 16S rRNA gene sequence similarity was approximately 97.5%, observed between the novel strains and Bacillus selenatarsenatis SF-1T. Several phenotypic characteristics, such as growth with 10% NaCl and assimilation of melibiose and lactose, were useful in the discrimination of this novel species from the closely related alkali-tolerant species Bacillus firmus and B. selenatarsenatis. DNA-DNA hybridization studies revealed reassociation values of less than 45% between strain KSC SF8bT and its closest genotypic neighbours. The combination of unique phenotypic and genotypic characteristics allowed the differentiation of these alkali- and halotolerant spore-forming strains from related Bacillus species, and a novel species, Bacillus canaveralius sp. nov., is proposed. The type strain is KSC SF8bT (=ATCC BAA-1493T=MTCC 8908T).David NewcombeAnne DekasShanmugam MayilrajKasthuri Venkateswaran2013-01-31T07:04:37Z2013-01-31T07:04:37Zhttp://crdd.osdd.net/open/id/eprint/1155This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11552013-01-31T07:04:37ZMolecular and biochemical studies of O-Nitrobenzoate biodegradation and bacterial diversity of a nitroaromatic contaminated site. Janmejay Pandey2011-12-08T19:36:02Z2012-04-03T07:07:45Zhttp://crdd.osdd.net/open/id/eprint/569This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5692011-12-08T19:36:02ZIntegrative approaches for assessing the ecological sustainability of in situ bioremediation.Application of microbial metabolic potential (bioremediation) is accepted as an environmentally benign and economical measure for decontamination of polluted environments. Bioremediation methods are generally categorized into ex situ and in situ bioremediation. Although in situ bioremediation methods have been in use for two to three decades, they have not yet yielded the expected results. Their limited success has been attributed to reduced ecological sustainability under environmental conditions. An important determinant of sustainability of in situ bioremediation is pollutant bioavailability. Microbial chemotaxis is postulated to improve pollutant bioavailability significantly; consequently, application of chemotactic microorganisms can considerably enhance the performance of in situ degradation. The environmental fate of degradative microorganisms and the ecological consequence of intervention constitute other important descriptors for the efficiency and sustainability of bioremediation processes. Integrative use of culture-dependent, culture-independent methods (e.g. amplified rDNA restriction analysis, terminal restriction fragment length polymorphism, denaturing/thermal gradient gel electrophoresis, phospholipid fatty acid, etc.), computational and statistical analyses has enabled successful monitoring of the above aspects. The present review provides a detailed insight into some of the key factors that affect the efficiency of in situ bioremediation along with a comprehensive account of the integrative approaches used for assessing the ecological sustainability of processes. The review also discusses the possibility of developing suicidal genetically engineered microorganisms for optimized and controlled in situ bioremediation.Janmejay PandeyArchana ChauhanR K Jain2011-12-08T19:36:49Z2011-12-08T19:36:49Zhttp://crdd.osdd.net/open/id/eprint/575This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5752011-12-08T19:36:49ZCognitive optimization of microbial PHB production in an optimally dispersed bioreactor by single and mixed cultures.Cognitive (or intelligent) models are often superior to mechanistic models for nonideal bioreactors. Two kinds of cognitive models--cybernetic and neural--were applied recently to fed-batch fermentation by Ralstonia eutropha in a bioreactor with optimum finite dispersion. In the present work, these models have been applied in simulation studies of co-cultures of R. eutropha and Lactobacillus delbrueckii. The results for both cognitive and mechanistic models have been compared with single cultures. Neural models were the most effective for both types of cultures and mechanistic models the least effective. Simulations with co-culture fermentations predicted more PHB than single cultures with all three types of models. Significantly, the predicted enhancements in PHB concentration by cognitive methods for mixed cultures were four to five times larger than the corresponding increases in biomass concentration. Further improvements are possible through a hybrid combination of all three types of models.Pratap R Patnaik2012-02-28T16:10:16Z2012-02-28T16:10:16Zhttp://crdd.osdd.net/open/id/eprint/1096This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10962012-02-28T16:10:16ZTransient response analysis of the eukaryotic chemosensory system to intra-cellular fluctuations.Like prokaryotic cells, those of eukaryotes are also subjected to noise from within the cells. While the cells have a built-in mechanism to attenuate the noise, conditions may arise where this is beyond the cell's ability to regulate. Start-up perturbations and those induced by metabolic shifts are examples of such situations. Then, it becomes useful to understand how the cells respond. For a eukaryotic chemosensory system, this has been studied by applying response coefficient analysis to a recent model. With even three dependent variables - an activator, an inhibitor, and a response element - the response coefficients differ widely with time and from one variable to another. These differences are interpreted in terms of the chemosensory mechanism and its robustness. The results complement similar recent studies of Escherichia coli chemotaxis, thus supporting their credibility and versatility.Pratap R Patnaik2011-12-08T19:33:45Z2012-04-02T06:44:09Zhttp://crdd.osdd.net/open/id/eprint/550This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5502011-12-08T19:33:45ZCritical role of RPI1 in the stress tolerance of yeast during ethanolic fermentation.Stress tolerance of yeast Saccharomyces cerevisiae during ethanolic fermentation is poorly understood due to the lack of genetic screens and conventional plate assays for studying this phenotype. We screened a genomic expression library of yeast to identify gene(s) that, upon overexpression, would prolong the survival of yeast cells during fermentation, with the view to understand the stress response better and to use the identified gene(s) in strain improvement. The yeast RPI1 (Ras-cAMP pathway inhibitor 1) gene was identified in such a screen performed at 38 degrees C; introducing an additional copy of RPI1 with its native promoter helped the cells to retain their viability by over 50-fold better than the wild type (WT) parent strain, after 36 h of fermentation at 38 degrees C. Disruption of RPI1 resulted in a drastic reduction in viability during fermentation, but not during normal growth, further confirming the role of this gene in fermentation stress tolerance. This gene seems to improve viability by fortifying the yeast cell wall, because RPI1 overexpression strain is highly resistant to cell lytic enzyme zymolyase, compared with the WT strain. As the RPI1 overexpression strain substantially retains cell viability at the end of fermentation, the cells can be reused in the subsequent round of fermentation, which is likely to facilitate economical production of ethanol.Rekha PuriaM Amin-ul MannanRohini Chopra-DewasthalyK Ganesan2012-02-28T16:12:20Z2015-01-07T06:45:11Zhttp://crdd.osdd.net/open/id/eprint/1083This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10832012-02-28T16:12:20ZBiocide-tolerant multidrug-resistant Acinetobacter baumannii clinical strains are associated with higher biofilm formation.Govindan RajamohanV B SrinivasanWondwossen A Gebreyes2012-02-28T16:11:39Z2012-04-03T06:53:35Zhttp://crdd.osdd.net/open/id/eprint/1088This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10882012-02-28T16:11:39ZMechanism of drug resistance in a clinical isolate of Vibrio fluvialis: involvement of multiple plasmids and integrons.The role of mobile genetic elements in imparting multiple drug resistance to a clinical isolate of Vibrio fluvialis (BD146) was investigated. This isolate showed complete or intermediate resistance to all of the 14 antibiotics tested. Polymerase chain reaction (PCR) revealed the presence of a class 1 integron and the absence of the SXT element in this isolate. The strain harboured a 7.5 kb plasmid and a very low copy number plasmid of unknown molecular size. Transformation of Escherichia coli with plasmid(s) from BD146 generated two kinds of transformants, one that harboured both of these plasmids and the other that harboured only the low copy number plasmid. PCR and antibiogram analysis indicated the association of the class 1 integron with the low copy number plasmid, which also conferred all the transferable resistance traits except trimethoprim to the parent strain. A BLAST search with the sequence of the 7.5kb plasmid showed that it was 99% identical to plasmid pVN84 from Vibrio cholerae O1 in Vietnam, indicating that these two plasmids are probably one and the same. To the best of our knowledge, this is the first report of horizontal transfer of a plasmid between V. fluvialis and V. cholerae.Neha RajparaArati PatelNeha TiwariJyotsana BahugunaAnita AntonyIpsita ChoudhuryAnuradha GhoshR K JainAmit GhoshAshima Kushwaha Bhardwaj2012-01-10T08:04:55Z2012-01-10T08:04:55Zhttp://crdd.osdd.net/open/id/eprint/28This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/282012-01-10T08:04:55ZHmrbase: a database of hormones and their receptors.Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, DrugPedia linkage etc. Hmrbase is available online for public from http://crdd.osdd.net/raghava/hmrbase/.Mamoon RashidDeepak SinglaArun SharmaManish KumarG.P.S. Raghava2011-12-08T19:37:19Z2011-12-08T19:37:19Zhttp://crdd.osdd.net/open/id/eprint/579This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5792011-12-08T19:37:19ZPentoxifylline induces apoptosis in vitro in cutaneous T cell lymphoma (HuT-78) and enhances FasL mediated killing by upregulating Fas expression.Constitutive nuclear factor-kappaB (NF-kappaB) is known to play an important role in the survival of HuT-78 cells, a cutaneous T cell lymphoma (CTCL) cell line. Here, we have demonstrated that pentoxifylline (PTX), a phosphodiesterase inhibitor, can trigger a series of events leading to apoptosis in HuT-78 cells without affecting NF-kappaB. Apoptosis was ascertained by sub-G1 peak analysis and TUNEL assay. Apoptosis induced by PTX in HuT-78 cells involved mitochondrial hyperpolarization, cytochrome c release, caspase-3 activation and PARP cleavage. Further, it was found that PTX treatment downregulated Bcl-xl and c-FLIP expression without affecting constitutive NF-kappaB but upregulated activator protein-1 (AP-1). Low concentration of PTX upregulated Fas and TRAIL expression in HuT-78 cells. In addition, PTX can act as a scavenger of reactive oxygen intermediate and it could enhance FasL mediated killing in HuT-78 cells. Our results taken together indicated that PTX may be a potential agent for killing CTCL cells.Loveena RishiSatindra GahlotMahesh KathaniaSekhar Majumdar2012-09-06T04:25:52Z2012-09-06T04:25:52Zhttp://crdd.osdd.net/open/id/eprint/1158This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11582012-09-06T04:25:52ZExploration of yeasts from selected niches of India and study of thermotolerance.Puja Saluja2012-09-06T07:11:52Z2012-09-06T07:11:52Zhttp://crdd.osdd.net/open/id/eprint/1169This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11692012-09-06T07:11:52ZPhage display for screening and identifying protein ligand interactions in malaria.Ashu Shah2012-02-28T16:10:01Z2012-02-28T16:10:01Zhttp://crdd.osdd.net/open/id/eprint/1098This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10982012-02-28T16:10:01ZEvidence for the presence of R250G mutation at the ATPase domain of topoisomerase II in an arsenite-resistant Leishmania donovani exhibiting a differential drug inhibition profile.Resistance to operational drugs is a major barrier to successful antileishmanial chemotherapy that demands development of novel drug intervention strategies based on rational approaches. Model drug resistance phenotypes, such as arsenite resistance used in the current study, facilitate our understanding of the mechanism of drug resistance and assist in identifying new drug target(s). The current study was undertaken to investigate the sensitivity of topoisomerase II (topo II) of arsenite-sensitive (Ld-Wt) and -resistant (Ld-As20) Leishmania donovani to antileishmanial/anti-topo II agents. The effect of antileishmanial/anti-topo II drugs on partially purified topo II enzyme from Ld-Wt and Ld-As20 revealed differential inhibition of topo II decatenation activity for the two strains, with a lower amount of drug required to inhibit activity by 50% in Ld-Wt compared with Ld-As20. Comparison of topo II sequences from both strains indicated a point mutation, R250G, in the ATPase domain of the resistant strain. Furthermore, the Arg-250 of the ATPase domain of topo II was observed to be conserved throughout different species of Leishmania. Variation in the topo II gene sequence between Ld-Wt and Ld-As20 is envisaged to be responsible for the differential behaviour of the enzymes from the two sources.Gaganmeet SinghMeghna ThakurPradip K ChakrabortiChinmoy S Dey2012-02-28T16:10:08Z2013-01-29T04:47:53Zhttp://crdd.osdd.net/open/id/eprint/1097This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10972012-02-28T16:10:08ZMonitoring atrazine uptake by a new fluorometric assayWe report here a new fluorometric method for monitoring atrazine uptake using a strain of Acinetobacter radioresistens. Around 40% decrease in the relative fluorescent intensity of the culture supernatant and a corresponding increase in the fluorescence in cell biomass was observed after 18 h of growth on the fluorescing substrate, which was indicative of the rapid entry of the compound into the bacterial cell. This fast and safe method is a new application in the field of environmental biotechnology and can be used as an additional approach to monitor uptake of other toxic compounds by different microorganisms and to screen for different pollutant degraders.P. SinghSoniya DhanjalK.V. SinghC Raman SuriSwaranjit Singh Cameotra2012-02-28T16:12:26Z2015-01-07T06:44:01Zhttp://crdd.osdd.net/open/id/eprint/1082This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10822012-02-28T16:12:26ZRole of AbeS, a Novel Efflux Pump of the SMR Family of Transporters, in Resistance to Antimicrobial Agents in Acinetobacter baumanniiIn this study, a chromosomally encoded putative drug efflux pump of the SMR family, named AbeS, from a
multidrug-resistant strain of Acinetobacter baumannii was characterized to elucidate its role in antimicrobial
resistance. Expression of the cloned abeS gene in hypersensitive Escherichia coli host KAM32 resulted in
decreased susceptibility to various classes of antimicrobial agents, detergents, and dyes. Deletion of the abeS
gene in A. baumannii confirmed its role in conferring resistance to these compounds.V. B. SrinivasanGovindan RajamohanWondwossen A Gebreyes2012-02-28T16:12:13Z2012-02-28T16:12:13Zhttp://crdd.osdd.net/open/id/eprint/1084This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/10842012-02-28T16:12:13ZGenetic relatedness and molecular characterization of multidrug resistant Acinetobacter baumannii isolated in central Ohio, USA.This study underscores the major role of carbapenem-hydrolyzing class D beta-lactamases, and in particular the acquired OXA-23, in the dissemination of imipenem-resistant A. baumannii. The co-occurrence of additional resistance determinant could also be a significant threat.Vijaya B SrinivasanGovindan RajamohanPreeti PancholiKurt StevensonDaniel TadessePrapas PatchaneeMario MarconWondwossen A Gebreyes2012-09-06T04:47:38Z2012-09-06T04:47:38Zhttp://crdd.osdd.net/open/id/eprint/1161This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/11612012-09-06T04:47:38ZMycobacteria and host cell: Studies on cell envelope components of Mycobacteria. Shilpy Srivastava2011-12-08T19:32:47Z2015-01-09T09:32:37Zhttp://crdd.osdd.net/open/id/eprint/544This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/5442011-12-08T19:32:47ZIsolation and characterization of an atrazine-degrading Rhodococcus sp. strain MB-P1 from contaminated soil.Rhodococcus sp. strain MB-P1 could be used as an ideal model system for in-situ degradation and restoration of ecological niches which are heavily contaminated with atrazine.Fazlur rahmanM BatraJanmejay PandeyC Raman SuriR K Jain