open: No conditions. Results ordered Creators, Title. 2024-03-28T09:27:33ZEPrintshttp://crdd.osdd.net/images/sitelogo.gifhttp://crdd.osdd.net/open/2012-02-14T10:32:09Z2012-02-14T10:32:09Zhttp://crdd.osdd.net/open/id/eprint/934This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9342012-02-14T10:32:09ZMolecular characterization of rice hsp101: complementation of yeast hsp104 mutation by disaggregation of protein granules and differential expression in indica and japonica rice types.HSP100 protein is an important component of the heat-shock response in diverse organisms. Using specific primers based on cDNA sequence, rice hsp101 gene was PCR-amplified and sequenced. Southern analysis revealed that there appears to be a single gene per haploid genome coding for HSP101 protein in rice. Northern analysis showed that expression of hsp101 transcript is strictly heat-inducible and induction is transient in nature. In the temperature regime tested, 45 degrees C treatment to intact rice seedlings for 2 h showed maximal levels of hsp101 mRNA. Rice full-length hsp101 cDNA complemented yeast mutant disrupted for its own hsp104 gene by insertional mutagenesis, with efficacy that was comparable with Arabidopsis hsp101 cDNA. Electron micrographic evidence suggested that rice hsp101 cDNA in yeast is active in re-solubilizing the stress-induced protein granules in the post-stress recovery period. Rice hsp101 cDNA expression in hsp104 deficient yeast also caused recovery in tolerance against arsenite. Western analyses showed that this protein is expressed more rapidly during the stress period and retained for longer duration in the post-stress recovery period in japonica rice as compared to indica rice types. This is the first report wherein plant HSP100 protein expression is correlated to disappearance of protein granules in the yeast cells and distinct rice type-dependent protein expression patterns are reported.Manu AgarwalChandan SahiSurekha Katiyar-AgarwalSangeeta AgarwalTodd YoungDaniel R GallieVishva Mitra SharmaK GanesanAnil Grover2013-10-22T11:05:28Z2013-10-30T10:58:04Zhttp://crdd.osdd.net/open/id/eprint/1477This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14772013-10-22T11:05:28ZStructural Studies of EPS 8-SH3 Domain with its complementary ProteinsVishal Agrawal2012-01-06T14:58:55Z2012-01-06T14:58:55Zhttp://crdd.osdd.net/open/id/eprint/243This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2432012-01-06T14:58:55ZOB-fold: growing bigger with functional consistency.It was predicted that the folding space for various protein sequences is restricted and a maximum of 1000 protein folds could be expected. Although, there were about 648 folds identified, general functional features of individual folds is not thoroughly studied. We selected OB-fold, which is supposed to be an oligonucleotide and oligosaccharide binding fold to study the general functional features. OB-fold is a small beta-barrel fold formed from 5 strands connected by modulating loops. We observed consistently 2 or 3 loops on the same face of barrel acting as clamps to bind to their ligands. Depending on the ligand, which could be a single or double stranded DNA/RNA or an oligosaccharide, and their conformational properties the loops change in length and sequence to accommodate various ligands. Different classes of OB-folded proteins were analyzed and found that the functional features are retained in spite of negligible sequence homology among various proteins studied.Vishal AgrawalK V Radha Kishan2012-01-06T14:57:19Z2012-01-06T14:57:19Zhttp://crdd.osdd.net/open/id/eprint/234This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2342012-01-06T14:57:19ZDelivery of antigen in allogeneic cells preferentially generates CD(4+) Th1 cells.We have examined the possibility of evoking antigen-specific T cell immune response by using allogeneic cells as a source of adjuvant and also as a vehicle to deliver antigen. The mice were immunized with different preparations of antigen-pulsed allogeneic and syngeneic splenocytes. It was observed during the study that the animals immunized with antigen-pulsed mitomycin C treated allogeneic cells elicited antigen specific CD(4+) Th1 cell response. Predominant release of IL-2, interferon (IFN)-gamma and IgG2a-isotype also occurred. In contrast, mice immunized with antigen-pulsed syngeneic cells chiefly enhanced the production of interleukin (IL)-4 and IgG1-isotype. Further, allogeneic macrophages induced better T cell response than B cells or splenocytes and prominently induced the expression of B7-1 and B7-2. Immunization with antigen-pulsed macrophages provided better recall responses compared to B cells. This was manifested by the high LFA-1alpha and low CD45RB expression on T cells. Because it is already known that mitomycin C-treated cells undergo apoptosis and dendritic cells engulf apoptotic cells, we therefore propose that generation of T cell response using antigen-pulsed allogeneic cells may be due to the engulfment of these cells by dendritic cells, which may then process and present antigen entrapped in allogeneic cells to activate naive CD(4+) T cells and differentiate them to Th1 cells. This study therefore provides a rational basis for manipulating antigen-specific responses by immunizing with antigen-pulsed allogeneic cells.J N AgrewalaS SuvasV SinghH Vohra2012-01-05T15:04:12Z2015-01-09T09:07:35Zhttp://crdd.osdd.net/open/id/eprint/248This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2482012-01-05T15:04:12ZClass I integrons and SXT elements in El Tor strains isolated before and after 1992 Vibrio cholerae O139 outbreak, Calcutta, India.We examined the distribution of class I integrons and SXT elements in Vibrio cholerae O1 El Tor strains, isolated in Calcutta, India, before and after the V. cholerae O139 outbreak in 1992. Class I integrons, with aadA1 gene cassette, were detected primarily in the pre-O139 strains; the SXT element was found mainly in the post-O139 strains.l AmitaS Roy ChowdhuryM ThungapathraT RamamurthyG B NairAmit Ghosh2012-02-14T10:31:24Z2012-03-22T09:35:43Zhttp://crdd.osdd.net/open/id/eprint/941This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9412012-02-14T10:31:24ZDegradation and detoxification of endosulfan isomers by a defined co-culture of two Bacillus strains.The degradation of alpha and beta isomers of endosulfan by a two-member bacterial co-culture was studied. Results were similar whether the two isomers were present individually or together, as in technical endosulfan. The degradation of both isomers was accompanied by the formation of endosulfan diol and endosulfan lactone. Accumulation of the metabolite, endosulfan sulfate was, however, not observed during the reaction with either of the isomers. The microbial degradation of endosulfan isomers was also accompanied by a decrease in its toxicity to the test organism Tubifex tubifex Müller.N. AwasthiA K SinghR K JainB S KhangarotA Kumar2012-01-06T14:56:55Z2012-01-06T14:56:55Zhttp://crdd.osdd.net/open/id/eprint/231This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2312012-01-06T14:56:55ZPrediction of promiscuous and high-affinity mutated MHC binders.The identification of peptides in an antigenic sequence that can bind with high affinity to a wide range of MHC alleles is one of the challenges in subunit vaccine design. The mutation of natural peptides is an alternative to obtaining peptides that can bind to a wide range of MHC alleles with high affinity. A large number of experiments are typically necessary to identify mutations that define high-affinity binding peptides. Therefore there is a need to develop a computational method for detecting amino acid mutations in a peptide for making it high-affinity or promiscuous MHC binders. This report describes a high-throughput computer driven solution for the identification of promiscuous and high-affinity mutated binders of 47 MHC class I alleles by introducing mutations in an antigenic sequence. The method implements quantitative matrices for creating optimal mutations in an antigenic sequence. It has two major options: (i) prediction of promiscuous MHC binders and (ii) prediction of high-affinity binders. In case of prediction of promiscuous binders, the server allows a user to select (i) permissible mutations in a peptide; (ii) MHC alleles to whom it should bind; and (iii) positions at which mutation is allowed. In the case of prediction of high-affinity binders, the server allows users to specify the positions that should be conserved in the native protein. In both cases, the method computes the type of mutations and position of mutations in 9-mer peptides required to have the desired results. The web server MMBPred is available at www.imtech.res.in/raghava/mmbpred/.Manoj BhasinG.P.S. Raghava2012-01-05T15:04:19Z2012-01-05T15:04:19Zhttp://crdd.osdd.net/open/id/eprint/249This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2492012-01-05T15:04:19ZMHCBN: a comprehensive database of MHC binding and non-binding peptides.MHCBN is a comprehensive database of Major Histocompatibility Complex (MHC) binding and non-binding peptides compiled from published literature and existing databases. The latest version of the database has 19 777 entries including 17 129 MHC binders and 2648 MHC non-binders for more than 400 MHC molecules. The database has sequence and structure data of (a) source proteins of peptides and (b) MHC molecules. MHCBN has a number of web tools that include: (i) mapping of peptide on query sequence; (ii) search on any field; (iii) creation of data sets; and (iv) online data submission. The database also provides hypertext links to major databases like SWISS-PROT, PDB, IMGT/HLA-DB, GenBank and PUBMED.Manoj BhasinHarpreet SinghG.P.S. Raghava2013-10-18T04:58:34Z2013-10-18T04:58:34Zhttp://crdd.osdd.net/open/id/eprint/1390This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13902013-10-18T04:58:34ZMalaria parasite and Infected Erythrocytes: Role of membrane Associated Antigens in Macromolecular Uptake.Souvik Bhattacharjee2012-02-14T10:30:34Z2012-02-14T10:30:34Zhttp://crdd.osdd.net/open/id/eprint/948This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9482012-02-14T10:30:34ZBiosurfactant-Enhanced Bioremediation of Polycyclic Aromatic HydrocarbonsA review. Biosurfactants are surface-active compds. synthesized by a wide variety of microorganisms. They are mols. that have both hydrophobic and hydrophilic domains and are capable of lowering the surface tension and the interfacial tension of the growth medium. Biosurfactants possess different chem. structures - lipopeptides, glycolipids, neutral lipids, and fatty acids. They are nontoxic biomols. that are also exhibit strong emulsification of hydrophobic compds. and form stable emulsions. Polycyclic arom. hydrocarbons (PAHs) can be toxic, mutagenic, and carcinogenic compds. that pollute the environment. They are released to the environment as a result of spillage of oil and byproducts of coal treatment processes. The low water soly. of PAHs limits their availability to microorganisms, which is a potential problem for bioremediation of PAH-contaminated sites. Microbially produced surfactants enhance the bioavailability of these hydrophobic compds. for bioremediation. Therefore, biosurfactant-enhanced soly. of PAHs has potential applications in bioremediation. on SciFinder (R)Swaranjit Singh CameotraJean-Marc Bollag2013-10-18T04:55:51Z2015-01-07T10:18:51Zhttp://crdd.osdd.net/open/id/eprint/1389This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13892013-10-18T04:55:51ZBiochemical and Functional Studies on PknA,an eukaryotic-type serine/threonine kinase from Mycobaterioum tuberclosisRachna Chaba2012-02-14T10:32:03Z2015-01-07T10:21:33Zhttp://crdd.osdd.net/open/id/eprint/935This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9352012-02-14T10:32:03ZApophysomyces elegans: an emerging zygomycete in India.Apophysomyces elegans was considered a rare but medically important zygomycete. We analyzed the clinical records of eight patients from a single center in whom zygomycosis due to A. elegans was diagnosed over a span of 25 months. We also attempted a DNA-based method for rapid identification of the fungi and looked for interstrain polymorphism using microsattelite primers. Three patients had cutaneous and subcutaneous infections, three had isolated renal involvement, one had rhino-orbital tissue infection, and the final patient had a disseminated infection involving the spleen and kidney. Underlying illnesses were found in two patients, one with diabetes mellitus and the other with chronic alcoholism. A history of traumatic implantation was available for three patients. All except two of the patients responded to surgical and/or medical therapy; the diagnosis for the two exceptions was made at the terminal stage of infection. Restriction enzyme (MboI, MspI, HinfI) digestion of the PCR-amplified internal transcribed spacer region helped with the rapid and specific identification of A. elegans. The strains could be divided into two groups according to their patterns, with clustering into one pattern obtained by using microsatellite [(GTG)(5) and (GAC)(5)] PCR fingerprinting. The study highlights the epidemiology, clinical spectrum, and diagnosis of emerging A. elegans infections.Arunaloke ChakrabartiA GhoshG S PrasadJ K DavidS GuptaA DasV SakhujaN K PandaS K SinghS DasT Chakrabarti2013-10-18T08:52:22Z2013-10-18T08:52:22Zhttp://crdd.osdd.net/open/id/eprint/1402This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14022013-10-18T08:52:22ZProtein Engineering Studies of StreptokinaseJayeeta Dhar2012-02-14T10:31:07Z2012-04-02T06:47:45Zhttp://crdd.osdd.net/open/id/eprint/944This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9442012-02-14T10:31:07ZWhy is glutathione (a tripeptide) synthesized by specific enzymes while TSH releasing hormone (TRH or thyroliberin), also a tripeptide, is produced as part of a prohormone protein?Dwaipayan GanguliC V SrikanthChitranshu KumarPurva VatsAnand K Bachhawat2012-02-13T15:19:02Z2015-01-08T09:11:46Zhttp://crdd.osdd.net/open/id/eprint/915This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9152012-02-13T15:19:02ZComparative studies on the microbial adsorption of heavy metalsA process of competitive biosorption of Cr(VI) and Fe(III) ions on Streptococcus equisimilis,Saccharomyces cerevisiae and Aspergillus niger is described and compared to single metal ion adsorption in solution. The ability of these three microorganisms to adsorb metal ions [Cr(VI) and Fe(III)], is shown as a function of metal concentration, pH, temperature, growth medium composition, culture age and contact time with the biosorbents. The effect of addition of an extra energy source in the form of glucose, fructose and sucrose in the adsorption medium is studied for the biosorption of metal ions by microorganisms. Freundlich constants are determined from the Freundlich adsorption isotherms for all the organisms. The adsorbed metals from the sorbents can be regenerated in situ with 0.1 M sodium hydroxide.Nisha GoyalS.C JainU C Banerjee2012-02-14T10:32:29Z2012-02-14T10:32:29Zhttp://crdd.osdd.net/open/id/eprint/931This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9312012-02-14T10:32:29ZDetermining dihedral angles and local structure in silk peptide by 13C-2H REDOR.13C-2H REDOR NMR experiments were performed on 30-residue (AlaGly)15 silk I mimics of Bombyx mori silk fibroin to gain structural details about the elusive structure of the silk I conformation. 13C,2H-labeling strategies are illustrated for measuring individual dihedral angles in peptides and for determining local structure by REDOR. A major turn of type II character is found in the region Gly(14)-Ala(17).Terry GullionRaghuvansh KishoreTetsuo Asakura2012-01-08T05:45:58Z2012-01-08T05:45:58Zhttp://crdd.osdd.net/open/id/eprint/204This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2042012-01-08T05:45:58ZBTEVAL: a server for evaluation of beta-turn prediction methods.This paper describes a web server BTEVAL, developed for assessing the performance of newly developed beta-turn prediction method and it's ranking with respect to other existing beta-turn prediction methods. Evaluation of a method can be carried out on a single protein or a number of proteins. It consists of clean data set of 426 non-homologous proteins with seven subsets of these proteins. Users can evaluate their method on any subset or a complete set of data. The method is assessed at amino acid level and performance is evaluated in terms of Qtotal, Qpredicted, Qobserved and MCC measures. The server also compares the performance of the method with other existing beta-turn prediction methods such as Chou-Fasman algorithm, Thornton's algorithm, GORBTURN, 1-4 and 2-3 Correlation model, Sequence coupled model and BTPRED. The server is accessible from http://imtech.res.in/raghava/bteval/Harpreet KaurG.P.S. Raghava2012-01-05T15:05:30Z2012-01-05T15:05:30Zhttp://crdd.osdd.net/open/id/eprint/252This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2522012-01-05T15:05:30ZPrediction of beta-turns in proteins from multiple alignment using neural network.A neural network-based method has been developed for the prediction of beta-turns in proteins by using multiple sequence alignment. Two feed-forward back-propagation networks with a single hidden layer are used where the first-sequence structure network is trained with the multiple sequence alignment in the form of PSI-BLAST-generated position-specific scoring matrices. The initial predictions from the first network and PSIPRED-predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross-validation on a set of 426 nonhomologous protein chains. The corresponding Q(pred), Q(obs), and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published beta-turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach.Harpreet KaurG.P.S. Raghava2012-01-06T14:59:25Z2012-01-06T14:59:26Zhttp://crdd.osdd.net/open/id/eprint/246This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2462012-01-06T14:59:25ZA neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment.In the present study, an attempt has been made to develop a method for predicting gamma-turns in proteins. First, we have implemented the commonly used statistical and machine-learning techniques in the field of protein structure prediction, for the prediction of gamma-turns. All the methods have been trained and tested on a set of 320 nonhomologous protein chains by a fivefold cross-validation technique. It has been observed that the performance of all methods is very poor, having a Matthew's Correlation Coefficient (MCC) </= 0.06. Second, predicted secondary structure obtained from PSIPRED is used in gamma-turn prediction. It has been found that machine-learning methods outperform statistical methods and achieve an MCC of 0.11 when secondary structure information is used. The performance of gamma-turn prediction is further improved when multiple sequence alignment is used as the input instead of a single sequence. Based on this study, we have developed a method, GammaPred, for gamma-turn prediction (MCC = 0.17). The GammaPred is a neural-network-based method, which predicts gamma-turns in two steps. In the first step, a sequence-to-structure network is used to predict the gamma-turns from multiple alignment of protein sequence. In the second step, it uses a structure-to-structure network in which input consists of predicted gamma-turns obtained from the first step and predicted secondary structure obtained from PSIPRED.Harpreet KaurG.P.S. Raghava2012-01-06T14:57:25Z2012-01-06T14:57:25Zhttp://crdd.osdd.net/open/id/eprint/235This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2352012-01-06T14:57:25ZA solid-phase method for evaluation of gold conjugate used in quantitative detection of antigen by immunogold-labeling electron microscopy.Rapid and sensitive screening for confirming the reactivity of reagents, before proceeding for electron microscopy, is highly desirable. ELISA-based methods have been shown to be highly efficient and successful for rapid prescreening and optimization of immunological as well as sample-processing reagents for the sensitive detection and quantitation of antigen by electron microscopy. The drawback of these methods lies in their inability to provide any information regarding the gold conjugate used for the final observed and measured signal. In this work, we demonstrate a simple and rapid, solid-phase method in ELISA format that is also suitable for evaluation and optimization of the gold conjugate. We have demonstrated the utility of this technique by screening for Vitreoscilla hemoglobin (VHb) antigen in cell lysates and confirming the results directly with immunogold-labeling transmission electron microscopy (TEM) of cell sections. The sensitivity of detection and quantitation of antigens by immuno-electron microscopy depends upon the assay procedure being optimized to obtain the best possible signal. Our study indicates that evaluation of gold conjugate by the solid-phase assay could help in the rapid optimization of this reagent for immunogold localization and quantification of antigens by TEM.Ramandeep KaurManoj Raje2012-02-14T10:30:49Z2012-02-14T10:30:49Zhttp://crdd.osdd.net/open/id/eprint/946This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9462012-02-14T10:30:49ZSH-3 fold proteins are structurally conserved and functionally divergent.K V Radha KishanVishal Agrawal2012-01-06T14:58:34Z2012-01-06T14:58:34Zhttp://crdd.osdd.net/open/id/eprint/241This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2412012-01-06T14:58:34ZCLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics.We describe a program (and a website) to reformat the ClustalX/ClustalW outputs to a format that is widely used in the presentation of sequence alignment data in SNP analysis and molecular systematic studies. This program, CLOURE, CLustal OUtput REformatter, takes the multiple sequence alignment file (nucleic acid or protein) generated from Clustal as input files. The CLOURE-D format presents the Clustal alignment in a format that highlights only the different nucleotides/residues relative to the first query sequence. The program has been written in Visual Basic and will run on a Windows platform. The downloadable program, as well as a web-based server which has also been developed, can be accessed at http://imtech.res.in/~anand/cloure.html.Davinder K KohliAnand K Bachhawat2012-01-06T14:58:19Z2012-03-28T09:32:46Zhttp://crdd.osdd.net/open/id/eprint/240This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2402012-01-06T14:58:19ZInvestigations into the polymorphisms at the ECM38 locus of two widely used Saccharomyces cerevisiae S288C strains, YPH499 and BY4742.The ECM38 gene encodes the gamma-glutamyl transpeptidase enzyme, an enzyme involved in glutathione turnover. The enzyme was found to be present in the S288C strain, BY4742, but absent in another widely used strain congenic to S288C, YPH499. Cloning and sequencing the genes from these yeasts indicated the presence of 11 single nucleotide polymorphisms in the coding region and eight single nucleotide polymorphisms in the promoter region of the ECM38 gene of YPH499 (but none in that of BY4742). One of the SNPs in the ECM38 ORF led to a G --> D conversion in a region conserved in all gamma-GT enzymes and was found to be responsible for the loss of activity in this strain. The presence of gamma-GT activity in other YPH strains led us to trace the origins of the polymorphisms in YPH499. Our results indicated that among the progenitor strains, YPH1 and YPH2, YPH1 carried the polymorphisms seen in YPH499 and also lacked the gamma-GT activity. The implications of these results for the use of these widely used S288C strains and the origin of these single nucleotide polymorphisms are presented.Chitranshu KumarRakesh SharmaAnand K Bachhawat2012-02-14T10:31:18Z2012-03-28T09:33:30Zhttp://crdd.osdd.net/open/id/eprint/942This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9422012-02-14T10:31:18ZUtilization of glutathione as an exogenous sulfur source is independent of gamma-glutamyl transpeptidase in the yeast Saccharomyces cerevisiae: evidence for an alternative gluathione degradation pathway.gamma-Glutamyl transpeptidase (gamma-GT) is the only enzyme known to be responsible for glutathione degradation in living cells. In the present study we provide evidence that the utilization of glutathione can occur in the absence of gamma-GT. When disruptions in the CIS2 gene encoding gamma-GT were created in met15Delta strains, which require organic sulfur sources for growth, the cells were able to grow well with glutathione as the sole sulfur source suggesting that a gamma-GT-independent pathway for glutathione degradation exists in yeast cells. The CIS2 gene was strongly repressed by ammonium and derepressed in glutamate medium, and was found to be regulated by the nitrogen regulatory circuit. The utilization of glutathione as a sulfur source was, however, independent of the nitrogen source in the medium, further underlining that the two degradatory pathways were distinct.Chitranshu KumarRakesh SharmaAnand K Bachhawat2012-01-05T15:06:26Z2012-01-05T15:06:26Zhttp://crdd.osdd.net/open/id/eprint/253This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2532012-01-05T15:06:26ZPeptide scanning-based identification of regions of gamma-II crystallin involved in thermal aggregation: evidence of the involvement of structurally analogous, helix-containing loops from the two double Greek key domains of the molecule.Gamma crystallin is one of three structural proteins present in great abundance in the fiber cells of the vertebrate eye lens. The protein displays a tendency to aggregate readily in the course of heating, cooling, being exposed to ultraviolet radiation, or rapid refolding. To investigate the molecular mechanisms underlying such aggregation, we have employed a peptide-scanning approach aimed at identifying regions of bovine gamma-II crystallin that may be involved in intermolecular interactions leading to aggregation, using assays that measure the competitive inhibition of such aggregation by reagents drawn from a group of contiguous (overlapping) peptides derived from the sequence of the protein itself. Our results suggest that two regions, comprising residues 61-74, and 145-159, play key roles in aggregative interactions. Intriguingly, the two regions (each containing a solvent-exposed, single-turn helix in the native structure) are located in structurally analogous positions in the two homologous double Greek key (beta sheet) domains of the protein, suggesting that helix-strand conversions may operate to facilitate intermolecular beta sheet interactions during aggregation.Bishwajit KunduAnshuman ShuklaPurnananda Guptasarma2012-02-14T10:31:58Z2015-01-08T10:03:19Zhttp://crdd.osdd.net/open/id/eprint/936This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9362012-02-14T10:31:58ZThe D1/D2 domain of the large-subunit rDNA of the yeast species Clavispora lusitaniae is unusually polymorphic.Ten different versions of the D1/D2 divergent domain of the large-subunit ribosomal DNA were identified among interbreeding members of the yeast species Clavispora lusitaniae. One major polymorphism, located in a 90-bp structural motif of the D2 domain, exists in two versions that differ by 32 base substitutions. Three other polymorphisms consist of a two-base substitution, a two-base deletion, and a single-base deletion, respectively. The polymorphisms are independent of one another and of the two mating types, indicating that the strains studied belong to a single, sexually active Mendelian population. Several strains were heterogeneous for one or more of the polymorphisms, and one strain was found to be automictic and capable of producing asci on its own by isogamous conjugation or by bud-parent autogamy. These observations suggest circumspection in the use of sequence divergence as the principal criterion for delimiting yeast species.M.A. LachanceH M DanielW MeyerG S PrasadS P GautamK Boundy-Mills2012-02-06T18:17:57Z2012-02-06T18:17:57Zhttp://crdd.osdd.net/open/id/eprint/897This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/8972012-02-06T18:17:57ZOverproduction of an alkali- and thermo-stable xylanase in tobacco chloroplasts and efficient recovery of the enzymeOverproduction of cellulolytic enzymes through conventional nuclear transformation approaches posed a major
challenge as they can potentially degrade the cell wall components and thereby affect transgenic plant growth
and development. In this study, we have tested the possibility to over produce an alkali-thermostable xylanase
gene from Bacillus sp. Strain NG-27 in tobacco plants through chloroplast expression. Our results showed that
the xylanase expression can reach up to 6% of the total soluble protein, a value comparable to high level expression
reported for several non-cellulolytic proteins in tobacco chloroplasts. The chloroplast-expressed xylanase
retained its activity even when the leaves were dried under sun or at 42 °C, offering flexibility in the
agricultural system in transport and storage. The recombinant enzyme was purified to homogeneity using single
step chromatography with more than 85% recovery. Most importantly, transgenic plants were indistinguishable
from the control untransformed plants in their morphology, growth and in seed setting. These results open up
new avenues for large scale production of several other industrially useful cellulolytic enzymes through chloroplast
expression.Sadhu LeelavathiNaveen GuptaShankar MaitiAmit GhoshVanga Siva Reddy2012-02-14T10:32:23Z2012-02-14T10:32:23Zhttp://crdd.osdd.net/open/id/eprint/932This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9322012-02-14T10:32:23ZAdenosine suppresses activation of nuclear factor-kappaB selectively induced by tumor necrosis factor in different cell types.Adenosine is an endogenous immunomodulator that has been shown to exhibit anti-inflammatory and immunosuppressive properties through a mechanism that is not fully established. Owing to the pivotal role of nuclear factor (NF)-kappaB in these responses, we tested the hypothesis that adenosine mediates its effects through suppression of NF-kappaB activation. We investigated the effects of adenosine on NF-kappaB activation induced by various inflammatory agents in human myeloid KBM-5 cells. The treatment of these cells with adenosine suppressed TNF-induced NF-kappaB activation, but had no effect on activation of another redox-sensitive transcription factor, AP-1. These effects were not restricted to myeloid cells, as NF-kappaB activation in other lymphocytic and epithelial cell types was also inhibited. The effect on TNF-induced NF-kappaB activation was selective as adenosine had minimal effect on NF-kappaB activation induced by H(2)O(2), PMA, LPS, okadaic acid, or ceramide, suggesting differences in the pathway leading to NF-kappaB activation by different agents. Adenosine also suppressed NF-kappaB-dependent reporter gene expression activated by TNF or by overexpression of TNFR1, TRAF 2, NIK, and p65 subunit of NF-kappaB. The suppression of TNF-induced NF-kappaB activation by adenosine was found not to be because of inhibition of TNF-induced IkappaBalpha phosphorylation and degradation or IkappaBalpha kinase activation. The suppression of TNF-induced NF-kappaB activation was unique to adenosine, as neither its metabolites (inosine, AMP, and ATP) nor pyrimidines (thymidine and uridine) had any effect. Overall, our results clearly demonstrate that adenosine selectively suppresses TNF-induced NF-kappaB activation, which may contribute to its role in suppression of inflammation and of the immune system.Sekhar MajumdarBharat B Aggarwal2012-02-14T10:31:34Z2015-01-07T05:39:24Zhttp://crdd.osdd.net/open/id/eprint/939This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9392012-02-14T10:31:34ZConcentration of a potent calcium oxalate monohydrate crystal growth inhibitor in the urine of normal persons and kidney stone patients by ELISA-based assay system employing monoclonal antibodies.Standardized calcium oxalate monohydrate (COM) crystal growth assay system was employed to study the ability of various test samples to influence growth rates of COM crystals. The inhibitory activity (IA) of various samples was expressed in terms of inhibitory units. Urine samples obtained from normal persons and kidney stone patients were found to have IA of 3.18 +/- 0.62 and 1.02 +/- 0.08, respectively. A potent inhibitor having molecular weight between 14.2 and 16.2 kDa was found to be primarily responsible for the differences observed in the urinary IAs between normal persons and kidney stone patients. The potent inhibitor was found to be tightly associated with a chromophore resembling Urobilirubin. An ELISA based assay system, using monoclonal antibodies against the above most potent inhibitor confirmed the difference observed in the urinary IA between the normal persons and kidney stone patients. This assay system has the potential to be routinely used to screen human beings for potential stone formers.Mehdi F MoghadamC TandonS AggarwalS K SinglaS K SinghS K SharmaGrish C VarshneyR K Jethi2012-01-05T15:05:11Z2012-01-05T15:05:11Zhttp://crdd.osdd.net/open/id/eprint/250This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2502012-01-05T15:05:11ZSingle-step purification of a protein-folding catalyst, the SlyD peptidyl prolyl isomerase (PPI), from cytoplasmic extracts of Escherichia coli.The protein-folding catalyst SlyD, a peptidyl prolyl cis-trans isomerase regulated by metal binding, was initially discovered as a major contaminant of non-denaturing immobilized metal-affinity chromatography (IMAC)-based procedures for the purification of heterologously expressed 6xHis-tagged proteins from Escherichia coli. Given its ability to bind weakly to nickel-nitrilotriacetic acid (Ni(2+)-NTA), protocols for the purification of SlyD currently use an initial non-denaturing IMAC step, followed by an ion-exchange chromatographic step and occasionally also other chromatographic steps. Here we demonstrate that using denaturing conditions instead of non-denaturing conditions, and by processing of large quantities of culture through small volumes of Ni(2+)-NTA resin to increase competition for binding, single-step purification of SlyD to homogeneity can be achieved directly from E. coli extracts, as assessed through spectroscopic and electrophoretic methods. The purified, denatured SlyD is shown to be capable of refolding to give rise to a native-like CD spectrum, establishing the utility of the procedure. The procedure also establishes SlyD to be the only E. coli protein capable of contaminating denaturing IMAC-based procedures.Sourav MukherjeeAnshuman ShuklaPurnananda Guptasarma2012-01-05T15:06:43Z2012-01-05T15:06:43Zhttp://crdd.osdd.net/open/id/eprint/255This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2552012-01-05T15:06:43ZIdentification of Uhp1, a ubiquitinated histone-like protein, as a target/mediator of Rhp6 in mating-type silencing in fission yeast.Mating-type silencing in Schizosaccharomyces pombe is brought about by cooperative interactions between cis-acting DNA sequences flanking mat2P and mat3M and the trans-acting factors, namely Swi6, Clr1-Clr4, Clr6, and Rik1. In addition, DNA repair gene rhp6, which plays a role in post-replication DNA repair and ubiquitination of proteins including histones, is also involved in silencing, albeit in a unique way; its effect on silencing and chromatin structure of the donor loci is dependent on their switching competence. Earlier, we hypothesized the existence of a mediator of Rhp6 that plays a role in reestablishment of the chromatin structure coincidentally with DNA replication associated with mating-type switching. Here we report the identification of a 22-kDa protein as an in vivo target and mediator of Rhp6 in mating-type silencing. The level of this protein is greatly elevated in sng1-1/rhp6(-) mutant and rhp6Delta as compared with wild type strain. Both the deletion and overexpression of the gene encoding this protein elicit switching-dependent loss of silencing. Furthermore, the 22-kDa protein undergoes Rhp6-dependent multiubiquitination and associates with mat2 locus during S phase in wild type cells. Interestingly, it contains a histone-fold motif similar to that of histone H2A, and like histone H2A, it interacts strongly with histone H2B in vitro. These results indicate that the 22-kDa protein, renamed as the ubiquitinated histone-like protein Uhp1, is an in vivo target/mediator of Rhp6 in silencing. Thus, regulation of association of Uhp1 with chromatin and ubiquitination followed by degradation may play a role in reestablishment of inactive chromatin structure at the silent mating-type loci.Alpana NareshSharanjot SainiJagmohan Singh2012-01-06T14:56:06Z2012-04-03T07:25:06Zhttp://crdd.osdd.net/open/id/eprint/226This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2262012-01-06T14:56:06ZBranching of o-nitrobenzoate degradation pathway in Arthrobacter protophormiae RKJ100: identification of new intermediates.We have earlier reported a novel reductive pathway for o-nitrobenzoate (ONB) degradation (at 0.5 mM) in Arthrobacter protophormiae RKJ100, which proceeds via the formation of o-hydroxylaminobenzoate (HABA) and anthranilate (AA). During growth of this organism at 40 times higher concentration (20 mM) of ONB, 3-hydroxyanthranilate (HAA) was identified as an intermediate by thin layer chromatography, gas chromatography and high performance liquid chromatography studies. Crude cell extracts of ONB-grown cells showed HAA 3,4-dioxygenase activity suggesting HAA as a terminal aromatic intermediate of the catabolic energy-yielding pathway as shown before in Pseudomonas fluorescens strain KU-7. HAA is further cleaved to 2-amino-3-carboxymuconic-6-semialdehyde by the action of HAA 3,4-dioxygenase. In this report we propose that ONB degradation occurs via the formation of HABA and the pathway branches at this point to form the two different aromatic intermediates AA and HAA by the action of a reductase and a mutase, respectively.Gunjan PandeyDebarati PaulR K Jain2012-01-06T14:57:04Z2012-01-06T14:57:04Zhttp://crdd.osdd.net/open/id/eprint/232This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2322012-01-06T14:57:04ZEffect of fluid dispersion on cybernetic control of microbial growth on substitutable substrates.Many fermentation media contain two or more substrates, which a microorganism utilizes for similar purposes. Depending on the conditions prior to and during a fermentation, the substrates may be utilized in succession or simultaneously. Since it is difficult to portray this behavior through mechanistic models, a cybernetic method was proposed earlier. Here the microorganism chooses the mode of substrate utilization that maximizes its own survival, usually expressed by the growth rate. In a fully dispersed bioreactor, simultaneous utilization generates higher growth rates but leads to low biomass concentrations since this utilization pattern is preferred at low concentrations of the substrates. In this study it has been shown that by allowing less than complete dispersion in the broth it is possible to shift from sequential to simultaneous utilization at high concentrations, thereby enabling both high growth rates and large biomass concentrations. This strategy thus allows the natural incomplete dispersion in large bioreactors to be gainfully exploited.P R Patnaik2012-01-06T14:58:02Z2012-01-06T14:58:02Zhttp://crdd.osdd.net/open/id/eprint/238This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2382012-01-06T14:58:02ZOn the performances of noise filters in the restoration of oscillatory behavior in continuous yeast cultures.Continuous flow microbial fermentations under industrial conditions are subject to the influx of noise, mainly through the feed stream. Noise upsets the normal deterministic behavior. For continuous cultures of Saccharomyces cerevisiae exhibiting oscillatory responses, four kinds of commonly used noise filters, three algorithmic and one neural, have been compared for their ability to restore noise-free oscillations. An auto-associative neural filter was the best, similar to earlier observations for other organisms under non-oscillatory conditions. This enhances the general applicability of neural filters for industrial scale fermentations.P R Patnaik2012-01-06T14:57:11Z2012-01-06T14:57:11Zhttp://crdd.osdd.net/open/id/eprint/233This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2332012-01-06T14:57:11ZOscillatory metabolism of Saccharomyces cerevisiae: an overview of mechanisms and models.The budding yeast Saccharomyces cerevisiae displays steady oscillations in continuous cultures under certain conditions. Oscillatory responses are important both metabolically and in process applications. Although much information has become available, a definitive theory to explain and model these oscillations is yet to be formulated. Models of oscillatory cultivation have focussed primarily either on intracellular reactions or on transport processes coupled to substantially lumped intracellular kinetics. This review discusses the development of the models and the directions they provide for a comprehensive model of oscillatory metabolism.Pratap R Patnaik2012-02-14T10:31:00Z2012-03-29T06:31:43Zhttp://crdd.osdd.net/open/id/eprint/945This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9452012-02-14T10:31:00ZEffect of nutrients on optimal production of biosurfactants by Pseudomonas putida—A gujarat oil field isolateNutritional requirements for maximal production
of biosurfactant by an oil field bacterium Pseudomonas
putida were determined. The optimal concentrations of nitrogen,phosphate, sulfur, magnesium, iron, potassium, sodium,calcium, and trace elements for maximal production of biosurfactants were ascertained, and a new “Pruthi and Cameotra” salt medium was formulated. Data show that maximal biomass (2.4 g L−1) and biosurfactant production (6.28 g L−1) takes place after 72 h of growth on 2% hexadecane. The biosurfactant was produced optimally over pH and temperature ranges of 6.4–7.2 and 30–40°C, respectively. That the highest biosurfactant yield was obtained during late log phase of growth indicates that the biosurfactant is a secondary metabolite.
V. PruthiSwaranjit Singh Cameotra2012-01-10T08:06:21Z2012-01-10T08:06:21Zhttp://crdd.osdd.net/open/id/eprint/93This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/932012-01-10T08:06:21ZOXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94.5% with 52.5% accuracy for alignments in the 0-10 percentage identity range. This suggests that further improvements in accuracy will be possible in the future.G.P.S. RaghavaStephen M J SearlePatrick C AudleyJonathan D BarberGeoffrey J Barton2012-02-14T10:32:16Z2012-02-14T10:32:16Zhttp://crdd.osdd.net/open/id/eprint/933This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9332012-02-14T10:32:16ZNewer products from old proteins: the case of streptokinase.Girish Sahni2012-01-06T14:57:34Z2012-01-06T15:18:07Zhttp://crdd.osdd.net/open/id/eprint/236This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2362012-01-06T14:57:34ZIntrinsic contributions of polar amino acid residues toward thermal stability of an ABC-ATPase of mesophilic origin.The nucleotide-binding subunit of phosphate-specific transporter (PstB) from mesophilic bacterium, Mycobacterium tuberculosis, is a unique ATP-binding cassette (ABC) ATPase because of its unusual ability to hydrolyze ATP at high temperature. In an attempt to define the basis of thermostability, we took a theoretical approach and compared amino acid composition of this protein to that of other PstBs from available bacterial genomes. Interestingly, based on the content of polar amino acids, this protein clustered with the thermophiles.Jyoti SarinG.P.S. RaghavaPradip K Chakraborti2012-02-14T10:31:13Z2015-01-19T05:30:45Zhttp://crdd.osdd.net/open/id/eprint/943This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9432012-02-14T10:31:13ZThe glutathione-mediated detoxification pathway in yeast: an analysis using the red pigment that accumulates in certain adenine biosynthetic mutants of yeasts reveals the involvement of novel genes.The glutathione-mediated pathway for the detoxification of endogenously and exogenously derived toxic compounds was investigated using a pigment that accumulates in certain adenine biosynthetic mutants of yeasts. The ade1 / ade2 mutants of Saccharomyces cerevisiae, when grown on adenine-limiting medium, accumulate a characteristic red pigment (ade pigment) in their vacuoles. The precursors of the ade pigments are toxic intermediates that form conjugates with glutathione, followed by their transport inside the vacuole. In this study, this red pigment was used as a phenotypic screen to obtain insight regarding new genes involved in the three phases of this detoxification pathway: the activation phase (phase I), the conjugation phase (phase II), and the efflux phase (phase III). Components of the phase III (efflux) pathway which includes, in addition to the previously characterized Ycf1p and Bpt1p, another member of the 'Ycf1p family', Bat1p, as well as a vacuolar H(+)-ATPase-dependent transport were identified. In the investigation of phase II (conjugation), it was found that glutathione S-transferases, encoded by GTT1 and GTT2,do not appear to play a role in this process. By contrast, two other previously characterized genes, the oxidative stress transcription factor gene, SKN7, and the yeast caesin protein kinase gene, YCK1, of S. cerevisiae do participate in this pathway.K G SharmaRupinder KaurAnand K Bachhawat2013-10-22T11:00:45Z2013-10-22T11:00:45Zhttp://crdd.osdd.net/open/id/eprint/1476This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14762013-10-22T11:00:45ZTargeting Bacteria Entrapped in Syngencic or Allogeneic Macrophages to Dendritic Cells :An Approach for the Induction of Pathogen Specific Protective Immunology
Naresh Sharma2012-02-14T10:32:44Z2012-02-14T10:32:44Zhttp://crdd.osdd.net/open/id/eprint/930This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9302012-02-14T10:32:44ZUrsolic acid inhibits nuclear factor-kappaB activation induced by carcinogenic agents through suppression of IkappaBalpha kinase and p65 phosphorylation: correlation with down-regulation of cyclooxygenase 2, matrix metalloproteinase 9, and cyclin D1.The process of tumorigenesis requires cellular transformation, hyperproliferation, invasion, angiogenesis, and metastasis. Several genes that mediate these processes are regulated by the transcription factor nuclear factor-kappaB (NF-kappaB). The latter is activated by various carcinogens, inflammatory agents, and tumor promoters. Thus, agents that can suppress NF-kappaB activation have the potential to suppress carcinogenesis. Ursolic acid, a pentacyclic triterpene acid, has been shown to suppress the expression of several genes associated with tumorigenesis, but whether ursolic acid mediates its effects through suppression of NF-kappaB is not understood. In the study described in the present report, we found that ursolic acid suppressed NF-kappaB activation induced by various carcinogens including tumor necrosis factor (TNF), phorbol ester, okadaic acid, H(2)O(2), and cigarette smoke. These effects were not cell type specific. Ursolic acid inhibited DNA binding of NF-kappaB consisting of p50 and p65. Ursolic acid inhibited IkappaBalpha degradation, IkappaBalpha phosphorylation, IkappaBalpha kinase activation, p65 phosphorylation, p65 nuclear translocation, and NF-kappaB-dependent reporter gene expression. Ursolic acid also inhibited NF-kappaB-dependent reporter gene expression activated by TNF receptor, TNF receptor-associated death domain, TNF receptor-associated factor, NF-kappaB-inducing kinase, IkappaBalpha kinase, and p65. The inhibition of NF-kappaB activation correlated with suppression of NF-kappaB-dependent cyclin D1, cyclooxygenase 2, and matrix metalloproteinase 9 expression. Thus, overall, our results indicate that ursolic acid inhibits IkappaBalpha kinase and p65 phosphorylation, leading to the suppression of NF-kappaB activation induced by various carcinogens. These actions of ursolic acid may mediate its antitumorigenic and chemosensitizing effects.Shishir ShishodiaSekhar MajumdarSanjeev BanerjeeBharat B Aggarwal2013-10-18T06:06:20Z2013-10-18T06:06:20Zhttp://crdd.osdd.net/open/id/eprint/1393This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13932013-10-18T06:06:20ZFolding and Stability of Sequence-recombined Proteins: Effects of Backbone Reversal and Secondary Structure ShufflingAnshuman Shukla2012-01-06T14:55:10Z2012-01-06T14:55:10Zhttp://crdd.osdd.net/open/id/eprint/221This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2212012-01-06T14:55:10ZA backbone-reversed all-beta polypeptide (retro-CspA) folds and assembles into amyloid nanofibres.The backbone-reversed or 'retro', form of a model all-beta-sheet protein, Escherichia coli CspA, was produced from a synthetic gene in E.coli in fusion with an N-terminal affinity tag. Following purification under denaturing conditions and dialysis-based removal of urea, the protein was found to fold into a soluble, poorly structured multimer. Upon concentration, this state readily transformed into amyloid nanofibres. Congo Red-binding amorphous forms were also observed. Since a beta-sheet-forming sequence is expected to retain high beta-sheet-forming propensity even after backbone reversal and given the fact that folding of retro-CspA occurs only to a poorly structured form, we conclude that the increase effected in protein concentration may be responsible for the formation of intermolecular beta-sheets, facilitating the bleeding away of the protein's conformational equilibrium into aggregates that generate well-formed fibres. Since every molecule in these fibres contains a peptide tag for binding Ni(2+), the fibres may provide a template for deposition of nickel to generate novel materials.Anshuman ShuklaManoj RajePurnananda Guptasarma2012-01-05T15:03:56Z2012-01-05T15:03:56Zhttp://crdd.osdd.net/open/id/eprint/247This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2472012-01-05T15:03:56ZA backbone-reversed form of an all-beta alpha-crystallin domain from a small heat-shock protein (retro-HSP12.6) folds and assembles into structured multimers.The structural consequences of polypeptide backbone reversal ("retro" modification) remain largely unexplored, in particular, for the retro forms of globular all-beta-sheet proteins. To examine whether the backbone-reversed form of a model all-beta-sheet protein can fold and adopt secondary and tertiary structure, we created and examined the recombinant retro form of a 110-residue-long polypeptide, an alpha-crystallin-like small heat-shock protein, HSP12.6, from C. elegans. Following intracellular overexpression in fusion with a histidine affinity tag in Escherichia coli, purification under denaturing conditions, and removal of denaturant through dialysis, retro-HSP12.6 was found to fold to a soluble state. The folded protein was examined using fluorescence and CD spectroscopy, gel filtration chromatography, non-denaturing electrophoresis, differential scanning calorimetry, and electron microscopy and confirmed to have adopted secondary structure and assembled into a multimer. Interestingly, like its parent polypeptide, retro-HSP12.6 did not aggregate upon heating; rather, heating led to a dramatic increase in structural content and the adoption of what would appear to be a very well folded state at high temperatures. However, this was essentially reversed upon cooling with some hysteresis being observed resulting in greater structural content in the heated-cooled protein than in the unheated protein. The heated-cooled samples displayed CD spectra indicative of structural content comparable to that of any naturally occurring globular protein. Attempts are being made to refine crystallization conditions for the folded protein.Anshuman ShuklaManoj RajePurnananda Guptasarma2012-01-10T08:06:25Z2012-01-10T08:06:25Zhttp://crdd.osdd.net/open/id/eprint/97This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/972012-01-10T08:06:25ZProPred1: prediction of promiscuous MHC Class-I binding sites.SUMMARY: ProPred1 is an on-line web tool for the prediction of peptide binding to MHC class-I alleles. This is a matrix-based method that allows the prediction of MHC binding sites in an antigenic sequence for 47 MHC class-I alleles. The server represents MHC binding regions within an antigenic sequence in user-friendly formats. These formats assist user in the identification of promiscuous MHC binders in an antigen sequence that can bind to large number of alleles. ProPred1 also allows the prediction of the standard proteasome and immunoproteasome cleavage sites in an antigenic sequence. This server allows identification of MHC binders, who have the cleavage site at the C terminus. The simultaneous prediction of MHC binders and proteasome cleavage sites in an antigenic sequence leads to the identification of potential T-cell epitopes. AVAILABILITY: Server is available at http://www.imtech.res.in/raghava/propred1/. Mirror site of this server is available at http://bioinformatics.uams.edu/mirror/propred1/ Supplementary information: Matrices and document on server are available at http://www.imtech.res.in/raghava/propred1/page2.htmlHarpreet SinghG.P.S. Raghava2012-01-06T14:58:10Z2012-01-06T14:58:10Zhttp://crdd.osdd.net/open/id/eprint/239This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2392012-01-06T14:58:10ZAn ELISA-based approach to optimize elution conditions for obtaining hapten-specific antibodies.The correct choice of the elution conditions to break an affinity interaction is important for the successful purification of biomolecules. The optimal elution buffer liberates the bound substance in a minimum volume and maintains the activity of the purified material. The present study demonstrates an enzyme-linked immunosorbent assay (ELISA)-based approach for selection of specific elution conditions for eluting antibodies against a small molecule (atrazine) from pooled sera. Six different elution conditions were tried for the removal of antibodies from the complex. Large-scale purification of anti-atrazine antibodies from the sera was done with a hapten-specific column using an amino-terminal crosslinked agarose gel. Efficacy in terms of total amount of recovery and binding affinities of eluted antibodies from the column were further investigated by ELISA. Results indicate that the ELISA-based elution approach is ideal for the selection of suitable elution buffer that can subsequently be utilized for affinity purification applications.K V SinghJasdeep KaurManoj RajeGrish C VarshneyC Raman Suri2012-01-06T14:57:48Z2012-01-06T14:57:48Zhttp://crdd.osdd.net/open/id/eprint/237This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2372012-01-06T14:57:48ZPhytoremediation of toxic aromatic pollutants from soil.The enormous growth of industrialization, and the use of numerous aromatic compounds in dyestuffs, explosives, pesticides and pharmaceuticals has resulted in serious environmental pollution and has attracted considerable attention continuously over the last two decades. Many aromatic hydrocarbons, nitroaromatic compounds, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, diauxins and their derivatives are highly toxic, mutagenic and/or carcinogenic to natural microflora as well as to higher systems including humans. The increasing costs and limited efficiency of traditional physicochemical treatments of soil have spurred the development of new remediation technologies. Phytoremediation is emerging as an efficient treatment technology that uses plants to bioremediate pollutants from soil environments. Various modern tools and analytical devices have provided insight into the selection and optimization of remediation processes by various plant species. Sites heavily polluted with organic contaminants require hyperaccumulators, which could be developed by genetic engineering approaches. However, efficient hyperaccumulation by naturally occurring plants is also feasible and can be made practical by improving their nutritional and environmental requirements. Thus, phytoremediation of organics appears a very promising technology for the removal of contaminants from polluted soil. In this review, certain aspects of plant metabolism associated with phytoremediation of organic contaminants and their relevant phytoremediation efforts are discussed.O V SinghR K Jain2012-01-06T14:59:02Z2015-01-09T09:28:31Zhttp://crdd.osdd.net/open/id/eprint/244This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2442012-01-06T14:59:02ZPhytoremediation: an overview of metallic ion decontamination from soil.In recent years, phytoremediation has emerged as a promising ecoremediation technology, particularly for soil and water cleanup of large volumes of contaminated sites. The exploitation of plants to remediate soils contaminated with trace elements could provide a cheap and sustainable technology for bioremediation. Many modern tools and analytical devices have provided insight into the selection and optimization of the remediation process by plant species. This review describes certain factors for the phytoremediation of metal ion decontamination and various aspects of plant metabolism during metallic decontamination. Metal-hyperaccumulating plants, desirable for heavily polluted environments, can be developed by the introduction of novel traits into high biomass plants in a transgenic approach, which is a promising strategy for the development of effective phytoremediation technology. The genetic manipulation of a phytoremediator plant needs a number of optimization processes, including mobilization of trace elements/metal ions, their uptake into the root, stem and other viable parts of the plant and their detoxification and allocation within the plant. This upcoming science is expanding as technology continues to offer new, low-cost remediation options.O V SinghS LabanaGunjan PandeyR BudhirajaR K Jain2012-02-14T10:31:47Z2012-04-03T06:58:23Zhttp://crdd.osdd.net/open/id/eprint/938This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9382012-02-14T10:31:47ZGluconic acid production under varying fermentation conditions byAspergillus nigerThe production of gluconic acid with respect to varying substrate concentrations in
submerged (SmF), semisolid-state (SmSF), surface (SF), and solid-state surface (SSF) fermentations
was analyzed. Under the various fermentation conditions the biomass and specific growth rate varied
with different concentrations of glucose. The highest level of gluconic acid (106.5g dm�3) with 94.7%
yield was obtained under SSF conditions. In all cases the maximumdegree of gluconic acid conversion
was observed at on initial substrate concentration of 120g dm�3. The rate of glucose uptake increased
on increasing the initial glucose concentration and glucose utilization was observed to be highest
(89–94%) in the SmSF process and was comparable with the SSF and SF processes. The maximumrate
of cell growth was obtained in all processes at an initial glucose concentration of 120g dm�3. The
gluconic acid production and change in pH were analyzed at varying time intervals and it was observed
that the SmF and SmSF processes were completed within 6 days of incubation whereas the highest
yield was observed after 12 days of incubation and continued thereafter in the SSF process.
# 2003 Society of Chemical IndustryOm V SinghR K JainRajesh P Singh2013-10-18T05:01:52Z2013-10-18T05:01:52Zhttp://crdd.osdd.net/open/id/eprint/1391This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13912013-10-18T05:01:52ZUnderstanding the Regulation of Antigen Specific T Helper Cells by Cytokines and Costimulatory Molecules Expressed on
distintct Antigen Presenting CellsVinod Singh2012-01-06T14:58:44Z2012-01-06T14:58:44Zhttp://crdd.osdd.net/open/id/eprint/242This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2422012-01-06T14:58:44ZDomain truncation studies reveal that the streptokinase-plasmin activator complex utilizes long range protein-protein interactions with macromolecular substrate to maximize catalytic turnover.To explore the interdomain co-operativity during human plasminogen (HPG) activation by streptokinase (SK), we expressed the cDNAs corresponding to each SK domain individually (alpha, beta, and gamma), and also their two-domain combinations, viz. alphabeta and betagamma in Escherichia coli. After purification, alpha and beta showed activator activities of approximately 0.4 and 0.05%, respectively, as compared with that of native SK, measured in the presence of human plasmin, but the bi-domain constructs alphabeta and betagamma showed much higher co-factor activities (3.5 and 0.7% of native SK, respectively). Resonant Mirror-based binding studies showed that the single-domain constructs had significantly lower affinities for "partner" HPG, whereas the affinities of the two-domain constructs were remarkably native-like with regards to both binary-mode as well as ternary mode ("substrate") binding with HPG, suggesting that the vast difference in co-factor activity between the two- and three-domain structures did not arise merely from affinity differences between activator species and HPG. Remarkably, when the co-factor activities of the various constructs were measured with microplasminogen, the nearly 50-fold difference in the co-factor activity between the two- and three-domain SK constructs observed with full-length HPG as substrate was found to be dramatically attenuated, with all three types of constructs now exhibiting a low activity of approximately 1-2% compared to that of SK.HPN and HPG. Thus, the docking of substrate through the catalytic domain at the active site of SK-plasmin(ogen) is capable of engendering, at best, only a minimal level of co-factor activity in SK.HPN. Therefore, apart from conferring additional substrate affinity through kringle-mediated interactions, reported earlier (Dhar et al., 2002; J. Biol. Chem. 277, 13257), selective interactions between all three domains of SK and the kringle domains of substrate vastly accelerate the plasminogen activation reaction to near native levels.Vasudha SundramJagpreet S NandaKammara RajagopalJayeeta DharAnita ChaudharyGirish Sahni2012-01-06T14:56:15Z2012-01-06T14:56:15Zhttp://crdd.osdd.net/open/id/eprint/227This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/2272012-01-06T14:56:15ZModulation of the expression of M150 on macrophages by Th1/Th2 cytokines and co-stimulatory molecules CD40, B7-1, B7-2 and ICAM-1.M150 is an 150-kDa protein associated with the surface of macrophages and is responsible chiefly for the activation of Th1 cells. It is a unique subset of the lysosome-associated membrane protein-1 glycoprotein and its co-stimulatory activity depends on its post-translational modification, which has a distinct glycosylation pattern restricted to macrophages. In the present study, we have observed that M150 is expressed constitutively on peritoneal but not splenic macrophages isolated from mice of different genetic backgrounds: Balb/c, C57BL/6 and C3He. However, M150 was expressed not only on peritoneal but also on splenic macrophages of non-obese diabetic (NOD) mice. Expression on splenic macrophages was induced by culture with lipopolysaccharide (LPS). Expression could also be significantly up-regulated by interferon (IFN)-gamma and granulocyte-macrophage colony stimulating factor (GM-CSF) but was inhibited by interleukin (IL)-10; IL-4 exhibited no effect. Further, cross-linking of B7-2, CD40, ICAM-1 but not B7-1 enhanced the level of M150 significantly. IFN-gamma and GM-CSF acted synergistically with CD40. The significance of these findings is that cytokines IFN-gamma, GM-CSF and IL-10 and the co-stimulatory molecules B7-2, CD40 and ICAM-1 can regulate the expression of M150 on macrophages.S SuvasH VohraJ N Agrewala2013-10-18T06:35:09Z2013-10-18T06:35:09Zhttp://crdd.osdd.net/open/id/eprint/1398This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13982013-10-18T06:35:09ZDevelopment of a Transposon Tagging System for Candida Albican and its Use to Identify Drug TargetsVibha Taneja nee Mahajan2013-10-18T06:09:59Z2013-10-18T06:09:59Zhttp://crdd.osdd.net/open/id/eprint/1394This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13942013-10-18T06:09:59ZStudies on Myo-inositdhexakisphosphate Degrading Enzyme from a Hyper-producing Strain of Aspergillus Niger Van TeighemPurva Vats2012-02-14T10:32:50Z2012-02-14T10:32:50Zhttp://crdd.osdd.net/open/id/eprint/929This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9292012-02-14T10:32:50ZIdentification of the lambda integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation.Lambda integrase (Int) is a heterobivalent DNA-binding protein that together with the accessory DNA-bending proteins IHF, Fis, and Xis, forms the higher-order protein-DNA complexes that execute integrative and excisive recombination at specific loci on the chromosomes of phage lambda and its Escherichia coli host. The large carboxyl-terminal domain of Int is responsible for binding to core-type DNA sites and catalysis of DNA cleavage and ligation reactions. The small amino-terminal domain (residues 1-70), which specifies binding to arm-type DNA sites distant from the regions of strand exchange, consists of a three-stranded beta-sheet, proposed to recognize the cognate DNA site, and an alpha-helix. We report here that a site on this alpha-helix is critical for both homomeric interactions between Int protomers and heteromeric interactions with Xis. The mutant E47A, which was identified by alanine-scanning mutagenesis, abolishes interactions between Int and Xis bound at adjacent binding sites and reduces interactions between Int protomers bound at adjacent arm-type sites. Concomitantly, this residue is essential for excisive recombination and contributes to the efficiency of the integrative reaction. NMR titration data with a peptide corresponding to Xis residues 57-69 strongly suggest that the carboxyl-terminal tail of Xis and the alpha-helix of the aminoterminal domain of Int comprise the primary interaction surface for these two proteins. The use of a common site on lambda Int for both homotypic and heterotypic interactions fits well with the complex regulatory patterns associated with this site-specific recombination reaction.David WarrenMy D SamKate ManleyDibyendu SarkarSang Yeol LeeMohamad AbbaniJonathan M WojciakRobert T ClubbArthur Landy2012-02-14T10:31:52Z2012-02-14T10:31:52Zhttp://crdd.osdd.net/open/id/eprint/937This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/9372012-02-14T10:31:52ZStructural characterization and artificial fiber formation of Bombyx mori silk fibroin in hexafluoro-iso-propanol solvent system.High-resolution solution (13)C-NMR and CD studies of Bombyx mori silk fibroin revealed the presence of an ordered secondary structure 3(10)-helix, in hexafluoro-iso-propanol (HFIP). The solid-state structure of the silk fibroin film prepared by drying it gently from the HFIP solution still keep the structure, 3(10)-helix, which was studied with high-resolution solid state (13)C-NMR. The structural transition from the 3(10)-helix to silk II structure, heterogeneous structure including antiparallel beta-sheet, occurred during the artificial spinning from the HFIP solution. The wide-angle x-ray diffraction and differential scanning calorimetry thermograms of the artificial spinning fiber after postspinning treatments were observed together with the stress-strain curves. The results emphasize that the molecular structures, controlled morphology, and mechanical properties of the protein-based synthetic polymers can be modulated for enhancing biocompatibility.Chenhua ZhaoJuming YaoHiromi MasudaRaghuvansh KishoreTetsuo Asakura