open: No conditions. Results ordered Creators, Title. 2024-03-29T13:21:47ZEPrintshttp://crdd.osdd.net/images/sitelogo.gifhttp://crdd.osdd.net/open/2015-02-10T11:46:19Z2015-02-10T11:46:19Zhttp://crdd.osdd.net/open/id/eprint/1606This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16062015-02-10T11:46:19ZClathrin-mediated hemoglobin endocytosis is essential for survival of Leishmania.Leishmania is auxotroph for heme. Previously, we have shown that Leishmania acquire heme from the degradation of endocytosed hemoglobin via a specific receptor located in the flagellar pocket. Here, we report the cloning and expression of clathrin heavy chain from Leishmania (Ld-CHC) and provide evidences that Ld-CHC is localized in flagellar pocket and regulates Hb-endocytosis in Leishmania. Kinetic analysis of Hb trafficking in GFP-Ld-CHC overexpressed Leishmania reveals that Hb is internalized through Ld-CHC coated region and remains associated with Ld-CHC containing vesicles at early time points of internalization and subsequently starts dissociating from Hb-containing vesicles at later time points indicating that clathrin-coating and uncoating regulate Hb trafficking in Leishmania. Interestingly, overexpression of dominant negative mutant of clathrin heavy chain of Leishmania (GFP-Ld-CHC-Hub) blocks the Hb internalization and causes severe growth defect in parasite. Moreover, we have shown that chlorpromazine, a pharmacological agent, blocks Hb internalization in Leishmania by depolymerizing Ld-CHC and thereby inhibits the growth of the parasites. Taken together, our results have shown that Hb endocytosis in Leishmania is a clathrin dependent process and is essential for the survival of the parasites.Shruti AgarwalRuchir RastogiDeepika GuptaNitin PatelManoj RajeAmitabha Mukhopadhyay2019-09-05T14:04:43Z2019-09-05T14:04:43Zhttp://crdd.osdd.net/open/id/eprint/2429This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24292019-09-05T14:04:43ZPHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors.Dicer, an RNase III enzyme, plays a vital role in the processing of pre-miRNAs for generating the miRNAs. The structural and sequence features on pre-miRNA which can facilitate position and efficiency of cleavage are not well known. A precise cleavage by Dicer is crucial because an inaccurate processing can produce miRNA with different seed regions which can alter the repertoire of target genes.Firoz AhmedRakesh Kaundalg Raghava2014-05-30T04:03:08Z2014-05-30T04:03:08Zhttp://crdd.osdd.net/open/id/eprint/1507This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15072014-05-30T04:03:08ZMultiple exosites distributed across the three domains of streptokinase co-operate to generate high catalytic rates in the streptokinase-plasmin activator complex.To examine the global function of the key surface-exposed loops of streptokinase, bearing substrate-specific exosites, namely, the 88-97 loop in the α domain, the 170 loop in the β domain, and the coiled-coil region (Leu321-Asn338) in the γ domain, mutagenic as well as peptide inhibition studies were carried out. Peptides corresponded to the primary structure of an exosite, either individual or stoichiometric mixtures of various disulfide-constrained synthetic peptide(s) inhibited plasminogen activation by streptokinase. Remarkably, pronounced inhibition of substrate plasminogen activation by the preformed streptokinase-plasmin activator complex was observed when complementary mixtures of different peptides were used compared to the same overall concentrations of individual peptides, suggesting co-operative interactions between the exosites. This observation was confirmed with streptokinase variants mutated at one, two, or three sites simultaneously. The single/double/triple exosite mutants of streptokinase showed a nonadditive, synergistic decline in kcat for substrate plasminogen activation in the order single > double > triple exosite mutant. Under the same conditions, zymogen activation by the various mutants remained essentially native- like in terms of nonproteolytic activation of partner plasminogen. Multisite mutants also retain affinity to form 1:1 stoichiometric activator complexes with plasmin when probed through sensitive equilibrium fluorescence studies. Thus, the present results strongly support a model of streptokinase action, wherein catalysis by the streptokinase-plasmin complex operates through a distributed network of substrate-interacting exosites resident across all three domains of the cofactor protein.Rachna AnejaManish DattSuman YadavGirish Sahni2019-09-05T11:33:35Z2019-09-05T11:33:35Zhttp://crdd.osdd.net/open/id/eprint/2463This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24632019-09-05T11:33:35ZIn silico models for B-cell epitope recognition and signaling.Tremendous technological advances in peptide synthesis and modification in recent years have resolved the major limitations of peptide-based vaccines. B-cell epitopes are major components of these vaccines (besides having other biological applications). Researchers have been developing in silico or computational models for the prediction of both linear and conformational B-cell epitopes, enabling immunologists and clinicians to identify the most promising epitopes for characterization in the laboratory. Attempts are also ongoing in systems biology to delineate the signaling networks in immune cells. Here we present all possible in silico models developed thus far in these areas.Hifzur Rahman AnsariG.P.S. Raghava2014-05-30T04:22:25Z2014-05-30T04:22:25Zhttp://crdd.osdd.net/open/id/eprint/1512This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15122014-05-30T04:22:25ZInteraction of silver nanoparticles withEscherichia coliand their cell envelope biomoleculesbe in the range of 11.25–22.5 µg ml−1. The growth kinetics curve shows that 25 µg ml−1 AgNPs strongly inhibits the bacterial growth. Confocal laser scanning electron microscopy (CLSM) shows that as the concentration of NPs increases, reduction in the number of cells was observed and at 50 µg ml−1 of NPs, 100% death was noticed. Scanning electron microscopy (SEM) shows cells were severely damaged with pits, multiple depressions, and indentation on cell surface and original rod shape has swollen into bigger size. High resolution-transmission electron microscopic (HR-TEM) micrograph shows that cells were severely ruptured. The damaged cells showed either localized or complete separation of the cell membrane. The NPs that anchor onto cell surface and penetrating the cells may cause membrane damage, which could result in cell lysis. The interaction of AgNPs to membrane biomolecules; lipopolysaccharide (LPS) and l-α-phosphatidyl-ethanolamine (PE) were investigated by attenuated total reflectance–fourier transform infrared (ATR–FTIR) spectroscopy. LPS and PE showed IR spectral changes after AgNPs exposure. The O-antigen part of LPS was responsible for interaction of NPs through hydrogen bonding. The phosphodiester bond of PE was broken by AgNPs, forming phosphate monoesters and resulting in the highly disordered alkyl chain. The AgNPs-induced structural changes in phospholipid may lead to the loss of amphiphilic properties, destruction of the membrane and cell leaking. The biomolecular changes in bacterial cell envelope revealed by ATR–FTIR provide a deeper understanding of cytotoxicity of AgNPs.Mohammad Azam AnsariHaris Manzoor KhanAijaz Ahmed KhanMohammad Kaleem AhmadAbbas Ali MahdiRuchita PalSwaranjit Singh Cameotra2015-02-10T11:00:30Z2019-09-04T09:08:29Zhttp://crdd.osdd.net/open/id/eprint/1597This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15972015-02-10T11:00:30ZMyo1c, an unconventional motor that maintains glomerular filtration function.
Podocytes and their specialized junctions "slit diaphragm" are key components of glomerular filtration system and their dysfunction is associated with impaired kidney function. We recently demonstrated that motor protein Myo1c mediates translocation of slit diaphragm proteins Neph1 and Nephrin from cytoplasm to podocytes cell membrane that is critical for renal function. In this study, we investigated physiological significance of Myo1c in maintaining glomerular filtration barrier using zebrafish as a model system. In addition, we performed structural and biochemical experiments to decipher the interacting regions in Myo1c and Neph1 that provides mechanistic insight into the assembly of Neph1 and its complexes at podocyte membrane. Knockdown of Myo1c in zebrafish using morpholinos impaired the glomerular filtration function. The solution structures of full length Myo1c in complex with the cytoplasmic domain of Neph1 was resolved using small/wide angle X-ray scattering. The structural analysis revealed multiple regions in Myo1c and Neph1 that mediate this interaction. Binding mutants derived from this analysis confirmed the validity of this approach and the imaging experiments further demonstrated the inability of these mutants to localize at podocyte cell membrane and rescue a renal phenotype in zebrafish Neph1 knockdown model. Collectively, these results support a critical role for Myo1c in renal physiology. Ehtesham Arif Leena MallikYogendra S RathoreBabita KumariMichael Ostap. AshishLawrence B HolzmanDeepak Nihalani2019-09-05T11:35:55Z2019-09-05T11:35:55Zhttp://crdd.osdd.net/open/id/eprint/2462This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24622019-09-05T11:35:55ZGenomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151.Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease. Mario L Arrieta-OrtizLuis M Rodríguez-RÁlvaro L Pérez-QuinteroLucie PoulinAna C DíazNathalia Arias RojasCesar TrujilloMariana Restrepo BenavidesRebecca BartJens BochTristan BoureauArmelle DarrassePerrine DavidThomas Dugé de BernonvillePaula FontanillaLionel GagnevinFabien GuérinMarie-Agnès JacquesEmmanuelle LauberPierre LefeuvreCesar MedinaEdgar MedinaNathaly MontenegroAlejandra Muñoz BodnarLaurent D NoëlJuan F Ortiz QuiñonesDaniela OsorioCarolina PardoPrabhu B PatilStéphane PoussierOlivier PruvostIsabelle Robène-SoustradeRobert P RyanJavier TabimaOscar G Urrego MoralesChristian VernièreSébastien CarrereValérie VerdierBoris SzurekSilvia RestrepoCamilo LópezRalf KoebnikAdriana Bernal2015-02-11T09:29:18Z2015-07-22T04:32:17Zhttp://crdd.osdd.net/open/id/eprint/1619This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16192015-02-11T09:29:18ZTruncated hemoglobin, HbN, is post-translationally modified in Mycobacterium tuberculosis and modulates host-pathogen interactions during intracellular infection.Mycobacterium tuberculosis (Mtb) is a phenomenally successful human pathogen having evolved mechanisms that allow it to survive within the hazardous environment of macrophages and establish long term, persistent infection in the host against the control of cell-mediated immunity. One such mechanism is mediated by the truncated hemoglobin, HbN, of Mtb that displays a potent O2-dependent nitric oxide dioxygenase activity and protects its host from the toxicity of macrophage-generated nitric oxide (NO). Here we demonstrate for the first time that HbN is post-translationally modified by glycosylation in Mtb and remains localized on the cell membrane and the cell wall. The glycan linkage in the HbN was identified as mannose. The elevated expression of HbN in Mtb and M. smegmatis facilitated their entry within the macrophages as compared with isogenic control cells, and mutation in the glycan linkage of HbN disrupted this effect. Additionally, HbN-expressing cells exhibited higher survival within the THP-1 and mouse peritoneal macrophages, simultaneously increasing the intracellular level of proinflammatory cytokines IL-6 and TNF-α and suppressing the expression of co-stimulatory surface markers CD80 and CD86. These results, thus, suggest the involvement of HbN in modulating the host-pathogen interactions and immune system of the host apart from protecting the bacilli from nitrosative stress inside the activated macrophages, consequently driving cells toward increased infectivity and intracellular survival.Swati AryaDeepti SethiSandeep SinghMangesh Dattu HadeVijender SinghPreeti RajuSathi Babu ChodisettiDeepshikha VermaGrish C VarshneyJ N AgrewalaKanak L Dikshit2013-06-24T10:53:29Z2013-06-24T10:53:29Zhttp://crdd.osdd.net/open/id/eprint/1306This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13062013-06-24T10:53:29ZCharacterization of two antimicrobial peptides produced by a halotolerant Bacillus subtilis strain SK.DU.4 isolated from a rhizosphere soil sample.A bacterial strain producing two antimicrobial peptides was isolated from a rhizosphere soil sample and identified as Bacillus subtilis based on both phenotypic and 16S rRNA gene sequence phylogenetic analysis. It grew optimally up to 14% NaCl and produced antimicrobial peptide within 24 h of growth. The peptides were purified using a combination of chemical extraction and chromatographic techniques. The MALDI-TOF analysis of HPLC purified fractions revealed that the strain SK.DU.4 secreted a bacteriocin-like peptide with molecular mass of 5323.9 Da and a surface-active lipopeptide (m/z 1056 Da). The peptide mass fingerprinting of low-molecular-weight bacteriocin exhibited significant similarity with stretches of secreted lipoprotein of Methylomicrobium album BG8 and displayed 70% sequence coverage. MALDI MS/MS analysis elucidated the lipopeptide as a cyclic lipopeptide with a β-hydroxy fatty acid linked to Ser of a peptide with seven α-amino acids (Asp-Tyr-Asn-Gln-Pro-Asn-Ser) and assigned it to iturin-like group of antimicrobial biosurfactants. However, it differed in amino acid composition with other members of the iturin family. Both peptides were active against Gram-positive bacteria, suggesting that they had an additive effect.Piyush BaindaraSanti M MandalNiharika ChawlaPradip Kumar SinghAnil Kumar PinnakaSuresh Korpole2013-06-24T11:23:22Z2013-06-24T12:04:40Zhttp://crdd.osdd.net/open/id/eprint/1297This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12972013-06-24T11:23:22ZDraft Genome Sequence of Rhodococcus ruber Strain BKS 20-38.We report the 6.1-Mb genome sequence of Rhodococcus ruber strain BKS 20-38, isolated from the palm tree rhizosphere soil of Bhitarkanika National Park, Odhisha, India. The draft genome sequence of strain BKS 20-38 consists of 6,126,900 bp, with a G+C content of 69.72%, 5,716 protein-coding genes, and 49 RNAs.Monu BalaShailesh KumarG.P.S. RaghavaShanmugam Mayilraj2019-09-05T14:03:03Z2019-09-05T14:03:03Zhttp://crdd.osdd.net/open/id/eprint/2430This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24302019-09-05T14:03:03ZlncRNome: a comprehensive knowledgebase of human long noncoding RNAs.The advent of high-throughput genome scale technologies has enabled us to unravel a large amount of the previously unknown transcriptionally active regions of the genome. Recent genome-wide studies have provided annotations of a large repertoire of various classes of noncoding transcripts. Long noncoding RNAs (lncRNAs) form a major proportion of these novel annotated noncoding transcripts, and presently known to be involved in a number of functionally distinct biological processes. Over 18,000 transcripts are presently annotated as lncRNA, and encompass previously annotated classes of noncoding transcripts including large intergenic noncoding RNA, antisense RNA and processed pseudogenes. There is a significant gap in the resources providing a stable annotation, cross-referencing and biologically relevant information. lncRNome has been envisioned with the aim of filling this gap by integrating annotations on a wide variety of biologically significant information into a comprehensive knowledgebase. To the best of our knowledge, lncRNome is one of the largest and most comprehensive resources for lncRNAs. Database URL: http://genome.igib.res.in/lncRNome.Deeksha BhartiyaKoustav PalSourav GhoshShruti KapoorSaakshi JalaliBharat PanwarSakshi JainSatish SatiShantanu SenguptaChetana SachidanandanG.P.S. RaghavaSridhar SivasubbuVinod Scaria2019-09-05T14:01:13Z2019-09-05T14:01:13Zhttp://crdd.osdd.net/open/id/eprint/2431This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24312019-09-05T14:01:13ZFlavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater.A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1(T), was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate reduction and ornithine decarboxylase activities and negative for citrate utilization, urease, oxidase, catalase and DNase activities. The predominant fatty acids were C16 : 0 3-OH, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, anteiso-C15 : 0, C16 : 0, C15 : 0 3-OH, and C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3). Strain N1(T) contained menaquinone 6 (MK-6) as the sole respiratory quinone. The only polyamine was homospermidine and the major polar lipids were phosphatidylethanolamine (PE), three unidentified aminolipids (AL1-AL3) and two unidentified lipids (L1, L2). The DNA G+C content of the strain was 36.3 mol%. 16S rRNA gene sequence analysis indicated that strain N1(T) was a member of the genus Flavobacterium and closely related to Flavobacterium resistens with pairwise sequence similarity of 96.5 %. Phylogenetic analysis showed that strain N1(T) clustered with Flavobacterium glycines and Flavobacterium daejeonense with a distance of 4.8 and 6.0 % (95.2 and 94.0 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, strain N1(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium nitratireducens sp. nov. is proposed. The type strain is N1(T) ( = MTCC 11155(T) = JCM 17678(T)).V BhumikaT N R SrinivasP Anil Kumar2019-09-05T13:59:35Z2019-09-05T13:59:35Zhttp://crdd.osdd.net/open/id/eprint/2432This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24322019-09-05T13:59:35ZMariniradius saccharolyticus gen. nov., sp. nov., a member of the family Cyclobacteriaceae isolated from marine aquaculture pond water, and emended descriptions of the genus Aquiflexum and Aquiflexum balticum.A novel marine, Gram-stain-negative, oxidase- and catalase- positive, rod-shaped bacterium, designated strain AK6(T), was isolated from marine aquaculture pond water collected in Andhra Pradesh, India. The fatty acids were dominated by iso-C15:0, iso-C17:1ω9c, iso-C15:1 G, iso-C17:0 3-OH and anteiso-C15:0. Strain AK6(T) contained MK-7 as the sole respiratory quinone and phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and seven unidentified lipids as polar lipids. The DNA G+C content of strain AK6(T) was 45.6 mol%. Phylogenetic analysis showed that strain AK6(T) formed a distinct branch within the family Cyclobacteriaceae and clustered with Aquiflexum balticum DSM 16537(T) and other members of the family Cyclobacteriaceae. 16S rRNA gene sequence analysis confirmed that Aquiflexum balticum DSM 16537(T) was the nearest neighbour, with pairwise sequence similarity of 90.1%, while sequence similarity with the other members of the family was <88.5%. Based on differentiating phenotypic characteristics and phylogenetic inference, strain AK6(T) is proposed as a representative of a new genus and species of the family Cyclobacteriaceae, as Mariniradius saccharolyticus gen. nov., sp. nov. The type strain of Mariniradius saccharolyticus is AK6(T) (=MTCC 11279(T)=JCM 17389(T)). Emended descriptions of the genus Aquiflexum and Aquiflexum balticum are also proposed.V BhumikaT N R SrinivasK RavinderP Anil Kumar2019-09-05T13:57:31Z2019-09-05T13:57:31Zhttp://crdd.osdd.net/open/id/eprint/2433This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24332019-09-05T13:57:31ZEarly folding events protect aggregation-prone regions of a β-rich protein.Protein folding and aggregation inevitably compete with one another. This competition is even keener for proteins with frustrated landscapes, such as those rich in β structure. It is interesting that, despite their rugged energy landscapes and high β sheet content, intracellular lipid-binding proteins (iLBPs) appear to successfully avoid aggregation, as they are not implicated in aggregation diseases. In this study, we used a canonical iLBP, cellular retinoic acid-binding protein 1 (CRABP1), to understand better how folding is favored over aggregation. Analysis of folding kinetics of point mutants reveals that the folding pathway of CRABP1 involves early barrel closure. This folding mechanism protects sequences in CRABP1 that comprise cores of aggregates as identified by nuclear magnetic resonance. The amino acid conservation pattern in other iLBPs suggests that early barrel closure may be a general strategy for successful folding and minimization of aggregation. We suggest that folding mechanisms in general may incorporate steps that disfavor aggregation.Ivan L BudyakBeena KrishnanAnna M Marcelino-CruzMylene C FerrolinoAnastasia ZhuravlevaLila M Gierasch2015-02-11T09:54:02Z2015-02-11T09:54:02Zhttp://crdd.osdd.net/open/id/eprint/1623This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16232015-02-11T09:54:02ZHuman IL10 gene repression by Rev-erbα ameliorates Mycobacterium tuberculosis clearance.Nuclear receptors modulate macrophage effector functions, which are imperative for clearance or survival of mycobacterial infection. The adopted orphan nuclear receptor Rev-erbα is a constitutive transcriptional repressor as it lacks AF2 domain and was earlier shown to be present in macrophages. In the present study, we highlight the differences in the relative subcellular localization of Rev-erbα in monocytes and macrophages. The nuclear localization of Rev-erbα in macrophages is subsequent to monocyte differentiation. Expression analysis of Rev-erbα elucidated it to be considerably more expressed in M1 phenotype in comparison with M2. Rev-erbα overexpression augments antimycobacterial properties of macrophage by keeping IL10 in a basal repressed state. Further, promoter analysis revealed that IL10 promoter harbors a Rev-erbα binding site exclusive to humans and higher order primates and not mouse, demonstrating a species barrier in its functionality. This direct gene repression is mediated by recruitment of co-repressors NCoR and HDAC3. In addition, our data elucidate that its overexpression reduced the survival of intracellular pathogen Mycobacterium tuberculosis by enhancing phagosome lysosome maturation, an event resulting from IL10 repression. Thus, these findings suggest that Rev-erbα bestows protection against mycobacterial infection by direct gene repression of IL10 and thus provide a novel target in modulating macrophage microbicidal properties.Vemika ChandraSahil MahajanAnkita SainiHedwin K DkharRavikanth NanduriElla B RajAshwani KumarPawan Gupta2013-10-21T10:58:28Z2015-01-07T11:22:03Zhttp://crdd.osdd.net/open/id/eprint/1466This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14662013-10-21T10:58:28ZIn-silico approches for designing inhibitor based on protein- small ligand interactionJagat S Chauhan2016-09-30T11:16:38Z2016-09-30T11:16:38Zhttp://crdd.osdd.net/open/id/eprint/1912This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/19122016-09-30T11:16:38ZIn silico platform for prediction of N-, O- and C-glycosites in eukaryotic protein sequences.Glycosylation is one of the most abundant and an important post-translational modification of proteins. Glycosylated proteins (glycoproteins) are involved in various cellular biological functions like protein folding, cell-cell interactions, cell recognition and host-pathogen interactions. A large number of eukaryotic glycoproteins also have therapeutic and potential technology applications. Therefore, characterization and analysis of glycosites (glycosylated residues) in these proteins is of great interest to biologists. In order to cater these needs a number of in silico tools have been developed over the years, however, a need to get even better prediction tools remains. Therefore, in this study we have developed a new webserver GlycoEP for more accurate prediction of N-linked, O-linked and C-linked glycosites in eukaryotic glycoproteins using two larger datasets, namely, standard and advanced datasets. In case of standard datasets no two glycosylated proteins are more similar than 40%; advanced datasets are highly non-redundant where no two glycosites' patterns (as defined in methods) have more than 60% similarity. Further, based on our results with several algorihtms developed using different machine-learning techniques, we found Support Vector Machine (SVM) as optimum tool to develop glycosite prediction models. Accordingly, using our more stringent and non-redundant advanced datasets, the SVM based models developed in this study achieved a prediction accuracy of 84.26%, 86.87% and 91.43% with corresponding MCC of 0.54, 0.20 and 0.78, for N-, O- and C-linked glycosites, respectively. The best performing models trained on advanced datasets were then implemented as a user-friendly web server GlycoEP (http://www.imtech.res.in/raghava/glycoep/). Additionally, this server provides prediction models developed on standard datasets and allows users to scan sequons in input protein sequences.Jagat Singh ChauhanAlka RaoG.P.S. Raghava2015-02-10T10:02:25Z2015-07-22T04:19:47Zhttp://crdd.osdd.net/open/id/eprint/1596This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15962015-02-10T10:02:25ZCooperation of CD86 signaling with TLR-2 in the activation of resting B cells: a novel BCR independent pathway of stimulating B cells (P1126) The molecules of adaptive and innate immunity cooperate with each other in inducing effective immune response. It is well established fact that B cells can be activated through BCR mediated signaling. Here, we report an alternative strategy of activating resting B cells (RB cells) through concurrent engagement of CD86 and Toll like receptor-2. Concomitant signaling through CD86 and TLR-2 significantly augmented the longevity and activation profile of RB cells. Further, these cells showed enhanced pinocytosis and receptor mediated endocytosis. Furthermore, these cells secreted high levels of IgM and IgG1 and showed better ratio of surface IgG/IgM. Moreover, this process of activation amplifies the population of marginal zone precursors, which connect innate and adaptive arms of immune response. There was also upregulation of set of genes involved in the B cell activation, proliferation, maturation and endocytosis. The data are well in agreement with the gene expression profiles and insinuates to further decipher the molecular mechanism behind this concurrence. An insight into the detailed mechanism may pave way to design vaccines based on this signaling strategy. Sathi Babu ChodisettiShweta JainJ N Agrewala2015-02-11T07:14:57Z2015-02-11T07:14:57Zhttp://crdd.osdd.net/open/id/eprint/1615This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16152015-02-11T07:14:57ZCdTe nanobioprobe based optoelectrochemical immunodetection of diabetic marker HbA1c.Highly luminescent water soluble CdTe quantum dots (QDs) were synthesized and conjugated with anti-HbA1c antibody to generate specific nanobioprobe. A sandwich immunoassay model was employed using capture HbA1c antibody as a specific receptor molecule and the QD-labeled secondary antibody as a dual (fluorescence cum electrochemical) tracer to quantify the concentration of HbA1c. A linear increase in current was observed for HbA1c analytical standards with a R(2) value of 0.990 and coefficient of variance ~5%. A comparison between HPLC and dual immunoassay for clinical samples showed a correlation coefficient of 89% and 96% for fluorescence and electrochemical detection methods respectively. The QD-based immunoassay shows great promise for rapid reproducible and cost effective analysis of HbA1c in clinical samples.Adity ChopraSatish TutejaNaresh SachdevaK K BhasinVijayender BhallaC Raman Suri2015-02-12T03:56:29Z2015-07-22T04:39:33Zhttp://crdd.osdd.net/open/id/eprint/1627This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16272015-02-12T03:56:29ZDevelopment of suitable solvent system for downstream processing of biopolymer pullulan using response surface methodology.Downstream processing is an important aspect of all biotechnological processes and has significant implications on quality and yield of the final product. Several solvents were examined for their efficacy on pullulan precipitation from fermentation broth. Interactions among four selected solvents and their effect on pullulan yield were studied using response surface methodology. A polynomial model was developed using D-optimal design and three contour plots were generated by performing 20 different experiments and the model was validated by performing optimization experiments. The results indicated that lower concentration of ethanol in combination with the other three solvents has resulted in higher yield of polymer from fermentation broth and the optimized solvent system was able to recover 1.44 times more pullulan as compared to the conventional ethanolic precipitation method. These observations may help in enhancing efficiency of pullulan recovery from fermentation broth and also result in reduced cost of production for the final product.Anirban Roy ChoudhuryParamita BhattacharjeeG S Prasad2015-02-11T09:33:49Z2015-02-11T09:33:49Zhttp://crdd.osdd.net/open/id/eprint/1620This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16202015-02-11T09:33:49ZUnique N-terminal arm of Mycobacterium tuberculosis PhoP protein plays an unusual role in its regulatory function.Mycobacterium tuberculosis PhoP, a master regulator involved in complex lipid biosynthesis and expression of unknown virulence determinants, is composed of an N-terminal receiver domain and a C-terminal effector domain. The two experimentally characterized PhoP orthologs, from Escherichia coli and Salmonella enterica, display vastly different regulatory capabilities. Here, we demonstrate that the 20-residue-long N-terminal arm unique to M. tuberculosis PhoP plays an essential role in the expanded regulatory capabilities of this important regulator. Although the arm is not required for overall structural stability and/or phosphorylation of the PhoP N-domain, strikingly it is essential for phosphorylation-coupled transcription regulation of target genes. Consistent with this view, arm truncation of PhoP is accompanied by a conformational change of the effector domain, presenting a block in activation subsequent to phosphorylation. These results suggest that presence of the arm, unique to this regulator that shares an otherwise highly conserved domain structure with members of the protein family, contributes to the mechanism of inter-domain interactions. Thus, we propose that the N-terminal arm is an adaptable structural feature of M. tuberculosis PhoP, which evolved to fine-tune regulatory capabilities of the transcription factor in response to the changing physiology of the bacilli within its host.Arijit Kumar DasVijjamarri Anil KumarRitesh Rajesh SevalkarRoohi BansalDibyendu Sarkar2019-07-10T10:09:51Z2019-07-11T14:13:30Zhttp://crdd.osdd.net/open/id/eprint/2199This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/21992019-07-10T10:09:51ZRegulation of Adipocyte Function by all-trans-Retinoic acid, Pyridoxal-5'-phosphate and Therapeutic ProteaseSandeep Dave2015-02-10T09:21:52Z2015-02-10T09:21:52Zhttp://crdd.osdd.net/open/id/eprint/1594This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15942015-02-10T09:21:52ZHaemoglobins of Mycobacteria: structural features and biological functions.The genus Mycobacterium is comprised of Gram-positive bacteria occupying a wide range of natural habitats and includes species that range from severe intracellular pathogens to economically useful and harmless microbes. The recent upsurge in the availability of microbial genome data has shown that genes encoding haemoglobin-like proteins are ubiquitous among Mycobacteria and that multiple haemoglobins (Hbs) of different classes may be present in pathogenic and non-pathogenic species. The occurrence of truncated haemoglobins (trHbs) and flavohaemoglobins (flavoHbs) showing distinct haem active site structures and ligand-binding properties suggests that these Hbs may be playing diverse functions in the cellular metabolism of Mycobacteria. TrHbs and flavoHbs from some of the severe human pathogens such as Mycobacterium tuberculosis and Mycobacterium leprae have been studied recently and their roles in effective detoxification of reactive nitrogen and oxygen species, electron cycling, modulation of redox state of the cell and facilitation of aerobic respiration have been proposed. This multiplicity in the function of Hbs may aid these pathogens to cope with various environmental stresses and survive during their intracellular regime. This chapter provides recent updates on genomic, structural and functional aspects of Mycobacterial Hbs to address their role in Mycobacteria.Kelly S DavidgeKanak L Dikshit2019-09-05T13:54:33Z2019-09-05T13:54:33Zhttp://crdd.osdd.net/open/id/eprint/2434This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24342019-09-05T13:54:33ZDraft Genome Sequence of Plant-Growth-Promoting Rhizobacterium Serratia fonticola Strain AU-AP2C, Isolated from the Pea Rhizosphere.Plant health can be augmented by plant-growth-promoting rhizobacteria (PGPR) that confer biofertilizer, phytostimulation, and biocontrol activities. Herein, we provide the high-quality draft genome sequence of Serratia fonticola strain AU-AP2C, a Gram-negative motile PGPR of the pea plant, conferring phosphate solubilization, ammonia production, and antifungal activity against Fusarium sp. The 4.9-Mb genome contains genes related to plant growth promotion and synthesis of siderophores. Usha DeviIndu KhatriNavinder KumarDeepak SharmaSrikrishna SubramanianAdesh K Saini2019-09-05T13:52:25Z2019-09-05T13:52:25Zhttp://crdd.osdd.net/open/id/eprint/2435This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24352019-09-05T13:52:25ZDrugMint: a webserver for predicting and designing of drug-like molecules.Identification of drug-like molecules is one of the major challenges in the field of drug discovery. Existing approach like Lipinski rule of 5 (Ro5), Operea have their own limitations. Thus, there is a need to develop computational method that can predict drug-likeness of a molecule with precision. In addition, there is a need to develop algorithm for screening chemical library for their drug-like properties.Sandeep Kumar DhandaDeepak SinglaAlok K MondalG.P.S. Raghava2019-09-05T13:51:15Z2019-09-05T13:51:15Zhttp://crdd.osdd.net/open/id/eprint/2436This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24362019-09-05T13:51:15ZDesigning of interferon-gamma inducing MHC class-II binders.The generation of interferon-gamma (IFN-γ) by MHC class II activated CD4+ T helper cells play a substantial contribution in the control of infections such as caused by Mycobacterium tuberculosis. In the past, numerous methods have been developed for predicting MHC class II binders that can activate T-helper cells. Best of author's knowledge, no method has been developed so far that can predict the type of cytokine will be secreted by these MHC Class II binders or T-helper epitopes. In this study, an attempt has been made to predict the IFN-γ inducing peptides. The main dataset used in this study contains 3705 IFN-γ inducing and 6728 non-IFN-γ inducing MHC class II binders. Another dataset called IFNgOnly contains 4483 IFN-γ inducing epitopes and 2160 epitopes that induce other cytokine except IFN-γ. In addition we have alternate dataset that contains IFN-γ inducing and equal number of random peptides.Sandeep Kumar DhandaPooja VirG.P.S. Raghava2019-07-10T08:59:12Z2019-07-11T16:09:57Zhttp://crdd.osdd.net/open/id/eprint/2192This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/21922019-07-10T08:59:12ZInterleukin-6 and Mycobacterial InfectionRajesh Kumar Dutta2019-07-12T11:46:08Z2019-07-12T15:06:39Zhttp://crdd.osdd.net/open/id/eprint/2215This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22152019-07-12T11:46:08ZUnderstanding the Molecular Mechanism of Cysteine Synthase Assembly and its Regulatory Role in bacterial Cysteine BiosynthesisMary Krishna Ekka2014-05-30T03:50:03Z2015-01-07T06:26:30Zhttp://crdd.osdd.net/open/id/eprint/1504This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15042014-05-30T03:50:03ZDevelopment of Suitable Solvent System for Downstream Processing of Biopolymer Pullulan Using Response Surface MethodologyDownstream processing is an important aspect of all biotechnological processes and has significant implications on
quality and yield of the final product. Several solvents were examined for their efficacy on pullulan precipitation from
fermentation broth. Interactions among four selected solvents and their effect on pullulan yield were studied using
response surface methodology. A polynomial model was developed using D-optimal design and three contour plots
were generated by performing 20 different experiments and the model was validated by performing optimization
experiments. The results indicated that lower concentration of ethanol in combination with the other three solvents
has resulted in higher yield of polymer from fermentation broth and the optimized solvent system was able to recover
1.44 times more pullulan as compared to the conventional ethanolic precipitation method. These observations may
help in enhancing efficiency of pullulan recovery from fermentation broth and also result in reduced cost of production for the final product.Dwayne EliasAnirban Roy ChoudhuryParamita BhattacharjeeG S Prasad2019-09-05T13:49:47Z2019-09-05T13:49:47Zhttp://crdd.osdd.net/open/id/eprint/2437This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24372019-09-05T13:49:47ZDelicate balance between functionally required flexibility and aggregation risk in a β-rich protein.Susceptibility to aggregation is general to proteins because of the potential for intermolecular interactions between hydrophobic stretches in their amino acid sequences. Protein aggregation has been implicated in several catastrophic diseases, yet we still lack in-depth understanding about how proteins are channeled to this state. Using a predominantly β-sheet protein whose folding has been explored in detail, cellular retinoic acid-binding protein 1 (CRABP1), as a model, we have tackled the challenge of understanding the links between a protein's natural tendency to fold, 'breathe', and function with its propensity to misfold and aggregate. We identified near-native dynamic species that lead to aggregation and found that inherent structural fluctuations in the native protein, resulting in opening of the ligand-entry portal, expose hydrophobic residues on the most vulnerable aggregation-prone sequences in CRABP1. CRABP1 and related intracellullar lipid-binding proteins have not been reported to aggregate inside cells, and we speculate that the cellular concentration of their open, aggregation-prone conformations is sufficient for ligand binding but below the critical concentration for aggregation. Our finding provides an example of how nature fine-tunes a delicate balance between protein function, conformational variability, and aggregation vulnerability and implies that with the evolutionary requirement for proteins to fold and function, aggregation becomes an unavoidable but controllable risk. Mylene C FerrolinoAnastasia ZhuravlevaIvan L BudyakBeena KrishnanLila M Gierasch2013-06-24T11:03:21Z2013-06-24T11:03:21Zhttp://crdd.osdd.net/open/id/eprint/1303This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13032013-06-24T11:03:21ZIn silico approaches for designing highly effective cell penetrating peptides.Cell penetrating peptides have gained much recognition as a versatile transport vehicle for the intracellular delivery of wide range of cargoes (i.e. oligonucelotides, small molecules, proteins, etc.), that otherwise lack bioavailability, thus offering great potential as future therapeutics. Keeping in mind the therapeutic importance of these peptides, we have developed in silico methods for the prediction of cell penetrating peptides, which can be used for rapid screening of such peptides prior to their synthesis.Ankur GautamKumardeep ChaudharyRahul KumarArun SharmaPallavi KapoorAtul TyagiG.P.S. Raghava2019-09-05T13:47:56Z2019-09-05T13:47:56Zhttp://crdd.osdd.net/open/id/eprint/2438This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24382019-09-05T13:47:56ZCarrier protein influences immunodominance of a known epitope: implication in peptide vaccine design.We investigated how the processing of a given antigen by antigen presenting cells (APC) is dictated by the conformation of the antigen and how this governs the immunodominance hierarchy. To address the question, a known immunodominant sequence of bacteriophage lambda repressor N-terminal sequence 12-26 [λR(12-26)] was engineered at the N and C termini of a heterologous leishmanial protein, Kinetoplastid membrane protein-11 (KMP-11); the resulting proteins were defined as N-KMP-11 and C-KMP-11 respectively. The presence of λR(12-26) in N-KMP-11 and C-KMP-11 was established by western blot analysis with antibody to λR(12-26) peptide. N-KMP-11 but not C-KMP-11 could stimulate the anti λR(12-26) T-cell clonal population very efficiently in the presence of APCs. Priming of BALB/c mice with N-KMP-11 or C-KMP-11 generated similar levels of anti-KMP-11 IgG, but anti-λR(12-26) specific IgG was observed only upon priming with N-KMP-11. Interestingly, uptake of both N-KMP-11 and C-KMP-11 by APCs was similar but catabolism of N-KMP-11 but not C-KMP-11 was biphasic and fast at the initial time point. Kratky plots of small angle X-ray scattering showed that while N-KMP-11 adopts flexible Gaussian type of topology, C-KMP-11 prefers Globular nature. To show that KMP-11 is not unique as a carrier protein, an epitope (SPITBTNLBTMBK) of Plasmodium yoelii (PY) apical membrane protein 1[AMA-1 (136-148)], is placed at the C and N terminals of a dominant T-cell epitope of ovalbumin protein OVA(323-339) and the resulting peptides are defined as PY-OVA and OVA-PY respectively. Interestingly, only OVA-PY could stimulate anti-OVA T-cells and produce IgG response upon priming of BALB/c mice with it. Thus for rational design of peptide vaccine it is important to place the dominant epitope appropriately in the context of the carrier protein.Moumita GhoshAshish K SolankiKoushik RoyReema R Dhoke. AshishSyamal Roy2019-09-05T13:45:16Z2019-09-05T13:45:16Zhttp://crdd.osdd.net/open/id/eprint/2439This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24392019-09-05T13:45:16ZLipidated promiscuous peptide augments the expression of MHC-II molecules on dendritic cells and activates T cells.In spite of the fact that BCG is the most widely used vaccine, tuberculosis (TB) continues to be a major killer disease in TB-endemic regions. Recently, many emerging evidences from the published literature indicate the role of environmental mycobacteria in blocking the processing and presentation of BCG antigens and thereby impairing with suboptimal generation of protective T cells. To surmount this problem associated with BCG, we constructed a novel lipopeptide (L91) by conjugating a promiscuous peptide consisting of CD4 + T-helper epitope of sequence of 91-110 of 16 kDa antigen of Mycobacterium tuberculosis to Pam2Cys, an agonist of Toll-like receptor-2.Uthaman GowthamanPradeep K RaiWeiguang ZengDavid C JacksonJ N Agrewala2019-07-11T09:07:49Z2019-07-11T16:03:10Zhttp://crdd.osdd.net/open/id/eprint/2203This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22032019-07-11T09:07:49ZStudies on regulatory role of virulence-associated response regulator PhoP in Mycobacterium tuberculosisRajni Goyal2019-09-05T13:40:48Z2019-09-05T13:40:48Zhttp://crdd.osdd.net/open/id/eprint/2441This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24412019-09-05T13:40:48ZIdentification of B-cell epitopes in an antigen for inducing specific class of antibodies.In the past, numerous methods have been developed for predicting antigenic regions or B-cell epitopes that can induce B-cell response. To the best of authors' knowledge, no method has been developed for predicting B-cell epitopes that can induce a specific class of antibody (e.g., IgA, IgG) except allergenic epitopes (IgE). In this study, an attempt has been made to understand the relation between primary sequence of epitopes and the class of antibodies generated.Sudheer GuptaHifzur Rahman AnsariAnkur GautamG.P.S. Raghava2019-09-05T13:42:54Z2019-09-05T13:42:54Zhttp://crdd.osdd.net/open/id/eprint/2440This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24402019-09-05T13:42:54ZIn silico approach for predicting toxicity of peptides and protein.Over the past few decades, scientific research has been focused on developing peptide/protein-based therapies to treat various diseases. With the several advantages over small molecules, including high specificity, high penetration, ease of manufacturing, peptides have emerged as promising therapeutic molecules against many diseases. However, one of the bottlenecks in peptide/protein-based therapy is their toxicity. Therefore, in the present study, we developed in silico models for predicting toxicity of peptides and proteins.Sudheer GuptaPallavi KapoorKumardeep ChaudharyAnkur GautamRahul KumarG.P.S. Raghava2019-07-11T09:05:54Z2019-08-09T15:11:43Zhttp://crdd.osdd.net/open/id/eprint/2210This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22102019-07-11T09:05:54ZInduction of the Inhibition of Immune Response by Caerulomycin A Krishna Gurram Rama2019-09-05T13:38:38Z2019-09-05T13:38:38Zhttp://crdd.osdd.net/open/id/eprint/2442This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24422019-09-05T13:38:38ZDevelopment of a model webserver for breed identification using microsatellite DNA marker.Identification of true to breed type animal for conservation purpose is imperative. Breed dilution is one of the major problems in sustainability except cases of commercial crossbreeding under controlled condition. Breed descriptor has been developed to identify breed but such descriptors cover only "pure breed" or true to the breed type animals excluding undefined or admixture population. Moreover, in case of semen, ova, embryo and breed product, the breed cannot be identified due to lack of visible phenotypic descriptors. Advent of molecular markers like microsatellite and SNP have revolutionized breed identification from even small biological tissue or germplasm. Microsatellite DNA marker based breed assignments has been reported in various domestic animals. Such methods have limitations viz. non availability of allele data in public domain, thus each time all reference breed has to be genotyped which is neither logical nor economical. Even if such data is available but computational methods needs expertise of data analysis and interpretation.Mir Asif Iquebal. SarikaSandeep Kumar DhandaVasu AroraSat Pal DixitGajendra P S RaghavaAnil RaiDinesh Kumar2019-09-05T13:36:54Z2019-09-05T13:36:54Zhttp://crdd.osdd.net/open/id/eprint/2443This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24432019-09-05T13:36:54ZEffects of alcohols on the stability and low-frequency local motions that control the slow changes in structural dynamics of ferrocytochrome c.To determine the effects of alcohols on the low-frequency local motions that control slow changes in structural dynamics of native-like compact states of proteins, we have studied the effects of alcohols on structural fluctuation of M80-containing Ω-loop by measuring the rate of thermally driven CO dissociation from a natively folded carbonmonoxycytochrome c under varying concentrations of alcohols (methanol, ethanol, 1-propanol, 2-propanol, 3°-butanol, 2,2,2-trifluoroethanol). As alcohol is increased, the rate coefficient of CO dissociation (k(diss)) first decreases in subdenaturing region and then increases on going from subdenaturing to denaturing milieu. This decrease in k(diss) is more for 2,2,2-trifluroethanol and 1-propanol and least for methanol, indicating that the first phase of motional constraint is due to the hydrophobicity of alcohols and intramolecular protein cross-linking effect of alcohols, which results in conformational entropy loss of protein. The thermal denaturation midpoint for ferrocytochrome c decreases with increase in alcohol, indicating that alcohol decrease the global stability of protein. The stabilization free energy (ΔΔG) in alcohols' solution was calculated from the slope of the Wyman-Tanford plot and water activity. The m-values obtained from the slope of ΔΔG versus alcohols plot were found to be more negative for longer and linear chain alcohols, indicating destabilization of proteins by alcohols through disturbance of hydrophobic interactions and hydrogen bonding.Rishu JainDeepak SharmaRajesh Kumar2013-02-14T06:12:46Z2013-02-14T06:12:46Zhttp://crdd.osdd.net/open/id/eprint/1289This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12892013-02-14T06:12:46ZCombinatorial Signaling through TLR-2 and CD86 Augments Activation and Differentiation of Resting B Cells.B cells are an integral component in mounting humoral immune responses and they are also crucial in programming T cell mediated immunity. Usually, B cell activation is initiated by recognition of antigen through B cell receptor (BCR), followed by its processing and presentation to T cells. But very little is known about BCR independent activation of B cells. Now, there is an increasing body of evidence indicating the combinatorial effect of innate and adaptive immune components in modulating the functions of B cells. In this study, we demonstrate the activation of resting B cells (RB) by simultaneous involvement of Toll like Receptor-2 (TLR-2) and costimulatory molecule, CD86. Interestingly, these B cells exhibited significant level of activation and proliferation. Furthermore, this process of activation leads to the differentiation of RB cells, preferably into marginal zone precursors (CD19(+)IgD(hi)IgM(hi)CD21/35(hi)CD23(hi)) in a shorter time window and showed increased secretion of IgG isotype. These RB cells also showed enhanced antigen uptake capacity. These observations were also substantiated by microarray gene expression results, which strengthen the notion that combinatorial signaling through innate and adaptive immune components enhances B cell mediated immune response. Thus, the present study elucidates a novel BCR independent B cell activation mechanism that links TLR-2 and CD86. Hence signaling of TLRs in conjunction with costimulatory molecules will substantially help in bolstering humoral immune response, which can be extrapolated to formulate vaccination strategies for diseases involving B cell-mediated immunity.Shweta JainSathi Babu ChodisettiJ N Agrewala2014-05-30T04:09:11Z2014-05-30T04:09:11Zhttp://crdd.osdd.net/open/id/eprint/1508This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15082014-05-30T04:09:11ZAgromyces arachidis sp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field.A Gram-positive, yellowish bacterium strain AK-1(T) was isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genus Agromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1(T) was closely related to Agromyces aurantiacus (98.6%) followed by Agromyces soli (98.3%), Agromyces tropicus (97.6%), Agromyces ulmi (97.3%), Agromyces flavus (97.2%), and Agromyces italicus (97.0%), whereas the sequence similarity values with respect to the other Agromyces species with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1(T) and other related strains were well below the threshold that is required for the proposal of a novel species. The DNA G + C content of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1(T) clearly indicate that the strain represents a novel species, for which the name Agromyces arachidis sp. nov. is proposed. The type strain is AK-1(T) (=MTCC 10524(T) = JCM 19251(T)).Chandandeep KaurAnil Kumar PinnakaNitin Kumar SinghMonu BalaShanmugam Mayilraj2013-06-24T11:27:07Z2013-06-24T12:04:15Zhttp://crdd.osdd.net/open/id/eprint/1295This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12952013-06-24T11:27:07ZDraft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T.We report the 8.5-Mb genome sequence of Amycolatopsis decaplanina strain DSM 44594(T), isolated from a soil sample from India. The draft genome of strain DSM 44594(T) consists of 8,533,276 bp with a 68.6% G+C content, 7,899 protein-coding genes, and 57 RNAs.Navjot KaurShailesh KumarMonu BalaG.P.S. RaghavaShanmugam Mayilraj2019-09-05T14:06:35Z2019-09-05T14:06:35Zhttp://crdd.osdd.net/open/id/eprint/2426This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24262019-09-05T14:06:35ZIsostructural unbranched alkyl-chains as tools for stabilizing β-turn structure.To investigate the structural role played by isostructural unbranched alkyl-chains on the conformational ensemble and stability of β-turn structures, the conformational properties of a designed model peptide: Plm-Pro-Gly-Pda (1, Plm: H3 C-(CH2)14-CONH-; Pda: -CONH- (CH2 )14 -CH3) have been examined and compared with the parent peptide: Boc-Pro-Gly-NHMe (2, Boc: tert-butoxycarbonyl; NHMe: N-methylamide). The characteristic (13)C NMR chemical-shifts of the Pro C(β) and C(γ) resonances ascertained the incidence of an all-trans peptide-bond in low polarity deuterochloroform solution. Using FTIR and (1) H NMR spectroscopy, we establish that apolar alkyl-chains flanking a β-turn promoting Pro-Gly sequence impart definite incremental stability to the well-defined hydrogen-bonded structure. The assessment of (1)H NMR derived thermodynamic parameters of the hydrogen-bonded amide-NHs via variable temperature indicate that much weaker hydrophobic interactions do contribute to the stability of folded reverse turn structures. The far-UV CD spectral patterns of 1 and 2 in 2,2,2-trifluoroethanol are consistent with Pro-Gly specific type II β-turn structure, concomitantly substantiate that the flanking alkyl-chains induce substantial bias in enhanced β-turn populations. In view of structural as well as functional importance of the Pro-Gly mediated secondary structures, besides biochemical and biological significance of proteins lipidation via myristoylation or palmytoilation, we highlight potential convenience of the unbranched Plm and Pda moieities not only as main-chain N- and C-terminal protecting groups but also to mimic and stabilize specific isolated secondary and supersecondary structural components frequently observed in proteins and polypeptides.Rajwant KaurRaghuvansh Kishore2019-07-11T09:05:28Z2019-07-11T16:54:52Zhttp://crdd.osdd.net/open/id/eprint/2209This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22092019-07-11T09:05:28ZIdentification of Molecular Target of Caerulomycin A and Description of its Mechanism of ActionSuneet Kaur2019-07-11T09:05:21Z2019-07-11T17:02:21Zhttp://crdd.osdd.net/open/id/eprint/2211This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22112019-07-11T09:05:21ZAnticancer agents and Cutaneous T Cell LymphomaMohammad Aslam Khan2014-05-30T04:25:19Z2015-01-07T07:17:04Zhttp://crdd.osdd.net/open/id/eprint/1513This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15132014-05-30T04:25:19ZPhenyl aldehyde and propanoids exert multiple sites of action towards cell membrane and cell wall targeting ergosterol in Candida albicansIn the present study, two phyto-compounds phenyl aldehyde (cinnamaldehyde) and propanoid (eugenol) were
selected to explore their modes of action against Candida albicans. Electron microscopy, flow cytometry and
spectroscopic assays were employed to determine the targets of these compounds. Treatment of C. albicans (CA04)
with sub-MICs of cinnamaldehyde (50 μg/mL) and eugenol (200 μg/mL) indicated multiple sites of action including
damages to cell walls, cell membranes, cytoplasmic contents and other membranous structures as observed under
electron microscopy. Concentration and time dependent increase in the release of cytoplasmic contents
accompanied with change in extracellular K+ concentration was recorded. Exposure of Candida cells at 4 × MIC of
cinnaamldehyde and eugenol resulted in 40.21% and 50.90% dead cells, respectively as revealed by flow cytometry
analysis. Treatment of Candida cells by cinnamaldehyde and eugenol at 0.5 × MIC showed 67.41% and 76.23%
reduction in ergosterol biosynthesis, respectively. The binding assays reflected the ability of compounds to bind
with the ergosterol. Our findings have suggested that the membrane damaging effects of phenyl aldehyde and
propanoids class of compounds is attributed to their ability to inhibit ergosterol biosynthesis and simultaneously
binding with ergosterol. Indirect or secondary action of these compounds on cell wall is also expected as revealed
by electron microscopic studies.Mohd Sajjad KhanIqbal AhmadSwaranjit Singh Cameotra2015-02-10T09:57:28Z2015-07-22T04:32:51Zhttp://crdd.osdd.net/open/id/eprint/1595This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15952015-02-10T09:57:28ZImmunomodulation through CD40 and TLR-4: an approach to control tuberculosis (P4516) The immune system have nature's one of the most fascinating mechanisms which continuously protects us against billions of pathogens. It operates through a very well organized network of cells that constantly rove, communicate and coordinate to protect the host. The cells of the immune system regulate through sequence of events involving myriad of molecules expressed on their surface (costimulatory molecules, toll-like receptors, etc.) and also by soluble mediators (cytokines, chemokines, defensins, complement components, etc.). Moreover, the intricate interaction of these molecules among different immune cells like T cells, B cells, dendritic cells (DCs), macrophages, etc., elicit their activation or inhibition, thereby conferring resistance against various pathogens and maintain homeostasis of the immune system. Signaling of these molecules that are expressed on the surface of immune cells can further enhance their efficacy in elimination of pathogens. The study conducted by us showed that concomitant signaling through CD40 and Toll-Like Receptor-4 augmented the production of nitric oxide and proinflammatory cytokines like IL-6, TNFa and IL-12 in Mycobacterium tuberculosis (Mtb) infected DCs. Further, activated DCs showed enhanced microbicidal function and significantly reduced the intracellular survival of Mtb. This study indicates that concomitant signaling through CD40 and TLR-4 can be employed as a therapeutic strategy to curb the intracellular growth of pathogens.Nargis KhanJ N Agrewala2018-04-05T02:49:37Z2018-04-05T02:49:37Zhttp://crdd.osdd.net/open/id/eprint/2083This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/20832018-04-05T02:49:37ZGleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardiiBACKGROUND:
The yeast Saccharomyces boulardii is used worldwide as a probiotic to alleviate the effects of several gastrointestinal diseases and control antibiotics-associated diarrhea. While many studies report the probiotic effects of S. boulardii, no genome information for this yeast is currently available in the public domain.
RESULTS:
We report the 11.4 Mbp draft genome of this probiotic yeast. The draft genome was obtained by assembling Roche 454 FLX + shotgun data into 194 contigs with an N50 of 251 Kbp. We compare our draft genome with all other Saccharomyces cerevisiae genomes.
CONCLUSIONS:
Our analysis confirms the close similarity of S. boulardii to S. cerevisiae strains and provides a framework to understand the probiotic effects of this yeast, which exhibits unique physiological and metabolic properties.Indu KhatriAkil AkhtarKamaldeep KaurRajul TomarGandham Satyanarayana PrasadThirumalai Nallan Chakravarthy RamyaSrikrishna Subramanian2018-09-19T08:56:31Z2018-09-19T08:56:31Zhttp://crdd.osdd.net/open/id/eprint/2117This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/21172018-09-19T08:56:31ZDraft Genome Sequence of the Opportunistic Human Pathogen Morganella morganii SC01.We report the 4.1-Mb draft genome sequence of Morganella morganii SC01, a gammaproteobacterium, isolated from an Indian human fecal sample.Indu KhatriChetna DurejaSaumya RaychaudhuriSrikrishna Subramanian2019-09-05T12:18:28Z2019-09-05T12:18:28Zhttp://crdd.osdd.net/open/id/eprint/2445This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24452019-09-05T12:18:28ZDraft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4.Nonpathogenic Pantoea spp. have been shown to confer biofertilizer and biocontrol activities, indicating their potential for increasing crop yield. Herein, we provide the high-quality genome sequence of Pantoea sp. strain AS-PWVM4, a Gram-negative motile plant growth-promoting rhizobacterium isolated from a pomegranate plant. The 4.9-Mb genome contains genes related to plant growth promotion and the synthesis of siderophores. Indu KhatriSukhvir KaurUsha DeviNavinder KumarDeepak SharmaSrikrishna SubramanianAdesh K Saini2013-09-24T09:22:51Z2013-09-24T09:22:56Zhttp://crdd.osdd.net/open/id/eprint/1309This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13092013-09-24T09:22:51ZEvidence of a new metabolic capacity in an emerging diarrheal pathogen: lessons from the draft genomes of Vibrio fluvialis strains PG41 and I21563
Background
Vibrio fluvialis is an emerging diarrheal pathogen for which no genome is currently available. In this work, draft genomes of two closely related clinical strains PG41 and I21563 have been explored.
Results
V. fluvialis strains PG41 and I21563 were sequenced on the Illumina HiSeq 1000 platform to obtain draft genomes of 5.3 Mbp and 4.4 Mbp respectively. Our genome data reveal the presence of genes involved in ethanolamine utilization, which is further experimentally confirmed by growth analysis.
Conclusions
Combined in silico and growth analysis establish a new metabolic capacity of V. fluvialis to harvest energy from ethanolamine.
Indu KhatriSakshi MahajanChetna DurejaSrikrishna SubramanianSaumya Raychaudhuri2019-07-13T09:31:15Z2019-07-13T12:53:10Zhttp://crdd.osdd.net/open/id/eprint/2234This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22342019-07-13T09:31:15ZUnderstanding the role of Fis in the context of the quorum sensing signal transduction in Vibrio cholerae and related Vibrio:Lesson from V. cholerae quorum sensing signal networkNeelam Khatri2019-07-11T09:07:10Z2019-07-11T16:28:12Zhttp://crdd.osdd.net/open/id/eprint/2205This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22052019-07-11T09:07:10ZDevelopment of in-silico tools for understanding Human-HIV interactions and designing of therapeutics against HIV Ravi Kumar2013-06-24T10:57:09Z2013-06-24T10:57:09Zhttp://crdd.osdd.net/open/id/eprint/1305This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13052013-06-24T10:57:09ZHybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.HIV-1 infects the host cell by interacting with the primary receptor CD4 and a coreceptor CCR5 or CXCR4. Maraviroc, a CCR5 antagonist binds to CCR5 receptor. Thus, it is important to identify the coreceptor used by the HIV strains dominating in the patient. In past, a number of experimental assays and in-silico techniques have been developed for predicting the coreceptor tropism. The prediction accuracy of these methods is excellent when predicting CCR5(R5) tropic sequences but is relatively poor for CXCR4(X4) tropic sequences. Therefore, any new method for accurate determination of coreceptor usage would be of paramount importance to the successful management of HIV-infected individuals.Ravi KumarG.P.S. Raghava2019-07-11T09:08:00Z2019-07-11T16:00:25Zhttp://crdd.osdd.net/open/id/eprint/2202This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22022019-07-11T09:08:00ZStudies on Peptide Deformylase from Intracelluar PathogensSanjay Kumar2013-06-24T11:20:39Z2013-06-24T12:05:04Zhttp://crdd.osdd.net/open/id/eprint/1298This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12982013-06-24T11:20:39ZDraft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14.We report the 5.8-Mb genome sequence of Rhodococcus triatomae BKS 15-14, isolated from an ant hill soil sample, collected from Bhitarkanika Mangrove Reserve Forest, Odisha, India. The draft genome of strain BKS 15-14 consists of 5,824,349 bp, with a G+C content of 69%, 5,387 protein-coding genes, and 57 RNAs.Shailesh KumarMonu BalaG.P.S. RaghavaShanmugam Mayilraj2015-02-11T09:50:29Z2015-02-11T09:50:29Zhttp://crdd.osdd.net/open/id/eprint/1622This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16222015-02-11T09:50:29ZRedox-dependent stability of the γ-glutamylcysteine synthetase enzyme of Escherichia coli: a novel means of redox regulation.Glutathione is a thiol-containing tripeptide that plays important roles in redox-related processes. The first step in glutathione biosynthesis is catalysed by γ-GCS (γ-glutamylcysteine synthetase). The crystal structure of Escherichia coli γ-GCS has revealed the presence of a disulfide bond. As the disulfide-bonding cysteine residues Cys372 and Cys395 are not well conserved among γ-GCS enzymes in this lineage, we have initiated a biochemical genetic strategy to investigate the functional importance of these and other cysteine residues. In a cysteine-free γ-GCS that was non-functional, suppressor analysis yielded combinations of cysteine and aromatic residues at the position of the disulfide bond, and one mutant that lacked any cysteine residues. Kinetic analysis of the wild-type and mutant enzymes revealed that the disulfide bond was not involved in determining the affinity of the enzyme towards its substrate, but had an important role in determining the stability of the protein, and its catalytic efficiency. We show that in vivo the γ-GCS enzyme can also exist in a reduced form and that the mutants lacking the disulfide bond show a decreased half-life. These results demonstrate a novel means of regulation of γ-GCS by the redox environment that works by an alteration in its stability.Shailesh KumarNeha KasturiaAmit SharmaManish DattAnand K Bachhawat2013-06-24T11:11:08Z2013-06-24T12:05:29Zhttp://crdd.osdd.net/open/id/eprint/1301This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13012013-06-24T11:11:08ZDraft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658.We report the 5.0-Mb genome sequence of the type species of the genus Citrobacter, Citrobacter freundii strain MTCC 1658, isolated from canal water. This draft genome sequence of C. freundii strain MTCC 1658(T) consists of 5,001,265 bp with a G+C content of 51.61%, 4,691 protein-coding genes, 70 tRNAs, and 10 rRNAs.Shailesh KumarChandandeep KaurKazuyuki KimuraMasahiro TakeoG.P.S. RaghavaShanmugam Mayilraj2013-06-24T11:18:12Z2013-06-24T12:02:03Zhttp://crdd.osdd.net/open/id/eprint/1299This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12992013-06-24T11:18:12ZDraft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15.We report the 7.3-Mbp genome sequence of Streptomyces gancidicus strain BKS 13-15, isolated from mangrove sediment samples collected from the Bhitar Kanika Mangrove Reserve Forest, Odissha, India. The draft genome of strain Streptomyces gancidicus strain BKS 13-15 consists of 7,300,479 bp with 72.6% G+C content, 6,631 protein-coding genes, and 71 RNAs.Shailesh KumarNavjot KaurNitin Kumar SinghG.P.S. RaghavaShanmugam Mayilraj2019-09-05T12:15:52Z2019-09-05T12:15:52Zhttp://crdd.osdd.net/open/id/eprint/2446This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24462019-09-05T12:15:52ZGenome annotation of Burkholderia sp. SJ98 with special focus on chemotaxis genes.Burkholderia sp. strain SJ98 has the chemotactic activity towards nitroaromatic and chloronitroaromatic compounds. Recently our group published draft genome of strain SJ98. In this study, we further sequence and annotate the genome of stain SJ98 to exploit the potential of this bacterium. We specifically annotate its chemotaxis genes and methyl accepting chemotaxis proteins. Genome of Burkholderia sp. SJ98 was annotated using PGAAP pipeline that predicts 7,268 CDSs, 52 tRNAs and 3 rRNAs. Our analysis based on phylogenetic and comparative genomics suggest that Burkholderia sp. YI23 is closest neighbor of the strain SJ98. The genes involved in the chemotaxis of strain SJ98 were compared with genes of closely related Burkholderia strains (i.e. YI23, CCGE 1001, CCGE 1002, CCGE 1003) and with well characterized bacterium E. coli K12. It was found that strain SJ98 has 37 che genes including 19 methyl accepting chemotaxis proteins that involved in sensing of different attractants. Chemotaxis genes have been found in a cluster along with the flagellar motor proteins. We also developed a web resource that provides comprehensive information on strain SJ98 that includes all analysis data (http://crdd.osdd.net/raghava/genomesrs/burkholderia/). Shailesh KumarSurendra VikramG.P.S. Raghava2015-02-10T11:39:02Z2015-07-22T03:45:47Zhttp://crdd.osdd.net/open/id/eprint/1604This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16042015-02-10T11:39:02ZBiosynthesis of gold and silver nanoparticles using a novel marine strain of Stenotrophomonas.The present study aims at exploiting marine microbial diversity for biosynthesis of metal nanoparticles and also investigates role of microbial proteins in the process of bio-mineralization of gold and silver. This is the first report for concurrent production of gold and silver nanoparticles (AuNPs and AgNPs) by extracellular secretion of a novel strain of Stenotrophomonas, isolated from Indian marine origin. This novel strain has faster rate kinetics for AgNPs synthesis than any other organism reported earlier. The nanoparticles were further characterized using UV-vis spectrophotometer, TEM, DLS and EDAX confirming their size ranging from 10-50 nm and 40-60 nm in dimensions for AuNPs and AgNPs, respectively. TEM analysis indicated formation of multi-shaped nanoparticles with heterogeneous size distribution in both the cases. Finally, the SDS-PAGE analysis of extracellular media supernatant suggested a potential involvement of certain low molecular weight secretory proteins in AuNPs and AgNPs biosynthesis.Ankit MalhotraKunzes DolmaNavjot KaurYogendra S RathoreAshish GangulyShanmugam MayilrajAnirban Roy Choudhury2019-09-05T12:14:05Z2019-09-05T12:14:05Zhttp://crdd.osdd.net/open/id/eprint/2447This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24472019-09-05T12:14:05ZIsolation and characterization of diverse antimicrobial lipopeptides produced by Citrobacter and Enterobacter.Increasing multidrug-resistance in bacteria resulted in a greater need to find alternative antimicrobial substances that can be used for clinical applications or preservation of food and dairy products. Research on antimicrobial peptides including lipopeptides exhibiting both narrow and broad spectrum inhibition activities is increasing in the recent past. Therefore, the present study was aimed at isolation and characterization of antimicrobial lipopeptide producing bacterial strains from fecal contaminated soil sample.Santi M MandalShalley SharmaAnil Kumar PinnakaAnnu KumariSuresh Korpole2015-02-10T09:12:32Z2015-07-20T06:07:14Zhttp://crdd.osdd.net/open/id/eprint/1593This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15932015-02-10T09:12:32ZNPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database.Plant-derived molecules have been highly valued by biomedical researchers and pharmaceutical companies for developing drugs, as they are thought to be optimized during evolution. Therefore, we have collected and compiled a central resource Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (NPACT, http://crdd.osdd.net/raghava/npact/) that gathers the information related to experimentally validated plant-derived natural compounds exhibiting anti-cancerous activity (in vitro and in vivo), to complement the other databases. It currently contains 1574 compound entries, and each record provides information on their structure, manually curated published data on in vitro and in vivo experiments along with reference for users referral, inhibitory values (IC(50)/ED(50)/EC(50)/GI(50)), properties (physical, elemental and topological), cancer types, cell lines, protein targets, commercial suppliers and drug likeness of compounds. NPACT can easily be browsed or queried using various options, and an online similarity tool has also been made available. Further, to facilitate retrieval of existing data, each record is hyperlinked to similar databases like SuperNatural, Herbal Ingredients' Targets, Comparative Toxicogenomics Database, PubChem and NCI-60 GI(50) data.Manu MangalParul SagarHarinder SinghG.P.S. RaghavaSubhash M Agarwal2019-07-12T11:55:32Z2019-07-12T11:55:32Zhttp://crdd.osdd.net/open/id/eprint/2217This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22172019-07-12T11:55:32ZGenetic and Biochemical Interactions between RNA Interference and Heterochromatin Assembly PathwaysJagpreet Singh Nanda2019-09-04T16:05:51Z2019-09-04T16:05:51Zhttp://crdd.osdd.net/open/id/eprint/2428This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24282019-09-04T16:05:51Z(D)-p-Hydroxyphenylglycine production by thermostable D-hydantoinase from Brevibacillus parabrevis-PHG1his study was aimed at the investigation of D-hydantoinase from newly isolated strains of bacteria for overproduction of D-p-hydroxyphenylglycine. It was also hoped to develop a D-hydantoinase with suitable physicochemical parameters to make a successful process for other D-amino acids. D-hydantoinase was isolated from a Gram positive bacterial strain PHG1, identified as Brevibacillus parabrevis based on 16S rRNA gene sequence analysis. The strain showed hydantoinase activity of 5.0 U/ml of broth with hydantoin as substrate, at a cell turbidity of 4.8 at 600 nm. The enzyme was purified to homogeneity with native and subunit molecular mass of ≈154 kDa and ≈43 kDa, respectively. The specific activity of the enzyme was found to be ≈750 μmole/min/mg. D,L-p-hydroxyphenylhydantoin was found to be the preferred substrate after unsubstituted hydantoin. The optimum temperature and pH for enzyme activity were 70°C and 8.5, respectively, with a half-life of 120 min at 70°C. Supplementing with 0.32 mM Mn2+ in the growth medium resulted in ≈3-fold increase in enzyme activity. Ninety-five percent conversion efficiency of D-hydantoinase for D,L-p-hydroxyphenylhydantoin (10% w/v) into N-carbamoyl-(D)-p-hydroxyphenylglycine, better pH-temperature stability and broad substrate specificity signify the usefulness of this enzyme for production of D-p-hydroxyphenylglycine and other D-amino acids of industrial importance.Hemraj NandanwarRajnikant PrajapatiG S Hoondal2019-09-05T14:12:10Z2019-09-05T14:12:10Zhttp://crdd.osdd.net/open/id/eprint/2423This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24232019-09-05T14:12:10ZEnhanced stability of newly isolated trimeric l-methionine-N-carbamoylase from Brevibacillus reuszeri HSN1 by covalent immobilization.Newly isolated and partially purified trimeric l-methionine-N-carbamoylase from Brevibacillus reuszeri HSN1 was immobilized by covalent coupling to a well-known support material, Eupergit® C. Approximately 80% enzyme activity yield was achieved with ≈61% binding of a soluble protein from a solution containing 5 mg/mL protein. The immobilized preparation was found to be quite unstable due to a poor multisubunit covalent interaction of trimeric enzyme. Additional cross-linking with polyaldehyde-dextran was done to sustain the biotechnological application of immobilized enzyme. The temperature and pH optima of immobilized enzyme were increased by 10°C and 0.5 unit, respectively. The enzyme was significantly stabilized and retained ≈93% enzyme activity when incubated at 60°C for 60 Min, whereas free enzyme lost ≈50% activity. It was recycled nine times with ≈100% conversion efficiency when batch experiments were carried out at 35°C, pH 7.5, for the 180 Min cycle, using 5% N-carbamoyl-l-methionine as the substrate. The half-life of the immobilized preparation was determined as 23 cycles and is significant. Approximately 50% of enzyme activity was retained even after 5 months of storage at 4°C, whereas free enzyme lost complete enzyme activity. Hence, we could enhance the stability of l-methionine-N-carbamoylase to make it a potential biocatalyst for biotechnological production of α-amino acids.Hemraj S NandanwarRakesh M VohraGurinder S Hoondal2019-09-05T14:14:11Z2019-11-11T11:04:33Zhttp://crdd.osdd.net/open/id/eprint/2422This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24222019-09-05T14:14:11ZTrimeric l-N-carbamoylase from newly isolated Brevibacillus reuszeri HSN1: a potential biocatalyst for production of l-α-amino acids.l-N-carbamoylase was isolated from Brevibacillus reuszeri HSN1 and purified to homogeneity in three steps, which is a reasonably short protocol for native l-N-carbamoylase. The enzyme purification protocol resulted in ≈60-fold purification of l-N-carbamoylase with specific activity of 145 µmol/Min/mg. The subunit and native molecular mass were found to be 44.3 and 132 kDa, respectively. Temperature and pH optima were determined as 50°C and 8.5, respectively. The enzyme had retained ≈86% activity at 50°C when incubated for 60 Min and the half-life was determined as 180 Min at 50°C. N-carbamoyl-l-methionine (l-N-CMet) was found to be a preferred substrate with Km and Vmax values of ≈13.5 mM and ≈103 µmol/Min/mg, respectively. The broad substrate specificity with derivatives of N-carbamoyl amino acids is advantageous to be a better biocatalyst for production of corresponding l-α-amino acids. The enzyme activity was enhanced by 73% in the presence of 0.8 mM Mn(2+) ion during the biotransformation. In the batch experiment, ≈97% conversion of 5.0% l-N-CMet into enantiomerically pure l-methionine was achieved in 10 H when carried out at pH 8.0, 45°C, and 15% wet (w/v) cell loading, under controlled conditions. The overall merits of this enzyme show promise as a potential biocatalyst for l-α-amino acid production.Hemraj S NandanwarRakesh M VohraGurinder S Hoondal2019-07-12T12:08:50Z2019-07-12T16:12:17Zhttp://crdd.osdd.net/open/id/eprint/2220This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22202019-07-12T12:08:50ZNanoparticles Based Biochemical Approaches for Monitoring Sulfonylurea Herbicides Yogesh Kumar Nangia2015-02-10T11:35:53Z2015-02-10T11:35:53Zhttp://crdd.osdd.net/open/id/eprint/1603This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16032015-02-10T11:35:53ZStudies on xylitol production by metabolic pathway engineered Debaryomyces hansenii.Debaryomyces hansenii is one of the most promising natural xylitol producers. As the conversion of xylitol to xylulose mediated by NAD(+) cofactor dependent xylitol dehydrogenase (XDH) reduces its xylitol yield, xylitol dehydrogenase gene (DhXDH)-disrupted mutant of D. hansenii having potential for xylose assimilating pathway stopping at xylitol, was used to study the effects of co-substrates, xylose and oxygen availability on xylitol production. Compared to low cell growth and xylitol production in cultivation medium containing xylose as the only substrate, XDH disrupted mutants grown on glycerol as co-substrate accumulated 2.5-fold increased xylitol concentration over those cells grown on glucose as co-substrate. The oxygen availability, in terms of volumetric oxygen transfer coefficient, kLa (23.86-87.96 h(-1)), affected both xylitol productivity and yield, though the effect is more pronounced on the former. The addition of extra xylose at different phases of xylitol fermentation did not enhance xylitol productivity under experimental conditions.Suksham PalVikas ChoudharyAnil KumarDipanwita BiswasAlok K MondalDebendra K Sahoo2019-09-05T12:12:06Z2019-09-05T12:12:06Zhttp://crdd.osdd.net/open/id/eprint/2448This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24482019-09-05T12:12:06ZGenome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio.Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883(T), the type strain of T. acidaminovorans, stain Z-9701(T) is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Krishna PalaniappanJan P Meier-KolthoffHazuki TeshimaMatt NolanAlla LapidusHope TiceTijana Glavina Del RioJan-Fang ChengCliff HanRoxanne TapiaLynne A GoodwinSam PitluckKonstantinos LioliosKonstantinos MavromatisIoanna PaganiNatalia IvanovaNatalia MikhailovaAmrita PatiAmy ChenManfred RohdeShanmugam MayilrajStefan SpringJohn C DetterMarkus GökerJames BristowJonathan A EisenVictor MarkowitzPhilip HugenholtzNikos C KyrpidesHans-Peter KlenkTanja Woyke2019-07-12T12:00:07Z2019-07-12T16:08:44Zhttp://crdd.osdd.net/open/id/eprint/2218This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22182019-07-12T12:00:07ZUNDERSTAND THE GLYCOSYLATED FORM OF INFLUENZA A HEMAGGLUTININ TRIMER:TOWARDS IDENTIFICATION OF A NOVEL DRUG SITEKalpana Pandey2019-07-12T11:40:07Z2019-07-12T15:09:07Zhttp://crdd.osdd.net/open/id/eprint/2214This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22142019-07-12T11:40:07ZStudies on Structural and Regulatory Mechanisms of Substrate Recognition and Catalysis by CarnosinaseVaibhav Kumar Pandya2019-07-11T09:08:19Z2019-07-11T15:42:53Zhttp://crdd.osdd.net/open/id/eprint/2201This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22012019-07-11T09:08:19ZIn silico analysis and prediction of aminoacyl-tRNA synthetases and their ligandsBharat Panwar2019-09-05T12:10:15Z2019-09-05T12:10:15Zhttp://crdd.osdd.net/open/id/eprint/2449This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24492019-09-05T12:10:15ZPrediction of vitamin interacting residues in a vitamin binding protein using evolutionary information.The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure.Bharat PanwarSudheer GuptaG.P.S. Raghava2019-07-12T12:04:17Z2019-07-12T16:10:31Zhttp://crdd.osdd.net/open/id/eprint/2219This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22192019-07-12T12:04:17ZSTRUCTURE-FUNCTION RELATIONSHIP OF HUMAN PLASMA GELSOLIN AND ITS MINIMAL VERSIONSNagesh Peddada2015-02-11T09:42:04Z2015-07-22T03:44:13Zhttp://crdd.osdd.net/open/id/eprint/1621This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16212015-02-11T09:42:04ZGlobal shapes of F-actin depolymerization-competent minimal gelsolins: insight into the role of g2-g3 linker in pH/Ca2+ insensitivity of the first half.Because of its ability to rapidly depolymerize F-actin, plasma gelsolin has emerged as a therapeutic molecule in different disease conditions. High amounts of exogenous gelsolin are, however, required to treat animal models of different diseases. Knowing that the F-actin depolymerizing property of gelsolin resides in its N terminus, we made several truncated versions of plasma gelsolin. The smaller versions, particularly the one composed of the first 28-161 residues, depolymerized the F-actin much faster than the native gelsolin and other truncates at the same molar ratios. Although G1-G3 loses its dependence on Ca(2+) or low pH for the actin depolymerization function, interestingly, G1-G2 and its smaller versions were found to regain this requirement. Small angle x-ray scattering-based shape reconstructions revealed that G1-G3 adopts an open shape in both the presence and the absence of Ca(2+) as well as low pH, whereas G1-G2 and residues 28-161 prefer collapsed states in Ca(2+)-free conditions at pH 8. The mutations in the g2-g3 linker resulted in the calcium sensitivity of the mutant G1-G3 for F-actin depolymerization activity, although the F-actin-binding sites remained exposed in the mutant G1-G3 as well as in the smaller truncates even in the Ca(2+)-free conditions at pH 8. Furthermore, unlike wild type G1-G3, calcium-sensitive mutants of G1-G3 acquired closed shapes in the absence of free calcium, implying a role of g2-g3 linker in determining the open F-actin depolymerizing-competent shape of G1-G3 in this condition. We demonstrate that the mobility of the G1 domain, essential for F-actin depolymerization, is indirectly regulated by the gelsolin-like sequence of g2-g3 linker.Nagesh PeddadaAmin SagarYogendra S RathoreVikas ChoudharyU Bharat K PattnaikNeeraj KhatriRenu GargAshish Ganguly2013-02-14T06:09:49Z2013-02-14T06:09:49Zhttp://crdd.osdd.net/open/id/eprint/1290This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12902013-02-14T06:09:49ZHIPdb: A Database of Experimentally Validated HIV Inhibiting Peptides.Besides antiretroviral drugs, peptides have also demonstrated potential to inhibit the Human immunodeficiency virus (HIV). For example, T20 has been discovered to effectively block the HIV entry and was approved by the FDA as a novel anti-HIV peptide (AHP). We have collated all experimental information on AHPs at a single platform.Abid QureshiNishant ThakurManoj Kumar2019-09-05T12:08:25Z2019-09-05T12:08:25Zhttp://crdd.osdd.net/open/id/eprint/2450This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24502019-09-05T12:08:25ZVIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.Selection of effective viral siRNA is an indispensable step in the development of siRNA based antiviral therapeutics. Despite immense potential, a viral siRNA efficacy prediction algorithm is still not available. Moreover, performances of the existing general mammalian siRNA efficacy predictors are not satisfactory for viral siRNAs. Therefore, we have developed "VIRsiRNApred" a support vector machine (SVM) based method for predicting the efficacy of viral siRNA.Abid QureshiNishant ThakurManoj Kumar2019-09-05T12:06:10Z2019-09-05T12:06:10Zhttp://crdd.osdd.net/open/id/eprint/2451This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24512019-09-05T12:06:10ZCaldimonas meghalayensis sp. nov., a novel thermophilic betaproteobacterium isolated from a hot spring of Meghalaya in northeast India.While studying the microbial diversity of hot springs of North-east India we isolated a strain AK31T from the Jakrem hot spring of Meghalaya. The strain formed light yellow colonies on nutrient agar and was Gram negative, non spore-forming rods, motile with single polar flagellum. The strain was positive for oxidase and catalase and hydrolysed starch and weakly urea. The predominant cellular fatty acids were C16:0 (34.8 %), C17:0 cyclo (27.1 %), C16:1 ω7c and/or iso-C15:0 2OH (summed feature 3) (9.6 %), C10:0 3OH (8.0 %), C12:0 (5.8 %), C14:0 (5.3 %) and C18:1 ω7c (5.3 %). Strain AK31T contained ubiquinone-8 as the major respiratory quinone and diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and one unidentified glycolipid as the polar lipids. The G + C content of the DNA of the strain AK31T was 66.7 mol%. The 16S rRNA gene sequence analysis indicated that strain AK31T was member of the genus Caldimonas and closely related to Caldimonas manganoxidans JCM 10698T and Caldimonas taiwanensis On1T with 96.9 % similarity and with Aquincola tertiaricarbonis L10T and Azohydromonas australica IAM 12664T with 96.5 and 96.4 % similarity respectively. Phylogenetic analyses indicated that the strain AK31T clustered with C. manganoxidans JCM 10698T and C. taiwanensis On1T with a phylogenetic distance of 3.25 %. Based on data from the current polyphasic study, strain AK31T is proposed as a novel species of the genus Caldimonas, for which the name Caldimonas meghalayensis sp. nov. is proposed. The type strain of C. meghalayensis is AK31T (= MTCC 11703T = JCM 18786T).K RakshakK Ravinder. NupurT N R SrinivasP Anil Kumar2019-09-04T15:51:23Z2019-09-04T15:51:23Zhttp://crdd.osdd.net/open/id/eprint/2427This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24272019-09-04T15:51:23ZImportance of C–H···O Intramolecular Hydrogen Bonding Across a Nonproteinogenic γ-Aminobenzoic Acid Residue: Stabilization of a Flat β-Strand-like TemplateThis paper describes the conformational characteristics of a nonproteinogenic γ-aminobenzoic acid (γ-Abz), investigated experimentally as well as theoretically. The single crystal X-ray diffraction analysis of the model system Boc-γ-Abz-NHMe (1) revealed the existence of an unusual β-strand-like molecular structure. The two weak unconventional C–H···O intramolecular hydrogen-bonds, i.e., main-chain to main-chain: Cβi+1–H···O═Ci+1 and main-chain to side-chain Cδi+1–H···O═Ci interactions, evidently stabilize the flat molecular topology. The favorable antiparallel β-strand mimics are held together by a network of cross-strand N–H···O intermolecular hydrogen bonds. Interestingly, the noncovalent β-sheet-like duplexes facilitate the fabrication of offset face-to-face aromatic–aromatic interactions, whereas the dimers of dimers are aligned edge-to-edge. The two-dimensional 1H NMR ROESY experiment ascertained the extraordinary stability of the rigid β-strand template and molecular self-assembly in a nonpolar environment. The ab initio molecular modeling substantiated the crystal molecular structure as the minimum energy conformer along with weak C–H···O intramolecular hydrogen bonds. The solid-state Fourier transform infrared spectral analysis sustained the participation of both amide-NHs in intermolecular hydrogen bonding. The highly ordered supramolecular architecture, engendered from a single preorganized molecular component, exploited a variety of strong as well as weak stabilizing forces as varied as N–H···O, C–H···O, Ar···Ar, and van der Waals and/or hydrophobic interactions.Muthusamy RameshPrasad V BharatamP VenugopalanRaghuvansh Kishore2019-07-10T09:34:46Z2019-07-11T09:04:11Zhttp://crdd.osdd.net/open/id/eprint/2194This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/21942019-07-10T09:34:46ZFunctional Analysis of NIK1 Orthologs from Pathogenic FungiAnmoldeep Randhawa 2019-07-11T09:07:38Z2019-07-11T16:19:59Zhttp://crdd.osdd.net/open/id/eprint/2204This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22042019-07-11T09:07:38ZStudies on a mycobacterial eukaryotic-type serine/theronine kinase and its interacting partnersSandeep Kaur Ravala2019-07-11T09:06:40Z2019-07-11T16:46:05Zhttp://crdd.osdd.net/open/id/eprint/2207This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22072019-07-11T09:06:40ZStudies on polymer based biopharmaceuticals delivery systemSanjay Rawat2019-09-05T12:01:40Z2019-09-05T12:01:40Zhttp://crdd.osdd.net/open/id/eprint/2453This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24532019-09-05T12:01:40ZPurification, biochemical characterization and self-assembled structure of a fengycin-like antifungal peptide from Bacillus thuringiensis strain SM1.An antifungal lipopeptide fengycin, producing strain SM1 was isolated from farm land soil sample and identified as Bacillus thuringiensis strain SM1 by using 16S rDNA analysis. Fengycin detected in the culture extract was further purified using HPLC and showed a molecular mass of 1492.8 Da by MALDI-TOF-MS analysis. Purified fengycin was allowed to construct their self-assembled structure onto a hydrophobic surface showing a clear improvement of antibacterial activity. In self-assembly, fengycin adapts a spherical micelle core shell like structure. Self-assembled fengycin may be a successful antimicrobial compound modifying its action from confined antifungal function. Besides it can open up a new area of research in supramolecular lipopeptide based compound making. This can revealed the mode of action of this unique self-assembled structure to fully evaluate its potential for use as an antimicrobial drug to control the emergence of bacterial infection. Anupam RoyDenial MahataDebarati PaulSuresh KorpoleOctavio L FrancoSanti M Mandal2019-09-05T12:03:29Z2019-09-05T12:03:29Zhttp://crdd.osdd.net/open/id/eprint/2452This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24522019-09-05T12:03:29ZNorA efflux pump inhibitory activity of coumarins from Mesua ferrea.The purpose of this investigation was to study the modulator and efflux pump inhibitor activity of coumarins isolated from Mesua ferrea against clinical strains as well as NorA-over expressed strain of Staphylococcus aureus 1199B. Seven coumarins were tested for modulator activity using ethidium bromide (EtBr) as a substrate. Compounds 1, 4-7 modulated the MIC of EtBr by ≥ 2 fold against wild type clinical strains of S. aureus 1199 and S. aureus 1199B, whereas compounds 4-7 modulated the MIC of EtBr by ≥ 16 fold against MRSA 831. Compounds 1, 4-7 also reduced the MIC of norfloxacin by ≥ 8 fold against S. aureus 1199B, and 4-6 reduced the MIC of norfloxacin by ≥ 8 fold against MRSA 831 at half of their MICs. Inhibition of EtBr efflux by NorA-overproducing S. aureus 1199B and MRSA 831 confirmed the role of compounds 4-6 as NorA efflux pump inhibitors (EPI). Dose-dependent activity at sub-inhibitory concentration (6.25 μg/mL) suggested that compounds 4 and 5 are promising EPI compared to verapamil against 1199B and MRSA 831 strains.Somendu K RoyNeela KumariSonika PahwaUdai C AgrahariKamlesh K BhutaniSanjay M JachakHemraj Nandanwar2015-02-11T10:00:18Z2015-02-11T10:00:18Zhttp://crdd.osdd.net/open/id/eprint/1625This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16252015-02-11T10:00:18ZAmine functionalized graphene oxide/CNT nanocomposite for ultrasensitive electrochemical detection of trinitrotoluene.Binding of electron-deficient trinitrotoluene (TNT) to the electron rich amine groups on a substrate form specific charge-transfer Jackson-Meisenheimer (JM) complex. In the present work, we report formation of specific JM complex on amine functionalized reduced graphene oxide/carbon nanotubes- (a-rGO/CNT) nanocomposite leading to sensitive detection of TNT. The CNT were dispersed using graphene oxide that provides excellent dispersion by attaching to CNT through its hydrophobic domains and solubilizes through the available OH and COOH groups on screen printed electrode (SPE). The GO was reduced electrochemically to form reduced graphene that remarkably increases electrochemical properties owing to the intercalation of high aspect CNT on graphene flakes as shown by TEM micrograph. The surface amine functionalization of dropcasted and rGO/CNT was carried out using a bi-functional cross linker ethylenediamine. The extent of amine functionalization on modified electrodes was confirmed using energy dispersive X-ray (EDX), X-ray photoelectron spectroscopy (XPS) and confocal microscopy. The FTIR and Raman spectra further suggested the formation of JM complex between amine functionalized electrodes and TNT leading to a shift in peak intensity together with peak broadening. The a-rGO/CNT nanocomposite prepared electrode surface leads to ultra-trace detection of TNT upto 0.01 ppb with good reproducibility (n=3). The a-rGO/CNT sensing platform could be an alternate for sensitive detection of TNT explosive for various security and environmental applications.Kavita SablokVijayender BhallaPriyanka SharmaRoohi KaushalShilpa ChaudharyC Raman Suri2019-07-10T09:49:00Z2019-07-12T08:43:54Zhttp://crdd.osdd.net/open/id/eprint/2196This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/21962019-07-10T09:49:00ZStructure-function studies of recombinant human Erythropoietin (rHuEpo)Jesse Sebastian Samuel2019-09-05T11:59:32Z2019-09-05T11:59:32Zhttp://crdd.osdd.net/open/id/eprint/2454This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24542019-09-05T11:59:32ZMarinilabilia nitratireducens sp. nov., a lipolytic bacterium of the family Marinilabiliaceae isolated from marine solar saltern.A Gram-negative, rod shaped, motile bacterium, was isolated from a marine solar saltern sample collected from Kakinada, India. Strain AK2(T) was determined to be positive for nitrate reduction, catalase, Ala-Phe-Pro-arylamidase, β-galactosidase, β-N-acetylglucosaminidase, β-glucosidase, β-xylosidase, α-glucosidase, α-galactosidase and phosphatase activities, hydrolysis of aesculin, Tween 20/40/60/80 and urea. It was determined to be negative for oxidase, lysine decarboxylase and ornithine decarboxylase activities and could not hydrolyze agar, casein, gelatin and starch. The predominant fatty acids were identified as iso-C(15:0) (28.2 %), anteiso-C(15:0) (23.2 %), iso-C(13:0) (19.9 %) and iso-C(15:0) 3-OH (13.9 %). Strain AK2(T) was found to contain menaquinone with seven isoprene units (MK-7) as the sole respiratory quinone and phosphatidylethanolamine, one unidentified phospholipid and three unidentified lipids as polar lipids. The 16S rRNA gene sequence analysis indicated the strain AK2(T) as a member of the genus Marinilabilia and is closely related to Marinilabilia salmonicolor with pair-wise sequence similarity of 98.2 %. Phylogenetic analysis of 16S rRNA gene revealed that the strain AK2(T) clustered with M. salmonicolor. However, DNA-DNA hybridization with M. salmonicolor JCM 21150(T) showed a relatedness of 48 ± 0.5 % with respect to strain AK2(T). The DNA G+C content of the strain was determined to be 40.2 mol%. Based on the phenotypic characteristics and phylogenetic inference, it is proposed that the strain AK2(T) represents a novel species of the genus Marinilabilia, for which the name Marinilabilia nitratireducens sp. nov. is proposed. The type strain of M. nitratireducens sp. nov. is AK2(T) (= MTCC 11402(T) = JCM 17679(T)).S ShalleyS Pradip KumarT Naga Radha SrinivasK SureshP Anil Kumar2015-02-11T09:07:47Z2015-06-04T04:15:22Zhttp://crdd.osdd.net/open/id/eprint/1616This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16162015-02-11T09:07:47ZThe ApMat marker can resolve Colletotrichum species: a case study with Mangifera indica. Fungal DiversAnthracnose disease caused by the Colletotrichum gloeosporioides species complex is a major problem worldwide. In this study, we investigated the phylogenetic diversity of 207 Indian Colletotrichum isolates, associated with symptomatic and asymptomatic tissues of mango, belonging to this species complex. Phylogenetic analyses were performed based on a 6-gene dataset (act, cal, chs1, gapdh, ITS and tub2), followed by ApMat sequence-analysis. The ApMat-based phylogeny was found to be superior as it provided finer resolution in most of the species-level clades. Importantly, the ApMat marker identified seven lineages within C. siamense sensu lato, including C. jasmini-sambac, C. hymenocallidis, C. melanocaulon, C. siamense sensu stricto and three undesignated, potentially novel lineages. In this study, C. fragariae sensu stricto, C. fructicola, C. jasmini-sambac, C. melanocaulon and five undesignated, potentially novel lineages were found to be associated with mango tissues. There is a need to develop a consensus among mycologists as to which genes should be used to define and delimit a Colletotrichum species and in the mean time mycologists should voluntarily restrain from describing new species based on inadequate datasets.Gunjan SharmaNavinder KumarBevan S. Weir, Kevin D. HydeBelle Damodara Shenoy,2013-10-21T10:50:26Z2014-03-31T08:20:25Zhttp://crdd.osdd.net/open/id/eprint/1463This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14632013-10-21T10:50:26ZAntibody functionalsed nanobioprobes: Characterization and bioessay development for phenylurea herbicidesPriyanka Sharma2015-02-11T09:57:28Z2015-02-11T09:57:28Zhttp://crdd.osdd.net/open/id/eprint/1624This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16242015-02-11T09:57:28ZPlasmon enhanced fluoro-immunoassay using egg yolk antibodies for ultra-sensitive detection of herbicide diuron.Plasmon enhanced fluorescence immunoassay (PEFI) format has been reported in developing a sensitive heterogeneous fluoroimmunoassay for monitoring the phenylurea herbicide diuron. Computer-assisted molecular modeling was carried out to study the conformational and electrostatic effects of synthesized hapten for producing highly specific egg yolk antibody against a phenyl urea herbicide diuron. The generated antibodies were labeled with fluorescein isothiocyanate at different molar ratios and used as tracer in the developed fluorescence based immunoassay. The sensitivity of the assay format was enhanced by using silver nanoparticles tagged with bovine serum albumin as a new blocking reagent in the developed PEFI format. Enhancer treatment on the developed immunoassay showed a significant improvement of fluorescence signal intensity with approximately 10 fold increase in assay sensitivity. The immunoassay has a detection limit of 0.01 ng mL(-1) with good signal precision (~2%) in the optimum working concentration range between 1 pg mL(-1) to 10 μg mL(-1) of diuron. These findings facilitate high throughput fluorescence-based processes that could be useful in biology, drug discovery and compound screening applications.Priyanka SharmaManil KukkarAshok K GanguliAman BhasinC Raman Suri2013-01-31T04:05:38Z2013-01-31T04:05:38Zhttp://crdd.osdd.net/open/id/eprint/1223This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12232013-01-31T04:05:38ZBio-functionalized graphene-graphene oxide nanocomposite based electrochemical immunosensing.We report a novel in-situ electrochemical synthesis approach for the formation of functionalized graphene-graphene oxide (fG-GO) nanocomposite on screen-printed electrodes (SPE). Electrochemically controlled nanocomposite film formation was studied by transmission electron microscopy (TEM) and Raman spectroscopy. Further insight into the nanocomposite has been accomplished by the Fourier transformed infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA) and X-ray diffraction (XRD) spectroscopy. Configured as a highly responsive screen-printed immunosensor, the fG-GO nanocomposite on SPE exhibits electrical and chemical synergies of the nano-hybrid functional construct by combining good electronic properties of functionalized graphene (fG) and the facile chemical functionality of graphene oxide (GO) for compatible bio-interface development using specific anti-diuron antibody. The enhanced electrical properties of nanocomposite biofilm demonstrated a significant increase in electrochemical signal response in a competitive inhibition immunoassay format for diuron detection, promising its potential applicability for ultra-sensitive detection of range of target analytes.Priyanka SharmaSatish K TutejaVijayender BhallaG ShekhawatVinayak P DravidC Raman Suri2013-06-24T11:33:59Z2013-07-18T04:34:22Zhttp://crdd.osdd.net/open/id/eprint/1293This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12932013-06-24T11:33:59ZSecreted glyceraldehye-3-phosphate dehydrogenase is a multifunctional autocrine transferrin receptor for cellular iron acquisition.The long held view is that mammalian cells obtain transferrin (Tf) bound iron utilizing specialized membrane anchored receptors. Here we report that, during increased iron demand, cells secrete the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) which enhances cellular uptake of Tf and iron.Navdeep SheokandSantosh KumarHimanshu MalhotraVikas TilluChaaya Iyengar RajeManoj Raje2019-09-05T11:46:01Z2019-09-05T11:46:01Zhttp://crdd.osdd.net/open/id/eprint/2460This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24602019-09-05T11:46:01ZDraft Genome Sequence of Cesiribacter andamanensis Strain AMV16T, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India.Here we report the 4.75-Mb genome of Cesiribacter andamanensis strain AMV16(T), isolated from a soil sample from a mud volcano in the Andaman Islands, India.Sisinthy ShivajiSreenivas AraZareena BegumT N R SrinivasAditya SinghAnil Kumar Pinnaka2019-07-12T11:50:08Z2019-07-12T11:50:08Zhttp://crdd.osdd.net/open/id/eprint/2216This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22162019-07-12T11:50:08ZInvestigation into and Validation of the prion function of Cut4p subunit of Anaphase promoting complex (APC) in Fission YeastPoonam Shukla2019-09-05T11:57:27Z2019-09-05T11:57:27Zhttp://crdd.osdd.net/open/id/eprint/2455This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24552019-09-05T11:57:27ZImproved method for linear B-cell epitope prediction using antigen's primary sequence.One of the major challenges in designing a peptide-based vaccine is the identification of antigenic regions in an antigen that can stimulate B-cell's response, also called B-cell epitopes. In the past, several methods have been developed for the prediction of conformational and linear (or continuous) B-cell epitopes. However, the existing methods for predicting linear B-cell epitopes are far from perfection. In this study, an attempt has been made to develop an improved method for predicting linear B-cell epitopes. We have retrieved experimentally validated B-cell epitopes as well as non B-cell epitopes from Immune Epitope Database and derived two types of datasets called Lbtope_Variable and Lbtope_Fixed length datasets. The Lbtope_Variable dataset contains 14876 B-cell epitope and 23321 non-epitopes of variable length where as Lbtope_Fixed length dataset contains 12063 B-cell epitopes and 20589 non-epitopes of fixed length. We also evaluated the performance of models on above datasets after removing highly identical peptides from the datasets. In addition, we have derived third dataset Lbtope_Confirm having 1042 epitopes and 1795 non-epitopes where each epitope or non-epitope has been experimentally validated in at least two studies. A number of models have been developed to discriminate epitopes and non-epitopes using different machine-learning techniques like Support Vector Machine, and K-Nearest Neighbor. We achieved accuracy from ∼54% to 86% using diverse s features like binary profile, dipeptide composition, AAP (amino acid pair) profile. In this study, for the first time experimentally validated non B-cell epitopes have been used for developing method for predicting linear B-cell epitopes. In previous studies, random peptides have been used as non B-cell epitopes. In order to provide service to scientific community, a web server LBtope has been developed for predicting and designing B-cell epitopes (http://crdd.osdd.net/raghava/lbtope/).Harinder SinghHifzur Rahman AnsariG.P.S. Raghava2015-02-10T09:09:04Z2015-02-10T09:09:04Zhttp://crdd.osdd.net/open/id/eprint/1592This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/15922015-02-10T09:09:04ZThe crystal structure reveals the molecular mechanism of bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II (Rv1415) from Mycobacterium tuberculosis.The enzymes 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBPS) and GTP cyclohydrolase II (GCHII) catalyze the initial steps of both branches of the bacterial riboflavin-biosynthesis pathway. The structures and molecular mechanisms of DHBPS and GCHII as separate polypeptides are known; however, their organization and molecular mechanism as a bifunctional enzyme are unknown to date. Here, the crystal structure of an essential bifunctional DHBPS/GCHII enzyme from Mycobacterium tuberculosis (Mtb-ribA2) is reported at 3.0 Å resolution. The crystal structure revealed two conformationally different molecules of Mtb-ribA2 in the asymmetric unit that form a dimer via their GCHII domains. Interestingly, analysis of the crystal packing revealed a long `helical-like oligomer' formed by DHBPS and GCHII functional homodimers, thus generating an `open-ended' unit-cell lattice. However, size-exclusion chromatography studies suggest that Mtb-ribA2 exists as a dimer in solution. To understand the discrepancy between the oligomerization observed in solution and in the crystal structure, the DHBPS (Mtb-DHBPS) and GCHII (Mtb-GCHII) domains of Mtb-ribA2 have been cloned, expressed and purified as His-tagged proteins. Size-exclusion chromatography studies indicated that Mtb-GCHII is a dimer while Mtb-DHBPS exists as a monomer in solution. Moreover, kinetic studies revealed that the GCHII activities of Mtb-ribA2 and Mtb-GCHII are similar, while the DHBPS activity of Mtb-ribA2 is much higher than that of Mtb-DHBPS alone. Taken together, the results strongly suggest that Mtb-ribA2 exists as a dimer formed through its GCHII domains and requires full-length Mtb-ribA2 for optimal DHBPS activity.Mirage SinghPankaj KumarSavita YadavRuchi GautamNidhi SharmaSubramanian Karthikeyan2019-07-12T11:32:40Z2019-07-12T15:13:48Zhttp://crdd.osdd.net/open/id/eprint/2213This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22132019-07-12T11:32:40ZThe Functional evaluation of variant HapR and HapR homologues in the context of DNA-Protein interactions:Lessons from a natural HapR variantNaorem Santa Singh2013-06-24T11:30:03Z2013-06-24T12:03:46Zhttp://crdd.osdd.net/open/id/eprint/1294This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12942013-06-24T11:30:03ZDraft Genome Sequence of Acinetobacter baumannii Strain MSP4-16.We report the 4.0-Mb draft genome sequence of Acinetobacter baumannii strain MSP4-16, isolated from a mangrove soil sample from Parangipettai (11°30'N, 79°47'E), Tamil Nadu, India. The draft genome sequence of strain MSP4-16 consists of 3,944,542 bp, with a G+C content of 39%, 5,387 protein coding genes, and 69 RNAs.Nitin Kumar SinghShailesh KumarG.P.S. RaghavaShanmugam Mayilraj2013-06-24T11:14:45Z2013-06-24T11:14:45Zhttp://crdd.osdd.net/open/id/eprint/1300This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13002013-06-24T11:14:45ZExiguobacterium himgiriensis sp. nov. a novel member of the genus Exiguobacterium, isolated from the Indian Himalayas.The taxonomic position of an orange coloured bacterium, strain K22-26(T) isolated from a soil sample was studied using a polyphasic approach. The organism had phenotypic and chemotaxonomic properties consistent with its allocation into the genus Exiguobacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain K22-26(T) belongs to the genus Exiguobacterium and was related to Exiguobacterium aurantiacum DSM 6208(T) (99.0 %) Exiguobacterium mexicanum DSM 16483(T) (98.6 %), Exiguobacterium aquaticum (98.6 %), Exiguobacterium aestuarii DSM 16306(T) (98.1 %), Exiguobacterium profundum DSM 17289(T) (98.1 %) and Exiguobacterium marinum DSM 16483(T) (97.9 %), whereas sequence similarity values with respect to other Exiguobacterium species with validly published names were between 92.5-94.0 %. The major polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major menaquinone was determined to be MK-7 (83 %) whereas MK-8 (11 %) and MK-6 (6 %) occur in smaller amounts. The peptidoglycan of the strain was found to contain L-lysine as the diagnostic diamino acid. The major fatty acids detected were iso C13:0 (11.2 %), anteiso C13:0 (15.4 %), iso C15:0 (13.2 %) and iso C17:0 (16.1 %). However, analysis of the DNA-DNA relatedness confirmed that strain K22-26(T) belongs to a novel species. The G + C content of the strain K22-26(T) was determined to be 50.1 mol %. The novel strain was distinguished from closely related type species of the genus Exiguobacterium using DNA-DNA relatedness and phenotypic data. Based on these differences, the strain K22-26(T) should be classified as a novel species of the genus Exiguobacterium, for which the name Exiguobacterium himgiriensis sp. nov. strain K22-26(T) (= MTCC 7628(T) = JCM 14260(T)) is proposed.Nitin Kumar SinghRevti RaichandIshwinder KaurChandandeep KaurSiddhika PareekShanmugam Mayilraj2018-09-19T08:20:27Z2018-09-19T08:20:31Zhttp://crdd.osdd.net/open/id/eprint/2119This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/21192018-09-19T08:20:27ZSubstitution of glutamate residue by lysine in the dimerization domain affects DNA binding ability of HapR by inducing structural deformity in the DNA binding domain.HapR has been given the status of a high cell density master regulatory protein in Vibrio cholerae. Though many facts are known regarding its structural and functional aspects, much still can be learnt from natural variants of the wild type protein. This work aims at investigating the nature of functional inertness of a HapR natural variant harboring a substitution of a conserved glutamate residue at position 117 which participates in forming a salt bridge by lysine (HapRV2G-E(117)K). Experimental evidence presented here reveals the inability of this variant to interact with various cognate promoters by in vitro gel shift assay. Furthermore, the elution profiles of HapRV2G-E(117)K protein along with the wild type functional HapRV2G in size-exclusion chromatography as well as circular dichroism spectra did not reflect any significant differences in its structure, thereby indicating the intactness of dimer in the variant protein. To gain further insight into the global shape of the proteins, small angle X-ray scattering analysis (SAXS) was performed. Intriguingly, increased radius of gyration of HapRV2G-E(117)K of 27.5 Å in comparison to the wild type protein from SAXS data analyses implied a significant alteration in the global shape of the dimeric HapRV2G-E(117)K protein. Structure reconstruction brought forth that the DNA binding domains were substantially "parted away" in this variant. Taken together, our data illustrates that substitution of the conserved glutamate residue by lysine in the dimerization domain induces separation of the two DNA binding domains from their native-like positioning without altering the dimeric status of HapR variant. Richa SinghYogendra Singh RathoreNaorem Santa SinghNagesh Peddada. AshishSaumya Raychaudhuri2019-07-11T09:06:25Z2019-07-11T16:36:55Zhttp://crdd.osdd.net/open/id/eprint/2206This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22062019-07-11T09:06:25ZUnderstanding the Structural Composition of TIR Domain in TLRs: Elucidating their Role in Functional AssemblyShikha Singh2013-06-24T11:38:49Z2015-07-22T03:37:47Zhttp://crdd.osdd.net/open/id/eprint/1292This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/12922013-06-24T11:38:49ZA communication network within the cytoplasmic domain of toll-like receptors has remained conserved during evolution.Toll/IL-1R (TIR) domain, that is, the cytoplasmic domain, in toll-like receptors (TLRs) from different species showed high sequence conservation in stretches spread across the surface as well as the core of the domain. To probe the structure-function significance of these residues, especially those coming from the core of TIR domains, we analyzed molecular dynamics trajectories of sequence similarity based models of human TIR domains. This study brought forth that N-terminal of the TIR domain simultaneously interacts with the flanking residues of the BB loop and central β-sheets. At the same time, residues of the central β-strands form favorable contacts with the DD loop and C-terminal, thus forming a two-way circuit between the N- and C-termini. In this work, the array of intradomain interactions is termed as communication network. Importantly, the "hubs" of this communication network were found to be conserved in all human TLRs. Earlier mutagenesis-function correlation work brought forth that certain mutations in the "core" of the TIR domain of TLR4 (e.g. in IFI767-769AAA and L815A) led to almost complete abrogation of signaling and reasoning for this dramatic loss-of-function has remained unclear, since these sites are not surface exposed. Using MD studies, we show here that this communication network gets disrupted in mutants of human TLR4 which were earlier reported to be functionally compromised. Extension of MD studies to heterodimer of TLR1/2 suggested that this evolutionarily conserved communication network senses the interactions formed upon dimerization and relays it to surfaces which are not involved in direct interdomain contacts.Shikha SinghKalpana PandeyYogendra S RathoreAmin SagarU Bharat K PattnaikAshish Ganguly2019-09-05T11:43:30Z2019-09-05T11:43:30Zhttp://crdd.osdd.net/open/id/eprint/2461This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24612019-09-05T11:43:30ZGenome Sequence of the "Indian Bison Type" Biotype of Mycobacterium avium subsp. paratuberculosis Strain SS.We report the 4.79-Mb genome sequence of the "Indian Bison Type" biotype of subsp. strain S5, isolated from a terminally sick Jamunapari goat at the CIRG (Central Institute for Research on Goats) farm in India. This draft genome will help in studying novelties of this biotype, which is widely distributed in animals and human beings in India.Shoor Vir SinghNaveen KumarShree Narayan SinghTapas BhattacharyaJagdip Singh SohalPravin Kumar SinghAjay Vir SinghBrajesh SinghKundan Kumar ChaubeySaurabh GuptaNitu SharmaShailesh KumarG.P.S. Raghava2013-06-24T11:07:22Z2015-01-07T11:19:02Zhttp://crdd.osdd.net/open/id/eprint/1302This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13022013-06-24T11:07:22ZOpen source software and web services for designing therapeutic molecules.Despite the tremendous progress in the field of drug designing, discovering a new drug molecule is still a challenging task. Drug discovery and development is a costly, time consuming and complex process that requires millions of dollar and 10-15 years to bring new drug molecules in the market. This huge investment and long-term process are attributed to high failure rate, complexity of the problem and strict regulatory rules, in addition to other factors. Given the availability of 'big' data with ever improving computing power, it is now possible to model systems which is expected to provide time and cost effectiveness to drug discovery process. Computer Aided Drug Designing (CADD) has emerged as a fast alternative method to bring down the cost involved in discovering a new drug. In past, numerous computer programs have been developed across the globe to assist the researchers working in the field of drug discovery. Broadly, these programs can be classified in three categories, freeware, shareware and commercial software. In this review, we have described freeware or open-source software that are commonly used for designing therapeutic molecules. Major emphasis will be on software and web services in the field of chemo- or pharmaco-informatics that includes in silico tools used for computing molecular descriptors, inhibitors designing against drug targets, building QSAR models, and ADMET properties.Deepak SinglaSandeep Kumar DhandaJagat S ChauhanAnshu BhardwajSamir K BrahmachariG.P.S. Raghava2013-06-24T11:00:42Z2013-06-24T11:00:42Zhttp://crdd.osdd.net/open/id/eprint/1304This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/13042013-06-24T11:00:42ZDesigning of inhibitors against drug tolerant Mycobacterium tuberculosis (H37Rv).Mycobacterium tuberculosis (M.tb) is the causative agent of tuberculosis, killing ~1.7 million people annually. The remarkable capacity of this pathogen to escape the host immune system for decades and then to cause active tuberculosis disease, makes M.tb a successful pathogen. Currently available anti-mycobacterial therapy has poor compliance due to requirement of prolonged treatment resulting in accelerated emergence of drug resistant strains. Hence, there is an urgent need to identify new chemical entities with novel mechanism of action and potent activity against the drug resistant strains.Deepak SinglaRupinder TewariAshwani KumarG.P.S. Raghava2019-07-12T11:25:09Z2019-07-12T15:02:43Zhttp://crdd.osdd.net/open/id/eprint/2212This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/22122019-07-12T11:25:09ZGLOBAL STRUCTURE ANALYSIS OF MONOCLONAL ANTIBODIES RECOGNIZING ENVELOPE COMPONENTS, gp120 AND gp41, OF HIV-1Ashish K Solanki2019-09-05T11:49:10Z2019-09-05T11:49:10Zhttp://crdd.osdd.net/open/id/eprint/2459This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24592019-09-05T11:49:10ZSilanimonas mangrovi sp. nov., a member of the family Xanthomonadaceae isolated from mangrove sediment, and emended description of the genus Silanimonas.A novel Gram-negative, rod-shaped, motile bacterium, designated strain AK13(T), was isolated from a sediment sample collected from mangrove of Namkhana, Sunderbans, West Bengal, India. Strain AK13(T) was positive for oxidase, DNase and lipase activities and negative for catalase, gelatinase, ornithine decarboxylase, lysine decarboxylase, nitrate reductase, aesculinase and urease activities. The fatty acids were dominated by iso-C(11 : 0), iso-C(11 : 0) 3-OH, iso-C(15 : 0), iso-C(16 : 0), iso-C(17 : 1)ω9c and summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH). Strain AK13(T) contained Q-8 as the major respiratory quinone and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, two unidentified aminolipids, one unidentified glycolipid and one unidentified lipid as the polar lipids. The DNA G+C content of strain AK13(T) was 55.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the type strain of Silanimonas lenta, of the family Xanthomonadaceae (phylum Proteobacteria), was the closest neighbour of strain AK13(T), with 95.2 % sequence similarity. Other members of the family showed sequence similarities <94.4 %. Based on the phenotypic characteristics and phylogenetic inference, strain AK13(T) is proposed as a member of a novel species of the genus Silanimonas, Silanimonas mangrovi sp. nov.; the type strain is AK13(T) (= MTCC 11082(T) = DSM 24914(T)). An emended description of the genus Silanimonas is also provided.T N R SrinivasT B KailashP Anil Kumar2019-09-05T11:55:29Z2019-09-05T11:55:29Zhttp://crdd.osdd.net/open/id/eprint/2456This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24562019-09-05T11:55:29ZRole of oxyRKP, a novel LysR-family transcriptional regulator, in antimicrobial resistance and virulence in Klebsiella pneumoniae.Klebsiella pneumoniae is a Gram-negative bacillus that causes serious infections in immunocompromised human hosts and exhibits significant multidrug resistance. In this study, we identified a novel lysR-family regulator (designated oxyR(KP)) in the genome of K. pneumoniae NTUH-K2044 whose functions have remained enigmatic so far. Functional characterization of the putative lysR regulator oxyR(KP) with respect to cellular physiology and antimicrobial susceptibility was performed by generating an isogenic mutant, ΔoxyR(KP) in a hypervirulent clinical isolate of K. pneumoniae. The K. pneumoniae oxyR(KP) mutant was sensitive to hyperosmotic and bile conditions. Disruption of oxyR(KP) increased the susceptibility of K. pneumoniae to oxidative (0.78947 mM hydrogen peroxide) and nitrosative (30 mM acidified nitrite) stress by ~1.4-fold and ~10-fold, respectively. Loss of the Klebsiella regulator led to a decrease in the minimum inhibitory concentrations for chloramphenicol (10-fold), erythromycin (6-fold), nalidixic acid (>50-fold) and trimethoprim (10-fold), which could be restored following complementation. The relative change in expression of resistance-nodulation-cell division super family (RND) efflux gene acrB was decreased by approximately fivefold in the oxyR(KP) mutant as evidenced by qRT-PCR. In a Caenorhabditis elegans model, the oxyR(KP) mutant exhibited significantly (P<0.01) lower virulence. Overall, results detailed in this report reflect the pleiotropic role of the oxyR(KP) signalling system and diversity of the resistance determinants in hypervirulent K1 serotype K. pneumoniae NTUH-K2044. Vijaya Bharathi SrinivasanAmitabha MondalManjunath VenkataramaiahNeeraj Kumar ChauhanGovindan Rajamohan2015-02-10T11:43:50Z2015-02-10T11:43:50Zhttp://crdd.osdd.net/open/id/eprint/1605This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16052015-02-10T11:43:50ZKpnEF, a new member of the Klebsiella pneumoniae cell envelope stress response regulon, is an SMR-type efflux pump involved in broad-spectrum antimicrobial resistance.Klebsiella pneumoniae has been frequently associated with nosocomial infections. Efflux systems are ubiquitous transporters that also function in drug resistance. Genome analysis of K. pneumoniae strain NTUH-K2044 revealed the presence of ∼15 putative drug efflux systems. We discuss here for the first time the characterization of a putative SMR-type efflux pump, an ebrAB homolog (denoted here as kpnEF) with respect to Klebsiella physiology and the multidrug-resistant phenotype. Analysis of hypermucoviscosity revealed direct involvement of kpnEF in capsule synthesis. The ΔkpnEF mutant displayed higher sensitivity to hyperosmotic (∼2.8-fold) and high bile (∼4.0-fold) concentrations. Mutation in kpnEF resulted in increased susceptibility to cefepime, ceftriaxone, colistin, erythromycin, rifampin, tetracycline, and streptomycin; mutated strains changed from being resistant to being susceptible, and the resistance was restored upon complementation. The ΔkpnEF mutant displayed enhanced sensitivity toward structurally related compounds such as sodium dodecyl sulfate, deoxycholate, and dyes, including clinically relevant disinfectants such as benzalkonium chloride, chlorhexidine, and triclosan. The prevalence of kpnEF in clinical strains broadens the diversity of antibiotic resistance in K. pneumoniae. Experimental evidence of CpxR binding to the efflux pump promoter and quantification of its expression in a cpxAR mutant background demonstrated kpnEF to be a member of the Cpx regulon. This study helps to elucidate the unprecedented biological functions of the SMR-type efflux pump in Klebsiella spp.Vijaya Bharathi SrinivasanGovindan Rajamohan2018-09-19T08:22:59Z2018-09-19T08:22:59Zhttp://crdd.osdd.net/open/id/eprint/2118This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/21182018-09-19T08:22:59ZAlanine-scanning mutagenesis of WH2 domains of VopF reveals residues important for conferring lethality in a Saccharomyces cerevisiae model.VopF, the type III effector molecule, has been implicated in the pathogenesis of non-O1, non-O139 strains of Vibrio cholerae. It is a protein of 530 amino acids, comprises of one formin homology 1-like (FH1-like) domain and three WASP homology 2 (WH2) domains. Previous works have demonstrated that WH2 domains are crucial for VopF function as a modulator of cellular actin homeostasis. Furthermore, domain deletion analysis also suggests that VopF variant constituted with only WH2 domain 3 is more efficient in restricting the growth of budding yeast than its congeners containing either only domain 1 or domain 2. Interestingly, a good degree of sequence diversity is present within each WH2 domain of VopF. In order to ascertain the importance of different amino acids in each WH2 domain, a systemic alanine scanning mutagenesis was employed. Using a yeast model system, the alanine derivatives of each amino acid of WH2 domain 1 and 3 of VopF were examined for growth restricting activity. Taken together, our mutagenesis results reveal the identification of critical residues of WH2 domain 1 and 3 of VopF.Ranjana TripathiVikas KaithwasChetna DurejaSaumya Raychaudhuri2015-02-10T11:15:05Z2015-02-10T11:15:05Zhttp://crdd.osdd.net/open/id/eprint/1600This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16002015-02-10T11:15:05ZArf-like GTPase Arl8b regulates lytic granule polarization and natural killer cell-mediated cytotoxicity.Natural killer (NK) lymphocytes contain lysosome-related organelles (LROs), known as lytic granules, which upon formation of immune synapse with the target cell, polarize toward the immune synapse to deliver their contents to the target cell membrane. Here, we identify a small GTP-binding protein, ADP-ribosylation factor-like 8b (Arl8b), as a critical factor required for NK cell-mediated cytotoxicity. Our findings indicate that Arl8b drives the polarization of lytic granules and microtubule-organizing centers (MTOCs) toward the immune synapse between effector NK lymphocytes and target cells. Using a glutathione S-transferase pull-down approach, we identify kinesin family member 5B (KIF5B; the heavy chain of kinesin-1) as an interaction partner of Arl8b from NK cell lysates. Previous studies showed that interaction between kinesin-1 and Arl8b is mediated by SifA and kinesin-interacting protein (SKIP) and the tripartite complex drives the anterograde movement of lysosomes. Silencing of both KIF5B and SKIP in NK cells, similar to Arl8b, led to failure of MTOC-lytic granule polarization to the immune synapse, suggesting that Arl8b and kinesin-1 together control this critical step in NK cell cytotoxicity.Amit TuliJerome ThieryAshley M JamesXavier MicheletMahak SharmaSalil GargKeri B SanbornJordan S OrangeJudy LiebermanMichael B Brenner2019-09-05T11:53:44Z2019-09-05T11:53:44Zhttp://crdd.osdd.net/open/id/eprint/2457This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24572019-09-05T11:53:44ZIn silico models for designing and discovering novel anticancer peptides.Use of therapeutic peptides in cancer therapy has been receiving considerable attention in the recent years. Present study describes the development of computational models for predicting and discovering novel anticancer peptides. Preliminary analysis revealed that Cys, Gly, Ile, Lys, and Trp are dominated at various positions in anticancer peptides. Support vector machine models were developed using amino acid composition and binary profiles as input features on main dataset that contains experimentally validated anticancer peptides and random peptides derived from SwissProt database. In addition, models were developed on alternate dataset that contains antimicrobial peptides instead of random peptides. Binary profiles-based model achieved maximum accuracy 91.44% with MCC 0.83. We have developed a webserver, which would be helpful in: (i) predicting minimum mutations required for improving anticancer potency; (ii) virtual screening of peptides for discovering novel anticancer peptides, and (iii) scanning natural proteins for identification of anticancer peptides (http://crdd.osdd.net/raghava/anticp/). Atul TyagiPallavi KapoorRahul KumarKumardeep ChaudharyAnkur GautamG.P.S. Raghava2013-10-21T11:11:31Z2013-10-21T11:11:31Zhttp://crdd.osdd.net/open/id/eprint/1468This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/14682013-10-21T11:11:31ZUnderstanding and Characterization of Genome of Barkholderia sp. strain SJ 98 using bioinformatics and experimental TechniquesSurendra Vikram2019-09-05T11:51:45Z2019-09-05T11:51:45Zhttp://crdd.osdd.net/open/id/eprint/2458This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24582019-09-05T11:51:45ZDraft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon.We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon, isolated from a pesticide-contaminated site. The draft genome sequence of strain SJCon will be helpful in studying the genetic pathways involved in the degradation of several aromatic compounds.Surendra VikramShailesh KumarBhumika VaidyaAnil Kumar PinnakaG.P.S. Raghava2015-02-12T03:52:37Z2015-07-20T06:08:48Zhttp://crdd.osdd.net/open/id/eprint/1626This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16262015-02-12T03:52:37ZGenes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98.Biodegradation of para-Nitrophenol (PNP) proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT) and hydroquinone (HQ) as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB) showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM) and p-benzoquinone reductase (BqR). Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ), while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ). Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions.Surendra VikramJanmejay PandeyShailesh KumarG.P.S. Raghava2015-02-10T11:48:49Z2015-02-10T11:48:49Zhttp://crdd.osdd.net/open/id/eprint/1607This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/16072015-02-10T11:48:49ZStructure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone.Serine acetyltransferase (SAT) catalyzes the limiting reaction in plant and microbial biosynthesis of cysteine. In addition to its enzymatic function, SAT forms a macromolecular complex with O-acetylserine sulfhydrylase. Formation of the cysteine regulatory complex (CRC) is a critical biochemical control feature in plant sulfur metabolism. Here we present the 1.75-3.0 Å resolution x-ray crystal structures of soybean (Glycine max) SAT (GmSAT) in apoenzyme, serine-bound, and CoA-bound forms. The GmSAT-serine and GmSAT-CoA structures provide new details on substrate interactions in the active site. The crystal structures and analysis of site-directed mutants suggest that His(169) and Asp(154) form a catalytic dyad for general base catalysis and that His(189) may stabilize the oxyanion reaction intermediate. Glu(177) helps to position Arg(203) and His(204) and the β1c-β2c loop for serine binding. A similar role for ionic interactions formed by Lys(230) is required for CoA binding. The GmSAT structures also identify Arg(253) as important for the enhanced catalytic efficiency of SAT in the CRC and suggest that movement of the residue may stabilize CoA binding in the macromolecular complex. Differences in the effect of cold on GmSAT activity in the isolated enzyme versus the enzyme in the CRC were also observed. A role for CRC formation as a molecular chaperone to maintain SAT activity in response to an environmental stress is proposed for this multienzyme complex in plants.Hankuil YiSanghamitra DeySangaralingam KumaranSoon Goo LeeHari B KrishnanJoseph M Jez