open: No conditions. Results ordered Creators, Title. 2024-03-28T08:01:01ZEPrintshttp://crdd.osdd.net/images/sitelogo.gifhttp://crdd.osdd.net/open/2020-06-29T15:46:43Z2020-07-29T10:27:58Zhttp://crdd.osdd.net/open/id/eprint/2580This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25802020-06-29T15:46:43ZVapBC22 toxin-antitoxin system from Mycobacterium tuberculosis is required for pathogenesis and modulation of host immune responseVirulence-associated protein B and C toxin-antitoxin (TA) systems are widespread in prokaryotes, but their precise role in physiology is poorly understood. We have functionally characterized the VapBC22 TA system from Mycobacterium tuberculosis. Transcriptome analysis revealed that overexpression of VapC22 toxin in M. tuberculosis results in reduced levels of metabolic enzymes and increased levels of ribosomal proteins. Proteomics studies showed reduced expression of virulence-associated proteins and increased levels of cognate antitoxin, VapB22 in the ΔvapC22 mutant strain. Furthermore, both the ΔvapC22 mutant and VapB22 overexpression strains of M. tuberculosis were susceptible to killing upon exposure to oxidative stress and showed attenuated growth in guinea pigs and mice. Host transcriptome analysis suggests upregulation of the transcripts involved in innate immune responses and tissue remodeling in mice infected with the ΔvapC22 mutant strain. Together, we demonstrate that the VapBC22 TA system belongs to a key regulatory network and is essential for M. tuberculosis pathogenesisSakshi AgarwalArun SharmaRania BouzeyenAmar DeepHarsh SharmaK Kiran MangalaparthiKeshava K DattaSaqib KidwaiHarsha GowdaRaghavan VaradarajanDatta Ravi SharmaKrishan Gopal ThakurRamandeep Singh2020-07-29T10:47:32Z2020-07-29T15:32:40Zhttp://crdd.osdd.net/open/id/eprint/2584This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25842020-07-29T10:47:32ZMsrA Efflux Pump Inhibitory Activity ofPiper cubebaL.f. and its Phytoconstituents againstStaphylococcus aureusRN4220MsrA, an efflux pump belonging to ATP-binding cassette (ABC) transporter family that conferred resistance to macrolides, was detected inStaphylococcus aureusstrains. Herein, we report the isolation of phytoconstituents fromPiper cubebafruit methanol extract and investigated their efflux pump inhibitory potential againstS. aureusMsrA pump. Four isolated compounds, viz. pellitorine, sesamin, piperic acid and tetrahydropiperine studied in combination with erythromycin inS. aureusRN4220, exhibited 2-8-fold reduction in minimum inhibitory concentration (MIC) of erythromycin. Pellitorine and sesamin decreased MIC of erythromycin by 8-fold. The real-time fluorometry-based efflux and accumulation studies of ethidium bromide (EtBr) onS. aureusRN4220 in the presence of these compounds showed reduced efflux and enhanced uptake, thus indicating inhibition of the efflux pump. Pellitorine showed significant post-antibiotic effect of erythromycin. The results revealed that the primary mechanism of action of these compounds involves steady ATP production impairment.Pallavi AhirraoRushikesh TambatNishtha ChandalNisha MaheyAnjoo KambojUpendra K. JainInder Pal SinghSanjay M. JachakHemraj Nandanwar2020-02-26T15:04:27Z2020-02-26T15:04:27Zhttp://crdd.osdd.net/open/id/eprint/2544This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25442020-02-26T15:04:27ZDesign of a thrombin inhibitory staphylokinase based plasminogen activator with anti-reocclusion potential.In the quest of a therapeutically improved thrombolytic drug, we designed and expressed a Staphylokinase based, recombinant fusion protein with fibrin specific clot lysis and anti-thrombin activities derived from human thrombomodulin, a transmembrane glycoprotein with anticoagulant properties, known to form a complex with thrombin and then activating Protein C. The fusion construct was expressed in the yeast Pichia pastoris for cost effective and facile production. The purified construct had comparable plasminogen activation and clot lysis capability as compared to native SAK in that it showed plasmin dependent Plasminogen activation, but exhibited significantly lower fibrinogenolysis (an indicator of fibrin-specific action) even at much higher doses than SAK. In addition, its successful activation of the thrombin-mediated Protein C anticoagulant pathway was reflected in increased in vitro plasma clotting time, as well as inhibition of clot bound thrombin, which led to nearly 15-25% lesser re-formation of fibrin clots after initial successful clot lysis in a specially designed in vitro assay for re-occlusion. Thus, this novel chimeric protein could be of high therapeutic potential as a thrombolytic drug with enhanced fibrin specific clot dissolving properties along with lower bleeding and re-thrombosis complications- a dire need today, especially in the treatment of thrombotic strokes.Kashika AroraNeeraj MaheshwariGirish Sahni2019-12-06T15:10:46Z2020-03-02T10:09:37Zhttp://crdd.osdd.net/open/id/eprint/2514This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25142019-12-06T15:10:46ZWhole genome mining reveals a diverse repertoire of lanthionine synthetases and lanthipeptides among the genus Paenibacillus.Lanthionine or methyllanthionine-containing lanthipeptides belongs to ribosomally synthesized and post-translationally modified peptides (RiPPs) family. Recent revolution in sequencing has made available huge genome sequence dataset of micro-organisms. In this study, we performed genome mining of the complete and partial genome sequences of 479 bacteria of the genus Paenibacillus to determine the diversity and distribution of lanthipeptide gene clusters.P BaindaraN NayuduS Korpole2020-12-31T04:38:35Z2020-12-31T06:29:20Zhttp://crdd.osdd.net/open/id/eprint/2625This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26252020-12-31T04:38:35ZTerminal Respiratory Oxidases: A Targetables Vulnerability of Mycobacterial Bioenergetics?Recently, ATP synthase inhibitor Bedaquiline was approved for the treatment of multi-drug resistant tuberculosis emphasizing the importance of oxidative phosphorylation for the survival of mycobacteria. ATP synthesis is primarily dependent on the generation of proton motive force through the electron transport chain in mycobacteria. The mycobacterial electron transport chain utilizes two terminal oxidases for the reduction of oxygen, namely the bc(1)-aa(3) supercomplex and the cytochrome bd oxidase. The bc(1)-aa(3) supercomplex is an energy-efficient terminal oxidase that pumps out four vectoral protons, besides consuming four scalar protons during the transfer of electrons from menaquinone to molecular oxygen. In the past few years, several inhibitors of bc(1)-aa(3) supercomplex have been developed, out of which, Q203 belonging to the class of imidazopyridine, has moved to clinical trials. Recently, the crystal structure of the mycobacterial cytochrome bc(1)-aa(3) supercomplex was solved, providing details of the route of transfer of electrons from menaquinone to molecular oxygen. Besides providing insights into the molecular functioning, crystal structure is aiding in the targeted drug development. On the other hand, the second respiratory terminal oxidase of the mycobacterial respiratory chain, cytochrome bd oxidase, does not pump out the vectoral protons and is energetically less efficient. However, it can detoxify the reactive oxygen species and facilitate mycobacterial survival during a multitude of stresses. Quinolone derivatives (CK-2-63) and quinone derivative (Aurachin D) inhibit cytochrome bd oxidase. Notably, ablation of both the two terminal oxidases simultaneously through genetic methods or pharmacological inhibition leads to the rapid death of the mycobacterial cells. Thus, terminal oxidases have emerged as important drug targets. In this review, we have described the current understanding of the functioning of these two oxidases, their physiological relevance to mycobacteria, and their inhibitors. Besides these, we also describe the alternative terminal complexes that are used by mycobacteria to maintain energized membrane during hypoxia and anaerobic conditions.Sapna BajeliNavin BaidManjot KaurGanesh P. PawarVinod ChaudhariAshwani Kumar2020-07-30T13:43:56Z2020-07-30T13:43:56Zhttp://crdd.osdd.net/open/id/eprint/2593This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25932020-07-30T13:43:56ZAn Electronic and Optically Controlled Bifunctional Transistor Based on a Bio−Nano Hybrid ComplexWe report an electronically and optically controlled bioelectronic field-effect transistor (FET) based on the hybrid film of photoactive bacteriorhodopsin and electronically conducting single-walled carbon nanotubes (SWNTs). Two-dimensional (2D) crystals of bacteriorhodopsin form the photoactive center of the bio–nano complex, whereas one-dimensional (1D) pure SWNTs provide the required electronic support. The redshift in the Raman spectra indicates the electronic doping with an estimated charge density of 3 × 106 cm–2. The hybrid structure shows a conductivity of 19 μS/m and semiconducting characteristics due to preferential binding with selective diameters of semiconducting SWNTs. The bioelectronic transistor fabricated using direct laser lithography shows both optical and electronic gating with a significant on/off switch ratio of 8.5 and a photoconductivity of 13.15 μS/m. An n-type FET shows complementary p-type characteristics under light due to optically controlled, electronic doping by the “proton-pumping” bacteriorhodopsin. The fabricated bioelectronic transistor exhibits both electronically and optically well-controlled bifunctionality based on the functionalized hybrid electronic material.Vikram BakarajuE.Senthil PrasadBrijesh MeenaHarsh Chaturvedi2020-04-27T11:24:30Z2020-04-27T11:24:30Zhttp://crdd.osdd.net/open/id/eprint/2560This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25602020-04-27T11:24:30ZPhylogenomic Insights into Diversity and Evolution of Nonpathogenic Strains Associated with Citrus. species are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal the existence of potential novel species and strains of following a nonpathogenic lifestyle. In the present study, we report whole-genome sequences of four nonpathogenic strains from citrus (NPXc). Taxonogenomics revealed the surprising diversity, as each of these three isolates were found to be potential novel species that together form a citrus-associated nonpathogenic species complex (NPXc complex). Interestingly, this NPXc complex is related to another nonpathogenic species, , from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to nonpathogenic isolates from walnut (NPXw); altogether, they form a potential taxonomic outlier of pathogenic species. Furthermore, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle-specific gene content dynamics. Primarily, genes essential for virulence (i.e., ype 1 ecretion ystem [T1SS], T2SS and its effectors, T3SS and its effectors, T4SS, T6SS, adhesins, and gene cluster) and adaptation (i.e., , iron uptake and utilization, xanthomonadin, and two-component systems) were depicted by comparative genomics of a community comprising diverse lifestyles. Overall, the present analysis confers that nonpathogenic isolates of diverse hosts phylogenomically converge and are evolving in parallel with their pathogenic counterparts. Hence, there is a need to understand the world of nonpathogenic isolates from diverse and economically important hosts. Genomic knowledge and resources of nonpathogenic strains will be invaluable in both basic and applied research of the genus is one of the top phytopathogenic bacteria and is the causal agent of citrus canker. Interestingly, is also reported to be associated with healthy citrus plants. The advent of the genomic era enabled us to carry out a detailed evolutionary study of a community associated with citrus and other plants. Our genome-based investigations have revealed hidden and extreme interstrain diversity of nonpathogenic strains from citrus plants, warranting further large-scale studies. This indicates an unexplored world of from healthy citrus plant species that may be coevolving as a species complex with the host, unlike the variant pathogenic species. The knowledge and genomic resources will be valuable in evolutionary studies exploring its hidden potential and management of pathogenic species.Kanika BansalSanjeet KumarPrabhu B Patil2020-04-27T11:12:54Z2020-04-27T11:12:54Zhttp://crdd.osdd.net/open/id/eprint/2559This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25592020-04-27T11:12:54ZExpression based biomarkers and models to classify early and late-stage samples of Papillary Thyroid Carcinoma.Recently, the rise in the incidences of thyroid cancer worldwide renders it to be the sixth most common cancer among women. Commonly, Fine Needle Aspiration biopsy predominantly facilitates the diagnosis of the nature of thyroid nodules. However, it is inconsiderable in determining the tumor's state, i.e., benign or malignant. This study aims to identify the key RNA transcripts that can segregate the early and late-stage samples of Thyroid Carcinoma (THCA) using RNA expression profiles.Sherry BhallaHarpreet KaurRishemjit KaurSuresh SharmaG.P.S. Raghava2020-02-05T10:13:09Z2020-02-05T10:13:09Zhttp://crdd.osdd.net/open/id/eprint/2538This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25382020-02-05T10:13:09ZA comprehensive review on microbial L-asparaginase: Bioprocessing, characterization and industrial applications.L-asparaginase (E.C.3.5.1.1.) is a vital enzyme which hydrolyzes L-asparagine to L-aspartic acid and ammonia. This property of L-asparaginase inhibits the protein synthesis in cancer cells, making L-asparaginase a mainstay of pediatric chemotherapy practices to treat acute lymphoblastic leukemia (ALL) patients. L-asparaginase is also recognized as one of important food processing agent. The removal of asparagine by L-asparaginase leads to the reduction of acrylamide formation in fried food items. L-asparaginase is produced by various organisms including animals, plants and microorganisms, however, only microorganisms which produce a substantial amount of this enzyme are of commercial significance. The commercial L-asparaginase for healthcare applications is chiefly derived from E. coli and Erwinia chrysanthemi. A high rate of hypersensitivity and adverse reactions limits the long term clinical use of L-asparaginase. Present review provides thorough information on microbial L-asparaginase bioprocess optimization including submerged fermentation (SmF) and solid state fermentation (SSF) for L-asparaginase production, downstream purification, its characterization and issues related to the clinical application including toxicity and hypersensitivity. Here we have highlighted the bioprocess techniques which can produce improved and economically viable yields of L-asparaginase from promising microbial sources in the current scenario where there is an urgent need for alternate L-asparaginase with less adverse effects. This article is protected by copyright. All rights reserved.Subhash ChandRichi V MahajanJai Prakash PrasadDebendra K SahooKanti Nandan MihooliyaMahesh S DharGirish Sharma2020-12-31T05:03:58Z2020-12-31T05:03:58Zhttp://crdd.osdd.net/open/id/eprint/2626This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26262020-12-31T05:03:58ZDeciphering the Structural Enigma of HLA Class-II Binding Peptides for Enhanced Immunoinformatics-based Prediction of Vaccine EpitopesVaccines remain the most efficacious means to avoid and eliminate morbid diseases associated with high morbidity and mortality. Clinical trials indicate the gaining impetus of peptide vaccines against diseases for which an effective treatment still remains obscure. CD4 T-cell-based peptide vaccines involve immunization with antigenic determinants from pathogens or neoplastic cells that possess the ability to elicit a robust T helper cell response, which subsequently activates other arms of the immune system. The available in silico predictors of human leukocyte antigen II (HLA-II) binding peptides are sequence-based techniques, which ostensibly have balanced sensitivity and specificity. Structural analysis and understanding of the cognate peptide and HLA-II interactions are essential to empirically derive a successful peptide vaccine. However, the availability of structure-based epitope prediction algorithms is inadequate compared with sequence-based prediction methods. The present study is an attempt to understand the structural aspects of HLA-II binders by analyzing the Protein Data Bank (PDB) complexes of pHLA-II. Furthermore, we mimic the peptide exchange mechanism and demonstrate the structural implication of an acidic environment on HLA-II binders. Finally, we discuss a structure-guided approach to decipher potential HLA-II binders within an antigenic protein. This strategy may accurately predict the peptide epitopes and thus aid in designing successful peptide vaccines.Deepyan ChatterjeePragya PriyadarshiniDeepjyoti Kumar DasKhurram MushtaqBalvinder SinghJ N Agrewala2020-04-04T17:44:20Z2020-04-04T17:44:20Zhttp://crdd.osdd.net/open/id/eprint/2554This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25542020-04-04T17:44:20ZEvolutionary insights into adaptation of Staphylococcus haemolyticus to human and non-human niches.Staphylococcus haemolyticus is a well-known member of human skin microbiome and an emerging opportunistic human pathogen. Presently, evolutionary studies are limited to human isolates even though it is reported from plants with beneficial properties and in environmental settings. In the present study, we report isolation of novel S. haemolyticus strains from surface sterilized rice seeds and compare their genome to other isolates from diverse niches available in public domain. The study showed expanding nature of pan-genome and revealed set of genes with putative functions related to its adaptability. This is seen by presence of type II lanthipeptide cluster in rice isolates, metal homeostasis genes in an isolate from copper coin and gene encoding methicillin resistance in human isolates. The present study on differential genome dynamics and role of horizontal gene transfers has provided novel insights into capability for ecological diversification of a bacterium of significance to human health.Vasvi ChaudhryPrabhu B Patil2020-12-17T09:49:19Z2020-12-17T09:49:19Zhttp://crdd.osdd.net/open/id/eprint/2623This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26232020-12-17T09:49:19ZSELECT-GLYCOCIN: a recombinant microbial system for expression and high-throughput screening of glycocinsGlycosylated bacteriocins (glycocins) are potential clean label food preservatives and new alternatives to antibiotics. Further development requires the availability of a method for laboratory evolution of glycocins, wherein the challenges to overcome include ensuring glycosylation in a heterologous host, avoiding potential toxicity of active glycocins to the host, and provisioning of a one-pot screening assay for active mutants. Employing EntS, a sequential O/S- di-glycosyltransferase from Enterococcus faecalis TX0104, a proof of the concept microbial system and high throughput screening assay (SELECT-GLYCOCIN) is developed for generation of O/S- linked glycopeptide libraries and screening of glycocins for desired activity/property. The method enabled enzyme-dependent in vivo glycosylation in the heterologous host and rapid screening of mutants of enterocin 96 (Ent96)- a glycocin active against food-borne pathogen L. monocytogenes. Using SELECT-GLYCOCIN, a library of random (1.5 X 10^3) and rational (17) mutants of Ent96 was generated. The mutants were screened for bioactivity to identify a total of 376 random and 14 rational mutants as bioactive. Downstream detailed analysis of 16 random and 14 rational mutants led to the identification of sequence- and or glyco-variants namely, G16E-H24Q, C13T, and Ent96-K4_K5insYYGNGV (PedioEnt96) as improved antimicrobials. To summaries, SELECT-GLYCOCIN provides a system and a generic method for discovery and screening of glycocins that can further be adapted to any known/unknown glycocins and can be employed in food preservatives’ and drug discovery programs.Pravinkumar ChoudharyAlka Rao2020-12-31T04:30:59Z2020-12-31T04:30:59Zhttp://crdd.osdd.net/open/id/eprint/2624This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26242020-12-31T04:30:59ZHybrid Dynamic Pharmacophore Models as Effective Tools to Identify Novel Chemotypes for Anti-TB Inhibitor Design: A Case Study With Mtb-DapBAntimicrobial resistance (AMR) is one of the most serious global public health threats as it compromises the successful treatment of deadly infectious diseases like tuberculosis. New therapeutics are constantly needed but it takes a long time and is expensive to explore new biochemical space. One way to address this issue is to repurpose the validated targets and identify novel chemotypes that can simultaneously bind to multiple binding pockets of these targets as a new lead generation strategy. This study reports such a strategy, dynamic hybrid pharmacophore model (DHPM), which represents the combined interaction features of different binding pockets contrary to the conventional approaches, where pharmacophore models are generated from single binding sites. We have considered Mtb-DapB, a validated mycobacterial drug target, as our model system to explore the effectiveness of DHPMs to screen novel unexplored compounds. Mtb-DapB has a cofactor binding site (CBS) and an adjacent substrate binding site (SBS). Four different model systems of Mtb-DapB were designed where, either NADPH/NADH occupies CBS in presence/absence of an inhibitor 2, 6-PDC in the adjacent SBS. Two more model systems were designed, where 2, 6-PDC was linked to NADPH and NADH to form hybrid molecules. The six model systems were subjected to 200 ns molecular dynamics simulations and trajectories were analyzed to identify stable ligand-receptor interaction features. Based on these interactions, conventional pharmacophore models (CPM) were generated from the individual binding sites while DHPMs were created from hybrid-molecules occupying both binding sites. A huge library of 1,563,764 publicly available molecules were screened by CPMs and DHPMs. The screened hits obtained from both types of models were compared based on their Hashed binary molecular fingerprints and 4-point pharmacophore fingerprints using Tanimoto, Cosine, Dice and Tversky similarity matrices. Molecules screened by DHPM exhibited significant structural diversity, better binding strength and drug like properties as compared to the compounds screened by CPMs indicating the efficiency of DHPM to explore new chemical space for anti-TB drug discovery. The idea of DHPM can be applied for a wide range of mycobacterial or other pathogen targets to venture into unexplored chemical space.Chinmayee ChoudhuryAnshu Bhardwaj2020-07-29T10:19:24Z2020-07-29T10:19:24Zhttp://crdd.osdd.net/open/id/eprint/2586This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25862020-07-29T10:19:24ZStructural basis of self-assembly in the lipid-binding domain of mycobacterial polar growth factor Wag31Wag31, or DivIVA, is an essential protein and a drug target in the human pathogen Mycobacterium tuberculosis that self-assembles at the negatively curved membrane surface to form a higher-order structural scaffold, maintains rod-shaped cellular morphology and localizes key cell-wall synthesizing enzymes at the pole for exclusive polar growth. The crystal structure of the N-terminal lipid-binding domain of mycobacterial Wag31 was determined at 2.3 angstrom resolution. The structure revealed a highly polar surface lined with several conserved charged residues that suggest probable sites for interactions with membrane lipids. Crystal-packing analysis revealed a previously unseen `dimer-of-dimers' assembly state of N-terminal Wag31, which is formed by antiparallel stacking of two coiled-coil dimers. Size-exclusion column-chromatography-coupled small-angle solution X-ray scattering data revealed a tetrameric form as a major assembly state of N-terminal Wag31 in solution, further supporting the crystal structure. The results suggest that, in addition to lipid binding, the N-terminal Wag31 can participate in self-assembly to form filamentous structures. Plausible models of linear self-assembly and branching of Wag31 filaments consistent with available data are suggested.Komal ChoukateBarnali Chaudhuri2020-12-31T06:49:37Z2020-12-31T06:49:37Zhttp://crdd.osdd.net/open/id/eprint/2630This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26302020-12-31T06:49:37ZHigher order assembling of the mycobacterial polar growth factor DivIVA/Wag31DivIVA or Wag31, which is an essential pole organizing protein in mycobacteria, can self-assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. The structural organization of polar scaffold formed by polymerization of coiled-coil rich Wag31, which is implicated in the anti-tubercular activities of amino-pyrimidine sulfonamides, remains to be determined. A single-site phosphorylation in Wag31 regulates peptidoglycan biosynthesis in mycobacteria. We report biophysical characterizations of filaments formed by mycobacterial Wag31 using circular dichroism, atomic force microscopy and small angle solution X-ray scattering. Atomic force microscopic images of the wild-type, a phospho-mimetic (T73E) and a phospho-ablative (T73A) form of Wag31 show mostly linear filament formation with occasional curving, kinking and apparent branching. Solution X-ray scattering data indicates that the phospho-mimetic forms of the Wag31 polymers are on average more compact than their phospho-ablative counterparts, which is likely due to the extent of bending/branching. Observed structural features in this first view of Wag31 filaments suggest a basis for higher order Wag31 scaffold formation at the pole.Komal ChoukateAanchal GuptaBrohmomoy BasuVrk KarmanMunia GanguliBarnali Chaudhuri2020-05-04T09:24:33Z2020-05-04T09:24:33Zhttp://crdd.osdd.net/open/id/eprint/2569This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25692020-05-04T09:24:33ZBoosting Photochemical Performance of GaN nanowall network photoanode with BacteriorhodopsinThe ever-increasing demand for renewable and clean energy sources has prompted the development of novel materials for photoelectrochemical (PEC) water splitting, but efficient solar to hydrogen conversion remains a big challenge. In this work, we report a bio-nanohybrid strategy in a photo-system to simultaneously enhance the charge separation and water splitting efficiency of photoanode (PA) by introducing Bacteriorhodopsin (bR), a natural proton pumping photosystem and GaN nanowall network (NWN), a direct band gap and corrosion-resistant semiconductor. The experimental study reveals that this combination of bR and GaN NWN has huge potential as a light-activated sensitizer as well as proton pumping source to achieve enhance photocurrent density in hydrogen evolution reaction (HER). Consequently, this synergistic effect in bR/GaN NWN PA gives rise to largely enhanced applied bias photon-to-current efficiency (ABPE) ~7.8% and photocurrent density (28.74 mA/cm2 at 1.0 V vs RHE). It is worth mentioning that the photocurrent density of bR/GaN NWN, to the best of our knowledge, is superior to previously reported bR-based PAs and bio-photoelectric devices reported till today for solar-to-hydrogen fuelPooja DeviAnupama ThakurDibyendu GhoshE.Senthil PrasadS.M. SgivaprasadR.K. SinhaParveen Kumar2020-04-27T11:46:57Z2020-04-27T11:46:57Zhttp://crdd.osdd.net/open/id/eprint/2563This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25632020-04-27T11:46:57ZComputing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics.Human leukocyte antigen (HLA) are essential components of the immune system that stimulate immune cells to provide protection and defense against cancer. Thousands of HLA alleles have been reported in the literature, but only a specific set of HLA alleles are present in an individual. The capability of the immune system to recognize cancer-associated mutations depends on the presence of a particular set of alleles, which elicit an immune response to fight against cancer. Therefore, the occurrence of specific HLA alleles affects the survival outcome of cancer patients. In the current study, prediction models were developed, using 401 cutaneous melanoma patients, to predict the overall survival (OS) of patients using their clinical data and HLA alleles. We observed that the presence of certain favorable superalleles like HLA-B55 (HR = 0.15, 95% CI 0.034-0.67), HLA-A01 (HR = 0.5, 95% CI 0.3-0.8), is responsible for the improved OS. In contrast, the presence of certain unfavorable superalleles such as HLA-B50 (HR = 2.76, 95% CI 1.284-5.941), HLA-DRB112 (HR = 3.44, 95% CI 1.64-7.2) is responsible for the poor survival. We developed prediction models using key 14 HLA superalleles, demographic, and clinical characteristics for predicting high-risk cutaneous melanoma patients and achieved HR = 4.52 (95% CI 3.088-6.609, -value = 8.01E-15). Eventually, we also provide a web-based service to the community for predicting the risk status in cutaneous melanoma patients (https://webs.iiitd.edu.in/raghava/skcmhrp/).Anjali DhallSumeet PatiyalHarpreet KaurSherry BhallaChakit AroraG.P.S. Raghava2020-07-29T10:34:13Z2020-07-29T15:34:13Zhttp://crdd.osdd.net/open/id/eprint/2588This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25882020-07-29T10:34:13ZMonomeric human soluble CD4 dimerizes at physiological temperature: VTSAXS data based modeling and screening of retardant moleculesEarlier, solution small angle X-ray scattering (SAXS) data at 10 degrees C showed that soluble CD4 (sCD4; 1 mg/ml) is monomer with shape similar to single chain in crystal structures of its dimer. Query remained whether the dimeric state of CD4 can form independent of packing effects of crystal? Taking cue from other systems, we explored heat induced possible association of native shapes of sCD4 by variable temperature SAXS (VTSAXS) experiments. The predominant particle size increased consistently with temperature and around 35-40 degrees C, the estimated mass indicated dimeric state in solution. Furthermore, the observed association was found to be reversible to certain extent. Using SAXS profile representing dimer and crystal structure of monomer, we solved models of CD4 dimers which were dominated by D4-D4 interactions and appeared ``wobbling'' about the crystal structure of dimeric CD4, convincing pre-existence of crystal-like association in solution. To break the dimerization, we theoretically screened for small molecules binding to dimeric interface of D4 domain. Additionally, as negative control or not expecting to interfere, we searched molecules preferentially docking on the apex of D1 domain. VTSAXS experiments of CD4 + molecules at similar to 1:3 molar ratio showed that as expected few D4 reactive hits could retard dimerization, yet surprisingly molecules which docked at D1 domain could also derail dimerization. Additional analysis led to conclusion that there lies a systematic communication network across the structural length of sCD4 which senses binding to self and other molecules, and our work can be used to develop new (or re-purpose known) molecules as CD4-reactive immunosuppressive agents. Communicated by Ramaswamy H. SarmaKanika DhimanSamir Kumar Nath. Ashish2020-07-29T10:45:27Z2020-07-29T10:45:27Zhttp://crdd.osdd.net/open/id/eprint/2590This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25902020-07-29T10:45:27ZNovel xylanase producing Bacillus strain X2: molecular phylogenetic analysis and its application for production of xylooligosaccharidesA Bacillus strain X2 that produced extracellular endo-xylanase (GH 11) (EC: 3.2.1.8) was isolated from the soil of the Northeast India region. This aerobic culture was Gram positive and endospore forming. Chemotaxonomic characterization showed variance with the fatty acid profile of related species in the Bacillus subtilis group. In Bacillus strain X2, distinct occurrence of iso-C14:0 lipids is absent in other related species. The 16S rRNA gene sequence homology showed 99% similarity with Bacillus subtilis subsp. inaquosorum. The phylogenetic analysis by the multilocus sequence analysis (MLSA) of the nucleotide sequence of six concatenated genes (16S rRNA, groEL, gyrA, polC, purH and rpoB) resolved the taxonomic position of the Bacillus strain X2 in the Bacillus subtilis subsp. group. The MLSA showed that it is a member of a clade that includes Bacillus subtilis subsp. stercoris. In in silico DNA–DNA hybridization (DDH), the highest matching score was obtained with Bacillus subtilis subsp. stercoris (87%). The in silico DDH of the genome (G + C 43.7 mol %) shared 48.5%, with Bacillus subtilis subsp. inaquosorum. The MLSA phylogenetic tree and the highest degree of DNA hybridization, indicating that it belongs to the Bacillus subtilis subspecies stercoris.Chandrabhan DhruwKhadim HusainVyas KumarVijay Chintaman Sonawane2020-12-31T07:11:11Z2020-12-31T07:11:11Zhttp://crdd.osdd.net/open/id/eprint/2632This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26322020-12-31T07:11:11ZArginine 37 of Glycine Linker Dictates Regulatory Function of HapRHapR is designated as a high cell density quorum sensing master regulatory protein of Vibrio cholerae. It is a member of the TetR family protein and functions both as an activator and a repressor by directly communicating with cognate promoters, thus controlling the expression of a plethora of genes in a density-dependent manner. Molecular insights reveal the domain architecture and further unveil the significance of a cross talk between the DNA binding domain and the dimerization domain for the functionality of the wild-type protein. The DNA binding domain is made up of three α-helices, where a helix-turn-helix motif spans between the helices α2 and α3. The essentiality of the glycine-rich linker linking helices α1 and α2 came into prominence while unraveling the molecular basis of a natural non-functional variant of HapR. Subsequently, the importance of linker length was demonstrated. The present study, involving a series of biochemical analyses coupled with molecular dynamics simulation, has illustrated the indispensability of a critical arginine within the linker at position 37 contributing to HapR-DNA binding activity.Manjula EkkaAbhisek MondalRicha SinghHimanshu SenSaumen DattaSaumya Raychaudhuri2020-07-29T10:17:10Z2020-07-29T10:17:10Zhttp://crdd.osdd.net/open/id/eprint/2585This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25852020-07-29T10:17:10ZThe Yeast Hsp70 Cochaperone Ydj1 Regulates Functional Distinction of Ssa Hsp70s in the Hsp90 Chaperoning PathwayHeat-shock protein (Hsp) 90 assists in the folding of diverse sets of client proteins including kinases and growth hormone receptors. Hsp70 plays a major role in many Hsp90 functions by interacting and modulating conformation of its substrates before being transferred to Hsp90s for final maturation. Each eukaryote contains multiple members of the Hsp70 family. However, the role of different Hsp70 isoforms in Hsp90 chaperoning actions remains unknown. Using v-Src as an Hsp90 substrate, we examined the role of each of the four yeast cytosolic Ssa Hsp70s in regulating Hsp90 functions. We show that the strain expressing stress-inducible or, and the not constitutively expressed or, as the sole Ssa Hsp70 isoform reduces v-Src-mediated growth defects. The study shows that although different Hsp70 isoforms interact similarly with Hsp90s, v-Src maturation is less efficient in strains expressing as the sole Hsp70. We further show that the functional distinction between and is regulated by its C-terminal domain. Further studies reveal that, which is known to assist substrate transfer to Hsp70s, interacts relatively weakly with compared with, which could be the basis for poor maturation of the Hsp90 client in cells expressing stress-inducible as the sole Ssa Hsp70. The study thus reveals a novel role of in determining the functional distinction among Hsp70 isoforms with respect to the Hsp90 chaperoning action.Deepika GaurPrashant SinghJyoti GuleriaArpit GuptaSatinderdeep KaurDeepak Sharma2020-11-27T04:14:04Z2020-11-27T04:14:04Zhttp://crdd.osdd.net/open/id/eprint/2618This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26182020-11-27T04:14:04ZEtiopathogenesis, Challenges and Remedies Associated With Female Genital Tuberculosis: Potential Role of Nuclear ReceptorsExtra-pulmonary tuberculosis (EPTB) is recognized mainly as a secondary manifestation of a primary tuberculosis (TB) infection in the lungs contributing to a high incidence of morbidity and mortality. The TB bacilli upon reactivation maneuver from the primary site disseminating to other organs. Diagnosis and treatment of EPTB remains challenging due to the abstruse positioning of the infected organs and the associated invasiveness of sample acquisition as well as misdiagnosis, associated comorbidities, and the inadequacy of biomarkers. Female genital tuberculosis (FGTB) represents the most perilous form of EPTB leading to poor uterine receptivity (UR), recurrent implantation failure and infertility in females. Although the number of TB cases is reducing, FGTB cases are not getting enough attention because of a lack of clinical awareness, nonspecific symptoms, and inappropriate diagnostic measures. This review provides an overview for EPTB, particularly FGTB diagnostics and treatment challenges. We emphasize the need for new therapeutics and highlight the need for the exaction of biomarkers as a point of care diagnostic. Nuclear receptors have reported role in maintaining UR, immune modulation, and TB modulation; therefore, we postulate their role as a therapeutic drug target and biomarker that should be explored inShalini GuptaPawan Gupta2020-02-26T15:02:20Z2020-02-26T15:02:20Zhttp://crdd.osdd.net/open/id/eprint/2545This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25452020-02-26T15:02:20ZTruncated Hemoglobin O Carries an Autokinase Activity and Facilitates Adaptation of Under Hypoxia. Although the human pathogen, (), is strictly aerobic and requires efficient supply of oxygen, it can survive long stretches of severe hypoxia. The mechanism responsible for this metabolic flexibility is unknown. We have investigated a novel mechanism by which hemoglobin O (HbO), operates and supports its host under oxygen stress. We discovered that the HbO exists in a phospho-bound state in and remains associated with the cell membrane under hypoxia. Deoxy-HbO carries an autokinase activity that disrupts its dimeric assembly into monomer and facilitates its association with the cell membrane, supporting survival and adaptation of under low oxygen conditions. Consistent with these observations, deletion of the O gene in bacillus Calmette-Guerin, which is identical to the O gene of , attenuated its survival under hypoxia and complementation of the O gene of rescued this inhibition, but phosphorylation-deficient mutant did not. These results demonstrated that autokinase activity of the HbO modulates its physiological function and plays a vital role in supporting the survival of its host under hypoxia. Our study demonstrates that the redox-dependent autokinase activity regulates oligomeric state and membrane association of HbO that generates a reservoir of oxygen in the proximity of respiratory membranes to sustain viability of under hypoxia. These results thus provide a novel insight into the physiological function of the HbO and demonstrate its pivotal role in supporting the survival and adaptation of under hypoxia.Mangesh Dattu HadeDeepti SethiHimani DattaSandeep SinghNaveen ThakurAjay ChhayaKanak L Dikshit2020-04-04T17:33:29Z2020-04-04T17:33:29Zhttp://crdd.osdd.net/open/id/eprint/2553This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25532020-04-04T17:33:29ZTaxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade.Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.Princy HiraPriya SinghAnil Kumar PinnakaSuresh KorpoleRup Lal2020-11-27T06:23:40Z2020-11-27T06:23:40Zhttp://crdd.osdd.net/open/id/eprint/2619This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26192020-11-27T06:23:40ZButyrate induced Tregs are capable of migration from the GALT to the pancreas to restore immunological tolerance during type-1 diabetes.Type-1 diabetes (T1D) is an autoimmune disease caused by progressive loss of insulin-producing beta cells in the pancreas. Butyrate is a commensal microbial-derived metabolite, implicated in intestinal homeostasis and immune regulation. Here, we investigated the mechanism of diabetes remission in non-obese diabetic (NOD) mice following butyrate administration. Sodium butyrate (150 mM) was administered to female NOD mice in drinking water after the onset of hyperglycemia (15-25 weeks age) and at 4 weeks of age (early-intervention group). Butyrate administration reduced the progression of hyperglycemia in diabetic mice and delayed onset of diabetes in the early-intervention group with a reduction in insulitis. Butyrate administration increased regulatory T cells (Tregs) in the colon, mesenteric lymph nodes, Peyer's patches, and its protective effects diminished upon depletion of Tregs. Further, an increase in alpha 4 beta 7, CCR9, and GPR15 expressing Tregs in the pancreatic lymph nodes (PLN) and pancreas in butyrate-treated mice suggested migration of gut-primed Tregs towards the pancreas. Finally, the adoptive transfer experiments demonstrated that induced Tregs from gut-associated lymphoid tissue can migrate towards the pancreas and PLN and delay the onset of diabetes. Our results thus suggest that early administration of butyrate can restore immunological tolerance during T1D via induction of Tregs with migratory capabilities.Neenu JacobShivani JaiswalDeep MaheshwariNayudu NallabelliNeeraj KhatriAlka BhatiaAmanjit BalVivek MalikSavita VermaRakesh Kumar Naresh Sachdeva2020-07-30T11:25:42Z2020-07-30T11:25:42Zhttp://crdd.osdd.net/open/id/eprint/2591This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25912020-07-30T11:25:42ZIn Vitro Evaluation of Antimicrobial Peptide Tridecaptin M in Combination with Other Antibiotics against Multidrug Resistant Acinetobacter baumanniiThe rapid emergence of antimicrobial resistance in Acinetobacter baumannii coupled with the dried pipeline of novel treatments has driven the search for new therapeutic modalities. Gram-negative bacteria have an extra outer membrane that serves as a permeability barrier for various hydrophobic and/or large compounds. One of the popular approaches to tackle this penetration barrier is use of potentiators or adjuvants in combination with traditional antibiotics. This study reports the in vitro potential of an antimicrobial peptide tridecaptin M in combination with other antibiotics against different strains of A. baumannii. Tridecaptin M sensitized the bacteria to rifampicin, vancomycin, and ceftazidime. Further, we observed that a tridecaptin M and rifampicin combination killed the bacteria completely in 4 h in an ex vivo blood infection model and was superior to rifampicin monotherapy. The study also found that concomitant administration of both compounds is not necessary to achieve the antimicrobial effect. Bacteria pre-treated with tridecaptin M (for 2-4 h) followed by exposure to rifampicin showed similar killing as obtained for combined treatment. Additionally, this combination hampered the survival of persister development in comparison to rifampicin alone. These findings encourage the future investigation of this combination to treat severe infections caused by extremely drug-resistant A. baumannii.Manoj JangraVrushali RakaHemraj Nandanwar2019-12-06T15:35:04Z2020-04-22T14:40:28Zhttp://crdd.osdd.net/open/id/eprint/2505This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25052019-12-06T15:35:04ZNitrincola tapanii sp. nov., a novel alkaliphilic bacterium from An Indian Soda Lake.A novel Gram-stain-negative bacterial strain designated as MEB193 was isolated from a sediment sample collected from Lonar Lake, India. The cells were motile, non-spore-forming and rod-shaped. The strain was oxidase- and catalase-positive. It grew optimally at pH 9.0 and at 1 % (w/v) NaCl concentration at 30 °C. Based on 16S rRNA gene sequence similarity, MEB193 belongs to genus , with ZV-19 (95.89 %) and 4CA (95.87 %) as its closest neighbours. The major fatty acid was summed feature 8 comprising Cω7c/Cω6c (52 %) followed by C (25 %). Phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG) were present as the major polar lipids. The draft genome obtained in this study was 2 793 747 bp and the G+C content was 50.79 mol%. Average nucleotide identity (71.76 %) and DNA-DNA hybridization (<20 %) values between strain MEB193 and 4CA confirmed the novelty of this new species. Based on phenotypic including chemotaxonomic and genotypic characterization data, strain MEB193 represents a new species of the genus for which the name sp. nov. is proposed. The type strain is MEB193 (=MCC 2863=JCM 31570 =KCTC 52390 ).Amaraja JoshiSonia ThiteDhiraj DhotreManju MoorthyNeetha JosephV Venkata RamanaYogesh Shouche2020-10-29T05:47:51Z2020-10-29T05:47:51Zhttp://crdd.osdd.net/open/id/eprint/2613This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26132020-10-29T05:47:51ZProspective evaluation of individual and consortia plant growth promoting rhizobacteria for drought stress amelioration in rice (Oryza sativaL.)Aim Rice (Oryza sativaL.) being the most important crop for human population in Asia region, accounts for 23% of the world's caloric intake. Due to the changing climatic conditions, the agricultural crops are experiencing vagaries of the weather more frequently leading to yield losses and even crop failure. The objective of this study was to find out a suitable consortium of bacterial inoculants which can make the crop resilient to drought stress. Methods Bacterial isolates from different habitats were characterized for salt tolerance and multiple plant growth promoting traits. Four separate treatments were formulated, with two treatments having individual bacterial strain as PGPR and the rest two having consortia of three bacterial isolates as PGPR. High yielding variety MTU1010 was selected for pot experiments and treated with individual as well as consortium of isolates. Drought was imposed for 10 days to different batch of the rice crop (variety MTU1010) at two stages of crop growth i.e., pre-flowering and flowering stages. Results Results indicated amelioration of drought stress with higher biomass accumulation, increased grain yield and reversal of stress indicators in plants inoculated with PGPR. The antioxidant enzyme activity of SOD, CAT, and GPOX declined by 24%, 20.5% and 20% in plants treated with bacterial inoculum as compared to un-inoculated control. Conclusions This study indicates that the plant beneficial microorganisms can be used to induce systematic tolerance to rice plants under drought stress and furthermore, application of consortium of PGPR has better probability to improve the coping capacity of the plants exposed to stress conditions.Bhawana JoshiAnita ChaudharyHarjodh SinghAnil Kumar Pinnaka2020-05-01T15:12:12Z2020-05-01T15:12:12Zhttp://crdd.osdd.net/open/id/eprint/2568This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25682020-05-01T15:12:12ZUnderstanding the rheology of novel guar-gellan gum composite hydrogelsHydrogels are hydrophilic polymeric materials, prepared from either synthetic or natural macromolecules. However, synthetic hydrogels are now gradually being replaced with natural hydrogels owing to their non-toxicity, biocompatibility and biodegradability. The present work focused on synthesizing novel composite hydrogels of guar gum and gellan. The synthesized guar-gellan composite hydrogels were further characterized rheologically to understand their functional properties. Arrhenius and power law models were fitted for elucidation of their steady flow behavior. Interestingly the guar-gellan composite hydrogels showed remarkable stability and maintained elasticity at high temperatures and angular frequency. The comprehensive analysis of rheological data of novel guar-gellan gum composite hydrogels suggested their potential advantages over gellan gum and its applicability in diverse industrial sectors.
Anjula KatochAnirban Roy Choudhury2020-04-16T12:12:19Z2020-04-16T12:12:19Zhttp://crdd.osdd.net/open/id/eprint/2556This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25562020-04-16T12:12:19ZMolecular and Biochemical Characterization of YeeF/YezG, a Polymorphic Toxin-Immunity Protein Pair From .Polymorphic toxins are important and widespread elements of bacterial warfare that help in restricting the growth of competitors, aiding kin selection, and shaping the bacterial communities. Although widespread, polymorphic toxin systems (PTS) have been extensively studied in Gram-negative bacteria, there are limited studies describing PTS in Gram-positive bacteria. The present study characterizes YeeF/YezG, a predicted member of a PF04740 family of the polymorphic toxin-immunity system from a Gram-positive bacteria . The expression of the C-terminal toxic domain of YeeF (YeeF-CT) causes growth inhibition and gross morphological changes in The observed toxic effects are neutralized by the co-expression of , a gene present downstream of , confirming YeeF-CT/YezG as a toxin/immunity protein pair. Biochemical and studies reveal that YeeF-CT causes toxicity due to its non-specific metal-dependent DNase activity. This is different from the previously reported RNase activity from the three toxins belonging to PF04740 family. Isothermal titration calorimetry (ITC) data analysis suggests that YeeF-CT binds YezG with a dissociation constant in the nanomolar range. Analytical ultracentrifugation studies revealed that YeeF-CT forms a homodimer and binds with two molecules of monomeric YezG immunity protein to form a 2:2 stochiometric heterotetrameric complex. Biolayer interferometry and electrophoretic mobility shift assays show that YeeF-CT/YezG/DNA forms a stable ternary complex implicating that YezG is an exosite inhibitor of YeeF-CT. This study extends the molecular targets of the toxins in the PF04740 family and thus, this family of toxins can be broadly classified as nucleases harboring either DNases or RNases activities.Soni KaundalAmar DeepGundeep KaurKrishan Gopal Thakur2020-02-26T15:07:03Z2020-02-26T15:07:03Zhttp://crdd.osdd.net/open/id/eprint/2543This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25432020-02-26T15:07:03ZExtensive genomic rearrangements along with distinct mobilome and TALome is associated with extreme pathotypes of a rice pathogen.Xanthomonas oryzae pv. oryzae (Xoo) is a serious pathogen of rice which displays tremendous inter-strain variation. The emergence of highly virulent strains of Xoo is a major threat to rice cultivation. Evolutionary insights into genome dynamics of highly virulent strains as compared to the less virulent ones are crucial for understanding the molecular basis of exceptional success of Xoo as a highly evolved plant pathogen. In the present study, we report a complete genome sequence of Xoo strains with extreme virulent pathotypes (XVPs) characterized based on their reaction towards ten resistance (Xa) genes. One strain, IXO1088 can overcome resistance mediated by all the ten resistance genes while the other strain IXO704 cannot overcome any of them. Interestingly, our investigation revealed that XVPs display dramatic variation in the genome structure with numerous rearrangements/inversions. Moreover, XPVs also possess distinct transposon content and prophage elements that may provide genomic flux required for the acquisition of novel gene cassettes and structural changes in the genome. Interestingly, analysis of transcription activator-like effector (TALE) proteins, which are major virulence determinants of Xanthomonas pathogen show marked variation in the TALE content and DNA binding domain of tal genes. Overall, the present study indicates the possible role of mobilomes and repetitive elements in major structural and sequence alterations, which may be leading to the emergence of novel and extreme pathotypes. The knowledge and resource of XVPs will be invaluable in the further systematic understanding of evolution and management of variant pathotypes of Xoo.Amandeep KaurKanika BansalPrabhu B Patil2020-10-29T06:51:25Z2020-10-29T06:51:25Zhttp://crdd.osdd.net/open/id/eprint/2615This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26152020-10-29T06:51:25ZStructure-Guided Designing and Evaluation of Peptides Targeting Bacterial TranscriptionThe mycobacterial RNA polymerase (RNAP) is an essential and validated drug target for developing antibacterial drugs. The β-subunit of Mycobacterium tuberculosis (Mtb) RNAP (RpoB) interacts with an essential and global transcription factor, CarD, and confers antibiotic and oxidative stress resistance to Mtb. Compromising the RpoB/CarD interactions results in the killing of mycobacteria, hence disrupting the RpoB/CarD interaction has been proposed as a novel strategy for the development of anti-tubercular drugs. Here, we describe the first approach to rationally design and test the efficacy of the peptide-based inhibitors which specifically target the conserved PPI interface between the bacterial RNAP β/transcription factor complex. We performed in silico protein-peptide docking studies along with biochemical assays to characterize the novel peptide-based inhibitors. Our results suggest that the top ranked peptides are highly stable, soluble in aqueous buffer, and capable of inhibiting transcription with IC50 > 50 μM concentration. Using peptide-based molecules, our study provides the first piece of evidence to target the conserved RNAP β/transcription factor interface for designing new inhibitors. Our results may hence form the basis to further improve the potential of these novel peptides in modulating bacterial gene expression, thus inhibiting bacterial growth and combating bacterial infections.Gundeep KaurSrajan KapoorSoni KaundalDipak DuttaKrishan Gopal Thakur2020-02-05T10:03:13Z2020-02-05T10:08:01Zhttp://crdd.osdd.net/open/id/eprint/2536This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25362020-02-05T10:03:13ZIdentification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data.The high mortality rate of hepatocellular carcinoma (HCC) is primarily due to its late diagnosis. In the past, numerous attempts have been made to design genetic biomarkers for the identification of HCC; unfortunately, most of the studies are based on small datasets obtained from a specific platform or lack reasonable validation performance on the external datasets. In order to identify a universal expression-based diagnostic biomarker panel for HCC that can be applicable across multiple platforms, we have employed large-scale transcriptomic profiling datasets containing a total of 2,316 HCC and 1,665 non-tumorous tissue samples. These samples were obtained from 30 studies generated by mainly four types of profiling techniques (Affymetrix, Illumina, Agilent, and High-throughput sequencing), which are implemented in a wide range of platforms. Firstly, we scrutinized overlapping 26 genes that are differentially expressed in numerous datasets. Subsequently, we identified a panel of three genes (, and as HCC biomarker using different feature selection techniques. Three-genes-based HCC biomarker identified HCC samples in training/validation datasets with an accuracy between 93 and 98%, Area Under Receiver Operating Characteristic curve (AUROC) in a range of 0.97 to 1.0. A reasonable performance, i.e., AUROC 0.91-0.96 achieved on validation dataset containing peripheral blood mononuclear cells, concurred their non-invasive utility. Furthermore, the prognostic potential of these genes was evaluated on TCGA-LIHC and GSE14520 cohorts using univariate survival analysis. This analysis revealed that these genes are prognostic indicators for various types of the survivals of HCC patients (e.g., Overall Survival, Progression-Free Survival, Disease-Free Survival). These genes significantly stratified high-risk and low-risk HCC patients (p-value <0.05). In conclusion, we identified a universal platform-independent three-genes-based biomarker that can predict HCC patients with high precision and also possess significant prognostic potential. Eventually, we developed a web server HCCpred based on the above study to facilitate scientific community (http://webs.iiitd.edu.in/raghava/hccpred/).Harpreet KaurAnjali DhallRajesh KumarG.P.S. Raghava2020-05-15T09:36:02Z2020-09-01T08:48:00Zhttp://crdd.osdd.net/open/id/eprint/2570This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25702020-05-15T09:36:02ZA potent enzybiotic against methicillin-resistant Staphylococcus aureus.Staphylococcus aureus is one of the most dreadful infectious agents, responsible for high mortality and morbidity in both humans and animals. The increased prevalence of multidrug-resistant (MDR) Staphylococcus aureus strains has limited the number of available treatment options, which calls for the development of alternative and effective modalities against MDR S. aureus. Endolysins are bacteriophage-derived antibacterials, which attack essential conserved elements of peptidoglycan that are vital for bacterial survival, making them promising alternatives or complements to existing antibiotics for tackling such infections. For developing endolysin lysin-methicillin-resistant-5 (LysMR-5) as an effective antimicrobial agent, we evaluated its physical and chemical characteristics, and its intrinsic antibacterial activity against staphylococcal strains, including methicillin-resistant Staphylococcus aureus (MRSA). In this study, we cloned, expressed, and purified LysMR-5 from S. aureus phage MR-5. In silico analysis revealed that LysMR-5 harbors two catalytic and one cell wall-binding domain. Biochemical characterization and LC-MS analysis showed that both catalytic domains were active and had no dependence on divalent ions for their action, Zn exerted a negative effect. The optimal lytic activity of the endolysin was at 37 °C/pH 7.0 and in the presence of ≥ 300 mM concentration of NaCl. Circular dichroism (CD) demonstrated a loss in secondary structure with an increase in temperature confirming the thermosensitive nature of endolysin. Antibacterial assays revealed that LysMR-5 was active against diverse clinical isolates of staphylococci. It showed high lytic efficacy against S. aureus ATCC 43300, as an endolysin concentration as low as 15 µg/ml was sufficient to achieve maximum lytic activity within 30 min and it was further confirmed by scanning electron microscopy. Our results indicate that rapid and strong bactericidal activity of LysMR-5 makes it a valuable candidate for eradicating multidrug-resistant S. aureus.Jasjeet KaurPrashant SinghDeepak SharmaKusum HarjaiSanjay Chhibber2020-04-16T12:05:35Z2020-04-16T12:05:35Zhttp://crdd.osdd.net/open/id/eprint/2555This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25552020-04-16T12:05:35ZMetagenomics analysis reveals features unique to Indian distal gut microbiota.Various factors including diet, age, geography, culture and socio-economic status have a role in determining the composition of the human gut microbiota. The human gut microbial composition is known to be altered in disease conditions. Considering the important role of the gut microbiome in maintaining homeostasis and overall health, it is important to understand the microbial diversity and the functional metagenome of the healthy gut. Here, we characterized the microbiota of 31 fecal samples from healthy individuals of Indian ethnic tribes from Ladakh, Jaisalmer and Khargone by shotgun metagenomic sequencing. Sequence analysis revealed that Bifidobacterium and Prevotella were the key microbes contributing to the differences among Jaisalmer, Khargone and Ladakh samples at the genus level. Our correlation network study identified carbohydrate-active enzymes and carbohydrate binding proteins that are associated with specific genera in the different Indian geographical regions studied. Network analysis of carbohydrate-active enzymes and genus abundance revealed that the presence of different carbohydrate-active enzymes is driven by differential abundance of genera. The correlation networks were different in the different geographical regions, and these interactions suggest the role of less abundant genera in shaping the gut environment. We compared our data with samples from different countries and found significant differences in taxonomic composition and abundance of carbohydrate-active enzymes in the gut microbiota as compared to the other countries.Kamaldeep KaurIndu KhatriAkil AkhtarSrikrishna SubramanianT N C Ramya2020-07-30T16:05:32Z2020-07-30T16:05:32Zhttp://crdd.osdd.net/open/id/eprint/2595This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25952020-07-30T16:05:32ZRecombinant expression, purification and PEGylation of Paneth cell peptide (cryptdin-2) with value added attributes against Staphylococcus aureusArticle
Open Access
Published: 22 July 2020
Recombinant expression, purification and PEGylation of Paneth cell peptide (cryptdin-2) with value added attributes against Staphylococcus aureus
Navneet Kaur, Rahul Dilawari, Amrita Kaur, Girish Sahni & Praveen Rishi
Scientific Reports volume 10, Article number: 12164 (2020) Cite this article
140 Accesses
1 Altmetric
Metricsdetails
Abstract
Cryptdins are disulfide-rich cationic antimicrobial peptides secreted by mouse Paneth cells and are known to exhibit potent antimicrobial activity against various deadly pathogens. Keeping in view the extremely low yield obtained from mouse Paneth cells and high cost of synthetic peptide(s), herein, we have attempted to produce cryptdin-2 in Escherichia coli using recombinant technology. To avoid lethal effects of peptide on the host cells, cryptdin-2 was expressed as a fusion protein with thioredoxin as fusion partner which yielded 40 mg/L protein in the soluble fraction. Subsequently, mature cryptdin-2 was cleaved from the fusion partner and purified by cation exchange chromatography. Since conjugation of poly(ethylene) glycol (PEG) has been known to improve the biological properties of biomolecules, therefore, we further attempted to prepare PEG-conjugated variant of cryptdin-2 using thiol specific PEGylation. Though the antimicrobial activity of PEGylated cryptdin-2 was compromised to some extent, but it was found to have enhanced serum stability for longer duration as compared to its un-modified forms. Also, it was found to exhibit reduced toxicity to the host cells. Further, its synergism with gentamicin suggests that PEGylated cryptdin-2 can be used with conventional antibiotics, thereby indicating its possibility to be used as an adjunct therapy.Navneet KaurRahul DilwariAmrita KaurGirish SahniPraveen Rishi2020-10-29T05:42:09Z2020-10-29T05:42:09Zhttp://crdd.osdd.net/open/id/eprint/2612This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26122020-10-29T05:42:09ZStructural insights into rice SalTol QTL located SALT proteinSalinity is one of the major stresses affecting rice production worldwide, and various strategies are being employed to increase salt tolerance. Recently, there has been resurgence of interest to characterize SalTol QTL harbouring number of critical genes involved in conferring salt stress tolerance in rice. The present study reports the structure of SALT, a SalTol QTL encoded protein by X-ray crystallography (PDB ID: 5GVY; resolution 1.66 angstrom). Each SALT chain was bound to one mannose via 8 hydrogen bonds. Compared to previous structure reported for similar protein, our structure showed a buried surface area of 900 angstrom (2) compared to only 240 angstrom (2) for previous one. Small-angle X-ray scattering (SAXS) data analysis showed that the predominant solution shape of SALT protein in solution is also dimer characterized by a radius of gyration and maximum linear dimension of 2.1 and 6.5 nm, respectively. The SAXS profiles and modelling confirmed that the dimeric association and relative positioning in solution matched better with our crystal structure instead of previously reported structure. Together, structural/biophysical data analysis uphold a tight dimeric structure for SALT protein with one mannose bound to each protein, which remains novel to date, as previous structures indicated one sugar unit sandwiched loosely between two protein chains.Navneet KaurAmin SagarPankaj Sharma. AshishPratap Kumar Pati2020-04-27T11:41:30Z2020-04-27T11:41:30Zhttp://crdd.osdd.net/open/id/eprint/2562This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25622020-04-27T11:41:30ZFoldscope as a primary diagnostic tool for oral and urinary tract infections and its effectiveness in oral health education.Due to its speed, accuracy and cost-effectiveness, microscopy has become an integral part of clinical examination for disease diagnosis. However, modern microscopes are very costly and require skilled personnel for their operation and maintenance, and specimen processing and analysis is labour-intensive. Further, lack of such expensive diagnostic tools in remote areas is a serious concern. Affordable point-of-care diagnostic tools are the most useful for timely disease diagnosis and management. The Foldscope is an affordable origami-based microscopy device composed of a series of paper clippings, which, upon assembly, can hold a specimen slide for observation, and this specimen can be viewed via a mobile phone camera attached to it. The present study evaluated the use of the Foldscope in the clinical diagnosis of oral and urinary tract infections and evaluated its efficacy as a motivational tool for improving oral health among school children in India. We qualitatively compared the Foldscope to a clinical microscope by examining five different types of clinical samples. Of the different types of clinical samples, the Foldscope was effective in detecting infection in dental plaque samples and urine samples. Thus, we further analysed 31 dental plaque samples of patients aged 3-13 years and 25 urine samples of patients aged 11-62 years. We also evaluated the use of the Foldscope as an educational tool for motivating oral hygiene among 80 school children aged 12 years and found that students in the Foldscope intervention group had better measures of oral hygiene than did students in the non-intervention group. In summary, our study indicated that the Foldscope is useful in detecting urinary tract infections and kidney stones in urine samples and is a useful motivational tool for oral health education among school-aged children. Furthermore, it may also be useful in oral health monitoring in resource poor settings. This article is protected by copyright. All rights reserved.T KaurS DahiyaS H SatijaS J NawalN KshetrimayumJ NingthoujamA K ChahalAlka Rao2020-11-16T09:54:25Z2020-11-16T09:54:25Zhttp://crdd.osdd.net/open/id/eprint/2617This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26172020-11-16T09:54:25ZMolecular Mechanism of Selective Substrate Engagement and Inhibitor Dis-engagement of Cysteine SynthaseO-acetyl serine sulfhydrylase (OASS), referred to as Cysteine Synthase (CS), synthesizes cysteine from O-acetyl serine (OAS) and sulfur in bacteria and plants. The inherent challenge for CS is to overcome 4-6 log-folds stronger affinity for its natural inhibitor, serine acetyltransferase (SAT), as compared to its affinity for substrate, OAS. Our recent study showed that CS employs a novel competitive-allosteric mechanism to selectively recruit its substrate in the presence of natural inhibitor [1]. In this study, we trace the molecular features that control selective substrate recruitment. To generalize our findings, we used CS from three different bacteria (Haemophilus, Salmonella, and Mycobacterium) as our model systems and analysed structural and substrate-binding features of wild type CS and its ~13 mutants. Results show that CS uses a non-catalytic residue, M120, located 20 Å away from the reaction centre, to discriminate in favour of substrate. M120A and background mutants display significantly reduced substrate binding, catalytic efficiency, and inhibitor binding. Results shows that M120 favours the substrate binding by selectively enhancing the affinity for the substrate and dis-engaging the inhibitor by 20-286 and 5-3 folds respectively. Together, M120 confers a net discriminative force in favour of substrate by 100-858 folds.Abhishek KaushikR. RahisuddinNeha SainiRavi P. SinghRajveer KaurSukirte KaulSangaralingam Kumaran2020-04-04T17:10:06Z2020-11-20T11:38:43Zhttp://crdd.osdd.net/open/id/eprint/2549This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25492020-04-04T17:10:06ZM. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.Class-II AP-endonuclease (XthA) and NAD+-dependent DNA ligase (LigA) are involved in initial and terminal stages of bacterial DNA base excision repair (BER), respectively. XthA acts on abasic sites of damaged DNA to create nicks with 3'OH and 5'-deoxyribose phosphate (5'-dRP) moieties. Co-immunoprecipitation using mycobacterial cell-lysate, identified MtbLigA-MtbXthA complex formation. Pull-down experiments using purified wild-type, and domain-deleted MtbLigA mutants show that LigA-XthA interactions are mediated by the BRCT-domain of LigA. Small-Angle-X-ray scattering, 15N/1H-HSQC chemical shift perturbation experiments and mutational analysis identified the BRCT-domain region that interacts with a novel 104DGQPSWSGKP113 motif on XthA for complex-formation. Isothermal-titration calorimetry experiments show that a synthetic peptide with this sequence interacts with MtbLigA and disrupts XthA-LigA interactions. In vitro assays involving DNA substrate and product analogs show that LigA can efficiently reseal 3'OH and 5'dRP DNA termini created by XthA at abasic sites. Assays and SAXS experiments performed in the presence and absence of DNA, show that XthA inhibits LigA by specifically engaging with the latter's BRCT-domain to prevent it from encircling substrate DNA. Overall, the study suggests a coordinating function for XthA whereby it engages initially with LigA to prevent the undesirable consequences of futile cleavage and ligation cycles that might derail bacterial BER.Taran KhanamMohammad AfsarAnkita ShuklaFaiyaz AlamSanjay KumarHoram SoyarKunzes Dolma. AshishMukesh PasupuletiKishore Kumar SrivastavaRavi Sankar AmpapathiRavishankar Ramachandran2020-12-31T06:57:49Z2020-12-31T06:57:49Zhttp://crdd.osdd.net/open/id/eprint/2631This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26312020-12-31T06:57:49ZExploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2The current life-threatening and tenacious pandemic eruption of coronavirus disease in 2019 (COVID-19) has posed a significant global hazard concerning high mortality rate, economic meltdown, and everyday life distress. The rapid spread of COVID-19 demands countermeasures to combat this deadly virus. Currently, there are no drugs approved by the FDA to treat COVID-19. Therefore, discovering small molecule therapeutics for treating COVID-19 infection is essential. So far, only a few small molecule inhibitors are reported for coronaviruses. There is a need to expand the small chemical space of coronaviruses inhibitors by adding potent and selective scaffolds with anti-COVID activity. In this context, the huge antiviral chemical space already available can be analysed using cheminformatic and machine learning to unearth new scaffolds. We created three specific datasets called “antiviral dataset” (N= 38,428) “drug-like “antiviral dataset” (N=20,963) and “anticorona dataset” (N= 433) for this purpose. We analyzed the 433 molecules of “anticorona dataset” for their scaffold diversity, physicochemical distributions, principal component analysis, activity cliffs, R-group decomposition, and scaffold mapping. The scaffold diversity of the “anticorona dataset” in terms of Murcko scaffold analysis demonstrates a thorough representation of diverse chemical scaffolds. However, physicochemical descriptor analysis and principal component analysis demonstrated negligible drug-like features for the “anticorona dataset” molecules. The “antiviral dataset” and “drug-like antiviral dataset” showed low scaffold diversity as measured by the Gini coefficient. The hierarchical clustering of the “antiviral dataset” against the “anticorona dataset” demonstrated little molecular similarity. We generated a library of frequent fragments and polypharmacological ligands targeting various essential viral proteins such as main protease, helicase, papain-like protease, and replicase polyprotein 1ab. Further structural and chemical features of the “anticorona dataset” were compared with SARS-CoV-2 repurposed drugs, FDA-approved drugs, natural products, and drugs currently in clinical trials. Using machine learning tool DCA (DMax Chemistry Assistant, we converted the “anticorona dataset” into an elegant hypothesis with significant functional biological relevance. Machine learning analysis uncovered that FDA approved drugs, Tizanidine HCl, Cefazolin, Raltegravir, Azilsartan, Acalabrutinib, Luliconazole, Sitagliptin, Meloxicam (Mobic), Succinyl sulfathiazole, Fluconazole, and Pranlukast could be repurposed as effective drugs for COVID-19. Fragment-based scaffold analysis and R-group decomposition uncovered pyrrolidine and the indole molecular scaffolds as the potent fragments for designing and synthesizing the novel drug-like molecules for targeting SARS-CoV-2. This comprehensive and systematic assessment of small-molecule viral therapeutics' entire chemical space realised critical insights to potentially privileged scaffolds that could aid in enrichment and rapid discovery of efficacious antiviral drugs for COVID-19.Abhinit KumarSaurabh LoharchSunil KumarRajesh P. RingeRaman Parkesh2020-12-31T05:16:52Z2020-12-31T05:16:52Zhttp://crdd.osdd.net/open/id/eprint/2627This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26272020-12-31T05:16:52ZSynthesis, biological evaluation and computational studies of acrylohydrazide derivatives as potential Staphylococcus aureus NorA efflux pump inhibitorsThe NorA efflux pump decreases the intracellular concentration of fluoroquinolones (ciprofloxacin, norfloxacin) by effluxing them from Staphylococcus aureus cells. The synthesis of novel acrylohydrazide derivatives was achieved using well-known reactions and were characterized by various spectroscopy techniques. The synthe-sized 50 compounds were evaluated for the NorA efflux pump inhibition activity against S. aureus SA-1199B (norA++) and K1758 (norA-) strains. The study provided two most active compounds viz. 19 and 52. Compound 19 was found to be most active in potentiating effect of norfloxacin and also it showed enhanced uptake, efflux inhibition in ethidium bromide assay. Further compound 19 also enhanced post antibiotic effect and reduced mutation prevention concentration of norfloxacin. The homology modeling study was performed to elucidate three-dimensional structure of NorA. Docking studies of potent molecules were done to find the binding affinity and interaction with active site residues. Further, all the tested compounds exhibited good ADME and drug-likeness properties insilico. Based on the in-silico studies and detailed in vitro studies, acrylohydrazides derivatives may be considered as potential NorA EPI candidates.Gautam KumarAmbati Goutami GodavariRushikesh TambatSiva KumarHemraj Nandanwar M. Elizabeth SobhiaSanjay M Jachak2020-09-24T09:07:43Z2020-09-24T09:07:43Zhttp://crdd.osdd.net/open/id/eprint/2582This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25822020-09-24T09:07:43ZCancerEnD: A database of cancer associated enhancersCancerEnD is an integrated resource developed for annotating 8524 unique expressed enhancers, associated genes, somatic mutations and copy number variations of 8063 cancer samples from 18 cancer types of TCGA. Somatic mutation data was taken from the COSMIC repository. To delineate the relationship of change in copy number of enhancer elements with the prognosis of cancer patients, survival analysis was done using the survival package in R. We identified 1762 overall survival associated enhancers, which can be used for prognostic purposes of cancer patients in a tissue-specific manner. CancerEnD (https://web.iiitd.edu.in/raghava/cancerend/) is developed on a user-friendly responsive template, that enables searching, browsing and downloading of the annotated enhancer elements in terms of gene expression, copy number variation and survival association. We hope it provides a promising avenue for researchers to facilitate the understanding of enhancer deregulation in tumorigenesis, and to identify new biomarkers for therapy and disease-diagnosis.Rajesh KumarAnjali LathwalVinod KumarSumeet PatiyalPawan Kumar RaghavGajendra P. S. Raghava2020-12-31T05:35:40Z2020-12-31T05:35:40Zhttp://crdd.osdd.net/open/id/eprint/2629This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26292020-12-31T05:35:40ZGenomic insights into evolution of extensive drug resistance in Stenotrophomonas maltophilia complexWe report first complete genomic investigation of extensive drug resistance (XDR) in a nosocomial Stenotrophomonas maltophilia complex strain that is resistant to mainstream drugs (trimethoprim/sulfamethoxazole and levofloxacin). Comprehensive genomic investigation revealed its exclusive fourteen dynamic regions and highly enriched resistome comprising of two sulfonamide resistance genes on two diverse super-integrons of chromosomal origin. In addition, both these integrons harbour array of antibiotic resistance and commonly used disinfectant's resistance genes linked to ISCR elements. Isolation of a novel XDR strain from Indian tertiary care unit belonging to novel ST with diverse array of resistance genes on ISCR linked super-integrons indicates extent and nature of selection pressure in hospitals. Since, repetitive elements have major role in their spread and due to limitations of draft genomes, there is an urgent need to employ complete genome-based investigation for tracking the emergence of XDR at global level and designing strategies of antimicrobial stewardship and disinfection.Sanjeet KumarKanika BansalPrashant P PatilAmandeep KaurSatinder KaurVivek JaswalVikas GautamPrabhu B Patil2020-09-24T09:45:14Z2020-09-24T09:45:14Zhttp://crdd.osdd.net/open/id/eprint/2606This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26062020-09-24T09:45:14ZVitamin D3-VDR-PTPN6 axis mediated autophagy contributes to the inhibition of macrophage foam cell formationMacrophage derived foam cells in atherosclerotic plaques are the major factor responsible for the pathogenesis of atherosclerosis (AS). During advanced AS, macrophage-specific macroautophagy/autophagy is dysfunctional. 1, 25-dihydroxy vitamin D3 (VitD3) and its receptor VDR (vitamin D receptor) are reported to inhibit foam cell formation and induce autophagy; however, the role of VitD3-VDR-induced autophagy and foam cell formation in AS has not been explored. Here we find that VitD3 significantly recovered oxidized low-density lipoprotein-impaired autophagy, as well as increased autophagy-mediated lipid breakdown in mouse bone marrow-derived macrophages and human monocyte-derived macrophages, thus inhibiting the conversion of macrophages into foam cells. Importantly, VitD3 functions through its receptor VDR to upregulate autophagy and attenuate the accumulation of lipids in macrophages. Moreover, this study is the first occasion to report the interesting link between VitD3 signaling and PTPN6/SHP-1 (protein tyrosine phosphatase non-receptor type 6) in macrophages. VitD3-induced autophagy was abrogated in the presence of the PTPN6/Ptpn6 shRNA or inhibitor. VDR along with RXRA (retinoid X receptor alpha), and NCOA1 (nuclear receptor coactivator 1), are recruited to a specific response element located on the gene promoter and induce PTPN6 expression. PTPN6 contributes to VitD3-mediated autophagy by regulating autophagy-related genes via activation of MAPK1 (mitogen-activated protein kinase 1) and CEBPB (CCAAT enhancer binding protein beta). Furthermore, expression of PTPN6 is also crucial for VitD3-mediated inhibition of macrophage foam cell formation through autophagy. Thus, VitD3-VDR-PTPN6 axis-regulated autophagy attenuates foam cell formation in macrophages.Sumit KumarRavikanth NanduriElla BhagyarajRashi KalraNancy AhujaAnuja P ChackoDrishti TiwariKanupriya SethiAnkita SainiVemika ChandraMonika JainShalini GuptaDeepak BhattPawan Gupta2020-05-01T14:21:21Z2020-05-01T14:21:21Zhttp://crdd.osdd.net/open/id/eprint/2566This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25662020-05-01T14:21:21ZA Method for Predicting Hemolytic Potency of Chemically Modified Peptides From Its Structure.In the present study, a systematic effort has been made to predict the hemolytic potency of chemically modified peptides. All models have been trained, tested, and evaluated on a dataset that contains 583 modified hemolytic peptides and a balanced number of non-hemolytic peptides. Machine learning techniques have been used to build the classification models using an immense range of peptide features that include 2D, 3D descriptors, fingerprints, atom, and diatom compositions. Random Forest based model developed using fingerprints as an input feature achieved maximum accuracy of 78.33% with AUC of 0.86 on the main dataset and accuracy of 78.29% with AUC of 0.85 on the validation dataset. Models developed in this study have been incorporated in a web server "HemoPImod" to facilitate the scientific community (http://webs.iiitd.edu.in/raghava/hemopimod/).Vinod KumarRajesh KumarPiyush AgrawalSumeet PatiyalG.P.S. Raghava2020-07-30T15:57:45Z2020-07-30T15:57:45Zhttp://crdd.osdd.net/open/id/eprint/2594This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25942020-07-30T15:57:45ZColorimetric and electrochemical detection of pathogens in water using silver ions as a unique probeThe manuscript highlights the efficacy of silver ions to act as a unique probe for the detection of bacterial contamination in water samples. The bacterial cell membrane adherence property of the silver ions was employed to develop two different bacterial detection assays employing colorimetric and electrochemical techniques. In one of the schemes, silver ion was used directly as a detector of bacteria in a colorimetric assay format, and in the other scheme surface-functionalized antibodies were used as a primary capture for specific detection of Salmonella enterica serovar Typhi. The colorimetric detection is based on silver-induced inhibition of urease activity and silver ion utilization by bacteria for the rapid screening of enteric pathogens in water. The specific detection of bacteria uses an antibody-based electrochemical method that employs silver as an electrochemical probe. The ability of silver to act as an electrochemical probe was investigated by employing Anodic Stripping Voltammetry (ASV) for targeted detection of Salmonella Typhi. For further insights into the developed assays, inductively coupled plasma mass spectrometry (ICP-MS) and transmission electron microscopy (TEM) studies were performed. The sensitivity of the developed assay was found to be 100 cfu mL−1 for colorimetric and 10 cfu mL−1 for electrochemical assay respectively.Virendra KumarAdity ChopraBhawana BishtVijayender Bhalla2020-12-17T09:40:23Z2020-12-17T09:40:23Zhttp://crdd.osdd.net/open/id/eprint/2621This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26212020-12-17T09:40:23ZDevelopment of Site-Specific PEGylated Granulocyte Colony Stimulating Factor With Prolonged Biological ActivityCurrently, amino-terminal PEGylated human granulocyte colony stimulating factor (huG-CSF) is used to prevent and treat neutropenia. Although huG-CSF has been used as a drug for more than 20 years, it has three significant drawbacks: (i) it relies on PEG aldehyde for PEGylation of the alpha-amino group of the first amino acid, and this leads to non-specific PEGylation of the epsilon amino group of lysine residues within the G-CSF; (ii) longer-acting G-CSF variants are desirable to reduce the risk of chemotherapy-associated neutropenia; and (iii) G-CSF cannot be administered on the day of chemotherapy. In an attempt to overcome the above drawbacks, we engineered cysteine variants of G-CSF to facilitate the maleimide PEG-based site-specific PEGylation that leads to a highly homogenous PEGylated product. Importantly, we have demonstrated that 20 kDa thiol-reactive PEG conjugated by maleimide chemistry to the Cys2 G-CSF variant exhibits leukocyte proliferative activity similar to that of the commercially available G-CSF conjugated with aldehyde PEG in a neutropenia mice model. Moreover, we have demonstrated that PEGylation of the cysteine variant of huG-CSF with higher molecular weight PEGs, such as 30 kDa PEG and 40 kDa PEG, leads to significantly prolonged leukocyte proliferation activity compared to the variant conjugated with 20 kDa PEG. Importantly, even a half-dose of the engineered variant conjugated with 40 kDa PEG exhibited significantly longer biological activity than the commercially available 20 kDa PEGylated huG-CSF. Finally, we have demonstrated that administration of the engineered variant conjugated with 40 kDa PEG on the day of administration of cyclophosphamide for inducing neutropenia in mice can alleviate neutropenia through leukocyte proliferation. In summary, this study provides the design of site-specific PEGylated huG-CSF variants with improved therapeutic potential. It opens the possibility of long-acting and same-day prophylactic administration of G-CSF after chemotherapy drug regimens. These results may pave the way for the development of potential G-CSF derivatives possessing longer half-lives and favorable clinical attributes.Monika KumariGirish SahniSonal Datta2020-07-29T10:38:22Z2020-07-29T10:38:22Zhttp://crdd.osdd.net/open/id/eprint/2583This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25832020-07-29T10:38:22ZIdentification of prognostic biomarkers for major subtypes of non-small-cell lung cancer using genomic and clinical dataPurpose Intra-tumor heterogeneity and high mortality among patients with non-small-cell lung carcinoma (NSCLC) emphasize the need to identify reliable prognostic markers unique to each subtype. Methods In this study, univariate cox regression and prognostic index (PI)-based approaches were used to develop models for predicting NSCLC patients' subtype-specific survival. Results Prognostic analysis of TCGA dataset identified 1334 and 2129 survival-specific genes for LUSC (488 samples) and LUAD (497 samples), respectively. Individually, 32 and 271 prognostic genes were found and validated in GSE study exclusively for LUSC and LUAD. Nearly, 9-10% of the validated genes in each subtype were already reported in multiple studies thus highlighting their importance as prognostic biomarkers. Strong literature evidence against these prognostic genes like ``ELANE'' (LUSC) and ``AHSG'' (LUAD) instigates further investigation for their therapeutic and diagnostic roles in the corresponding cohorts. Prognostic models built on five and four genes were validated for LUSC HR = 2.10,pvalue = 1.86 x 10(-5)] and LUAD HR = 2.70,pvalue = 3.31 x 10(-7)], respectively. The model based on the combination of age and tumor stage performed well in both NSCLC subtypes, suggesting that despite having distinctive histological features and treatment paradigms, some clinical features can be good prognostic predictors in both. Conclusion This study advocates that investigating the survival-specific biomarkers restricted to respective cohorts can advance subtype-specific prognosis, diagnosis, and treatment for NSCLC patients. Prognostic models and markers described for each subtype may provide insight into the heterogeneity of disease etiology and help in the development of new therapeutic approaches for the treatment of NSCLC patients.Anjali LathwalRajesh KumarChakit AroraG.P.S. Raghava2020-09-24T08:57:42Z2020-09-24T08:59:28Zhttp://crdd.osdd.net/open/id/eprint/2604This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26042020-09-24T08:57:42ZOvirusTdb: A database of oncolytic viruses for the advancement of therapeutics in cancerOne of the emerging technologies to fight against cancer is oncolytic virus-based immunotherapy. Recently, the FDA approved an oncolytic virus T-vec for the treatment of melanoma. To facilitate the scientific community, we build a manually-curated repository of oncolytic viruses called OvirusTdb (https://webs.iiitd.edu.in/raghava/ovirustdb/). The repository maintains comprehensive information on therapeutically important oncolytic viruses with 5927 records where each record has 25 fields such as the virus species, cancer cell line, synergism with anti-cancer drugs, and many more. It stores information on 09 types of DNA, 15 types of RNA; 300 recombinant and 09 wild-type viral strains; tested against 124 cancer types and 427 cancer cell lines. Approximately, 1047 records suggest improved anti-cancer response using the combinatorial approach with chemotherapeutic agents. Nearly, 3243 and 1506 records indicate cancer cell death via apoptosis induction and immune activation, respectively. OvirusTdb may facilitate researchers in designing and discovering new oncolytic viruses for effective cancer treatment.Anjali LathwalRajesh KumarG.P.S. Raghava2020-05-01T14:24:30Z2020-05-01T14:24:30Zhttp://crdd.osdd.net/open/id/eprint/2564This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25642020-05-01T14:24:30ZComputer-aided designing of oncolytic viruses for overcoming translational challenges of cancer immunotherapy.Wild-type and genetically engineered oncolytic viruses (OVs) represent powerful therapeutic agents in cancer immunotherapy. Several OV species are in clinical trials for cancer treatment. Preclinical and clinical trials revealed several issues related to OV therapy in terms of viral delivery, spread, antiviral immune response, and tumor resistance. Here, we suggest some promising computational strategies that can overcome these issues. The strategies include predicting and prioritizing tumor-homing peptides, anticancer peptides, neoantigens, and miRNA response elements in the viral genome. The combination of computational approaches with genetic engineering could enhance the safety, delivery, oncolysis, and antitumor immune responses of OVs.Anjali LathwalRajesh KumarG.P.S. Raghava2020-09-24T09:34:02Z2020-09-24T09:34:02Zhttp://crdd.osdd.net/open/id/eprint/2605This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26052020-09-24T09:34:02ZA multiple T cell epitope comprising DNA vaccine boosts the protective efficacy of Bacillus Calmette–Guérin (BCG) against Mycobacterium tuberculosisBackground: Approximately 80% - 90% of individuals infected with latent Mycobacterium tuberculosis (Mtb)
remain protected throughout their life-span. The release of unique, latent-phase antigens are known to have
a protective role in the immune response against Mtb. Although the BCG vaccine has been administered for
nine decades to provide immunity against Mtb, the number of TB cases continues to rise, thereby raising
doubts on BCG vaccine efficacy. The shortcomings of BCG have been associated with inadequate processing
and presentation of its antigens, an inability to optimally activate T cells against Mtb, and generation of
regulatory T cells. Furthermore, BCG vaccination lacks the ability to eliminate latent Mtb infection. With these
facts in mind, we selected six immunodominant CD4 and CD8 T cell epitopes of Mtb expressed during latent,
acute, and chronic stages of infection and engineered a multi-epitope-based DNA vaccine (C6).
Result: BALB/c mice vaccinated with the C6 construct along with a BCG vaccine exhibited an expansion of
both CD4 and CD8 T cell memory populations and augmented IFN-γ and TNF-α cytokine release.
Furthermore, enhancement of dendritic cell and macrophage activation was noted. Consequently, illustrating
the elicitation of immunity that helps in the protection against Mtb infection; which was evident by a
significant reduction in the Mtb burden in the lungs and spleen of C6 + BCG administered animals.
Conclusion: Overall, the results suggest that a C6 + BCG vaccination approach may serve as an effective
vaccination strategy in future attempts to control TB.Sudeep K MauryaMohammad AqdasDeepjyoti Kumar DasSandeep SinghSajid NadeemGurpreet KaurJ N Agrewala2020-11-27T06:57:24Z2020-11-27T06:57:39Zhttp://crdd.osdd.net/open/id/eprint/2620This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26202020-11-27T06:57:24ZSpecifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretationMitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.Elizabeth M. McCormick Marie T. LottMatthew C. DulikLishuang Shen Marcella AttimonelliOrnella VitaleAmel KaraaRenkui BaiDaniel E Pineda-AlvarezLarry N. Singh Christine M StanleyStacey WongAnshu BhardwajDaria Merkurjev Rong MaoNeal SondheimerShiping ZhangVincent ProcaccioDouglas C WallaceXiaowu Gai Marni J. Falk2021-01-04T04:03:17Z2022-08-10T03:31:53Zhttp://crdd.osdd.net/open/id/eprint/2635This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26352021-01-04T04:03:17ZRunx proteins mediate protective immunity against Leishmania donovani infection by promoting CD40 expression on dendritic cellsThe level of CD40 expression on dendritic cells (DCs) plays a decisive role in disease protection during Leishmania donovani (LD) infection. However, current understanding of the molecular regulation of CD40 expression remains elusive. Using molecular, cellular and functional approaches, we identified a role for Runx1 and Runx3 transcription factors in the regulation of CD40 expression in DCs. In response to lipopolysaccharide (LPS), tumor necrosis factor alpha (TNFα) or antileishmanial drug sodium antimony gluconate (SAG), both Runx1 and Runx3 translocated to the nucleus, bound to the CD40 promoter and upregulated CD40 expression on DCs. These activities of Runx proteins were mediated by the upstream phosphatidylinositol 3-kinase (PI3K)-Akt pathway. Notably, LD infection attenuated LPS- or TNFα-induced CD40 expression in DCs by inhibiting PI3K-Akt-Runx axis via protein tyrosine phosphatase SHP-1. In contrast, CD40 expression induced by SAG was unaffected by LD infection, as SAG by blocking LD-induced SHP-1 activation potentiated PI3K-Akt signaling to drive Runx-mediated CD40 upregulation. Adoptive transfer experiments further showed that Runx1 and Runx3 play a pivotal role in eliciting antileishmanial immune response of SAG-treated DCs in vivo by promoting CD40-mediated type-1 T cell responses. Importantly, antimony-resistant LD suppressed SAG-induced CD40 upregulation on DCs by blocking the PI3K-Akt-Runx pathway through sustained SHP-1 activation. These findings unveil an immunoregulatory role for Runx proteins during LD infection.Akhtar Md. NausadManish MishraVinod YadavRavindra GujarSunaina LalRaj KumarNeeraj KhatriPradip Sen2020-04-04T17:13:19Z2020-04-04T17:13:19Zhttp://crdd.osdd.net/open/id/eprint/2550This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25502020-04-04T17:13:19ZStudies on efficient production of a novel l-asparaginase by a newly isolated IGS-131 and its heterologous expression in .In the current study, the production of novel glutaminase free l-asparaginase from a new microbial source ( IGS-131) is reported. Optimization of l-asparaginase production using conventional and statistical optimization techniques resulted in an enzyme yield of 37.63 IU/mL, which was 3.45-fold higher than the initial enzyme activity (i.e., 10.91 IU/mL). l-Asparaginase production from . IGS-131 was successfully carried out at the bioreactor level and investigations on the effect of agitation rates showed a maximum asparaginase yield of 38.88 IU/mL after 24 h fermentation at 400 rpm. The l-asparaginase gene from this source, showing 78% identity with a reported sequence in GenBank, was expressed in rosetta DE3. The molecular weight of the recombinant protein was determined as 35.6 kDa. Downstream processing of recombinant l-asparaginase resulted in a purified protein concentration of 62.53 mg/L, which showed good free radical scavenging activity of 62%. The current findings provide promising results for a process of l-asparaginase production from . IGS-131. Furthermore, the recombinant production of this enzyme could help in avoiding the complexity of down streaming processes associated with the purification of this enzyme from wild-type organisms.Kanti N MihooliyaJitender NandalAlka KumariSidhanta NandaHimanshu VermaDebendra K Sahoo2020-09-30T04:34:55Z2020-09-30T04:34:55Zhttp://crdd.osdd.net/open/id/eprint/2607This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26072020-09-30T04:34:55ZA novel function ofMycobacterium tuberculosischaperonin paralog GroEL1 in copper homeostasisAmong the two GroEL paralogs inMycobacterium tuberculosis, GroEL1 and GroEL2, GroEL1 has a characteristic histidine-rich C terminus. Since histidine richness is likely to be involved in metal binding, we attempted to decipher the role of GroEL1 in chelating metals and the consequence onM. tuberculosisphysiology. Isothermal titration calorimetry showed that GroEL1 binds copper and other metals. Mycobacterial viability assay, redox balance, and DNA protection assay concluded that GroEL1 protects from copper stressin vitro. Solution X-ray scattering and constrained modeling of GroEL1 -/+ copper ions showed reorientation of the apical domain as seen in functional assembly. We conclude that the duplication of chaperonin genes inM. tuberculosismight have led to their evolutionary divergence and consequent functional divergence of chaperonins.Yusuf Ansari MohammadSakshi D. BatraHina OjhaKanina Dhiman. AshishJaya S TyagiShekhar C Mande2020-06-02T09:49:27Z2020-09-24T08:36:45Zhttp://crdd.osdd.net/open/id/eprint/2573This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25732020-06-02T09:49:27ZSynthesis and Rheological Characterization of a Novel Shear Thinning Levan Gellan HydrogelShear thinning hydrogels are majorly employed in biomedical and cosmetic industry. However, the application of such chemically modified hydrogels is limited due to their high gelation time and chemical toxicity. The present study attempts to address these issues by synthesizing a novel quick setting, non-toxic hydrogel composed of biodegradable polysaccharides, levan and gellan. Comprehensive rheological analysis was conducted to understand the shear thinning and self-healing behaviour of the hydrogel. Frequency sweeps indicated that remarkable mechanical properties were exhibited by the composite hydrogels. Furthermore, the hydrogel exhibited an ease of injectability as demonstrated by strain sweep experiments. This study can, therefore, act as a pioneer for establishment of natural polysaccharide-based shear thinning hydrogels for possible application in various sectors.Revathy NairAnirban Roy Choudhury2020-08-14T10:45:29Z2020-08-14T10:45:29Zhttp://crdd.osdd.net/open/id/eprint/2596This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25962020-08-14T10:45:29ZIntestinal microbiota disruption limits the isoniazid mediated clearance ofMycobacterium tuberculosisin miceTuberculosis (TB) continues to remain a global threat due to the emergence of drug-resistantMycobacterium tuberculosis(Mtb) strains and toxicity associated with TB drugs. Intestinal microbiota has been reported to affect the host response to immunotherapy and drugs. However, how it affects the potency of first-line TB drug isoniazid (INH) is largely unknown. Here, we examined the impact of gut microbial dysbiosis on INH efficiency to killMtb. In this study, we employed in vivo mouse model, pretreated with broad-spectrum antibiotics (Abx) cocktail to disrupt their intestinal microbial population prior toMtbinfection and subsequent INH therapy. We demonstrated that microbiota disruption results in the impairment of INH-mediatedMtbclearance, and aggravated TB-associated tissue pathology. Further, it suppressed the innate immunity and reduced CD4 T-cell response againstMtb. Interestingly, a distinct shift of gut microbial profile was noted with abundance ofEnterococcusand reduction ofLactobacillusandBifidobacteriumpopulation. Our results show that the intestinal microbiota is crucial determinant in efficacy of INH to killMtband impacts the host immune response against infection. This work provides an intriguing insight into the potential links between host gut microbiota and potency of INH.Shikha NegiSusanta PahariHilal BashirJ N Agrewala2019-12-05T14:01:13Z2020-06-29T10:04:53Zhttp://crdd.osdd.net/open/id/eprint/2489This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24892019-12-05T14:01:13ZInduction of autophagy through CLEC4E in combination with TLR4: an innovative strategy to restrict the survival of .Host-directed therapies are gaining considerable impetus because of the emergence of drug-resistant strains of pathogens due to antibiotic therapy. Therefore, there is an urgent need to exploit alternative and novel strategies directed at host molecules to successfully restrict infections. The C-type lectin receptor CLEC4E and Toll-like receptor TLR4 expressed by host cells are among the first line of defense in encountering pathogens. Therefore, we exploited signaling of macrophages through CLEC4E in association with TLR4 agonists (C.T) to control the growth of (). We observed significant improvement in host immunity and reduced bacterial load in the lungs of infected mice and guinea pigs treated with C.T agonists. Further, intracellular killing of was achieved with a 10-fold lower dose of isoniazid or rifampicin in conjunction with C.T than the drugs alone. C.T activated MYD88, PtdIns3K, STAT1 and RELA/NFKB, increased lysosome biogenesis, decreased and gene expression and enhanced macroautophagy/autophagy. Macrophages from autophagy-deficient ( knockout or knockdown) mice showed elevated survival of . The present findings also unveiled the novel role of CLEC4E in inducing autophagy through MYD88, which is required for control of growth. This study suggests a unique immunotherapeutic approach involving CLEC4E in conjunction with TLR4 to restrict the survival of through autophagy. 3MA: 3 methyladenine; AO: acridine orange; Atg5: autophagy related 5; AVOs: acidic vesicular organelles; BECN1: beclin 1, autophagy related; BMDMs: bone marrow derived macrophages; bw: body weight; C.T: agonists of CLEC4E (C/TDB) and TLR4 (T/ultra-pure-LPS); CFU: colony forming unit; CLEC4E/Mincle: C-type lectin domain family 4, member e; CLR: c-type lectin receptor; INH: isoniazid; LAMP1: lysosomal-associated membrane protein 1; Mφ: infected C.T stimulated macrophages; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MDC: monodansylcadaverine; MTOR: mechanistic target of rapamycin kinase; MYD88: myeloid differentiation primary response 88; NFKB: nuclear factor of kappa light polypeptide gene enhance in B cells; NLR: NOD (nucleotide-binding oligomerization domain)-like receptors; PFA: paraformaldehyde; PPD: purified protein derivative; PtdIns3K: class III phosphatidylinositol 3-kinase; RELA: v-rel reticuloendotheliosis viral oncogene homolog A (avian); RIF: rifampicin; RLR: retinoic acid-inducible gene-I-like receptors; TDB: trehalose-6,6´-dibehenate; TLR4: toll-like receptor 4; Ultra-pure-LPS: ultra-pure lipopolysaccharide-EK; V-ATPase: vacuolar-type H ATPase.Susanta PahariShikha NegiMohammad AqdasEusondia ArnettLarry S SchlesingerJaved N Agrewala2020-02-05T10:22:03Z2020-02-05T10:22:03Zhttp://crdd.osdd.net/open/id/eprint/2540This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25402020-02-05T10:22:03ZNAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence.N-acetylglucosamine (NAG) belongs to the eight essential saccharides that are required to maintain the optimal health and precise functioning of systems ranging from bacteria to human. In the present study, we have developed a method, NAGbinder, which predicts the NAG-interacting residues in a protein from its primary sequence information. We extracted 231 NAG-interacting nonredundant protein chains from Protein Data Bank, where no two sequences share more than 40% sequence identity. All prediction models were trained, validated, and evaluated on these 231 protein chains. At first, prediction models were developed on balanced data consisting of 1,335 NAG-interacting and noninteracting residues, using various window size. The model developed by implementing Random Forest using binary profiles as the main principle for identifying NAG-interacting residue with window size 9, performed best among other models. It achieved highest Matthews Correlation Coefficient (MCC) of 0.31 and 0.25, and Area Under Receiver Operating Curve (AUROC) of 0.73 and 0.70 on training and validation data set, respectively. We also developed prediction models on realistic data set (1,335 NAG-interacting and 47,198 noninteracting residues) using the same principle, where the model achieved MCC of 0.26 and 0.27, and AUROC of 0.70 and 0.71, on training and validation data set, respectively. The success of our method can be appraised by the fact that, if a sequence of 1,000 amino acids is analyzed with our approach, 10 residues will be predicted as NAG-interacting, out of which five are correct. Best models were incorporated in the standalone version and in the webserver available at https://webs.iiitd.edu.in/raghava/nagbinder/.Sumeet PatiyalPiyush AgrawalVinod KumarAnjali DhallRajesh KumarGaurav MishraG.P.S. Raghava2020-10-20T04:44:09Z2020-10-20T04:44:09Zhttp://crdd.osdd.net/open/id/eprint/2610This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26102020-10-20T04:44:09ZExploration of space to achieve scientific breakthroughsLiving organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
Binod PrasadPeter RichterNithya VedakedathRocco MancinelliMarcus KrugerSebastian M. StrauchDaniela GrimmPhilippe DarrietJean-Paul ChapelJacob CohenMichael Lebert2019-12-05T14:11:56Z2019-12-05T14:11:56Zhttp://crdd.osdd.net/open/id/eprint/2485This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/24852019-12-05T14:11:56ZSynthesis of a novel gellan-pullulan nanogel and its application in adsorption of cationic dye from aqueous medium.The current study focused on synthesizing a novel gellan-pullulan composite nanogel via chemical crosslinking with DPPH. The physical and rheological properties of the synthesised nanogel was assessed by determining its particle size, zeta potential and effect of temperature and stress on viscosity of nanogels. Furthermore, the novel nanogel was assessed for its ability to ameliorate water resources by efficiently adsorbing cationic dyes. Methylene blue (MB) was used as a model cationic dye compound in the study. The adsorption capacity of nanogels for MB was evaluated by fitting different isotherm models and understanding thermodynamics and kinetics of the process. It was revealed from the overall analysis that nanogels had the property to adsorb MB in multilayer alignment. The gellan-pullulan composite nanogel was found to have better adsorption capability as compared to native gellan nanogel. This is the first report of gellan-pullulan nanogel and its application for cationic dye adsorption.. RichaAnirban Roy Choudhury2020-04-27T11:36:40Z2020-04-27T11:36:40Zhttp://crdd.osdd.net/open/id/eprint/2561This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25612020-04-27T11:36:40ZpH mediated rheological modulation of chitosan hydrogels.Chitosan (CS) hydrogels are used widely for multifarious applications in diverse fields due to the property of pH responsiveness. This study aims to explain the sensitivity of CS hydrogels to alteration in pH due to change in the concentration of acetic acid, which is a solvent for CS. Studies on changes in rheological properties in this regard are still scarce. The present study evaluated the change in rheological properties of the CS hydrogels by studying the flow behaviour, creep recovery and thixotropic property. The obtained data were used to fit mathematical models, like power law model and Herschel-Bulkley model to gain a vivid understanding of the rheological properties of CS hydrogel. Overall analyses revealed that the CS hydrogels, irrespective of the pH, were highly elastic in nature and exhibited significant creep recovery. However, the steady flow behaviour and thixotropy varied substantially with variation in pH.. RichaAnirban Roy Choudhury2020-06-29T15:36:02Z2020-06-30T12:30:40Zhttp://crdd.osdd.net/open/id/eprint/2579This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25792020-06-29T15:36:02ZSurfactin Like Broad Spectrum Antimicrobial Lipopeptide Co-produced With Sublancin From Bacillus subtilis Strain A52: Dual Reservoir of BioactivesAn antimicrobial substance producing strain designated as A52 was isolated from a marine sediment sample and identified as Bacillus sp., based on 16S rRNA gene sequence analysis. The ANI and dDDH analysis of the genome sequence displayed high identity with two strains of B. subtilis sub sp. subtilis. Strain A52 yielded two antimicrobial peptides (AMPs) that differed in activity spectrum. MALDI mass spectrometry analysis of HPLC purified fractions revealed mass of peptides as 3881.6 and 1061.9 Da. The antiSMASH analysis of genome sequence unraveled presence of identical biosynthetic cluster involved in production of sublancin from B. subtilis sub sp. subtilis strain 168, which yielded peptide with identical mass. The low molecular weight peptide is found to be a cyclic lipopeptide containing C16 β-hydroxy fatty acid that resembled surfactin-like group of biosurfactants. However, it differed in fatty acid composition and antimicrobial spectrum in comparison to other surfactins produced by strains of B. subtilis. It exhibited broad spectrum antibacterial activity, inhibited growth of pathogenic strains of Candida and filamentous fungi. Further, it exhibited hemolytic activity, but did not show phytotoxic effect in seed germination experiment. The emulgel formulation of surfactin-like lipopeptide showed antimicrobial activity in vitro and did not show any irritation effects in animal studies using BALB/c mice. Moreover, surfactin-like lipopeptide displayed synergistic activity with fluconazole against Candida, indicating its potential for external therapeutic applications.Deepika SharmaShelley Sardul SinghPiyush BaindaraShikha SharmaNeeraj KhatriVishakha GroverPrabhu B PatilSuresh Korpole2020-12-31T11:17:44Z2020-12-31T11:17:44Zhttp://crdd.osdd.net/open/id/eprint/2634This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26342020-12-31T11:17:44ZHeat induces end to end repetitive association in P. furiosusl-asparaginase which enables its thermophilic propertyIt remains undeciphered how thermophilic enzymes display enhanced stability at elevated temperatures. Taking l-asparaginase from P. furiosus (PfA) as an example, we combined scattering shapes deduced from small-angle X-ray scattering (SAXS) data at increased temperatures with symmetry mates from crystallographic structures to find that heating caused end-to-end association. The small contact point of self-binding appeared to be enabled by a terminal short β-strand in N-terminal domain, Leu179-Val-Val-Asn182 (LVVN). Interestingly, deletion of this strand led to a defunct enzyme, whereas suplementation of the peptide LVVN to the defunct enzyme restored structural frameworkwith mesophile-type functionality. Crystal structure of the peptide-bound defunct enzyme showed that one peptide ispresent in the same coordinates as in original enzyme, explaining gain-of lost function. A second peptide was seen bound to the protein at a different location suggesting its possible role in substrate-free molecular-association. Overall, we show that the heating induced self-assembly of native shapes of PfA led to an apparent super-stable assembly.Pankaj SharmaRachana TomarShiv Pratap Singh YadavMaulik D BadmaliaSamir K Nath. AshishBishwajit Kundu2020-12-31T05:23:39Z2020-12-31T05:23:39Zhttp://crdd.osdd.net/open/id/eprint/2628This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26282020-12-31T05:23:39ZA non-classical route of efficient plant uptake verified with fluorescent nanoparticles and root adhesion forces investigated using AFMClassical plant uptake is limited to hydrophilic or water-dispersible material. Therefore, in order to test the uptake behaviour of hydrophobic particles, here, we tested the fate of hydrophobic particles (oleylamine coated Cu2-xSe NPs (CS@OA)) in comparison to hydrophilic particles (chitosan-coated Cu2-xSe NPs (CS@CH)) by treatment on the plant roots. Surprisingly, hydrophobic CS@OA NPs have been found to be similar to 1.3 times more efficient than hydrophilic CS@CH NPs in tomato plant root penetration. An atomic force microscopy (AFM) adhesion force experiment confirms that hydrophobic NPs experience non-spontaneous yet energetically favorable root trapping and penetration. Further, a relative difference in the hydrophobic vs. hydrophilic NPs movement from roots to shoots has been observed and found related to the change in protein corona as identified by two dimensional-polyacrylamide gel electrophoresis (2D-PAGE) analysis. Finally, the toxicity assays at the give concentration showed that Cu2-xSe NPs lead to non-significant toxicity as compared to control. This technology may find an advantage in fertilizer application.Sandeep SharmaMohd MuddassirSaraladevi MuthusamyPardeep Kumar VaishnavManish SinghDeepak SharmaSelvaraju KanagarajanVijayakumar Shanmugam2020-10-29T05:33:10Z2020-10-29T05:33:10Zhttp://crdd.osdd.net/open/id/eprint/2611This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26112020-10-29T05:33:10ZAmino acid residues important for D-galactose recognition by the F-type lectin, Ranaspumin-4.F-type lectins are typically L-fucose binding proteins with characteristic L-fucose-binding and calciumbinding sequence motifs, and an F-type lectin fold. An exception is Ranaspumin-4, an F-type lectin of the Tungra frog, Engystomops pustulosus. Ranaspumin-4 is D-galactose specific and does not bind to L-fucose although it has the conserved L-fucose binding sequence motif and shares overall sequence similarity with other F-type lectins. Here, we report the detailed glycan-binding profile of wild-type Ranaspumin-4 using hemagglutination inhibition assays, flow cytometry assays and enzyme-linked lectin assays, and identify residues important for D-galactose recognition using rational site-directed mutagenesis. We demonstrate that Ranaspumin-4 binds to terminal D-galactose in alpha or beta linkage with preference for alpha 1-3, alpha 1-4,beta 1-3, and beta 1-4 linkages. Further, we find that a methionine residue (M31) in Ranaspumin-4 that occurs in place of a conserved Gln residue (in other F-type lectins), supports D-galactose recognition. Resides Q42 and F156 also likely aid in D-galactose recognition. (C) 2020 Elsevier Inc. All rights reserved.Shailza SharmaSonal MahajanSonali SunsunwalAasawari KhairnarT N C Ramya2020-02-26T14:58:21Z2020-04-04T17:36:08Zhttp://crdd.osdd.net/open/id/eprint/2542This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25422020-02-26T14:58:21ZKringles of substrate plasminogen provide a "catalytic switch" in plasminogen to plasmin turnover by Streptokinase.To understand the role of substrate plasminogen kringles in its differential catalytic processing by the streptokinase - human plasmin (SK-HPN) activator enzyme, Fluorescence Resonance Energy Transfer (FRET) model was generated between the donor labeled activator enzyme and the acceptor labeled substrate plasminogen (for both kringle rich Lys plasminogen - LysPG, and kringle less microplasminogen - µPG as substrates). Different steps of plasminogen to plasmin catalysis i.e. substrate plasminogen docking to scissile peptide bond cleavage, chemical transformation into proteolytically active product, and the decoupling of the nascent product from the SK-HPN activator enzyme were segregated selectively using (1) FRET signal as a proximity sensor to score the interactions between the substrate and the activator during the cycle of catalysis, (2) active site titration studies and (3) kinetics of peptide bond cleavage in the substrate. Remarkably, active site titration studies and the kinetics of peptide bond cleavage have shown that post docking chemical transformation of the substrate into the product is independent of kringles adjacent to the catalytic domain. Stopped-flow based rapid mixing experiments for kringle rich and kringle less substrate plasminogen derivatives under substrate saturating and single-cycle turn-over conditions have shown that the presence of kringle domains adjacent to the catalytic domain in the macromolecular substrate contributes by selectively speeding up the final step, namely the product release/expulsion step of catalysis by the streptokinase-plasmin(ogen) activator enzyme.Vandna SharmaShekhar KumarGirish Sahni2020-02-05T10:10:59Z2020-02-05T10:10:59Zhttp://crdd.osdd.net/open/id/eprint/2537This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25372020-02-05T10:10:59ZFacile One Pot Greener Synthesis of Sophorolipid Capped Gold Nanoparticles and its Antimicrobial Activity having Special Efficacy Against Gram Negative Vibrio cholerae.Microbes develop several strategies to survive in the adverse condition such as biofilm formation, attaining non-dividing state, altering drug target or drug, thereby increases the burden of drug dosage. To combat these issues, nanoparticles have shown an alternative approach for new treatment strategy but synthesis via chemical synthetic route limits their application in biomedical field. Here, green method for the synthesis of gold nanoparticles using sophorolipid (SL) is discussed that is characterized by various techniques. Initially, the antimicrobial activity was checked against metabolically active state of microbes; Gram-positive Staphylococcus aureus and Gram-negative Vibrio cholerae using XTT assay and growth kinetics assay. Results suggested higher efficacy of nanoparticles for Gram-negative, therefore further analyzed against Escherichia coli that confirmed its potency for the same. AuNPs-SL also signifies its efficiency at least metabolically active state; non dividing cells and biofilm of these microbes. Induced morphological changes were studied by SEM that revealed AuNPs-SL led to disruption of cell membrane and leakage of intracellular fluid to the surroundings. Inhibition of respiratory enzymes activity also plays a crucial role in bactericidal action as indicated by LDH assay. Synergy of AuNPs-SL with different antibiotics was also analyzed using checkerboard assay. These results suggested the possible use of AuNPs-SL as an antimicrobial therapy in the field of nanomedicine.Sristy ShikhaSaumya Ray ChaudhuriMani Shankar Bhattacharyya2020-02-05T10:18:52Z2020-04-04T17:41:51Zhttp://crdd.osdd.net/open/id/eprint/2539This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25392020-02-05T10:18:52ZMetabolic switching of during hypoxia is controlled by the virulence regulator PhoP. (Mtb) retains the ability to establish an asymptomatic latent infection. A fundamental question in mycobacterial physiology is to understand the mechanisms involved in hypoxic stress, a critical player in persistence. Here, we show that the virulence regulator PhoP responds to hypoxia, the dormancy signal and effectively integrates hypoxia with nitrogen metabolism. We also provide evidence to demonstrate that both under nitrogen limiting conditions and during hypoxia, locus controls key genes involved in nitrogen metabolism. Consistently, under hypoxia shows growth attenuation even with surplus nitrogen, the alternate electron acceptor, and complementation of the mutant restores bacterial growth. Together, our observations provide new biological insights into the role of PhoP in integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR. The results have significant implications on the mechanism of intracellular survival and growth of the tubercle bacilli under a hypoxic environment within the phagosome. Mtb retains the unique ability to establish an asymptomatic latent infection. To understand the mechanisms involved in hypoxic stress which plays a critical role in persistence, we show that the virulence regulator PhoP is linked to hypoxia, the dormancy signal. In keeping with this, was shown to play a major role in Mtb growth under hypoxia even in presence of surplus nitrogen, the alternate electron acceptor. Our results showing regulation of hypoxia-responsive genes provide new biological insights into role of the virulence regulator in metabolic switching by sensing hypoxia and integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR.Prabhat Ranjan SinghVijjamarri Anil KumarDibyendu Sarkar2020-09-24T09:03:51Z2020-09-24T09:03:51Zhttp://crdd.osdd.net/open/id/eprint/2581This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25812020-09-24T09:03:51ZComparative genome analysis and characterization of a MDR Klebsiella variicolaKlebsiella variicola is an emerging pathogen responsible for causing blood-stream infections, urinary and respiratory tract related diseases in humans. In this report, we describe the genome sequence data and phenotypic characterization of K. variicola strain KV093 isolated from India. Comparative genome sequence analysis revealed the presence of genes linked with virulence, iron acquisition and transport, type 1 and type 3 pili, secretion systems including the capsular gene cluster. The plant-associated genes such as nitrogen fixation, growth and defense mechanisms against oxidative stress were also identified. On performing antibiotic susceptibility testing, growth inhibition, and stress challenge assays it was observed that the drug resistant K. variicola KV093 exhibited cross resistance to various antibiotics, antiseptics, including disinfectants. This report highlights the arsenal of virulence and antibiotic resistance determinants in K. variicola KV093, an effort emphasizing the current pressing need for regular surveillance of K. variicola strains especially in India.Vijaya Bharathi SrinivasanGovindan Rajamohan2020-10-29T06:02:10Z2020-10-29T06:02:10Zhttp://crdd.osdd.net/open/id/eprint/2614This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26142020-10-29T06:02:10ZPseudomonas karstica sp. nov. and Pseudomonas spelaei sp. nov., isolated from calcite moonmilk deposits from cavesA taxonomic study of two fluorescent Pseudomonas strains (HJ/4(T) and SJ/9/1(T)) isolated from calcite moonmilk samples obtained from two caves in the Moravian Karst in the Czech Republic was carried out. Results of initial 16S rRNA gene sequence analysis assigned both strains into the genus Pseudomonas and showed Pseudomonas yamanorum 8H1(T) as their closest neighbour with 99.8 and 99.7% 16S rRNA gene similarities to strains HJ/4(T) and SJ/9/1(T). respectively. Subsequent sequence analysis of rpoD, rpoB and gyrB housekeeping genes confirmed the highest similarity of both isolates to P. yamanorum 8H1(T). but phylogeny and sequences similarities implied that they are representatives of two novel species within the genus Pseudomonas. Further study comprising whole-genome sequencing followed by average nucleotide identity and digital DNA-DNA hybridization calculations, repetitive sequence-based PCR fingerprinting with the REP and ERIC primers, automated ribotyping with the EcoRl restriction endonuclease, cellular fatty acid analysis, quinone and polar lipid characterization, and extensive biotyping confirmed clear separation of both analysed strains from the remaining Pseudomonas species and showed that they represent two novel species within the genus Pseudomonas for which the names Pseudomonas karstica sp. nov. (type strain HJ/4(T) =CCM 7891(T) =LMG 27930(T)) and Pseudomonas spelaei sp. nov. (type strain SJ/9/1(T)=CCM 7893(T)=LMG 27931(T)) are suggested.Pavel SvecMarcel KosinaMichal ZemanPavla HolochovaStanislava KralovaEva NemcovaLenka Micenkova. UrvashiVipin GuptaUtkarsh SoodRup LalSuresh Korpole2020-04-04T17:18:53Z2020-05-15T09:46:27Zhttp://crdd.osdd.net/open/id/eprint/2551This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25512020-04-04T17:18:53ZAn evaluation of liposome-based diagnostics of pulmonary and extrapulmonary tuberculosis.: Tuberculosis (TB) is still one of the major global health threats and delayed diagnosis or misdiagnosis continues to fuel the global epidemic. The conventional diagnostic approaches have shortcomings that might hinder the process of diagnosis of the disease and ultimately affect the prognosis.: We emphasize on the process of the synthesis of liposomes, its physicochemical properties affecting the formulation and their utilization in the field of molecular diagnostics for TB. The review also sheds a light on other nanoparticle-based molecular diagnostic approaches for TB. Despite the advent of science, we are yet to have a diagnostic tool that is simple, rapid, sensitive, and specific, and most importantly, one that enables us to demarcate patients with active tuberculosis from those with quiescent lesions, prior vaccination, or other diseases.: The utility of liposomes for diagnostic purposes has been attempted so as to overcome the challenges posed by conventional diagnostic tools for Tuberculosis. Through this review we present insights into liposome formulation and selection processes, various studies that report the use of liposome-based diagnostic tools for tuberculosis, as well as the limitations associated with the same that can be improvised to make the technology more efficient.Nikunj TandelAnish Z JosephAishwarya JoshiPriya ShramaRavi Pn MishraRajeev K TyagiPrakash S Bisen2020-06-10T09:57:52Z2020-06-10T09:57:52Zhttp://crdd.osdd.net/open/id/eprint/2576This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25762020-06-10T09:57:52ZMalariaNikunj TandelRajeev K Tyagi2020-09-24T08:51:02Z2020-09-24T08:51:02Zhttp://crdd.osdd.net/open/id/eprint/2603This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26032020-09-24T08:51:02ZEvaluation of novobiocin and telmisartan for anti-CHIKV activityChikungunya has re-emerged as an epidemic with global distribution and high morbidity, necessitating the need for effective therapeutics. We utilized already approved drugs with a good safety profile used in other diseases for their new property of anti-chikungunya activity. It provides a base for a fast and efficient approach to bring a novel therapy from bench to bedside by the process of drug-repositioning. We utilized an in-silico drug screening with FDA approved molecule library to identify inhibitors of the chikungunya nsP2 protease, a multifunctional and essential non-structural protein required for virus replication. Telmisartan, an anti-hypertension drug, and the antibiotic novobiocin emerged among top hits on the screen. Further, SPR experiments revealed strong in-vitro binding of telmisartan and novobiocin to nsP2 protein. Additionally, small angle x-ray scattering suggested binding of molecules to nsP2 and post-binding compaction and retention of monomeric state in the protein-inhibitor complex. Protease activity measurement revealed that both compounds inhibited nsP2 protease activity with IC50 values in the low micromolar range. More importantly, plaque formation assays could show the effectiveness of these drugs in suppressing virus propagation in host cells. We propose novobiocin and telmisartan as potential inhibitors of chikungunya replication. Further research is required to establish the molecules as antivirals of clinical relevance against chikungunya.Praveen Kumar TripathiAnjali SoniShiv Pratap Singh YadavAnkit KumarSiva RaghavenderPradeep SharmaSunil Sujhatha. AshishBhyravabhotla JayaramAshok Kumar Patel2020-06-10T10:25:35Z2020-06-10T12:36:14Zhttp://crdd.osdd.net/open/id/eprint/2577This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25772020-06-10T10:25:35ZRole of Novel Drug Delivery Vehicles in NanobiomedicineMedical Nanotechnology and Nanomedicine introduces non-experts to the world of nanomedicine and its evolving organizational infrastructure. Considering the fluid nature of nano breakthroughs and the delicate balance between benefits and consequences as they apply to medicine, readers at all levels will gain a practical, understandable base of information on these developments so that they may take the greatest advantage of them. This practical reference investigates the impact of nanotechnology on applications in medicine and biomedical sciences, and the broader societal and economic effects. Eschewing technological details, it focuses on enhancing awareness of the business, regulatory, and administrative aspects of medical applications. It gives readers a critical, balanced, and realistic evaluation of existing nanomedicine developments and future prospects and provides an ideal foundation upon which to plan and make decisions.Rajeev K Tyagi2020-07-30T11:41:23Z2020-10-20T04:19:22Zhttp://crdd.osdd.net/open/id/eprint/2592This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25922020-07-30T11:41:23ZSynthesis of Bioactive Complex Small Molecule-Ciprofloxacin Conjugates and Evaluation of Their Antibacterial ActivityConjugates between pharmaceuticals and small molecules enable access to a vast chemical space required for the discovery of new lead molecules with modified therapeutic potential. However, the dearth of specific chemical reactions that are capable of functionalizing drugs and bioactive natural products presents a formidable challenge for preparing their conjugates. Here, we report a support-free CuI-nanoparticle-catalyzed strategy for conjugating electron-deficient and electron-rich terminal alkynes with a ciprofloxacin methyl ester. Our conjugation technique exploits the late-stage functionalization of bioactive natural products such as tocopherol, vasicinone, amino acids, and pharmaceuticals such as aspirin and paracetamol to provide conjugates in excellent yields under mild and green conditions. This protocol also enabled the synthesis of (hetero)arene-ciprofloxacin 1,4-disubstituted 1,2,3-triazoles in good yields and high regioselectivities. These synthesized ciprofloxacin conjugates were evaluated in vitro for their antibacterial activity against a panel of relevant bacteria. A significant number of conjugates showed comparable activity against Gram-positive and Gram-negative bacteria. Moreover, some conjugates exhibited less toxicity than ciprofloxacin against two mammalian cell lines, suggesting the utility for the future investigation of these compounds for in vivo efficacy and pharmacokinetic studies.Rahul UpadhyayRahul KumarManoj JangraRohit RanaOnkar S NayalHemraj NandanwarSushil K Maurya2020-10-20T04:13:07Z2020-10-20T04:13:07Zhttp://crdd.osdd.net/open/id/eprint/2608This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26082020-10-20T04:13:07ZParaclostridium dentum, a novel species with pathogenic features isolated from human dental plaque sampleA strictly anaerobic bacterial strain designated as SKVG24 was isolated from subgingival dental plaque samples of patients suffering from periodontitis. Cells were stained Gram-positive, rod shaped with endospore. The strain showed negative reaction to catalase and oxidase enzymes, but positive for gelatinase activity. Optimal growth was observed at 37 °C temperature and 7.0 pH. The 16S rRNA gene sequence BLAST analysis assigned strain SKVG24 to the genus Paraclostridium as it displayed 99.93% identity with P. benzoelyticum JC272T followed by P. bifermentans ATCC 638T (99.79%). However, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of the whole genome sequence showed <97% and <70% identity, respectively, with type strains of all closely related species. The G + C content of the DNA was 28.7 mol%. Total lipids profile showed presence of glycolipids as major lipids. Pathogenic features like hemolysis, gelatin hydrolysis and production of volatile sulfur compounds exhibited by strain SKVG24T were analogous to those observed in the established oral pathogenic strains. Further, whole genome sequence analysis confirmed the presence of genes encoding virulence factors and provided genomic insights on adaptation of the strain in oral environment. Based on the phenotypic and genetic differences with phylogenetic relatives, strain SKVG24T is proposed to represent a new species of the genus Paraclostridium with potential pathogenic ability, for which the name Paraclostridium dentum sp. nov., is suggested. The proposed type strain is SKVG24T (MTCC 12836T; = JCM 32760T).. UrvashiStanzin ChoksketAshish SharmaDeepika SharmaVishakha GroverSuresh Korpole2020-04-04T17:29:42Z2020-04-04T17:29:42Zhttp://crdd.osdd.net/open/id/eprint/2552This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25522020-04-04T17:29:42ZBacterial Populations in Subgingival Plaque Under Healthy and Diseased Conditions: Genomic Insights into Oral Adaptation Strategies by sp. Strain DISK7.Human oral cavity is a complex habitat comprising about 700 microbial species and represents the most complex microbiota after gastrointestinal tract. In fact, oral microbiota directly influences health, metabolism and immune responses of the host. Metagenomic studies based on 16S rDNA profiling has reported the inhabitant bacteria mainly belonging to phyla , , , , and . Therefore, it is essential to isolate these strains and characterize in detail to understand their interaction. We have isolated strains from subgingival plaque from healthy to diseased individuals and the molecular characterization based on 16S rRNA gene sequence analysis showed predominance of , specifically members of the genus . Species of and were also found in significant number, which are considered as secondary colonizers. However, the population of was decreased in diseased conditions with the increase in opportunistic pathogenic strains pertaining to genera like , , , and . Further, we have also made an attempt to gain genomic insights on adaptation features and interactions of an isolate, sp. strain DISK7 by performing whole genome sequencing and analysis, subsequently biochemical characterization to explore its functional and metabolic properties for the development as probiotic agent.. UrvashiDeepika SharmaShikha SharmaVijay PalRup LalPrabhu PatilVishakha GroverSuresh Korpole2020-03-02T10:03:40Z2020-03-02T10:03:40Zhttp://crdd.osdd.net/open/id/eprint/2546This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25462020-03-02T10:03:40ZAntioxidant and Wound Healing Property of Gelsolin in 3T3-L1 Cells.Delineation of factors which affect wound healing would be of immense value to enable on-time or early healing and reduce comorbidities associated with infections or biochemical stress like diabetes. Plasma gelsolin has been identified earlier to significantly enable injury recovery compared to placebo. This study evaluates the role of rhuGSN for its antioxidant and wound healing properties in murine fibroblasts (3T3-L1 cell line). Total antioxidant capacity of rhuGSN increased in a concentration-dependent manner (0.75-200 g/mL). Cells pretreated with 0.375 and 0.75 g/mL rhuGSN for 24 h exhibited a significant increase in viability in a MTT assay. Preincubation of cells with rhuGSN for 24 h followed by oxidative stress induced by exposure to HO for 3 h showed cytoprotective effect. rhuGSN at 12.5 and 25 g/mL concentration showed an enhanced cell migration after 20 h of injury in a scratch wound healing assay. The proinflammatory cytokine IL-6 levels were elevated in the culture supernatant. These results establish an effective role of rhuGSN against oxidative stress induced by HO and in wound healing of 3T3-L1 fibroblast cells.Bhavna VaidBhupinder Singh ChopraSachin RautAmin SagarMaulik D Badmalia. AshishNeeraj Khatri2020-06-02T10:40:29Z2020-06-02T10:40:42Zhttp://crdd.osdd.net/open/id/eprint/2575This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25752020-06-02T10:40:29ZHalocatena pleomorpha Gen. Nov. Sp. Nov., an Extremely Halophilic Archaeon of Family Halobacteriaceae Isolated From Saltpan Soil.A novel archaeal strain designated as SPP-AMP-1T was isolated from saltpan soil, using the serial dilution method on a halophilic archaeal medium supplemented with ampicillin. Cells were both rod-shaped and pleomorphic in nature, non-motile, unable to produce acid from a variety of sugars or grow anaerobically with different substrates (l-arginine) and electron acceptors (DMSO, nitrate). Optimal growth was observed at 42 °C, 3.4-4.2 M NaCl and pH 7.2. Cells did not lyse in distilled water and grew in the absence of Mg2+ ions. Phylogenetic analysis based on the sequences of 16S rRNA gene, amino acid sequence of β'-subunit of RNA polymerase and 400 conserved proteins retrieved from the whole genome assemblies showed that strain SPP-AMP-1T was distantly related to any existing genera within the family Halobacteriaceae. MK-8 was the only quinone detected. Polar lipid analysis showed a unique combination of diethyl derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, glycosyl-mannosyl-glucosyl diether and sulphated glycosyl-mannosyl-glucosyl diether as the major lipids. The G+C content of genomic DNA is 57.7 mol%. The phenotypic, phylogenetic and genomic data supported the concept of the novel genus status of strain SPP-AMP-1T in the family Halobacteriaceae for which the name Halocatena pleomorpha gen. nov., sp. nov., is proposed; the type strain is SPP-AMP-1T (=JCM 31368T=KCTC 4276T=MTCC 12579T).Ashish VermaYash PalPravin KumarSrinivasan Krishnamurthi2020-12-31T11:04:40Z2020-12-31T11:06:18Zhttp://crdd.osdd.net/open/id/eprint/2633This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26332020-12-31T11:04:40ZIsolation and Taxonomic Characterization of Novel Haloarchaeal Isolates From Indian Solar Saltern: A Brief Review on Distribution of Bacteriorhodopsins and V-Type ATPases in HaloarchaeaHaloarchaea inhabit high salinity environments worldwide. They are a potentially rich source of crucial biomolecules like carotenoids and industrially useful proteins. However, diversity in haloarchaea present in Indian high salinity environments is poorly studied. In the present study, we isolated 12 haloarchaeal strains from hypersaline Kottakuppam, Tamil Nadu solar saltern in India. 16S rRNA based taxonomic characterization of these isolates suggested that nine of them are novel strains that belong to genera Haloarcula, Halomicrobium, and Haloferax. Transmission electron microscopy suggests the polymorphic nature of these haloarchaeal isolates. Most of the haloarchaeal species are known to be high producers of carotenoids. We were able to isolate carotenoids from all these 12 isolates. The UV-Vis spectroscopy-based analysis suggests that bacterioruberin and lycopene are the major carotenoids produced by these isolates. Based on the visual inspection of the purified carotenoids, the isolates were classified into two broad categories i.e., yellow and orange, attributed to the differences in the ratio of bacterioruberin and lycopene as confirmed by the UV-Vis spectral analysis. Using a PCR-based screening assay, we were able to detect the presence of the bacteriorhodopsin gene (bop) in 11 isolates. We performed whole-genome sequencing for three bop positive and one bop negative haloarchaeal isolates. Whole-genome sequencing, followed by pan-genome analysis identified multiple unique genes involved in various biological functions. We also successfully cloned, expressed, and purified functional recombinant bacteriorhodopsin (BR) from one of the isolates using Escherichia coli as an expression host. BR has light-driven proton pumping activity resulting in the proton gradient across the membrane, which is utilized by V-Type ATPases to produce ATP. We analyzed the distribution of bop and other accessory genes involved in functional BR expression and ATP synthesis in all the representative haloarchaeal species. Our bioinformatics-based analysis of all the sequenced members of genus Haloarcula suggests that bop, if present, is usually inserted between the genes coding for B and D subunits of the V-type ATPases operon. This study provides new insights into the genomic variations in haloarchaea and reports expression of new BR variant having good expression in functional form in E. coli.Dipesh Kumar VermaChetna ChaudharyLatika SinghChandni SidhuBusi SiddhardhaE.Senthil PrasadKrishan Gopal Thakur2022-03-29T04:20:28Z2022-03-29T04:20:28Zhttp://crdd.osdd.net/open/id/eprint/2761This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/27612022-03-29T04:20:28ZIsolation and Taxonomic Characterization of Novel Haloarchaeal Isolates From Indian Solar Saltern: A Brief Review on Distribution of Bacteriorhodopsins and V-Type ATPases in Haloarchaea (vol 11, 554927, 2020)Haloarchaea inhabit high salinity environments worldwide. They are a potentially rich source of crucial biomolecules like carotenoids and industrially useful proteins. However, diversity in haloarchaea present in Indian high salinity environments is poorly studied. In the present study, we isolated 12 haloarchaeal strains from hypersaline Kottakuppam, Tamil Nadu solar saltern in India. 16S rRNA based taxonomic characterization of these isolates suggested that nine of them are novel strains that belong to genera Haloarcula, Halomicrobium, and Haloferax. Transmission electron microscopy suggests the polymorphic nature of these haloarchaeal isolates. Most of the haloarchaeal species are known to be high producers of carotenoids. We were able to isolate carotenoids from all these 12 isolates. The UV-Vis spectroscopy-based analysis suggests that bacterioruberin and lycopene are the major carotenoids produced by these isolates. Based on the visual inspection of the purified carotenoids, the isolates were classified into two broad categories i.e., yellow and orange, attributed to the differences in the ratio of bacterioruberin and lycopene as confirmed by the UV-Vis spectral analysis. Using a PCR-based screening assay, we were able to detect the presence of the bacteriorhodopsin gene (bop) in 11 isolates. We performed whole-genome sequencing for three bop positive and one bop negative haloarchaeal isolates. Whole-genome sequencing, followed by pan-genome analysis identified multiple unique genes involved in various biological functions. We also successfully cloned, expressed, and purified functional recombinant bacteriorhodopsin (BR) from one of the isolates using Escherichia coli as an expression host. BR has light-driven proton pumping activity resulting in the proton gradient across the membrane, which is utilized by V-Type ATPases to produce ATP. We analyzed the distribution of bop and other accessory genes involved in functional BR expression and ATP synthesis in all the representative haloarchaeal species. Our bioinformatics-based analysis of all the sequenced members of genus Haloarcula suggests that bop, if present, is usually inserted between the genes coding for B and D subunits of the V-type ATPases operon. This study provides new insights into the genomic variations in haloarchaea and reports expression of new BR variant having good expression in functional form in E. coli.Dipesh Kumar VermaChetna ChaudharyLatika SinghChandni SidhuBusi SiddhardhaSenthil E. PrasadKrishan Gopal Thakur2020-10-20T04:29:02Z2020-10-20T04:29:02Zhttp://crdd.osdd.net/open/id/eprint/2609This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/26092020-10-20T04:29:02ZBiochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the IsolateHaloarchaea are salt-loving archaea and potential source of industrially relevant halotolerant enzymes. In the present study, three reddish-pink, extremely halophilic archaeal strains, namely wsp1 (wsp-water sample Pondicherry), wsp3, and wsp4, were isolated from the Indian Solar saltern. The phylogenetic analysis based on 16S rRNA gene sequences suggests that both wsp3 and wsp4 strains belong to Halogeometricum borinquense while wsp1 is closely related to Haloferax volcanii species. The comparative genomics revealed an open pangenome for both genera investigated here. Whole-genome sequence analysis revealed that these isolates have multiple copies of industrially/biotechnologically important unique genes and enzymes. Among these unique enzymes, for recombinant expression and purification, we selected four putative α-amylases identified in these three isolates. We successfully purified functional halotolerant recombinant Amy2, from wsp1 using pelB signal sequence-based secretion strategy using Escherichia coli as an expression host. This method may prove useful to produce functional haloarchaeal secretory recombinant proteins suitable for commercial or research applications. Biochemical analysis of Amy2 suggests the halotolerant nature of the enzyme having maximum enzymatic activity observed at 1 M NaCl. We also report the isolation and characterization of carotenoids purified from these isolates. This study highlights the presence of several industrially important enzymes in the haloarchaeal strains which may potentially have improved features like stability and salt tolerance suitable for industrial applications.Dipesh Kumar VermaGunjan VasudevaChandni SidhuAnil Kumar PinnakaE.Senthil PrasadKrishan Gopal Thakur2020-06-02T10:16:54Z2020-06-02T10:16:54Zhttp://crdd.osdd.net/open/id/eprint/2574This item is in the repository with the URL: http://crdd.osdd.net/open/id/eprint/25742020-06-02T10:16:54ZCloning, Characterization, and Structural Modeling of an Extremophilic Bacterial Lipase Isolated From Saline Habitats of the Thar DesertLipases have a characteristic folding pattern of α/β-hydrolase with mostly parallel β-sheets, flanked on both sides by α-helixes in the structure. The active site is formed by a catalytic triad (serine, aspartic/glutamic acid, and histidine), which is highly conserved. In this study, we have used an integrated experimental and computational approach to identify the extremophilic microbial lipases from the saline habitats of the Thar Desert of Rajasthan. Lipase-producing bacteria were screened and a few samples showed significant lipase activity in both quantitative and qualitative experiments. 16S rRNA sequence analysis of the isolate F1 showed that its sequence is quite similar to that of Bacillus licheniformis and Bacillus haynesii, indicating that this isolate belongs to a new subspecies of Bacillus. The isolate F7 showed maximum sequence identity with Bacillus tequilensis strain 10b. The isolate F7 sequence analysis provided a clear testimony that it can be a new strain of Bacillus tequilensis. The F7 lipase exhibited optimal activity at 60 °C and pH 9. Structural modeling of the F7 lipase revealed that it has a highly conserved alpha/beta hydrolase fold at the sequence and structural level except for the N-terminal region. Interestingly, residue Glu128 was different from the template structure and showed the hydrogen bonding between the side chain of Glu128 and side chains of Asn35 and Gln152 amino acids. Besides, this amino acid also showed salt bridge interaction between Glu128--Lys101. These interactions may be assisting in preserving the stability and activity of lipase at high temperatures and in alkaline pH conditions. The information gathered from this investigation will guide in the rational designing of new more potential extremophilic lipase.Swati VermaRajinder KumarDeepak SharmaHukum GahlotPushpender Kumar SharmaGautam Kumar Meghawanshi