Jayadev Joshi

Jayadev Joshi
Cleveland Clinic · Department of Genomic Medicine

About

53
Publications
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395
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Introduction

Publications

Publications (53)
Article
Full-text available
Background Computational methods based on initial screening and prediction of peptides for desired functions have proven to be effective alternatives to lengthy and expensive biochemical experimental methods traditionally utilized in peptide research, thus saving time and effort. However, for many researchers, the lack of expertise in utilizing pro...
Article
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Aims Allergic airway disease manifestation is induced by lysophosphatidylcholine (LPC) through CD1d-restricted Natural killer T (NKT) cells. Choline chloride (ChCl) and LPC both have the “choline” moiety in their structure and this may interplay the effect in allergic airway disease pathway. Main methods To test the hypothesis, mice were sensitize...
Article
Full-text available
Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve, and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galax...
Article
Full-text available
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely acc...
Article
Measurement of traffic emissions has gained a lot of interest in recent times due to its contribution to urban pollution. This paper reports the outcome from an unmanned aerial vehicle (UAV) based measurement of PM concentration near an urban roadway at Kolkata, India. A total of 54 flights were carried out for simultaneous measurements of PM1, PM2...
Article
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DNA methylation, catalyzed by DNA methyltransferase (DNMT), is a well-characterized epigenetic modification in cancer cells. In particular, promoter hypermethylation of AR and ESR1 results in loss of expression on Androgen Receptor (AR) and Estrogen Receptor (ER), respectively, and is associated with a hormone refractory state. We now report that G...
Article
Low-cost sensors have the potential to revolutionize air pollution research by providing high spatial resolution data. However, data accuracy from the low-cost sensors remains a major concern. Therefore, it is necessary to evaluate the performance of the low-cost sensors. The current study evaluated the performance of two such low cost PM (particul...
Article
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As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the po...
Preprint
Full-text available
Computational methods based on initial screening and prediction of peptides for desired functions have been proven effective alternatives to the lengthy and expensive methods traditionally utilized in peptide research, thus saving time and effort. However, for many researchers, the lack of expertise in utilizing programming libraries and the lack o...
Chapter
Bioinformatics and chemoinformatics are rapidly evolving fields that demand sophisticated algorithms and methods to handle complex data such as genomics data, medical imaging, and electronic medical records. These data can be categorized as big data. During the past few decades, computational methods have impacted biomedical research dramatically....
Preprint
Full-text available
Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize, retrieve, and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to m...
Article
Bacillus anthracis is the causative agent of anthrax in humans, bovine, and other animals. B. anthracis pathogenesis requires differentiation of dormant spores into vegetative cells. The spores inherit cellular components as phenotypic memory from the parent cell, and this memory plays a critical role in facilitating the spores’ revival. Since meta...
Preprint
Full-text available
Bacillus anthracis is the causative agent of anthrax in humans, bovine, and other animals. B. anthracis pathogenesis requires differentiation of dormant spores into vegetative cells. The spores inherit cellular components as phenotypic memory from the parent cell, and this memory plays a critical role in facilitating the spores' revival. Because me...
Article
Full-text available
Therapeutic hypothermia has proven benefits in critical care of a number of diseased states, where inflammation and oxidative stress are the key players. Here, we report that adenosine monophosphate (AMP) triggered hypometabolic state (HMS), 1-3 hours after lethal total body irradiation (TBI) for a duration of 6 hours, rescue mice from radiation-in...
Article
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Drug discovery field has tremendously progressed during last few decades, however, an effective radiation countermeasure agent for the safe administration to the victims of radiation exposure is still unavailable. This multi-model study is aimed at elucidating the mechanistic aspects of a novel podophyllotoxin and rutin combination (henceforth refe...
Article
Full-text available
Background: The lack of a safe and effective drug against radiation injury is a major hurdle in management of these diseases. Owing to unprecedented radionuclear threats and accidents that may occur, screening of Johns Hopkins Clinical Compound Library (JHCCL) was carried out in zebrafish embryos for identifying novel radio modulators against letha...
Article
Full-text available
Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins is not studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation....
Article
Ligand bound beta 2 adrenergic receptor (β2AR) crystal structures are in use for screening of compound libraries for identifying inducers and blockers. However, in case of G protein coupled receptors (GPCR), docking and binding energy (BE) calculations are not enough to discriminate agonist and antagonists. Absence of a reliable model for discrimin...
Article
Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9–22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-...
Article
Full-text available
Abstract The Johns Hopkins Clinical Compound Library (JHCCL), a collection of Food and Drug Administration (FDA)-approved small molecules (1400), was screened in silico for identification of novel β2AR blockers and tested for hematopoietic stem cell (HSC) expansion and radioprotection in zebrafish embryos. Docking studies, followed by the capacity...
Article
Full-text available
Mycobacterium ulcerans, the causative agent of Buruli ulcer in humans, is unique among the members of Mycobacterium genus due to the presence of the virulence determinant megaplasmid pMUM001. This plasmid encodes multiple virulence-associated genes, including mup011, which is an uncharacterized Ser/Thr protein kinase (STPK) PknQ. In this study, we...
Article
Drug repositioning is an approach of significant translatability, and the present study was undertaken to screen a collection of FDA approved small-molecule clinical compounds for identification of novel radioprotective agents. Screening of JHCCL (Johns Hopkins Clinical Compound Library), a collection of 1,400 FDA approved small molecules, lead to...
Article
Pseudomonas is a highly versatile bacterium at the species level with great ecological significance. These genetically and metabolically diverse species have undergone repeated taxonomic revisions. We propose a strategy to identify Pseudomonas up to species level, based on the unique features of their 16S rDNA (rrs) gene sequence, such as the frame...
Article
Full-text available
Cycloxygenase-2 (COX-2) is well established for its role in inflammation, cancer and has also been reported to play a significant role in radiation induced inflammation and bystander effect. It has already been reported to have a role in protection against radiation induced damage, suggesting it to be an important target for identifying novel radia...
Article
Cycloxygenase-2 (COX-2) is well established for its role in inflammation, cancer and has also been reported to play a significant role in radiation induced inflammation and bystander effect. It has already been reported to have a role in protection against radiation induced damage, suggesting it to be an important target for identifying novel radia...
Article
Full-text available
To explore bacterial diversity for elucidating genetic variability in acylhomoserine lactone (AHL) lactonase structure, we screened 800 bacterial strains. It revealed the presence of a quorum quenching (QQ) AHL-lactonase gene (aiiA) in 42 strains. These 42 strains were identified using rrs (16S rDNA) sequencing as Bacillus strains, predominantly B....
Article
Full-text available
Traditionally, drugs are discovered by testing compounds synthesized in time consuming multi-step processes against a battery of invivo biological screens. Promising compounds are then further studied in development, where their pharmacokinetic properties, metabolism and potential toxicity were investigated. Here, we present a study on herbal lead...
Article
The specificity of drug targets is a great challenge in the pharma-proteomics field of cancer biology. In particular, bioinformatics methods based on complex networks and Gene Ontologies (GOs) are very useful in this area. This work reviews some bioinformatics concepts and previous studies related to Colorectal Cancer (CRC) research using GOs, comp...
Data
Full-text available
Figures S1-S15 'Guide trees' for phylogenetic famework. File contains 'Guide trees' for all the 15 Clostridium spp. used to develop phylogenetic framework sequences for this study.
Data
Table S1 Clostridium species. File contains rrs sequences of Clostridium species which occurred with low frequency and the number of sequences used in this study http://rdp.cme.msu.edu/.
Data
Figure S16 Phylogenetic tree of 16S rDNA of Clostridium spp. and Framework sequences. File contains a neighbor - joining analysis of rrs sequences of Swine fecal bacterium, Clostridiaceae bacterium and unidentified eubacterium - 31 along with 56 of phylogenetic framework.
Data
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Figure S17 Phylogenetic tree of 84 16S rDNA sequences of 'novel' Clostridium species. File contains a neighbor - joining analysis of 56 representative novel Clostridium sequences.
Data
Full-text available
Figures S18-S19 Phylogenetic tree of 16S rDNA of novel Clostridium spp. and low frequency Clostridium spp. File contains a neighbor - joining analysis performed on the rrs sequences of novel Clostridium sp. (Additional file 4: Table S2) 56 along with 83 representatives of Clostridium sp. known to occur at low frequency (Additional file 4: Table S3)...
Data
Table S22 Nucleotide signatures. File contains nucleotide signatures of rrs sequences common to Clostridium sp. used for developing framework sequences.
Data
Tables S23-S26 Representative motifs for Clostridium botulinum and C. perfringens. File contains details of rrs sequences of Clostridium botulinum and C. perfringens used for drawing Regular Expression Diagram of signatures presented in Additional file 8: Figures S20-S23.
Data
Tables S2-S3 'Novel' and low frequency Clostridium spp. File contains representative rrs sequences of unsegregated Clostridium sp. (novel) and Clostridium spp. with small population sizes.
Data
Table S4 RE sites with low frequency. File contains low frequency in silico Restriction Enzymes cut sites in rrs sequences of different Clostridium spp.
Data
Figures S20-S36 Regular expression diagram. File contains regular expression diagram of signatures (nucleotides) of rrs sequences of 15 Clostridium spp. obtained through MEME suite.
Data
Table S5-S21 Motifs for 15 Clostridium spp. File represents motifs obtained for Clostridium botulinum (128 rrs sequences) through MEME suite and the frequency of their occurrence across other Clostridium spp. using BioEdit.
Article
Full-text available
Bacterial taxonomy and phylogeny based on rrs (16S rDNA) sequencing is being vigorously pursued. In fact, it has been stated that novel biological findings are driven by comparison and integration of massive data sets. In spite of a large reservoir of rrs sequencing data of 1,237,963 entries, this analysis invariably needs supplementation with othe...
Article
The specificity of drug targets is a great challenge in the pharma-proteomics field of cancer biology. In particular, bioinformatics methods based on complex networks and Gene Ontologies (GOs) are very useful in this area. This work reviews some bioinformatics concepts and previous studies related to Colorectal Cancer (CRC) research using GOs, comp...

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