A5058179549- Pneumonia and Respiratory Infections
- Insect symbiosis and bacterial influences
- Streptococcal Infections and Treatments
- Genomics and Phylogenetic Studies
- Bacterial Infections and Vaccines
- Infrared Target Detection Methodologies
- Parasitic Diseases Research and Treatment
- Neonatal and Maternal Infections
- Video Surveillance and Tracking Methods
- Antimicrobial Resistance in Staphylococcus
- Respiratory viral infections research
- Advanced Measurement and Detection Methods
- CRISPR and Genetic Engineering
- Opinion Dynamics and Social Influence
- Helicobacter pylori-related gastroenterology studies
- Image and Object Detection Techniques
- Single-cell and spatial transcriptomics
- Complex Network Analysis Techniques
- Advanced Vision and Imaging
- Invertebrate Immune Response Mechanisms
- Social Media and Politics
- Genomics and Chromatin Dynamics
- Calibration and Measurement Techniques
- NF-κB Signaling Pathways
- Infective Endocarditis Diagnosis and Management
Indian Institute of Technology Indore
2024
Amity University
2024
Instruments Research & Development Establishment
2016-2023
University of Maryland, Baltimore
2011-2021
Harvard University
2017-2018
Boston Public Library
2018
Arizona State University
2016
Rutgers, The State University of New Jersey
2014
J. Craig Venter Institute
2007-2008
Washington University in St. Louis
2007
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D tracks, allowing users to combine various data types, synchronize multiple modalities, share fully customizable views with others. demonstrate its utility in exploring different experimental conditions, comparing the results analyses, creating interactive snapshots collaborators broader public. HiGlass...
Although common among bacteria, lateral gene transfer—the movement of genes between distantly related organisms—is thought to occur only rarely bacteria and multicellular eukaryotes. However, the presence endosymbionts, such as Wolbachia pipientis , within some eukaryotic germlines may facilitate bacterial transfers host genomes. We therefore examined genomes for evidence transfer events from their hosts. found confirmed into four insect nematode species that range nearly entire genome...
ABSTRACT The group A streptococcus (GAS) is a strict human pathogen responsible for wide spectrum of diseases. Although GAS genome sequences are available, functional genomic analyses have been limited. We developed mariner -based transposon, osKaR , designed to perform Transposon-Site Hybridization (TraSH) in and successfully tested its use several invasive serotypes. complex mutant library M1T1 strain 5448 was subjected negative selection blood identify genes important fitness this...
To better understand Neisseria meningitidis genomes and virulence, microarray comparative genome hybridization (mCGH) data were collected from one cinerea , two lactamica gonorrhoeae 48 isolates. For N. these isolates are diverse clonal complexes, invasive carriage strains, all major serogroups. The platform represented strains MC58, Z2491 FAM18, FA1090. By comparing to sequences, the core insertions/deletions (e.g. capsule locus, type I secretion system) related pathogenicity identified,...
It is unclear whether Streptococcus pneumoniae in biofilms are virulent and contribute to development of invasive pneumococcal disease (IPD). Using electron microscopy we confirmed the mature a continuous-flow-through line model determined that biofilm formation occurred discrete stages with composed primarily dead pneumococci. Challenge mice equal colony forming units planktonic pneumococci bacteria were highly attenuated for but not nasopharyngeal colonization. Biofilm numerous serotypes...
ABSTRACT Streptococcus pneumoniae is an opportunistic pathogen that colonizes the nasopharynx. Herein we show carbon availability distinct between nasopharynx and bloodstream of adult humans: glucose absent from nasopharynx, whereas galactose abundant. We demonstrate pneumococcal neuraminidase A (NanA), which cleaves terminal sialic acid residues host glycoproteins, exposed on surface septal epithelial cells, thereby increasing its during colonization. observed S. mutants deficient in NanA...
For over 130 years, invasive pneumococcal disease has been associated with the presence of extracellular planktonic pneumococci, i.e. diplococci or short chains in affected tissues. Herein, we show that Streptococcus pneumoniae invade myocardium instead replicate within cellular vesicles and transition into non-purulent biofilms. Pneumococci mature cardiac microlesions exhibited salient biofilm features including intrinsic resistance to antibiotic killing an matrix. Dual RNA-seq subsequent...
Lateral gene transfer (LGT) from bacterial Wolbachia endosymbionts has been detected in ~20% of arthropod and nematode genome sequencing projects. Many these transfers are large contain a substantial part the genome.Here, we re-sequenced three D. ananassae genomes Asia Pacific that LGTs Wolbachia. We find multiple copies transferred to Drosophila nuclear all lines. In line Indonesia, DNA nearly identical size sequence yielding an even coverage mapped reads over genome. contrast, lines Hawaii...
Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea , we have identified conserved regions that represent potentially functional sequences overlooked by previous genome annotation methods. A total 454,274 whole shotgun covering 283 Mb (0.44×) estimated 650 were searched against genome, (CAGSs) identified. Of these 229,735 regions, 167,357 fell within or intersected existing gene models, while 60,378 located in previously unannotated...
ABSTRACT CsrRS (or CovRS) is a two-component regulatory system that controls expression of multiple virulence factors in the important human pathogen group B Streptococcus (GBS). We now report global gene studies GBS strains 2603V/R and 515 their isogenic csrR csrS mutants. Together with data reported previously for strain NEM316, results reveal conserved 39-gene regulon. In vitro phosphorylation-dependent binding recombinant CsrR to promoter regions both positively negatively regulated...
Group A Streptococcus (GAS) has a rich evolutionary history of horizontal transfer among its core genes. Yet, despite extensive genetic mixing, GAS strains have discrete ecological phenotypes. To further our understanding the molecular basis for phenotypes, comparative genomic hybridization set 97 diverse to pangenome microarray was undertaken, and association accessory genes with emm genotypes that define tissue tropisms infection determined. Of 22 nonprophage gene regions (AGRs)...
Abstract Background Numerous methods exist for enriching bacterial or mammalian mRNA prior to transcriptome experiments. Yet there persists a need enrich in non-mammalian animal systems. For example, insects contain many important and interesting obligate intracellular bacteria, including endosymbionts vector-borne pathogens. Such bacteria are difficult study by traditional methods. Therefore, genomics has greatly increased our understanding of these bacteria. Efficient subtraction needed...
Halyomorpha halys (Stål) (Insecta:Hemiptera;Pentatomidae), commonly known as the Brown Marmorated Stink Bug (BMSB), is an invasive pest of mid-Atlantic region United States, causing economically important damage to a wide range crops. Native Asia, BMSB was first observed in Allentown, PA, USA, 1996, and this now well-established throughout US beyond. In addition serious threat poses agriculture, has become nuisance homeowners, invading home gardens congregating large numbers human-made...
Transcriptional regulatory mechanisms likely contribute to the etiology of inflammatory bowel disease (IBD), as genetic variants associated with are disproportionately found at elements. However, transcription factors regulating colonic inflammation unclear. To identify these factors, we mapped epigenomic changes in epithelium upon inflammation. Epigenetic marks transcriptional elements responded dynamically and indicated a shift epithelial factor networks. Active enhancer chromatin...
Macrolide resistance, emerging in Streptococcus pneumoniae and other Gram-positive bacteria, is increasingly due to efflux pumps encoded by mef/mel(msr) operons found on discrete mobile genetic elements. The regulation of these elements not well understood. We identified the mef(E)/mel transcriptional start, localized promoter, demonstrated attenuation transcription as a mechanism macrolide-inducible mef-mediated macrolide resistance S. pneumoniae. start site was guanine 327 bp upstream...
Abstract Despite numerous advances in genomics and bioinformatics, technological hurdles remain to examine host-microbe transcriptomics. Sometimes the transcriptome of either or both can be ascertained merely by generating more sequencing reads. However, many cases exist where bacterial mRNA needs enriched further enable cost-effective pathogen endosymbiont. While a suitable method is commercially available for mammalian samples this type, development such methods has languished invertebrate...
Abstract Background Lymphatic filariasis is a neglected tropical disease afflicting more than 120 million people, while another 1.3 billion people are at risk of infection. The nematode worm Brugia malayi one the causative agents and exists in mutualistic symbiosis with Wolbachia bacteria. Since extensive lateral gene transfer occurs frequently between its hosts, we sought to measure extent such LGT B. by whole genome sequencing -depleted worms. Results A considerable fraction (at least...
Abstract We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D tracks, allowing users to combine various data types, synchronize multiple modalities, share fully customizable views with others. demonstrate its utility in exploring different experimental conditions, comparing the results analyses, creating interactive snapshots collaborators broader public....
Abstract Enrichment methodologies enable the analysis of minor members in multi-species transcriptomic data. We compared standard enrichment bacterial and eukaryotic mRNA to a targeted using an Agilent SureSelect (AgSS) capture for Brugia malayi , Aspergillus fumigatus Wolbachia endosymbiont B. ( w Bm). Without introducing significant systematic bias, AgSS quantitatively enriched samples, resulting more reads mapping target organism. The AgSS-enriched libraries consistently had positive...
Abstract Background Streptococcus pneumoniae is a leading cause of childhood morbidity and mortality worldwide, despite the availability effective pneumococcal vaccines. Understanding molecular interactions between bacterium host will contribute to control prevention disease. Results We used combination adherence assays, mutagenesis functional genomics identify novel factors involved in adherence. By contrasting these processes two strains, TIGR4 G54, we showed that invasion capacities vary...
Group B Streptococcus (GBS) is an important pathogen responsible for a variety of diseases in newborns and the elderly. A clinical GBS isolate considered nontypable (NT) when serological methods fail to identify it as one nine known serotypes. Eight isolates (designated A1–A4, B1–B4) showed PFGE profiles similar that serotype V strain expressing R1, R4 surface proteins. These unique were further characterized by immunologic genetic methods. Rabbit sera A1 A2 reacted weakly with concentrated...
Abstract Background Viral upper respiratory tract infections are associated with increased colonization by Streptococcus pneumoniae but the mechanisms underlying this relationship unclear. The objective of study is to describe a comprehensive picture cellular interaction between adhering bacteria and host cells in presence or absence viral co-infection. Results Gene expression profiles Detroit-562 pharyngeal cells, which were either mock-infected infected human syncytial virus (RSV)...
Here, we present a comprehensive transcriptomics data set of Brugia malayi , its Wolbachia endosymbiont w Bm, and vector host. This study samples from 16 stages across the entire B. life cycle, including stage 1 through 4 larvae, adult males females, embryos, immature microfilariae, mature microfilariae.