rohita sinha - Academia.edu (original) (raw)

Papers by rohita sinha

$Research paper thumbnail of Commensal \u3ci\u3eEscherichia coli\u3c/i\u3e Strains Can Promote Intestinal Inflammation via Differential Interleukin-6 Production$

Escherichia coli is a facultative anaerobic symbiont found widely among mammalian gastrointestina... more Escherichia coli is a facultative anaerobic symbiont found widely among mammalian gastrointestinal tracts. Several human studies have reported increased commensal E. coli abundance in the intestine during inflammation; however, host immunological responses toward commensal E. coli during inflammation are not well-defined. Here, we show that colonization of gnotobiotic mice with different genotypes of commensal E. coli isolated from healthy conventional microbiota mice and representing distinct populations of E. coli elicited strain-specific disease phenotypes and immunopathological changes following treatment with the inflammatory stimulus, dextran sulfate sodium (DSS). Production of the inflammatory cytokines GM-CSF, IL-6, and IFN-y was a hallmark of the severe inflammation induced by E. coli strains of Sequence Type 129 (ST129) and ST375 following DSS administration. In contrast, colonization with E. coli strains ST150 and ST468 caused mild intestinal inflammation and triggered on...

An additional file is available along with the online version of this paper. Additional file 1 no... more An additional file is available along with the online version of this paper. Additional file 1 not only contains the Figures S1â 45 but also contains a detailed description of the nature of files and data shared on ( http://cage.unl.edu/DataPeptide ). (DOCX 14611Â kb)

Antiviral Research, 2021

Because ganciclovir resistance mutations in the cytomegalovirus UL97 gene most commonly occur at ... more Because ganciclovir resistance mutations in the cytomegalovirus UL97 gene most commonly occur at codons 460, 520 and 590-607, diagnostic genotyping for drug resistance has often omitted the analysis of codons below 440. However, the UL97 kinase inhibitor maribavir selects for distinctive resistance mutations at codons 409 and 411, and ganciclovir/maribavir resistance mutations have also been described in the ATP binding region starting at codon 335. Expanded genotypic testing of UL97 codons 335-440 in 1535 clinical specimens disclosed 10 uncharacterized sequence variants that were phenotyped for ganciclovir and maribavir susceptibility. Notable findings included low-grade ganciclovir resistance conferred by amino acid substitutions K359N and E362D, decreased maribavir susceptibility of L348V, and maribavir hypersensitivity of V345I and E362D. Recently published substitutions F342Y and K359E/Q were also confirmed. The data indicate that mutations in the UL97 ATP binding region may arise in clinical specimens to affect the interpretation of ganciclovir and maribavir resistance. This region should now be included in the standard diagnostic genotyping of UL97, especially with the introduction of maribavir into therapeutic use.

IMA Fungus, 2018

The biosynthetic pathway for amanitins and related cyclic peptides in deadly Amanita (Amanitaceae... more The biosynthetic pathway for amanitins and related cyclic peptides in deadly Amanita (Amanitaceae) PXVKURRPV UHSUHVHQWV WKH ¿UVW NQRZQ ULERVRPDO F\FOLF SHSWLGH SDWKZD\ LQ WKH Fungi. Amanitins are found outside of the genus in distantly related agarics Galerina (Strophariaceae) and Lepiota (Agaricaceae $ ORQJVWDQGLQJ TXHVWLRQ LQ WKH ¿HOG SHUVLVWV ZK\ LV WKLV SDWKZD\ SUHVHQW LQ WKHVH SK\ORJHQHWLFDOO\ GLVMXQFW DJDULFV" 7ZR GHDGO\ mushrooms, A. pallidorosea and A. subjunquillea, were deep sequenced, and sequences of biosynthetic genes encoding MSDINs (cyclic peptide precursor) and prolyl oligopeptidases (POPA and POPB) were obtained. The two Amanita VSHFLHV \LHOGHG DQG 06',1V UHVSHFWLYHO\ ,Q DGGLWLRQ WZR 06',1 VHTXHQFHV ZHUH FORQHG from L. brunneoincarnata basidiomes. The toxin MSDIN genes encoding amatoxins or phallotoxins from the three genera were compared, and a phylogenetic tree constructed. Prolyl oligopeptidase B (POPB), a key enzyme in the biosynthetic pathway, was used in phylogenetic reconstruction to infer the evolutionary history of the genes.

Applied and environmental microbiology, 2014

Fresh pork sausage is produced without a microbial kill step and therefore chilled or frozen to c... more Fresh pork sausage is produced without a microbial kill step and therefore chilled or frozen to control microbial growth. In this report, the microbiota in a chilled fresh pork sausage model produced with or without an antimicrobial combination of sodium lactate and sodium diacetate was studied using a combination of traditional microbiological methods and deep pyrosequencing of 16S rRNA gene amplicons. In the untreated system, microbial populations rose from 10(2) to 10(6) CFU/g within 15 days of storage at 4°C, peaking at nearly 10(8) CFU/g by day 30. Pyrosequencing revealed a complex community at day 0, with taxa belonging to the Bacilli, Gammaproteobacteria, Betaproteobacteria, Actinobacteria, Bacteroidetes, and Clostridia. During storage at 4°C, the untreated system displayed a complex succession, with species of Weissella and Leuconostoc that dominate the product at day 0 being displaced by species of Pseudomonas (P. lini and P. psychrophila) within 15 days. By day 30, a secon...

Genome biology, Jan 17, 2014

BackgroundIndividuality in the species composition of the vertebrate gut microbiota is driven by ... more BackgroundIndividuality in the species composition of the vertebrate gut microbiota is driven by a combination of host and environmental factors that have largely been studied independently. We studied the convergence of these factors in a G10 mouse population generated from a cross between two strains to search for quantitative trait loci (QTLs) that affect gut microbiota composition or ileal Immunoglobulin A (IgA) expression in mice fed normal or high fat diets.ResultsWe found 42 microbiota-specific QTLs in 27 different genomic regions that affect the relative abundances of 39 taxa, including four QTL that were shared between this G10 population and the population previously studied at G4. Several of the G10 QTLs show apparent pleiotropy. Eight of these QTLs, including four at the same site on chromosome 9, show significant interaction with diet, implying that diet can modify the effects of some host loci on gut microbiome composition. Utilization patterns of IghV variable regions...

PloS one, 2018

Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompl... more Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. The complexity of the lung microbial community in COPD patients has been highlighted in recent years. Evidence suggests that transplantation, medications, age, and disease severity influence microbial community membership. However, the dynamics of the lung microbiome in stable COPD patients remain poorly understood. In this study, we completed a longitudinal 16S ribosomal RNA survey of the lung microbiome on replicate sputum samples collected from 4 former smokers with COPD (Stage 2) within a 2-day time period. Samples from each individual over the two-day period were similar based on α-diversity, principle component analysis and taxonomy at the phyla and genera level. Sputum samples from COPD patients were also collected between 2-9 months of follow-up. Data suggest an increased variability of the sputum microbiota when comparing samples collected ≤...

PLOS ONE, 2020

Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United ... more Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United States. DFUs are colonized by complex microbial communities, and infection is one of the most common reasons for diabetes-related hospitalizations and amputations. In this study, we examined how DFU microbiomes respond to initial sharp debridement and offloading and how the initial composition associates with 4 week healing outcomes. We employed 16S rRNA next generation sequencing to perform microbial profiling on 50 samples collected from 10 patients with vascularized neuropathic DFUs. Debrided wound samples were obtained at initial visit and after one week from two DFU locations, wound bed and wound edge. Samples of the foot skin outside of the wounds were also collected for comparison. We showed that DFU wound beds are colonized by a greater number of distinct bacterial phylotypes compared to the wound edge or skin outside the wound. However, no significant microbiome diversity changes occurred at the wound sites after one week of standard care. Finally, increased initial abundance of Gram-positive anaerobic cocci (GPAC), especially Peptoniphilus (p < 0.05; n = 5 subjects), was associated with impaired healing; thus, GPAC's abundance could be a predictor of the wound-healing outcome.

Journal of microbiological methods, Apr 1, 2017

Changes in the gastrointestinal microbial community are frequently associated with chronic diseas... more Changes in the gastrointestinal microbial community are frequently associated with chronic diseases such as Inflammatory Bowel Diseases. However, understanding the relationship of any individual taxon within the community to host physiology is made complex due to the diversity and individuality of the gut microbiota. Defined microbial communities such as the Altered Schaedler Flora (ASF) help alleviate the challenges of a diverse microbiota by allowing one to interrogate the relationship between individual bacterial species and host responses. An important aspect of studying these relationships with defined microbial communities is the ability to measure the population abundance and dynamics of each member. Herein, we describe the development of an improved ASF species-specific and sensitive real-time quantitative polymerase chain reaction (qPCR) for use with SYBR Green chemistry to accurately assess individual ASF member abundance. This approach targets hypervariable regions V1 thr...

Open Forum Infectious Diseases, 2018

BackgroundRates and risk factors for recurrent enterococcal bloodstream infection (R-EBSI) and wh... more BackgroundRates and risk factors for recurrent enterococcal bloodstream infection (R-EBSI) and whether the same genetic lineage causes index EBSI and R-EBSI are unknown in patients with acute leukemia (AL) receiving chemotherapy.MethodsNinety-two AL patients with EBSI from 2010 to 2015 were included. Enterococcal bloodstream infection was defined by 31 positive blood cultures for Enterococcus faecium or Enterococcus faecalis and fever, hypotension, or chills. Clearance was defined by 31 negative cultures 324 hours after last positive culture and defervescence. Recurrent enterococcal bloodstream infection was defined by a positive blood culture for Enterococcus 324 hours after clearance. Categorical variables were reported as proportions and compared by the χ2 test. Continuous variables were summarized by median and interquartile range (IQR) and compared by the Wilcoxon-Mann-Whitney Test. P values <.05 were considered significant. Whole-genome sequencing was performed on available...

BMC genomics, Jan 21, 2015

Functional assignments for short-read metagenomic data pose a significant computational challenge... more Functional assignments for short-read metagenomic data pose a significant computational challenge due to perceived unpredictability of alignment behavior and the inability to infer useful functional information from translated protein-fragments/peptides. To address this problem, we have examined the predictability of short peptide alignments by systematically studying alignment behavior of large sets of short peptides generated from well-characterized proteins as well as hypothetical proteins in the KEGG database. Using test sets of peptides modeling the length and phylogenetic distributions of short-read metagenomic data, we observed that peptides from well-characterized proteins had indistinguishable alignments to proteins from the same orthologous family and proteins from different families. Nonetheless, the patterns contained remarkable phylogenetic and structural signals, with alignments of even very short peptides naturally restricted to their orthologous family and/or protein...

Rapid accumulation of experimental data on protein-protein complexes drives the paradigm shift in... more Rapid accumulation of experimental data on protein-protein complexes drives the paradigm shift in protein docking from ‘traditional, ’ template free approaches to template based techniques. Homology docking algorithms based on sequence similarity between target and template complexes can account for up to 20 % of known protein-protein interactions. When highly homologous templates for the target complex are not available, but the structure of the target monomers is known, docking by local structural alignment may provide an adequate solution. Such an algorithm was developed based on the structural comparison of monomers to co-crystallized interfaces. A library of the interfaces was generated from co-crystallized protein-protein complexes in PDB. The partial structure alignment algorithm was validated on the DOCKGROUND benchmark sets. The optimal performance of the partial (interface) structure alignment was achieved with the interface residues defined by 12Å distance across the inte...

The increasing availability of co-crystallized protein-protein complexes provides an opportunity ... more The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values,12 A ˚ across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 A˚, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 A ˚ cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-sca...

2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017

Accurate characterization of pathogenic microbes that may be present in food or clinical samples ... more Accurate characterization of pathogenic microbes that may be present in food or clinical samples is essential in the design of appropriate intervention strategies. Inherent genomic patterns (codon-biases and rate of evolution) do simplify the classification of microbes at most taxonomic levels (genus and above), but mostly blur classification at Species/Strain levels. Hence, their classification at these finer taxonomic levels requires high-resolution genomic-data that provide SNP (Single Nucleotide Polymorphism) level precision. Existing classification methods involve either targeted amplification of sero-specific genes (serotyping and MLST) or sequencing of the entire microbial genome, both of which require extra time and resources. We present a computational approach, which harnesses the power of the metagenomic NGS-data and object-detection abilities of Convolutional Neural Networks (CNN)(Inception V3), for precise classification of pathogens by converting genomic-data (NGS-read...

mBio

Bifidobacterium species are recognized as important, beneficial microbes in the human gut microbi... more Bifidobacterium species are recognized as important, beneficial microbes in the human gut microbiome, and their ability colonize individuals at different stages of life is influenced by poorly understood interactions between host, dietary, environmental, and ecological factors. The common marmoset is an emerging nonhuman primate model with a short maturation period, making this model amenable to study of the microbiome throughout a life history.

Clinical Journal of the American Society of Nephrology

Background and objectivesSubclinical acute rejection is associated with poor outcomes in kidney t... more Background and objectivesSubclinical acute rejection is associated with poor outcomes in kidney transplant recipients. As an alternative to surveillance biopsies, noninvasive screening has been established with a blood gene expression profile. Donor-derived cellfree DNA (cfDNA) has been used to detect rejection in patients with allograft dysfunction but not tested extensively in stable patients. We hypothesized that we could complement noninvasive diagnostic performance for subclinical rejection by combining a donor-derived cfDNA and a gene expression profile assay.Design, setting, participants, & measurementsWe performed a post hoc analysis of simultaneous blood gene expression profile and donor-derived cfDNA assays in 428 samples paired with surveillance biopsies from 208 subjects enrolled in an observational clinical trial (Clinical Trials in Organ Transplantation-08). Assay results were analyzed as binary variables, and then, their continuous scores were combined using logistic ...

American Journal of Transplantation

Donor-derived cell-free DNA (dd-cfDNA) has been evaluated as a rejection marker in organ transpla... more Donor-derived cell-free DNA (dd-cfDNA) has been evaluated as a rejection marker in organ transplantation. This study sought to assess the utility of dd-cfDNA to diagnose graft injury in liver transplant recipients (LTR) and as a predictive biomarker prior to different causes of graft dysfunction. Plasma from single and multicenter LTR cohorts was analyzed for dd-cfDNA. Phenotypes of treated biopsy-proven acute rejection (AR, N=57), normal function (TX, N=94), and acute dysfunction no rejection (ADNR; N=68) were divided into training and test sets. In the training set, dd-cfDNA was significantly different between AR vs. TX (AUC 0.95, 5.3% cutoff) and AR vs. ADNR (AUC 0.71, 20.4% cutoff). Using these cutoffs in the test set, the accuracy and NPV were 87% and 100% (AR vs. TX) and 66.7% and 87.8% (AR vs. ADNR). Blood samples collected serially from LTR demonstrated incremental elevations in dd-cfDNA prior to the onset of graft dysfunction (AR>ADNR), but not in TX. Dd-cfDNA also decreased following treatment of rejection. In conclusion, serial elevation of dd-cfDNA identifies pre-clinical graft injury in the context of normal liver function tests and is greatest in rejection. This biomarker may help detect early signs of graft injury and rejection to inform LTR management strategies.

Open Forum Infectious Diseases

Background Cell-free DNA (cfDNA) has emerged as an important clinical specimen to probe for patho... more Background Cell-free DNA (cfDNA) has emerged as an important clinical specimen to probe for pathogenic microbes, especially in organ transplant patients where the same data can be used to predict allograft rejection. Recent reports described viral, bacterial or the complete microbial diversity in plasma following cfDNA sequencing. The prevalence of certain viral families (anelloviridae) is associated with immunosuppressant dosage and the risk of antibody mediated rejection. While being informative, the cfDNA reads are inherently shorter in length (~160bp or 2x75bp) and predominated by the host DNA (~97-99%), causing challenges in their taxonomic annotation and lower specificity. Here we present a computational protocol which minimizes these challenges by merging the concept of “Reference-assisted Assembly” with K-mer profiles of NGS data, for highly sensitive and specific microbial detection. Methods We developed a pipeline in which non-host NGS data (reads not mapped to the human g...

Biology of Blood and Marrow Transplantation

Introduction Viral infections are commonly reported in immunocompromised patients such as hematop... more Introduction Viral infections are commonly reported in immunocompromised patients such as hematopoietic stem cell transplant recipients. While there are several reports on the effect of individual viruses, such as CMV, there is increasing evidence that the composition of the blood-virome may reflect the immune status of patients. High resolution virome analysis may provide an accurate measure of a patient's immune status as well as provide pathogen surveillance. Next generation sequencing (NGS) of cell-free DNA (cfDNA) purified from plasma is being investigated for assessment of diseases such as graft vs host disease, making unbiased sequence data readily available for analyses of a patient's virome. Here we present a computational tool (Vira-ome) which probes the presence of a targeted panel of DNA viruses following NGS sequencing of cfDNA. Method We developed a pipeline which initially removes host DNA reads, then performs a reference-assisted assembly operation. The resulting assemblies were then passed to a K-mer profile based taxonomic classifier for annotation to the species level. We trained the K-mer based classifier for 3 different K-mer values using ∼14,000 DNA-virus genomes representing 36 prevalent and pathogenic species. Predictions of three different K-mer classifiers were used to make final predictions, applying a majority-wins rule. We tested our method on 30 simulated (1, 2, or 3 species mix with 50,100 or 500 NGS reads each) and 29 clinical samples obtained from a biorepository. Results The Vira-ome tool utilized cfDNA NGS data to screen for the presence of a targeted set of nine pathogenic viruses (human adenovirus, human herpesvirus 1, 2, 6, 7 and 8, BK polyomavirus, human parvovirus B19, JC polyomavirus, KI polyomavirus, WU polyomavirus, torque teno virus, Epstein Barr virus, human cytomegalovirus, and varicella-zoster virus). On the simulated set of viral sample mixes, our protocol had 100% accuracy with no false-positive predictions. For 29 clinical samples, our pipeline predicted: (A) Torque teno virus in 13/29 samples, (B) pathogenic viruses in 11/15 cases were predominated by BK polyomavirus (7/15 samples) and (C) at least one viral species in 10/14 cases. Selected samples were then analyzed by qPCR, which confirmed the presence of BKV, JCV, HHV7 and EBV in 8/9, 3/4, 1/1, 2/2 samples, respectively. Viral loads ranged from 6 – 106 copies/mL. Five samples predicted positive for the adenovirus, were not confirmed by qPCR, emphasizing the need of in vitro validation for in silico predictions. Conclusions The Vira-ome tool, designed to detect pathogenic viruses using cfDNA data, performed well both on simulated and clinical samples with a majority of results confirmed by qPCR. Our results emphasize how computational predictions can complement clinical diagnostic approaches.