
Renesh BedreTexas A&M University | TAMU
Renesh Bedre
PhD
About
53
Publications
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Introduction
Dr. Renesh Bedre is a Bioinformatics scientist at Texas A&M AgriLife Research. Dr. Renesh Bedre lead the Computational Biology and Bioinformatics program and employ bioinformatics, statistical, and machine learning methods to mine and analyze high-throughput transcriptomics and genomics (omics) data generated from the rapidly growing RNA and DNA sequencing technologies.
Dr. Renesh Bedre primarily uses Python and R for data analysis and visualization. He uses Nextflow for computational pipelines
Additional affiliations
August 2011 - August 2016
August 2011 - present
August 2009 - August 2011
Education
August 2011 - December 2015
August 2009 - August 2011
Publications
Publications (53)
Background and Aim: Reflux esophagitis is characterized by the erosions of esophagus due to gastric acids. H2-Recptor antagonists are considered as effective therapy. We compared sucralfate with H2-receptor antagonist for treatment of reflux esophagitis.
Methods: Seven studies are selected from different databases (PUBMED, MEDLINE, COCHRANE LIBRARY...
Long intergenic non-coding RNAs (lincRNAs) are emerging as regulators of protein-coding genes (PCGs) in many plant and animal developmental processes and stress responses. In this study, we characterize the genome-wide lincRNAs in potatoes responsive to a vascular bacterial disease presumably caused by Candidatus Liberibacter solanacearum (CLso). A...
Genome editing of the NPR3 gene in potatoes conferred resistance to fastidious pathogens, Candidatus Liberibacter solanacearum, a causative agent of potato Zebra Chip diseases
Candidatus Liberibacter spp.” are insect-vectored, fastidious, and vascular-limited phytopathogens. They are the presumptive causal agents of potato zebra chip, tomato vein clearing, and the devastating citrus greening disease worldwide. There is an urgent need to develop new strategies to control them. In this study, we characterized a dual-specif...
Ascorbic acid (AsA), or vitamin C, is an essential nutrient for humans. In plants, AsA functions as an antioxidant during normal metabolism or in response to stress. Spinach is a highly nutritious green leafy vegetable that is consumed fresh, cooked or as a part of other dishes. One current goal in spinach breeding programs is to enhance quality an...
Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality cont...
Continuous development in low-cost and high-throughput sequencing technologies provides a wealth of genetic information to study the complex gene regulatory mechanisms and defense systems in the plants. Modern genomics and bioinformatics have surged the genome sequencing and molecular research of horticultural plants. This Special Issue focuses on...
Although the role of plant defense mechanisms against viruses are relatively well studied in dicots and in incompatible plant-microbe interactions, studies of their roles in compatible interactions and in grasses are lagging behind. In this study, we leveraged the emerging grass model
BrachypodiumPanicum mosaic virus
A major bottleneck in identifying therapies to control citrus greening and other devastating plant diseases caused by fastidious pathogens is our inability to culture the pathogens in defined media or axenic cultures. As such, conventional approaches for antimicrobial evaluation (genetic or chemical) rely on time-consuming, low-throughput and inher...
Modulation of Salicylic Acid Receptor Activity Confers Resistance to Potato Zebra Chip Disease
Motivation
Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various q...
Genome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popul...
Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a...
Core Ideas
High‐throughput imaging and genomic information can be combined to optimize marker development.
Genome‐wide association studies identified loci associated with plant growth traits.
We identified candidate genes associated with plant growth and development.
Despite advances in sequencing for genotyping, the lack of rapid, accurate, and r...
Anthracnose (Colletotrichum dematium) is an important disease in spinach (Spinacia oleracea). Sources of resistance must be identified, and molecular tools must be developed to expedite cultivar development. In this study, a diverse collection of 276 spinach accessions was scored for anthracnose disease severity. We then evaluated marker identifica...
Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane’s large, complex genome, and the variable chromosome numbers an...
Alternative splicing (AS) is a crucial posttranscriptional mechanism of gene expression which promotes transcriptome and proteome diversity. At the molecular level, splicing and AS involves recognition and elimination of intronic regions of a precursor messenger RNA (pre-mRNA) and joining of exonic regions to generate the mature mRNA. AS generates...
Alternative splicing (AS) is a key posttranscriptional process in eukaryotes that promotes transcriptome and proteome diversity during growth, development, and response to stress. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to absence of a high-quality sequenced reference genome, its complex genome architecture a...
Table S1 Sequences of primers used in the study.
Figure S1 Nuclear localization of SaADF2.
Figure S2 SDS‐PAGE analysis of N‐terminal 6X‐His‐tagged OsADF2 (a), SaADF2 (b) and OsADF2/6α after ammonium sulphate precipitation and Ni‐NTA resin purification. CL; Cell Lysate, FT; Column Flow Through, W1/2; Wash 1/2, F1; Fraction 1, 200 mm Imidazole eluate containing purified protein; F2; Fraction 2, 25...
Data S1 Comparison of differentially expressed genes among WT, SaADF2‐OE and OsADF2‐OE).
Appendix S1 Descriptive legends to supporting figures.
Data S2 Gene ontology of genes differentially expressed in ADF2‐overexpressers vis‐à‐vis WT under control and drought.
Data S3 KEGG enrichment analysis for differentially expressed genes.
Method S1 Supporting experimental procedures.
Actin depolymerizing factors (ADFs) maintain the cellular actin network dynamics by regulating severing and disassembly of actin filaments in response to environmental cues. An ADF isolated from a monocot halophyte, Spartina alterniflora (SaADF2) imparted significantly higher level of drought and salinity tolerance when expressed in rice than its r...
A comparative transcriptome analysis was performed using the genes significantly differentially expressed in cotton, corn and peanut in response to aflatoxin producing fungus Aspergillus flavus with an objective of identifying candidate resistance genes in cotton. Two-way analyses identified 732 unique genes to be differentially regulated by the fu...
Understanding plant-microbe interactions is critical for enhancing productivity in our food and bioenergy related cropping systems. With the support of the DOE-JGI community science program, this project aims to develop comprehensive gene atlas maps for diverse bioenergy grass-microbe interactions, including pathogenic (viruses, fungi, bacteria) an...
Motivation: Genome-scale studies using next-generation sequencing technologies generate substantial lists of differentially-expressed genes. The gene lists need to be further analyzed to identify overrepresented genes and functions in order to guide downstream analyses. Currently available gene enrichment tools rely on functional classifications ba...
Drought stress is a constant threat to rice production worldwide. Most modern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits. Identification of genes (QTLs)/markers associa...
Quantitative trait loci identified for grain yield under non-stressed control using Cocodrie/Vandana F2:3 families.
Genic SSR markers derived from the Cocodrie and Vandana transcriptome used for mapping of Cocdrie/Vandana F2 progenies.
Single nucleotide polymorphism (SNP) markers placed in the genetic map of Cocodrie/Vandana F2 progenies.
Linkage map of the F2 individuals showing distribution of the markers on 12 chromosomes. QTLs for grain yield under greenhouse drought are shown in red rectangles and QTLs for grain yield under non-stressed control are in green rectangles. Markers identified through single marker analysis and within the QTL interval are depicted in bold red fonts.
Markers associated with grain yield under drought stress in F2:3 families of Cocodrie/Vandana from single marker analysis and mean grain yield (g) per plant on each genotype (A, homozygous for Vandana alleles; B, homozygous for Cocodrie alleles; H, heterozygous).
Analysis of the grain yield of F2:3 progenies of Cocodrie × Vandana under greenhouse drought conditions.
Genes within QTLs on chromosomes 1, 5, 8, and 9.
Alternative splicing (AS) promotes transcriptome and proteome diversity in plants, which influences growth and development, and host responses to stress. Advancements in next-generation sequencing, bioinformatics, and computational biology tools have allowed biologists to investigate AS landscapes on a genome-wide scale in several plant species. Fu...
Many bacteria encode biosynthetic proteins that produce a vast array of natural products. These compounds are often synthesized during host invasion as they function as virulence factors. In addition, such secondary metabolites have yielded numerous molecular scaffolds with pharmaceutical and clinical importance. The gene clusters that encode prote...
Background
Soil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, halophytes have attracted attention of the biologists to understand their salt adaptation mechanisms. Spartina alterniflora (smooth...
Nucleotide/nucleoside analogues (antiviral therapy) are used in the therapy of HBeAg positive and HBeAg negative chronic hepatitis B. We analyzed ten selected randomized controlled with 2557 patients to estimate the effect of antiviral drugs in chronic hepatitis B with compared to placebo. Virological response, biochemical response, histological re...
Aflatoxins are toxic and potent carcinogenic metabolites produced from the fungi Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive preharvest and postharvest conditions. United States federal regulations restrict the use of aflatoxin contaminated cottonseed at >20 ppb for animal feed. Several strategies ha...
MicroRNAs have been shown to be involved in regulating plant's response to environmental stresses, including salinity. There is no report yet on the miRNA-mediated posttranscriptional regulation of salt stress response of a grass halophyte by miRNAs. Here we report on the deep-sequencing followed by expression validation through (s)qRT-PCR of a sel...
Soil salinity is one of the most serious environmental factors that affect crop productivity worldwide. Inevitable global climate change leading to rise in sea water level would exacerbate degradation of irrigation systems and contamination of ground water resources, which render conventional agricultural practices impossible due to the sensitivity...
Salt and drought stresses negatively affect rice yield. The magnitude of yield reduction depends on the genotype and developmental stage of the plant, and the severity of the stress. While natural variations for stress tolerance exist in the primary and secondary gene pool of rice, conventional breeding to develop salt and drought tolerant varietie...
Soil salinity negatively affects growth and yield of most crop plants. Plants respond to salinity through physiological and biochemical adjustments that involve a coordinate regulation and expression of a cascade of genes. Naturally highly salt tolerant plants, such as halophytes, have been of particular interest to understand the biology of their...
Sugarcane (Saccharum hybrids), being a (sub)tropical crop, is sensitive to sub-freezing temperatures. Cold temperatures limit the length of its growing season and affect the growth and development, thereby causing significant crop losses before and after harvest. Lack of freeze tolerance among the available sugarcane germplasm in Louisiana is attri...