Bacterial fauna associating with chironomid larvae from lakes of Bengaluru city, India - A 16s rRNA gene based identification
Publication date: Available online 3 March 2017 Source:Genomics Data Author(s): Ramprasad Kuncham, Thiyagarajan Sivapraksam, R Puneeth Kumar, P Sreenath, Ravi Nayak, Tha. Thayumanavan, Gopireddy V. Subba Reddy Chironomid larvae that inhabit in aquatic sediments play an important role as vector for bacterial pathogens. Its life cycle consists of four stages i.e. eggs, larvae, pupae and adult. In the present study we identified bacterial species associated with whole larvae of chironomids from 11 lake sediments of Bangalore region using 16s rRNA gene Sanger sequencing. We found that larvae from all lake sediments as...
Source: Genomics Data - March 3, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Thermoanaerobacterium sp. strain PSU-2 isolated from thermophilic hydrogen producing reactor
Publication date: Available online 28 February 2017 Source:Genomics Data Author(s): Sompong O-Thong, Peerawat Khongkliang, Chonticha Mamimin, Apinya Singkhala, Poonsuk Prasertsan, Nils-Kåre Birkeland Thermoanaerobacterium sp. strain PSU-2 was isolated from thermophlic hydrogen producing reactor and subjected to draft genome sequencing on 454 pyrosequencing and annotated on RAST. The draft genome sequence of strain PSU-2 contains 2,552,497 bases with an estimated G+C content of 35.2%, 2555 CDS, 8 rRNAs and 57 tRNAs. The strain had a number of genes responsible for carbohydrates metabolic, amino acids and derivative...
Source: Genomics Data - February 28, 2017 Category: Genetics & Stem Cells Source Type: research
Metagenome analysis of the root endophytic microbial community of Indian rice (O. sativa L.)
This study reports the root endophytic microbial community profile in rice (Oryza sativa L.), the largest food crop of Asia, using 16S rRNA gene amplicon sequencing. Metagenome of OS01 and OS04 consisted of 11,17,900 sequences with 300Mbp size and average 55.6% G+C content. Data of this study are available at NCBI Bioproject (PRJNA360379). The taxonomic analysis of 843 OTU's showed that the sequences belonged to four major phyla revealing dominance of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria. Results reveal the dominance of Bacillus as major endophytic genera in rice roots, probably playing a key role i...
Source: Genomics Data - February 28, 2017 Category: Genetics & Stem Cells Source Type: research
Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA
Publication date: Available online 27 February 2017 Source:Genomics Data Author(s): Ashish Pathak, Ashvini Chauhan, Paul Stothard, Stefan Green, Mark Maienschein-Cline, Rajneesh Jaswal, John Seaman Savannah River Site (SRS), an approximately 800-km2 former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistance to high concentrations of Uranium (U) and Nickel (Ni) were isolated from the Steeds Pond soils located within the SRS site. One...
Source: Genomics Data - February 27, 2017 Category: Genetics & Stem Cells Source Type: research
Impact of aspirin on the transcriptome of Streptococcus pneumoniae D39
Publication date: Available online 27 February 2017 Source:Genomics Data Author(s): Muhammad Afzal, Sulman Shafeeq Aspirin or acetylsalicylic acid (ASA) is a medicine used to treat pain, fever, and inflammation. Here, we for the very first time reported the genome-wide transcriptional profiling of aspirin-regulated genes in Streptococcus pneumoniae in the presence of 5mM aspirin in chemically-defined medium (CDM) using microarray analysis. Our results showed that expression of several genes was differentially expressed in the presence of aspirin. These genes were further grouped into COG (Clusters of Orthologous Groups...
Source: Genomics Data - February 27, 2017 Category: Genetics & Stem Cells Source Type: research
Hypothalamic transcriptome analysis of congenic-derived F2 mice (chromosome 17:3 –45Mb) exhibiting preferential carbohydrate (versus fat) intake
Publication date: Available online 24 February 2017 Source:Genomics Data Author(s): Brenda K. Richards, Claudia Kappen, Susan Newman (Source: Genomics Data)
Source: Genomics Data - February 24, 2017 Category: Genetics & Stem Cells Source Type: research
Novel quorum quenching enzymes identified from draft genome of Roseomonas sp. TAS13
Publication date: Available online 21 February 2017 Source:Genomics Data Author(s): Eri Nasuno, Tomohiro Suzuki, Ryoko Suzuki, Chigusa Okano, Takeshi Kurokura, Ken-ichi Iimura, Norihiro Kato Roseomonas sp. strain TAS13 isolated from an activated sludge sample degrades N-acylhomoserine lactones (AHLs) that are widely utilized as a signal in bacterial quorum sensing systems. The draft genome of Roseomonas sp. TAS13 contains 816 contigs (total 5,078,941bp) which carries 4760 protein-coding genes and 52 tRNA genes (DDBJ/EMBL/GenBank accession numbers BDLP01000001 through BDLP01000816). (Source: Genomics Data)
Source: Genomics Data - February 21, 2017 Category: Genetics & Stem Cells Source Type: research
SVMRFE based approach for prediction of most discriminatory gene target for type II diabetes
Publication date: Available online 17 February 2017 Source:Genomics Data Author(s): Atul Kumar, D. Jeya Sundara Sharmila, Sachidanand Singh Type II diabetes is a chronic condition that affects the way our body metabolizes sugar. The body's important source of fuel is now becoming a chronic disease all over the world. It is now very necessary to identify the new potential targets for the drugs which not only control the disease but also can treat it. Support vector machines are the classifier which has a potential to make a classification of the discriminatory genes and non-discriminatory genes. SVMRFE a modification o...
Source: Genomics Data - February 17, 2017 Category: Genetics & Stem Cells Source Type: research
Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation
Publication date: Available online 14 February 2017 Source:Genomics Data Author(s): Aide Lasa, Jesús L. Romalde To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are de...
Source: Genomics Data - February 14, 2017 Category: Genetics & Stem Cells Source Type: research
Genome-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer
Publication date: Available online 14 February 2017 Source:Genomics Data Author(s): Matias A. Bustos, Matthew P. Salomon, Nellie Nelson, Sandy C. Hsu, Maggie L. DiNome, Dave S.B. Hoon, Diego M. Marzese Triple-negative breast cancer (TNBC), especially the subset with a basal phenotype, represents the most aggressive subtype of breast cancer. Unlike other solid tumors, TNBCs harbor a low number of driver mutations. Conversely, we and others have demonstrated a significant impact of epigenetic alterations, including DNA methylation and histone post-translational modifications, affecting TNBCs. Due to the promising re...
Source: Genomics Data - February 14, 2017 Category: Genetics & Stem Cells Source Type: research
Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system
Publication date: Available online 6 February 2017 Source:Genomics Data Author(s): Sandeep Ghatak, Yiping He, Sue Reed, Terence Strobaugh, Peter Irwin Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and ...
Source: Genomics Data - February 5, 2017 Category: Genetics & Stem Cells Source Type: research
Genome sequences of 12 isolates of the EU1 lineage of Phytophthora ramorum, a fungus-like pathogen that causes extensive damage and mortality to a wide range of trees and other plants
Publication date: Available online 6 February 2017 Source:Genomics Data Author(s): Judith Turner, Paul O'Neill, Murray Grant, Rick A. Mumford, Richard Thwaites, David J. Studholme Here we present genome sequences for twelve isolates of the invasive pathogen Phytophthora ramorum EU1. The assembled genome sequences and raw sequence data are available via BioProject accession number PRJNA177509. These data will be useful in developing molecular tools for specific detection and identification of this pathogen. Image 1 Specifications [standardized info for the reader] Organism/cell line/tissue Twelve isolates of the...
Source: Genomics Data - February 5, 2017 Category: Genetics & Stem Cells Source Type: research
Virulence genome analysis of Pseudomonas aeruginosa VRFPA10 recovered from patient with scleritis
In this study, we investigated a P. aeruginosa VRFPA10 genome which exhibited susceptibility to commonly used drugs in vitro but the patient had poor prognosis due to its hyper virulent nature. Genomic analysis of VRFPA10 deciphered multiple virulence factors and P.aeruginosa Genomic Islands (PAGIs) VRFPA10 genome which correlated with hyper virulence nature of the organism. The genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession numbers LFMZ01000001-LFMZ01000044. Image 1 Specifications Organism/cell line/tissue Pseudomonas aeruginosa Strain VRFPA10 Sex N/A Sequence or Array type ION PGM Data...
Source: Genomics Data - February 5, 2017 Category: Genetics & Stem Cells Source Type: research
Red-legged partridge (Alectoris rufa) de-novo transcriptome assembly and identification of gene-related markers
In this study, RNA-sequencing and de-novo assembly of genes expressed in different immune tissues were performed. The raw FASTQ files were submitted to the NCBI SRA database with accession number PRJNA289204. A total of 94.2 million reads were obtained and assembled into 51,403 contigs using OASES software. The final annotated partridge immune transcriptome comprises almost 7000 unigenes, available as FASTA in the supplementary material. A total of 12,828 microsatellites and 33,857 Single Nucleotide Polymorphisms (SNPs) were identified. The candidate gene sequences and the large number of potential genetic markers from the...
Source: Genomics Data - February 4, 2017 Category: Genetics & Stem Cells Source Type: research
RNA-Seq analysis of human cell lines established from normal and neoplastic esophageal squamous epithelium
Publication date: Available online 5 February 2017 Source:Genomics Data Author(s): Ichiro Akagi, Osamu Ishibashi Esophageal cancer (EC) is the eighth most common cancer globally in 2012 and predominantly occurs in the man (Enzinger and Mayer, 2003; Conteduca et al., 2012) [1,2]. EC is classified mainly into two types, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, accounting for 60–70% and 20–30% of all EC cases, respectively. In a previous statistical study it was reported that the numbers of new EC cases and EC-related deaths worldwide in 2008 were estimated to be 482,300 and 406,800, re...
Source: Genomics Data - February 4, 2017 Category: Genetics & Stem Cells Source Type: research
