Project description:DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively Combination of these methods enabled the reconstruction of the complete genome sequence of M oxyfera from the metagenome and identification of the functionally relevant enzymes and genes
Project description:SPF leghorn chickens were infected with C. jejuni. The cecum were collected at 8h post infection for total RNA isolation. The significantly expressed microRNAs between infected and non-infected chickens were identified through Solexa sequencing technology.
Project description:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.
Project description:White leghorn layers were infected with Salmonella Enteritidis. The cecum were collected at 7 days post infection for total RNA isolation. The significantly expressed microRNAs between infected and non-infected chickens were identified through Solexa sequencing technology.
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
Project description:To profile the expression of circulating microRNAs (miRNAs) of mice in experimental sepsis by cecal ligation and puncture (CLP), the whole blood samples were obtained from C57BL/6 mice at 4, 8, and 24 h following CLP for miRNA expression analysis using a miRNA array (The Mouse & Rat miRNA OneArray® v3). Briefly, mice were anesthetized with a combination of ketamine and xylazine as the anesthetic/analgesic agents and a midline abdominal incision was made. The cecum was mobilized, ligated in the middle of cecum below the ileocecal valve, punctured once with a 21 G needle, and a little stool was squeeze out of the cecum to induce polymicrobial peritonitis. The abdominal wall was closed in two layers. Sham-operated mice underwent the same procedure, including opening the peritoneum and exposing the bowel, but without ligation and needle perforation of the cecum.
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
