Project description:This RNA-Seq study of gene expression in M. tuberculosis was done as part of the FLUTE project (NIH grant U19-AI107774, Eric Rubin, program director).
Project description:This RNA-Seq study of gene expression in M. tuberculosis was done as part of the FLUTE project (NIH grant U19-AI107774, Eric Rubin, program director).
Project description:Microbial RNAseq analysis of cecal and fecal samples collected from mice colonized with the microbiota of human twins discordant for obesity. Samples were colleted at the time of sacrifice, or 15 days after colonization from mice gavaged with uncultured or cultured fecal microbiota from the lean twins or their obese co-twins. Samples were sequenced using Illumina HiSeq technology, with 101 paired end chemistry.
Project description:Mammalian feces can be collected non-invasively during field research and provides valuable information on the ecology and evolution of the host individuals. Undigested food objects, genome/metagenome, steroid hormones, and stable isotopes obtained from fecal samples provide evidence on diet, host/symbiont genetics, and physiological status of the individuals. However, proteins in mammalian feces have hardly been studied, which hampers the molecular investigations into the behavior and physiology of the host individuals. Here, we apply mass spectrometry-based proteomics to fecal samples (n = 10) that were collected from infant, juvenile, and adult captive Japanese macaques (Macaca fuscata) to describe the proteomes of the host, food, and intestinal microbes. The results show that fecal proteomics is a useful method to investigate dietary changes along with breastfeeding and weaning, to reveal the organ/tissue and taxonomy of dietary items, and to estimate physiological status inside intestinal tracts. These types of insights are difficult or impossible to obtain through other molecular approaches. Most mammalian species are facing extinction risk and there is an urgent need to obtain knowledge on their ecology and evolution for better conservation strategy. The fecal proteomics framework we present here is easily applicable to wild settings and other mammalian species, and provides direct evidence of their behavior and physiology.
Project description:Purpose: The goal of this study is to compare colonic transcriptional responses following ex-vivo colonization with fecal samples collected from multiple sclerosis patients, before and after Propionic acid treatment and between the patients that responded or not to the therapy. Methods: Bulk whole-tissue mRNA profiles of 13-day-old wild-type mice colons were generated by deep sequencing, in triplicate, using Illumina NextSeq platform.
Project description:To elucidate potential mechanisms of U19/EAF2 action, we performed cDNA microarray analysis and identified 202 mRNA transcripts regulated by U19/EAF2 in the mouse ventral prostate. Of these transcripts, 167 are network eligible genes, with 63 associated with cancer and 24 with reproductive system diseases. Bioinformatics analysis indicated that U19/EAF2 knockout activates the RAS-BRAF-ERK signaling pathway, which is known to play important roles in carcinogenesis.
Project description:To elucidate potential mechanisms of U19/EAF2 action, we performed cDNA microarray analysis and identified 202 mRNA transcripts regulated by U19/EAF2 in the mouse ventral prostate. Of these transcripts, 167 are network eligible genes, with 63 associated with cancer and 24 with reproductive system diseases. Bioinformatics analysis indicated that U19/EAF2 knockout activates the RAS-BRAF-ERK signaling pathway, which is known to play important roles in carcinogenesis. prostate wild type and U19/EAF2 knockout