Institution
California Institute for Quantitative Biosciences
Nonprofit•San Francisco, California, United States•
About: California Institute for Quantitative Biosciences is a nonprofit organization based out in San Francisco, California, United States. It is known for research contribution in the topics: Protein structure & Population. The organization has 896 authors who have published 1183 publications receiving 100512 citations.
Topics: Protein structure, Population, Gene, RNA, CRISPR
Papers published on a yearly basis
Papers
More filters
••
TL;DR: Increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease.
Abstract: Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
7,032 citations
••
Broad Institute1, Commonwealth Scientific and Industrial Research Organisation2, Massachusetts Institute of Technology3, Hebrew University of Jerusalem4, Science for Life Laboratory5, Pittsburgh Supercomputing Center6, Oklahoma State University–Stillwater7, Griffith University8, University of Wisconsin-Madison9, Dresden University of Technology10, California Institute for Quantitative Biosciences11, Flanders Institute for Biotechnology12, Parco Tecnologico Padano13, United States Department of Agriculture14, Purdue University15, Indiana University16
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
Abstract: De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
6,369 citations
01 Jun 2010
TL;DR: Results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.
Abstract: MicroRNAs (miRNAs) are endogenous approximately 22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (>/=84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.
3,444 citations
••
TL;DR: A ribosomesome-profiling strategy based on the deep sequencing of ribosome-protected mRNA fragments is presented and enables genome-wide investigation of translation with subcodon resolution and is used to monitor translation in budding yeast under both rich and starvation conditions.
Abstract: Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.
3,416 citations
••
TL;DR: In this paper, the authors used ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels, showing that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.
Abstract: MicroRNAs (miRNAs) are endogenous approximately 22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (>/=84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.
3,401 citations
Authors
Showing all 907 results
Name | H-index | Papers | Citations |
---|---|---|---|
Carlos Bustamante | 161 | 770 | 106053 |
Christopher T. Walsh | 139 | 819 | 74314 |
Jonathan S. Weissman | 132 | 357 | 91528 |
Jennifer A. Doudna | 126 | 461 | 72967 |
Peter Walter | 126 | 841 | 71580 |
Kevan M. Shokat | 124 | 462 | 52630 |
Sanjay Kumar | 120 | 2052 | 82620 |
Andrej Sali | 119 | 430 | 74984 |
Carolyn R. Bertozzi | 118 | 691 | 61006 |
Graham R. Fleming | 113 | 573 | 51107 |
James A. Wells | 112 | 462 | 50847 |
Alma L. Burlingame | 107 | 610 | 43486 |
Nevan J. Krogan | 104 | 396 | 47254 |
John Kuriyan | 103 | 274 | 46431 |
Richard M. Karp | 100 | 312 | 69006 |