Recent lbnl_bs_gen items

PyroTag: Pyrosequencing as a Powerful Tool to Study the Diversity of Microbial Community

Wed, 13 Dec 2017 00:00:00 +0000

At JGI, major efforts have been spent on using the 16S RNA sequencing to study the composition of bacterial community. Currently, 16S rRNA genes from a microbial community are amplified with conserved PCR primers and the mixed amplicon is cloned and sequenced using traditional Sanger sequencing method. Using Roche GS FLX amplicon sequencing method, individual amplicon can be sequenced directly on the platform, producing hundreds of thousand ~;250 bp tags of the full length 16S rRNA gene. We call this pipeline PyroTag. The benefit of the PyroTag technology includes higher resolution and less bias than traditional PCR and cloning based sequencing. The disadvantage is that the read length is short as we used FLX reagent kit for the study. The aim for this study is to systematically test the effect of amplicon length and 16S rRNA regions targeted on diversity coverage of complex microbial community. The goal is to develop a standard PyroTag pipeline to provide to broad range JGI...

PyroTag: Pyrosequencing as a Powerful Tool to Study the Diversity of microbial Community

Tue, 12 Dec 2017 00:00:00 +0000

PyroTag: Pyrosequencing as a Powerful Tool to Study the Diversity of microbial Community

Metagenomic Bacterial Finishing at JGI

Mon, 11 Dec 2017 00:00:00 +0000

Metagenomic Bacterial Finishing at JGI

Comparing Two Approaches for Cloning Trace Amount of DNA

Thu, 7 Dec 2017 00:00:00 +0000

Comparing Two Approaches for Cloning Trace Amount of DNA

Development of High Throughput Processes for Constructing Illumina Libraries

Wed, 6 Dec 2017 00:00:00 +0000

As the demand of constructing Illumina libraries increases, we have started to modify the library construction protocol to adapt the use of multichannel pipette and 96-well plates. With the few simple modification steps, we have doubled the library production efficiency. These modifications include the shearing of DNA with Covaris E210, and the cleaning of enzymatic reactions and fragment size selection with SPRI beads and a magnetic plate holder. We have also designed a set of molecular barcodes to enable the sequencing of many libraries in parallel. The requirements of these barcodes include 4 bases, balanced GC, and at least 2 bases difference between barcodes. The barcode is attached to the adaptor so it does not require third sequencing primer and the barcoded library can be run on the same flowcell/run with other non-barcoded libraries. We have begun to assess the ability to assign reads and the potential bias towards certain barcodes after pooling different number of libraries....

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

Tue, 28 Nov 2017 00:00:00 +0000

BackgroundEnteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts. Methane production in the rumen is strongly connected to microbial hydrogen production through fermentation processes. In this study, we investigate the contribution that rumen bacteria make to methane yield phenotypes in sheep.ResultsUsing deep sequence metagenome and metatranscriptome datasets in combination with 16S rRNA gene amplicon sequencing...

meraculous: de novo genome assembly with short paired-end reads

Fri, 18 May 2012 00:00:00 +0000

meraculous: de novo genome assembly with short paired-end reads

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

Thu, 9 Sep 2010 00:00:00 +0000

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

Comparative genomics and evolution of eukaryotic phospholipid biosynthesis

Wed, 30 Jan 2008 00:00:00 +0000

Comparative genomics and evolution of eukaryotic phospholipid biosynthesis

Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca

Wed, 29 Aug 2007 00:00:00 +0000

Thermobifida fusca is a moderately thermophilic soil bacterium that belongs to Actinobacteria. 3 It is a major degrader of plant cell walls and has been used as a model organism for the study of 4 secreted, thermostable cellulases. The complete genome sequence showed that T. fusca has a 5 single circular chromosome of 3642249 bp predicted to encode 3117 proteins and 65 RNA6 species with a coding density of 85 percent. Genome analysis revealed the existence of 29 putative 7 glycoside hydrolases in addition to the previously identified cellulases and xylanases. The 8 glycosyl hydrolases include enzymes predicted to exhibit mainly dextran/starch and xylan 9 degrading functions. T. fusca possesses two protein secretion systems: the sec general secretion 10 system and the twin-arginine translocation system. Several of the secreted cellulases have 11 sequence signatures indicating their secretion may be mediated by the twin-arginine12 translocation system. T. fusca has...