FY 2014 Archives - Page 17 of 19

May 29, 2014

Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer

Zymomonas mobilis subsp. mobilis is one of the most rigorous ethanol-producing organisms known to date, considered by many to be the prokaryotic alternative to yeast. The two most applied Z. mobilis subsp. mobilis strains, ZM4 and CP4, derive from Recife, Brazil, and have been isolated from sugarcane fermentations. Of these, ZM4 was the first Z…. [Read More]

May 29, 2014

Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline… [Read More]

May 29, 2014

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin… [Read More]

May 29, 2014

Non-contiguous finished genome sequence and description of Clostridium dakarense sp. nov

Clostridium dakarense strain FF1(T), is the type strain of Clostridium dakarense sp. nov., a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the fecal flora of a 4-month-old Senegalese child suffering from gastroenteritis. C. dakarense sp. nov. strain FF1(T) is an obligate anaerobic Gram-positive bacillus. Here we… [Read More]

May 29, 2014

IMG/M 4 version of the integrated metagenome comparative analysis system

IMG/M (http://img.archive.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M’s data content and analytical tools have expanded continuously since its first version was released in 2007. Since… [Read More]

May 29, 2014

IMG 4 version of the integrated microbial genomes comparative analysis system

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released… [Read More]

May 29, 2014

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated… [Read More]

May 29, 2014

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of… [Read More]

May 29, 2014

Bayesian analysis of congruence of core genes in prochlorococcus and synechococcus and implications on horizontal gene transfer

It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. “Universal proteins” have been used to infer the organismal phylogeny, but have been criticized as being only the “tree of one percent.” Currently,… [Read More]

May 29, 2014

Cloud-Enabled Microscopy and Droplet Microfluidic Platform for Specific Detection of Escherichia coli in Water

We report an all-in-one platform – ScanDrop – for the rapid and specific capture, detection, and identification of bacteria in drinking water. The ScanDrop platform integrates droplet microfluidics, a portable imaging system, and cloud-based control software and data storage. The cloud-based control software and data storage enables robotic image acquisition, remote image processing, and rapid… [Read More]