PacBio 2014 User Group Meeting Presentation Slides: Anne Deslattes Mays of Georgetown University discussed how PacBio provided the necessary full-length isoform information to allow characterization of isoform distribution by sub-cell population.
Complete genome sequences of a H2O2-resistant psychrophilic bacterium Colwellia sp. Arc7-D isolated from Arctic Ocean sediment
Colwellia sp. Arc7-D, a psychrophilic H2O2-resisitant bacterium, was isolated from Arctic Ocean sediment. Here we describe the complete genome of Colwellia sp. Arc7-D. The genome has one circular chromosome of 4,305,442?bp (37.67?mol%?G?+?C content), consisting of 3526 coding genes, 77 tRNA genes, as well as five rRNA operons as 16S–23S-5S rRNA and one rRNA operon as 16S-23S-5S-5S. According to KEGG analysis, strain Arc7-D encodes 23 genes related with antioxidant activity including superoxide dismutase, glutathione peroxidase, glutathione reductase and catalase. However, many additional genes affiliated with anti-oxidative stress were also identified, such as aconitase, thioredoxin and ascorbic acid.
Next generation sequencing characterizes HLA diversity in a registry population from the Netherlands.
Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, -DRB3/4/5, and -DQB1 assignments of 1009 unrelated volunteers for the unrelated donor registry in The Netherlands. The analysis characterizes all HLA exons and introns for class I alleles; at least exons 2 to 3 for HLA-DRB1; and exons 2 to 6 for HLA-DQB1. Of the distinct alleles present, there are 229 class I and 71 class II; 36 of these alleles are novel. The majority (approximately 98%) of the cumulative allele frequency at each locus is contributed by alleles that appear three or more times. Alleles encoding protein variation outside of the antigen recognition domains are 0.6% of the class I assignments and 5.3% of the class II assignments. © 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
The complete genome sequence of the denitrifying bacterium Marinobacter sp. Arc7-DN-1 isolated from Arctic Ocean sediment
The general features and genome characteristics of the denitrifying bacterium Marinobacter sp. Arc7-DN-1, isolated from Arctic Ocean sediment, are described. Marinobacter sp. Arc7-DN-1 uses NO3- or NH4+ as the sole nitrogen source to grow at low temperatures. The strain can grow at a wide range of temperatures (0–30?°C) and NaCl concentration (15–90‰). The genome has one circular chromosome of 4,300,456?bp (57.64?mol%?G?+?C content), consisting of 4012 coding genes, including 50 tRNAs and three rRNA operons as 16S-23S-5S rRNA. On the basis of the KEGG analysis, strain Arc7-DN-1 encodes 43 proteins related to nitrogen metabolism, including a complete denitrifying pathway and an assimilatory nitrate reduction pathway.