Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels

The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica

Methane observations from the Greenhouse Gases Observing SATellite: Comparison to ground‐based TCCON data and model calculations

We report new short-wave infrared (SWIR) column retrievals of atmospheric methane (X_(CH4)) from the Japanese Greenhouse Gases Observing SATellite (GOSAT) and compare observed spatial and temporal variations with correlative ground-based measurements from the Total Carbon Column Observing Network (TCCON) and with the global 3-D GEOS-Chem chemistry transport model. GOSAT X_(CH4) retrievals are compared with daily TCCON observations at six sites between April 2009 and July 2010 (Bialystok, Park Falls, Lamont, Orleans, Darwin and Wollongong). GOSAT reproduces the site-dependent seasonal cycles as observed by TCCON with correlations typically between 0.5 and 0.7 with an estimated single-sounding precision between 0.4–0.8%. We find a latitudinal-dependent difference between the X_(CH4) retrievals from GOSAT and TCCON which ranges from 17.9 ppb at the most northerly site (Bialystok) to −14.6 ppb at the site with the lowest latitude (Darwin). We estimate that the mean smoothing error difference included in the GOSAT to TCCON comparisons can account for 15.7 to 17.4 ppb for the northerly sites and for 1.1 ppb at the lowest latitude site. The GOSAT X_(CH4) retrievals agree well with the GEOS-Chem model on annual (August 2009 – July 2010) and monthly timescales, capturing over 80% of the zonal variability. Differences between model and observed X_(CH4) are found over key source regions such as Southeast Asia and central Africa which will be further investigated using a formal inverse model analysis

Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process.

Genomic data generated from clinical Vibrio cholerae O1 isolates collected over a five year period in an area of Kolkata, India with seasonal cholera outbreaks allowed a detailed genetic analysis of serotype switching that occurred from Ogawa to Inaba and back to Ogawa. The change from Ogawa to Inaba resulted from mutational disruption of the methyltransferase encoded by the wbeT gene. Re-emergence of the Ogawa serotype was found to result either from expansion of an already existing Ogawa clade or reversion of the mutation in an Inaba clade. Our data suggests that such transitions are not random events but rather driven by as yet unidentified selection mechanisms based on differences in the structure of the O1 antigen or in the serotype-determining wbeT gene

Propaganda With the World at War

As the world was swept into war for the second time during the twentieth century, countries across the globe turned to propaganda to increase support for the war and commitment to victory. Drawing upon propagandist films and posters from major Allied and Axis countries, several themes emerge, such as hatred for the enemy, provided a boost in civilian morale, and encouraged women’s participation in the workforce. Patriotism materialized through these films and posters, but it is through the savvy world leaders that it stuck. This new wave of world leaders (Franklin D. Roosevelt, Winston Churchill, Adolf Hitler) were not like any before them, a group of men who were media-savvy, outspoken, influential, and effective public speakers. Through the use of media and public speeches, these leaders pulled their respective countries from the depths of despair to war powers, which saw civilians and soldiers alike rallying for the cause. This paper examines the effect of propaganda on civilians, both before the war, and during

Exome-wide association study of pancreatic cancer risk

We conducted a case-control exome-wide association study to discover germline variants in coding regions that affect risk for pancreatic cancer, combining data from 5 studies. We analyzed exome and genome sequencing data from 437 patients with pancreatic cancer (cases) and 1922 individuals not known to have cancer (controls). In the primary analysis, BRCA2 had the strongest enrichment for rare inactivating variants (17/437 cases vs 3/1922 controls) (P=3.27x10(-6); exome-wide statistical significance threshold P<2.5x10(-6)). Cases had more rare inactivating variants in DNA repair genes than controls, even after excluding 13 genes known to predispose to pancreatic cancer (adjusted odds ratio, 1.35, P=.045). At the suggestive threshold (P<.001), 6 genes were enriched for rare damaging variants (UHMK1, AP1G2, DNTA, CHST6, FGFR3, and EPHA1) and 7 genes had associations with pancreatic cancer risk, based on the sequence-kernel association test. We confirmed variants in BRCA2 as the most common high-penetrant genetic factor associated with pancreatic cancer and we also identified candidate pancreatic cancer genes. Large collaborations and novel approaches are needed to overcome the genetic heterogeneity of pancreatic cancer predisposition