Prevalence of antimicrobial resistance among serotypes of Campylobacter jejuni isolates from cattle and poultry in Japan

Penner serotypes of C. jejuni in a total of 601 isolates from apparently healthy cattle, layer and broiler chickens in Japan were examined between 2001 and 2006. Predominant serotypes were B (O: 2, 19.1%), D (O: 4, 13.5%), Y (O: 37, 7.3%) and G (O: 8, 5.8%), whereas the remaining serotypes made up less than 5% of the total isolates. The frequency of ampicillin resistance in serotype G (65.6%) was significantly higher than in serotypes D (12.5%), B (11.2%), and Y (0%). Our results suggest that serotype is one factor contributing to the prevalence of ampicillin resistance in C. jejuni isolates.     

Assessment of Metabolome Annotation Quality: A Method for Evaluating the False Discovery Rate of Elemental Composition Searches

Background

In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed.

Methodology/Principal Findings

The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30–50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries.

Conclusions/Significance

High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data.     

Post‐glacial distribution of a Mongolian mayfly inferred from population genetic analysis

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In vitro expansion of mouse primordial germ cell‐like cells recapitulates an epigenetic blank slate

The expansion of primordial germ cells (PGCs), the precursors for the oocytes and spermatozoa, is a key challenge in reproductive biology/medicine. Using a chemical screening exploiting PGC‐like cells (PGCLCs) induced from mouse embryonic stem cells (ESCs), we here identify key signaling pathways critical for PGCLC proliferation. We show that the combinatorial application of Forskolin and Rolipram, which stimulate cAMP signaling via different mechanisms, expands PGCLCs up to ~50‐fold in culture. The expanded PGCLCs maintain robust capacity for spermatogenesis, rescuing the fertility of infertile mice. Strikingly, during expansion, PGCLCs comprehensively erase their DNA methylome, including parental imprints, in a manner that precisely recapitulates genome‐wide DNA demethylation in gonadal germ cells, while essentially maintaining their identity as sexually uncommitted PGCs, apparently through appropriate histone modifications. By establishing a paradigm for PGCLC expansion, our system reconstitutes the epigenetic “blank slate” of the germ line, an immediate precursory state for sexually dimorphic differentiation.     

Metabolic switching of astringent and beneficial triterpenoid saponins in soybean is achieved by a loss‐of‐function mutation in cytochrome P450 72A69

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Discovery of novel 2-(4-aryl-2-methylpiperazin-1-yl)-pyrimidin-4-ones as glycogen synthase kinase-3β inhibitors

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