General microbiology and science, June 24

Metabolomics, metagenomics, phages in the human gut, arsenic poisoning in China, and a big award for Dengue research.


Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities – Paul E. Abraham – Current Protocols in Bioinformatics

“In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. “

Review: The human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva – Anton Amann – Journal of Breath Research

“Fecal volatiles have been implicated in differentiating certain infectious bowel diseases such as Clostridium difficile, Campylobacter, Salmonella and Cholera. They have also been used to differentiate other non-infectious conditions such as irritable bowel syndrome and inflammatory bowel disease.”

Metagenomics and DNA structure

Sequencing the Strange Communities: Taking on Metagenomics – Aaron Krol – Bio-IT World

““Communities are made up of organisms that interact,” says Jonathan Eisen, a professor at the School of Medicine and the College of Biological Sciences at the University of California, Davis. “They’re not made up of short reads of Illumina sequences. And we need to stitch those together into organisms in order to make useful predictions, and interpretation of experimental data.””

Gene positioning and genome function – Nidhi Vishnoi, Jie Yao – Frontiers in Biology

” In this review, we discuss some recent findings as well as experimental tools to investigate subnuclear gene positioning and to explore its implications in genome functions.”

Phages and viruses

Classification and quantification of bacteriophage taxa in human gut metagenomes – Alison S Waller – ISME Journal 

“Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. “


Enzymatic Treatment of Specimens before DNA Extraction Directly Influences Molecular Detection of Infectious Agents – Pablo Goldschmidt – PLOS ONE

“The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification.”


Sustainable Sciences Institute (SSI) Awarded $1 Million to Battle Growing Threat to Global Public Health: Mosquito-borne Dengue Virus – PR Web

“SSI, a San Francisco nonprofit founded by Eva Harris, UC Berkeley Professor of Infectious Disease and Vaccinology and former MacArthur “Genius” award winner, has worked to minimize the threat of potentially fatal Dengue disease for 15 years. With the latest award of $1 million dollars, Harris and other SSI investigators will be able to extend their reach and speed up their efforts.”

Infection and host response

Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection – Laxmi Yeruva – mBio

“To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. “

Immunity to gastrointestinal nematodes: mechanisms and myths – Richard K. Grencis – Immunological Reviews

“This review aims to discuss the recent discoveries in both host protection and immunoregulation against gastrointestinal nematodes, placing the data in context of the specific life cycles imposed by the different parasites studied and the future challenges of considering the mucosal/immune axis to encompass host, parasite, and microbiome in its widest sense.”

Tailored immunity at mucosae – Yasmine Belkaid – Immunological Reviews

“This issue of Immunological Reviews presents articles from investigators involved in the exploration of the mechanisms by which mucosal barrier sites induce and control innate and adaptive immune responses.”

Detection of bacteria in blood and other sites

Rapid Detection of Enterobacteriaceae Producing Extended Spectrum Beta-Lactamases Directly From Positive Blood Cultures by Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) – Marina Oviaño – Clinical Microbiology and Infection

“In the assay, 141 blood cultures were tested, 13 out of them were real bacteremias and 128 corresponded to blood culture bottles seeded with bacterial clinical isolates. Bacteremias were analyzed by MALDI-TOF after a positive growth result and the 128 remaining blood cultures 24 hours after the bacterial seeding. “

General microbiology and ecology

The quest for a unified view of bacterial land colonization – Hao Wu – ISME Journal

“Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. “

Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes – Akinori Yabuki – ISME Journal

“Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate.”

Arsenic metabolism

Arsenic Pollution Sows Despair in Chinese Cancer Village (slideshow)- Yahoo News

“Xiong Demin could not have foreseen that the mine he worked at for 32 years would leave his home village poisoned and hundreds of residents, including himself and his wife, stricken with cancer.”

Dr. Bik’s Picks – Evolution Edition

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials – Kieren J. Mitchell – Molecular Biology and Evolution

“We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species”

Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals – Zhen Liu – Molecular Biology and Evolution

“By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency bat, Stoliczka’s trident bat (Aselliscus stoliczkanus). “

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape – Yasunori Ichihashi – PNAS

“Utilizing the natural variation in leaf morphology between tomato and two related wild species, we identified a gene network module that leads to a dynamic rewiring of interactions in the whole leaf developmental gene regulatory network. “


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