General microbiome and science, July 8

Metabolic networks, CRISPR induced immunity, and influence of extraction methods and primers on microbiome analysis. Plus some smallpox in the Lost&Found, and a big citation scandal in SAGE journals.

Microbial ecology / metabolomics

Screen Shot 2014-07-08 at 10.07.56 PMIdentifying All Moiety Conservation Laws in Genome-Scale Metabolic Networks – Andrea De Martino – PLOS ONE

“ Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism.”

Emergent

Emergent Biosynthetic Capacity in Simple Microbial Communities – Hsuan-Chao Chiu – PLOS Computational Biology

“We specifically focus on detecting emergent biosynthetic capacity – instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. “

DIET ArchaeaDirect Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri – Amelia-Elena Rotaru – Applied and Environmental Microbiology

“M. barkeri is the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H2 or electrons derived from DIET for CO2 reduction. “

Optimal defenseOptimal Defense Strategies in an Idealized Microbial Food Web under Trade-Off between Competition and Defense – Selina Våge – PLOS ONE

“ Under coexistence with a competition specialist, a balance of competitive and defensive ability of the defense strategist was found to be evolutionarily stable, whereas stronger defense was optimal under increased nutrient levels in the absence of the pure competition specialist.”

Microbial detection

Screen Shot 2014-07-08 at 10.13.13 PMHuman Herpes Viruses Are Associated with Classic Fever of Unknown Origin (FUO) in Beijing Patients – Weimin Zhou – PLOS ONE

“HHVs are associated with Chinese patients (especially for children) with classic FUO. Our study adds perspective to the aetiological and clinical characteristics of classic FUO in beijing patients.”

Phages and viruses

Screen Shot 2014-07-08 at 10.13.31 PMCRISPR-Induced Distributed Immunity in Microbial Populations – Lauren M. Childs – PLOS ONE

“We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities.”

Techniques

Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems – Perrine Cruaud – Applied and Environmental Microbiology

“Thanks to statistical and diversity analyses as well as inference of operational taxonomic unit (OTU) networks, we show that (i) while DNA extraction methods do not seem to affect the results for some samples, they can lead to dramatic changes for others; and (ii) the choice of amplification and sequencing primers also considerably affects the microbial community detected in the samples.”

Dengue

Sanofi’s dengue vaccine first to complete phase 3 – Gunjan Sinha – Nature Biotechnology

“Banking on approval, Sanofi has already started production, a move some have described as a “huge gamble” in light of the vaccine’s disappointing results from earlier studies, says Mark Clark, a pharmaceuticals analyst at Deutsche Bank in London.”

Microbes in the News

Found: Forgotten Vials of Smallpox – Maryn McKenna – Wired.com (also see CDC Media Statement)

“Workers clearing out an old storage room on the Bethesda, Md. campus of the National Institutes of Health have found a forgotten box of vials that contain smallpox.”

The Bacteria That Got Spread Throughout The US By Military Testing – Esther Inglis-Arkell – IO9

“Have you ever heard of serratia marcescens bacteria? Today they are a cause of hospital infections. In the 1960s, they were secretly sprayed across Washington, San Francisco, and New York.”

Manage Your Microbes – Laura Stec – Palo Alto Online

“I’ve been researching this wonderful advance in science for Manage Your Microbes, a cook class at Belmont Library on July 29th. “

Science, Publishing, and Career

SAGE Publications busts “peer review and citation ring,” 60 papers retracted – Retraction Watch

SAGE announces the retraction of 60 articles implicated in a peer review and citation ring at the Journal of Vibration and Control (JVC). “

13 Subtle Ways Women Are Treated Differently At Work – Jenna Goudreau – Business Insider

“Both men and women hold these views but often don’t even realize it. “It’s hard to fight this,” says Rivers, but awareness is key.

Dr. Bik’s Picks

Combining colour and temperature: A blue object is more likely to be judged as warm than a red object – Hsin-Ni Ho – Nature Scientific Reports

“It is commonly believed that reddish colour induces warm feelings while bluish colour induces cold feelings. We, however, demonstrate an opposite effect when the temperature information is acquired by direct touch.”

MandarinSequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication – G Albert Wu – Nature Biotechnology

“Here we sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and show that cultivated types derive from two progenitor species. “

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