General microbiology and science digest, October 7, 2014

Transmission of Staph aureus in the hospital, a new assembler tool, metabolomics of the human gut microbiome, and a polio virus spill in Belgium.

More Microbes

Absence of Patient-to-Patient Intrahospital Transmission of Staphylococcus aureus as Determined by Whole-Genome Sequencing – S. Wesley Long – mBio

“To identify patient-to-patient intrahospital transmission using high-resolution genetic analysis, we sequenced the genomes of a consecutive set of 398 S. aureus isolates from sterile-site infections. “

Bioinformatics

Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs – Matthew Scholz, Chien-Chi Lo & Patrick S. G. Chain – Nature Scientific Reports

“MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. “

Inferring phylogenies of evolving sequences without multiple sequence alignment – Cheong Xin Chan – Nature Scientific Reports

“Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. “

Gut Check: Exploring Your Microbiome – Coursera / University of Colorado Boulder

“Join us on a guided tour of the human gut and its microscopic inhabitants.”

Metabolomics

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Microbes in the news

* Petri Dish: The third branch of life – David Woodland – Summit Daily

“In addition to being an interesting branch on the tree of life, archaebacteria have turned out to be an incredibly valuable source of new products for science and industry. “

Pharmaceutical Giant GlaxoSmithKline “Accidentally” Released 45 Liters of Concentrated Live Polio Virus in the Environment – Global Research

“As reported to ECDC by Belgian authorities, on 2 September 2014, following a human error, 45 litres of concentrated live polio virus solution were released into the environment by the pharmaceutical company, GlaxoSmithKline (GSK), in Rixensart city, Belgium.”

Science, publishing and career

* Science is innate! (behind a paywall, even at Stanford) – Jack A Gilbert – Genome Biology

“….when I am asked, as I often am, about how my research findings have influenced my day-to-day activities, I like to take a step back and think about what it means to be a scientist.”

Why I have taken a leave of absence from Science: to protest the abrupt firing of 4 colleagues – Michael Balter – Letter to Science

“Thus it is particularly painful and sad for me to tell you that I will be taking a three-month leave of absence in protest of recent events at Science and within its publishing organization, the American Association for the Advancement of Science (AAAS).

Bik’s Picks

Killer whales learn to communicate like dolphins – Science Daily

“…killer whales can engage in cross-species vocal learning: when socialized with bottlenose dolphins, they shifted the sounds they made to more closely match their social partners.”

NASA selects astrobiologists to study life origins and extraterrestrial possibilities – Jim Algar – Tech Times

“NASA announced 5-year grants adding up to nearly $50 million for seven research groups across the U .S. to study life in the universe and its origins, distribution, evolution and future.”

The most passive aggressive acknowledgement ever – BioDataGanache – SciEasterEggs

“The authors in this paper put some serious time in on this sucker, and they wanted to make a statement about it.”

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