General microbiology and science, October 14, 2014

A living review of multivariate techniques, spatial organizations of bacterial genomes, and metabolomics of wetlands, pigs, marine bacteria and free-living humans.

Bioinformatics

* A Guide to Statistical Analysis in Microbial Ecology: a community-focused, living review of multivariate data analyses – Pier Luigi Buttigieg – FEMS Microbiology Ecology

“we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists”

Techniques

New approaches to understanding the spatial organization of bacterial genomes – Tung BK Le, Michael T Laub – Current Opinion in Microbiology

“Here, we review the current arsenal of techniques used to query chromosome structure”

Development of Clamping Probe for Rare DNA Detection using Universal Primers – Meyong il Kim – E-FAS Journal

“In this study, we evaluated the efficiency of rare gene detection for two kinds of clamping probes which were successfully utilized for eukaryotic symbiont analysis”

Metabolomics

Microbial community metabolic function in subsurface flow constructed wetlands of different designs – Mark Button – Ecological Engineering

“Microbial community function followed a clear gradient along the flow direction. Metabolic profiles were system specific (horizontal, vertical, and aerated).”

A high fat, high choleststerol diet leads to changes in metabolite patterns in pigs – a metabolomic study – Jianghao Sun – Food Chemistry

“Extracts of plasma, fecal and urine samples from pigs fed high fat or basal regular diets for 11 weeks were analyzed using ultra-high performance liquid chromatography with high-resolution mass spectrometry “

Free-living individuals – as in “not in prison”?
An NMR metabolomics approach reveals a combined-biomarkers model in a wine interventional trial with validation in free-living individuals of the PREDIMED study – Rosa Vázquez-Fresno – Metabolomics

A High-Resolution LC-MS-Based Secondary Metabolite Fingerprint Database of Marine Bacteria – Liang Lu – Nature Scientific Reports

“Till now, 1,430 bacterial strains spanning 168 known species collected from different marine environments were cultured and profiled. “

Viruses and phages

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses – Eric G. Sakowski – PNAS USA

“We identify ribonucleotide reductase (RNR) genes as superior markers of viral diversity. RNR genes are distributed over a broad range of viruses”

More microbiology

Strength in Diversity – Daniel J. Wolter, Lucas R. Hoffman – Cell Host & Microbe

“In this issue of Cell Host & Microbe, Hammer et al. (2014) show that distinct, slow-growing bacteria have better in vitro and in vivo growth and virulence when cocultured than in isolation. “

The Journal of Infectious Diseases has a special Issue on Polio: The Final Phase of Polio Eradication and Endgame Strategies for the Post-Eradication Era – Journal of Infectious Diseases

Science, publishing, career

Correcting the scientific record: An introduction to retractions – Bonnie Swoger – Scientific American

“Although the system is far from perfect, the retraction process is one of the ways in which the scientific literature corrects itself over time.”

 

Bik’s Picks

When Racism Was a Science – ‘Haunted Files: The Eugenics Record Office’ Recreates a Dark Time in a Laboratory’s Past – Joshua A. Krisch – New York Times

“In its heyday, the office was the premier scientific enterprise at Cold Spring Harbor. There, bigoted scientists applied rudimentary genetics to singling out supposedly superior races and degrading minorities. “

Paul Ryan: Science doesn’t get climate change – Jane C. Timm – MSNBC

“A full 97% of researchers taking a stance on climate change say it’s man-made, as do 97-98% of the most frequently-published climate scientists. But according to Wisconsin Rep. Paul Ryan, they’re all wrong.”

Get fish fry with a side of science at ‘Science of the Supper Club’ this Friday – Lindsay Christians – The Capital Times

“Science is everywhere, even at a Friday night fish fry. That’s the message of a new event this Friday called “Science of Supper Clubs,” part of the four-day Wisconsin Science Festival held at various venues around the state.”

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