General microbiology and science, August 5, 2014

Antibiotic resistance, phages, bioinformatics tools, and how to present your research in 3 minutes.

Antibiotic resistance

The Natural Environment May Be the Most Important Source of Antibiotic Resistance Genes – Desmond Keith O’Toole – mBio

“I found the recent paper by Wichmann et al. (1) of great interest, and it illustrates an aspect of antibiotic resistance that has concerned me for a long time, namely, the origin of that resistance.”

Phages and viruses

Pervasive domestication of defective prophages by bacteria – Louis-Marie Bobay, Marie Touchon, and Eduardo P. C. Rocha – PNAS USA

“We identified over 300 vertically inherited prophages within enterobacterial genomes. Some of these elements are very old and might predate the split between Escherichia coli and Salmonella enterica. “

Bioinformatics tools

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm – Yu-Wei Wu, Yung-Hsu Tang, Susannah G Tringe, Blake A Simmons and Steven W Singer – Microbiome

“We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads.”

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification – Lőrinc S. Pongor – PLOS ONE

“We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. “

More microbes

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever – Zhemin Zhou, Angela McCann, François-Xavier Weill, Camille Blin, Satheesh Nair, John Wain, Gordon Dougan, and Mark Achtman – PNAS

“We identified seven modern lineages among 149 genomes on the basis of 4,584 SNPs in the core genome and estimated that Paratyphi A originated 450 y ago. “

Bacillus subtilis chromosome organization oscillates between two distinct patterns – Xindan Wang, Paula Montero Llopis, and David Z. Rudner – PNAS USA

“We propose that the distinct organization patterns observed for bacterial chromosomes reflect a common organization–segregation mechanism, and that simple modifications to it underlie the unique patterns observed in different species.”

Microbes in the news

Researchers Find Surprises in Human Microbiome – Carol Potera – BioScience

But “some forms of autism may have an etiology that lies in the gut, not the brain,” says Sarkis Mazmanian of the California Institute of Technology.

Science and publishing

Science Speak – Rina Shaikh-Lesko – The Scientist

“Contests that challenge young scientists to explain their research without jargon are turning science communication into a competitive sport.”

Researcher’s death shocks Japan – David Cyranoski – Nature Newsblog

“Yoshiki Sasai, one of Japan’s top stem-cell researchers, died this morning (5 August) in an apparent suicide. “

Bik’s Picks

The color red distorts time perception for men, but not for women – Masahiro Shibasaki & Nobuo Masataka – Nature Scientific Reports

“The results showed that the perceived duration of a red screen was longer than was that of a blue screen. However, the results reflected sex differences; men, but not women, overestimated the duration of the red screen. “

Gray’s paradox: A fluid mechanical perspective – Rahul Bale, Max Hao, Amneet Pal Singh Bhalla, Namrata Patel & Neelesh A. Patankar – Nature Scientific Reports

“Nearly eighty years ago, Gray reported that the drag power experienced by a dolphin was larger than the estimated muscle power – this is termed as Gray’s paradox. We provide a fluid mechanical perspective of this paradox.”


Total darkness at night key to success of breast cancer therapy, study shows – Science Daily

“Exposure to light at night, which shuts off nighttime production of the hormone melatonin, renders breast cancer completely resistant to tamoxifen, a widely used breast cancer drug, says a new study. “



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