General microbiology and science, August 26, 2014

Here, we have CRISPRs, phages, marine metagenomics, a universal bacterial/archaeal primer (The One?), single-cell genomics, light and bacteria, and Bik’s Picks.

Phages and CRISPRs

Abundant and Diverse Clustered Regularly Interspaced Short Palindromic Repeat Spacers in Clostridium difficile Strains and Prophages Target Multiple Phage Types within This Pathogen – Katherine R. Hargreaves – mBio

“We detected multiple matches between spacers and regions in 31 C. difficile phage and prophage genomes”

Evolutionary consequences of intra-patient phage predation on microbial populations
Kimberley D Seed – eLife

“Here, we show that predatory interactions of a phage with an important environmentally transmitted pathogen, Vibrio cholerae, can modulate the evolutionary trajectory of this pathogen during the natural course of infection within individual patients.”

Metagenomics

* Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery
Rosalba Barone – Frontiers in Marine Science

“We report examples of several hydrolytic enzymes and natural products isolated by functional sequenced-based and function- screening strategies assisted by new high-throughput DNA sequencing technology and recent bioinformatics tools.”

Bioinformatics

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data – Peter Skewes-Cox – PLOS ONE

“Here, we constructed HMMER3-compatible profile hidden Markov models (profile HMMs) from all the virally annotated proteins in RefSeq in an automated fashion using a custom-built bioinformatic pipeline. “

 

Techniques

I hope they developed two primers, not just one! Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing – Shunsuke Takahashi – PLOS ONE

“Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace×Large white×Duroc) using an Illumina MiSeq next-generation sequencer.”

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods – Charles F. A. de Bourcy – PLOS ONE

“Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). “

This abstract is so vague, I am not sure where to file this under – A Robust and Adaptable High Throughput Screening Method to Study Host-Microbiota Interactions in the Human Intestine – Tomas de Wouters – PLOS ONE

“In this study, we developed a robust and reproducible methodology to combine these two biological systems for high throughput application”

LC Sciences and Norgen Biotek will be conducting a free informational webinar describing 16S rRNA Sequencing and presenting a few application examples.

“If you are interested in attending the webinar, simply reply to news@lcsciences.com and we would be happy to send the webinar details.”

More microbiology

The Immune System in Children with Malnutrition — A Systematic Review
Maren Johanne Heilskov Rytter – PLOS ONE

“A systematic literature search was done in PubMed, and additional articles identified in reference lists and by correspondence with experts in the field. “

Photodynamic Therapy Using Systemic Administration of 5-Aminolevulinic Acid and a 410-nm Wavelength Light-Emitting Diode for Methicillin-Resistant Staphylococcus aureus-Infected Ulcers in Mice – Kuniyuki Morimoto – PLOS ONE

“5-aminolevulinic acid photodynamic therapy accelerated wound healing and decreased bacterial counts on ulcer surfaces; in contrast, vancomycin treatment did not accelerate wound healing.”

Light Scattering Sensor for Direct Identification of Colonies of Escherichia coli Serogroups O26, O45, O103, O111, O121, O145 and O157 – Yanjie Tang- PLOS ONE

“SMAC was chosen for exhaustive scatter image library development, and 36 additional strains of O157:H7 and 11 non-O157 serovars were examined, with each serogroup producing unique differential scatter patterns.”

Science and publishing

Protecting human research participants in the age of big data – Susan T. Fiskea, and Robert M. Hauser – PNAS USA

“IRB review does not apply to Facebook and other private enterprises, yet they generate data that can benefit humanity”

Bik’s Picks

Magpies don’t like shiny things – Sarah Zielinski – Science News

“Magpies deserve our apology. Apparently humans have been unnecessarily maligning the birds for centuries. “

Richard III ate like a king before biting the dust – Bruce Bower – Science News

“Well-known royal’s brief reign included a sudden shift to fancy food and drink”

What type of researcher are you? Take the Quiz – Roche Life Science

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