General microbiology and science, June 23

Amplification of 18S rRNA genes, metabolomics, phages, and the scientific way to cut a cake.

Bacteria are everywhere

This article is citing a study that was published in 1992, not sure why they reporting about it now, but here it is:
Earpieces can multiply bacteria 11 times in ear – Tribune

“Besides concerns about deafness, there are also issues regarding use of earpieces and bacteria. A study which measured bacteria levels on audio headsets provided on commercial airline flights entitled “Changes in the microbial flora of airline headset devices after their use,” published in the journal, The Laryngoscope, brings interesting conclusions. “

Anti-bacterial bag-for-life could prevent rise in food poisoning when 5p plastic bag charge comes into force – Independent UK

“Paul Morris, the managing director, said: “Multi-use bags which can carry raw meat one week and vegetables or clothing the next is a concern of many industry experts; this bag provides a solution to the problem.””

Amplification and sequencing techniques 

Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes – Alle A. Y. Lie – Applied and Environmental Microbiology

“Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. “

Targeted and Highly Multiplexed Detection of Microorganisms by Employing an Ensemble of Molecular Probes – Weihong Xu – Applied and Environmental Microbiology

“To profile the microbial diversity in environmental and clinical samples, we have devised and employed molecular probe technology, which detects and identifies bacteria that do and do not grow in culture.”

Metabolomics and mass spectrometry

This one is published by the not-so-trustworthy Omics group, but it sounds interesting:
Optimisation of Sample Preparation for Direct SPME-GC-MS Analysis of Murine and Human Faecal Volatile Organic Compounds for Metabolomic Studies (links to PDF)
– Reade S – Analytical & Bioanalytical Techniques

“We evaluated different aspects of sample preparation when processing murine and human faecal samples through a pipeline involving solid phase micro-extraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS)”

Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth – David Kentner – PNAS

“Here, we show that infected host cells maintain normal central metabolism for energy production and host cell survival. However, Shigella captures the entire host metabolism output and degrades it further to acetate.”

Beyond the Matrix-Assisted Laser Desorption Ionization (MALDI) Biotyping Workflow: in Search of Microorganism-Specific Tryptic Peptides Enabling Discrimination of Subspecies – Maria-Theresia Gekenidis – Applied and Environmental Microbiology

“Here, it is shown that combining tryptic digestion of the acid/organic solvent extracted (classical biotyping preparation) and resolubilized proteins, nano-liquid chromatography (nano-LC), and subsequent identification of the peptides by MALDI-tandem TOF (MALDI-TOF/TOF) mass spectrometry increases the discrimination power to the level of subspecies.”

Phages and viruses

Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread –
Victoriya V. Volkova – Applied and Environmental Microbiology

“Using the model and the most liberal assumptions about transduction efficiency and resistance gene frequency, we approximated the upper numerical limits (“worst-case scenario”) of gene transfer through specialized and generalized transduction in E. coli by enteric coliphages when the transduced genetic segment is picked at random. “

Tolerance of a Phage Element by Streptococcus pneumoniae Leads to a Fitness Defect during Colonization – Hilary K. DeBardeleben – Journal of Bacteriology

“Here, we examined a clinical isolate that carries a novel prophage element, designated Spn1, which was detected in both integrated and episomal forms. Surprisingly, both lytic and lysogenic Spn1 genes were expressed under routine growth conditions.”

Comparison of Five Bacteriophages as Models for Viral Aerosol Studies – Nathalie Turgeon – Applied and Environmental Microbiology

“The presence of viruses in collected air samples was detected by culture and quantitative PCR (qPCR). Our results showed that these selected five phages behave differently when aerosolized and sampled. “

Microbial detection in blood and normally sterile sites

Molecular revolution in the diagnosis of microbial brain abscesses – AK Mishra – European Journal of Clinical Microbiology & Infectious Diseases

“This article reviews the applications of the currently available tools for the etiological diagnosis of a brain abscess.”

General microbiology

Nitrogen stress response and stringent response are coupled in Escherichia coli – Daniel R. Brown – Nature Communications

“Here, we show that transcription of relA, a key gene responsible for the synthesis of ppGpp, is activated by NtrC during nitrogen starvation.”

Stenotrophomonas comparative genomics reveals genes and functions that
differentiate beneficial and pathogenic bacteria – Peyman Alavi – BMC Genomics

“We used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S. maltophilia and the plant-associated strains S. maltophilia R551-3 and S. rhizophila DSM14405T (both are biocontrol agents)”

Emergence of bacterial vortex explained – Science Daily

When a bunch of B. subtilis bacteria are confined within a droplet of water, a very strange thing happens. The chaotic motion of individual swimmers spontaneously organizes into a swirling vortex, with bacteria on the outer edge of the droplet moving in one direction while those on the inside move the opposite direction. “

Dr. Bik’s Picks

Screen Shot 2014-06-23 at 11.53.49 PMScientists tie social behavior to activity in specific brain circuit – Stanford University

“The new findings, published June 19 in Cell, may throw light on psychiatric disorders marked by impaired social interaction such as autism, social anxiety, schizophrenia and depression, said the study’s senior author, Karl Deisseroth, MD, PhD, a professor of bioengineering and of psychiatry and behavioral sciences. 

Scientists use X-rays to look at how DNA protects itself from UV light – Science Daily

The molecular building blocks that make up DNA absorb ultraviolet light so strongly that sunlight should deactivate them — yet it does not. Now scientists have made detailed observations of a ‘relaxation response’ that protects these molecules, and the genetic information they encode, from UV damage.”

Cut your cake and keep it (fresh), too – Eliza Barclay – NPR

“The ordinary method of cutting out a wedge is very faulty,” wrote Sir Francis Galton, a British mathematician, in a 1906 letter to the journal Nature concerning the scientific principles of cake-cutting.”

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