Category Archives: Infection and transplantation

General microbiology and science, June 25

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Arsenic profiling in rats, Bacillus in space, and antibiotic resistance in populations. And Dr. Bik’s Picks featuring butterflies, mummies and unfeelability cloaks.

Microbes in space

Screen Shot 2014-06-25 at 10.31.28 PMBacillus anthracis-Like Bacteria and Other B. cereus Group Members in a Microbial Community Within the International Space Station: A Challenge for Rapid and Easy Molecular Detection of Virulent B. anthracis – Sandra P. van Tongeren – PLOS ONE

“In this study we show the presence of B. anthracis-like bacteria and other members of the B. cereus group in a microbial community within the human environment of the International Space Station and their preliminary identification by using conventional culturing as well as molecular techniques including 16S rDNA sequencing, PCR and real-time PCR. “

Metagenomics

Screen Shot 2014-06-25 at 10.31.54 PMElucidation of Operon Structures across Closely Related Bacterial Genomes – Chuan Zhou – PLOS ONE

“Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes.”

Antibiotic resistance

Screen Shot 2014-06-25 at 10.32.23 PMOptimization of lag time underlies antibiotic tolerance in evolved bacterial populations – Ofer Fridman – Nature

“Here we followed the evolution of bacterial populations under intermittent exposure to the high concentrations of antibiotics used in the clinic and characterized the evolved strains in terms of both resistance and tolerance. “

Arsenic metabolism

Screen Shot 2014-06-25 at 10.32.54 PMThe metabolomic profiling of serum in rats exposed to arsenic using UPLC/Q-TOF MS – Cheng Wang – Toxicology Letters

“The aim of this study is to determine the impact of chronic arsenic exposure on the metabolism of organism, and find the metabolites changes by using metabolomic techniques. “

Screen Shot 2014-06-25 at 10.33.15 PMInvestigation of arsenic species stability by HPLC-ICP-MS in plants stored under different conditions for 12 months – Clarice D.B. Amaral – Microchemical Journal

“For the As species here studied it can be concluded that lyophilization and cryogenic grinding strategies were the most suitable sample pretreatments for As speciation in plant tissue.”

Science and careers

Screen Shot 2014-06-25 at 10.33.54 PMLove in the lab: Close collaborators – Kerri Smith – Nature

“Romance often sparks between colleagues, and scientists are no different. Nature profiles four super-couples who have combined love and the lab.”

Dr. Bik’s Picks

Screen Shot 2014-06-25 at 10.35.06 PMMetagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman – Frank Maixner – PLOS ONE

“Initially, the metagenomic data of the Iceman’s genomic survey was screened for bacterial ribosomal RNA (rRNA) specific reads. Through ranking the reads by abundance a relatively high number of rRNA reads most similar to T. denticola was detected. “

Screen Shot 2014-06-25 at 10.35.42 PMA magnetic compass aids monarch butterfly migration – Patrick A Guerra – Nature Communications

“Here we use flight simulator studies to show that migrants indeed possess an inclination magnetic compass to help direct their flight equatorward in the fall. “

Screen Shot 2014-06-25 at 10.36.07 PMAn elasto-mechanical unfeelability cloak made of pentamode metamaterials –
T. Bückmann – Nature Communications

“Here, inspired by invisible core-shell nanoparticles in optics, we design an approximate elasto-mechanical core-shell ‘unfeelability’ cloak based on pentamode metamaterials. “

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General microbiology and science, June 24

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Metabolomics, metagenomics, phages in the human gut, arsenic poisoning in China, and a big award for Dengue research.

Metabolomics

Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities – Paul E. Abraham – Current Protocols in Bioinformatics

“In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. “

Review: The human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva – Anton Amann – Journal of Breath Research

“Fecal volatiles have been implicated in differentiating certain infectious bowel diseases such as Clostridium difficile, Campylobacter, Salmonella and Cholera. They have also been used to differentiate other non-infectious conditions such as irritable bowel syndrome and inflammatory bowel disease.”

Metagenomics and DNA structure

Sequencing the Strange Communities: Taking on Metagenomics – Aaron Krol – Bio-IT World

““Communities are made up of organisms that interact,” says Jonathan Eisen, a professor at the School of Medicine and the College of Biological Sciences at the University of California, Davis. “They’re not made up of short reads of Illumina sequences. And we need to stitch those together into organisms in order to make useful predictions, and interpretation of experimental data.””

Gene positioning and genome function – Nidhi Vishnoi, Jie Yao – Frontiers in Biology

” In this review, we discuss some recent findings as well as experimental tools to investigate subnuclear gene positioning and to explore its implications in genome functions.”

Phages and viruses

Classification and quantification of bacteriophage taxa in human gut metagenomes – Alison S Waller – ISME Journal 

“Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. “

Techniques

Enzymatic Treatment of Specimens before DNA Extraction Directly Influences Molecular Detection of Infectious Agents – Pablo Goldschmidt – PLOS ONE

“The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification.”

Dengue

Sustainable Sciences Institute (SSI) Awarded $1 Million to Battle Growing Threat to Global Public Health: Mosquito-borne Dengue Virus – PR Web

“SSI, a San Francisco nonprofit founded by Eva Harris, UC Berkeley Professor of Infectious Disease and Vaccinology and former MacArthur “Genius” award winner, has worked to minimize the threat of potentially fatal Dengue disease for 15 years. With the latest award of $1 million dollars, Harris and other SSI investigators will be able to extend their reach and speed up their efforts.”

Infection and host response

Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection – Laxmi Yeruva – mBio

“To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. “

Immunity to gastrointestinal nematodes: mechanisms and myths – Richard K. Grencis – Immunological Reviews

“This review aims to discuss the recent discoveries in both host protection and immunoregulation against gastrointestinal nematodes, placing the data in context of the specific life cycles imposed by the different parasites studied and the future challenges of considering the mucosal/immune axis to encompass host, parasite, and microbiome in its widest sense.”

Tailored immunity at mucosae – Yasmine Belkaid – Immunological Reviews

“This issue of Immunological Reviews presents articles from investigators involved in the exploration of the mechanisms by which mucosal barrier sites induce and control innate and adaptive immune responses.”

Detection of bacteria in blood and other sites

Rapid Detection of Enterobacteriaceae Producing Extended Spectrum Beta-Lactamases Directly From Positive Blood Cultures by Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) – Marina Oviaño – Clinical Microbiology and Infection

“In the assay, 141 blood cultures were tested, 13 out of them were real bacteremias and 128 corresponded to blood culture bottles seeded with bacterial clinical isolates. Bacteremias were analyzed by MALDI-TOF after a positive growth result and the 128 remaining blood cultures 24 hours after the bacterial seeding. “

General microbiology and ecology

The quest for a unified view of bacterial land colonization – Hao Wu – ISME Journal

“Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. “

Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes – Akinori Yabuki – ISME Journal

“Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate.”

Arsenic metabolism

Arsenic Pollution Sows Despair in Chinese Cancer Village (slideshow)- Yahoo News

“Xiong Demin could not have foreseen that the mine he worked at for 32 years would leave his home village poisoned and hundreds of residents, including himself and his wife, stricken with cancer.”

Dr. Bik’s Picks – Evolution Edition

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials – Kieren J. Mitchell – Molecular Biology and Evolution

“We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species”

Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals – Zhen Liu – Molecular Biology and Evolution

“By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency bat, Stoliczka’s trident bat (Aselliscus stoliczkanus). “

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape – Yasunori Ichihashi – PNAS

“Utilizing the natural variation in leaf morphology between tomato and two related wild species, we identified a gene network module that leads to a dynamic rewiring of interactions in the whole leaf developmental gene regulatory network. “

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General microbiology and science, June 23

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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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Microbiome and general biology, June 20

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It was a quiet day on the microbiome research front, so there will only be one post today. But, with vampire bats, Bacillus anthracis, and fish-eating spiders, it’s a good one!

Pregnancy and Birth

Screen Shot 2014-06-20 at 10.08.36 PMStudy Finds Certain Birth Defects are more Common in Hispanics – Cheri Cheng

“”One of the things that caught our eye was, while Hispanics represent 17 percent of the population, 24 percent of premature babies are Hispanic,” said Dr. Edward McCabe, senior vice president and chief medical officer of the March of Dimes, a nonprofit organization.”

Animal models of human microbiota

BacillusColonic Immune Suppression, Barrier Dysfunction, and Dysbiosis by Gastrointestinal Bacillus anthracis Infection – Yaíma L. Lightfoot – PLOS ONE

“Herein, we investigated the pathogenesis of GI anthrax in animals orally infected with toxigenic non-encapsulated B. anthracis Sterne strain (pXO1+ pXO2−) spores that resulted in rapid animal death.”

Screen Shot 2014-06-20 at 9.53.32 PMBiology Students Study Stomach Bacteria – Pengxeu Thao – University of Minnesota Morris

“Wyckoff and her students are spending the summer studyingHelicobacter pylori (H. pylori), a Gram-negative bacterium found in the human stomach.”

Amphibian microbiome

AmphibCool Temperatures Reduce Antifungal Activity of Symbiotic Bacteria of Threatened Amphibians – Implications for Disease Management and Patterns of Decline – Joshua H. Daskin – PLOS ONE

“We characterized, at a range of temperatures approximating natural seasonal variation, the anti-Bd activity of bacterial symbionts from the skins of three species of rainforest tree frogs (Litoria nannotis, Litoria rheocola, and Litoria serrata)”

Plant microbiology

Screen Shot 2014-06-20 at 10.09.21 PMScientists look to bacteria to protect crop yields in the face of climate change – Jennifer Huizen – E&E Publishing

“If proved effective, this technology would decrease the amount of key nutrients like nitrogen and, most notably, water needed by the plant, while increasing the yield,” said Lin Myat, a postdoctoral fellow of molecular biology and genetics at Cornell “

belongs to

Screen Shot 2014-06-20 at 10.06.07 PMβ-Carboxysomal proteins assemble into highly organized structures in Nicotiana chloroplasts – Myat T. Lin – The Plant Journal

“We demonstrate that a foreign protein can be targeted with a 17-amino-acid CcmN peptide to the shell proteins inside chloroplasts. Our experiments establish the feasibility of introducing carboxysomes into chloroplasts for the potential compartmentalization of Rubisco or other proteins.”

Food microbiology

Screen Shot 2014-06-20 at 10.23.17 PMHaley Oliver: Master of Meat – Jef Akst – The Scientist

“In her own lab at Purdue University, Oliver studies the spread of Listeria in other foods, such as melons, and investigates sanitation strategies that may limit contamination and increase food shelf life. “

Infection and host response

InflammationInflammation: Gone with Translation – Carola G. Vinuesa, Thomas Preiss – PLOS Genetics

“Over the last few years, a number of studies have investigated global gene activation induced by pathogen-derived stimuli to gain insights into the modes of induction of the inflammatory mediators and regulators.”

Dengue

Screen Shot 2014-06-20 at 9.18.31 PMThe Need for More Research and Public Health Interventions on Dengue Fever in Burkina Faso – Valéry Ridde – PLOS Neglected Tropical Diseases

“…our aim in this article is to draw attention to the need for rapid deployment of research and interventions on dengue fever in Burkina Faso, because it appears to have been overlooked, with the focus being, instead, on malaria.”

Dengue NKTInvariant NKT Cell Response to Dengue Virus Infection in Human
Ponpan Matangkasombut – PLOS Neglected Tropical Diseases

“iNKT cells activation were analyzed by the expression of CD69 by flow cytometry. Their cytokine production was then analyzed after α-GalCer stimulation”

General microbiology

Screen Shot 2014-06-20 at 9.19.15 PMVampire Bats and Rabies: Toward an Ecological Solution to a Public Health Problem – Benjamin Stoner-Duncan – PLOS Neglected Tropical Diseases

“In the first half of 2011, 21 school-age children and two adults died of rabies transmitted by the common vampire bat (Desmodus rotundus) in and around the small rural village of Yupicusa in the Peruvian Amazon”

VectorCrossing the Interspecies Barrier: Opening the Door to Zoonotic Pathogens – Christian Gortazar – PLOS Pathogens

“The species barriers separating nonhuman animal species from humans represent a major hurdle for effective exposure to, infection by, and subsequent spread of zoonotic pathogens among humans”

Screen Shot 2014-06-20 at 9.35.19 PMHuman sweat can reduce bacteria fighting capabilities – ZeeNews

“A new research has revealed that human sweat can diminish bacteria-fighting qualities of brass objects like door knobs and taps within an hour of contact.”

 

Dr. Bik’s Picks

Screen Shot 2014-06-20 at 10.11.49 PMFish Predation by Semi-Aquatic Spiders: A Global Pattern – Martin Nyffeler – PLOS ONE

“More than 80 incidences of fish predation by semi-aquatic spiders – observed at the fringes of shallow freshwater streams, rivers, lakes, ponds, swamps, and fens – are reviewed.”

Screen Shot 2014-06-20 at 10.15.09 PMUS sets up honey bee loss task force – BBC News

“In the plan announced on Friday, Mr Obama directed the EPA and the agriculture department to lead a government-wide task force to develop a strategy within six months to fight bee and other pollinator declines.“

Screen Shot 2014-06-20 at 10.17.07 PMStrict diet suspends development, doubles lifespan of worms – Science Daily

“Researchers at Duke University found that taking food away from C. elegans triggers a state of arrested development: while the organism continues to wriggle about, foraging for food, its cells and organs are suspended in an ageless, quiescent state. “

Screen Shot 2014-06-20 at 10.26.39 PMFinding thoughts in speech: How human brain processes thoughts during natural communication – Science Daily

“The novelty of the authors’ approach is that the participants were not instructed to think and talk about a given topic in an experimental setting. “

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Human microbiome, June 19

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The journal Immunity has a special with several great papers on (gut) microbiome and diet. And even Martha Stewart is writing about the microbiome! In style, of course.

Oral microbiome

Screen Shot 2014-06-19 at 10.50.07 PMMining the Mouth’s Many Microbes – Tracy Vence – The Scientist

““The whole world passes through the oral cavity,” said Purnima Kumar, an assistant professor of periodontology at the Ohio State University College of Dentistry. This makes investigating the microbial communities present in the mouth a challenge.”

Gut microbiome

Screen Shot 2014-06-19 at 10.49.36 PMFinding the Missing Links among Metabolites, Microbes, and the Host – Pieter C. Dorrestein – Immunity

“Here, we provide our perspective on these connections and outline a systematic research program that could turn these individual links into a broader network that allows us to understand how these components interact. “

Screen Shot 2014-06-19 at 10.51.41 PMMining the Human Gut Microbiota for Effector Strains that Shape the Immune System – Philip P. Ahern – Immunity

“Here, we discuss a scalable, less biased approach for identifying effector strains in complex microbial communities that impact immune function. The approach begins by identifying uncultured human fecal microbiota samples that transmit immune phenotypes to germ-free mice.”

Screen Shot 2014-06-19 at 10.51.09 PMDiet, Metabolites, and “Western-Lifestyle” Inflammatory Diseases – Alison N. Thorburn – Immunity

“This review highlights what is currently known about diet, metabolites, and their associated immune pathways in relation to the development of inflammatory disease.”

Screen Shot 2014-06-19 at 10.52.28 PMInflammatory Bowel Disease as a Model for Translating the Microbiome – Curtis Huttenhower – Immunity

“IBD thus represents perhaps the most comprehensive current model for understanding the human microbiome’s role in complex inflammatory disease. Here, we review the influences of the microbiota on IBD and its potential for translational medicine.”

Screen Shot 2014-06-19 at 10.54.48 PMCulturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics – Grégory Dubourg – International Journal of Antimicrobial Agents

“Culturomics was performed on four stool samples from patients treated with large-scale antibiotics to assess the diversity of their gut flora in comparison with other culture-dependent studies. Pyrosequencing of the V6 region was also performed and was compared with a control group.”

Screen Shot 2014-06-19 at 10.55.24 PMLong-term monitoring of the human intestinal microbiota from the 2nd week to 13 years of age – Akihito Endo – Anaerobe

“Few long term follow-up studies have been reported and we therefore characterized the development of intestinal microbiota of ten subjects from the 2nd week of life to 13 years of age. PCR-denaturing gradient gel electrophoresis combined with several bacterial group-specific primer sets demonstrated the colonization steps of defined bacterial groups in the microbiota”

Respiratory microbiome

Time between sputum sample collection and storage significantly influences bacterial sequence composition from Cystic Fibrosis respiratory infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Aliquots were stored at room temperature before freezing at -80°C for increasing intervals up to 72 hour period. Samples were treated with propidium monoazide, to distinguish live from dead cells, prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterise the bacterial composition.”

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Human Pharyngeal Microbiome May Play a Protective Role in Respiratory Tract Infections – Zhancheng Gao – Genomics, Proteomics & Bioinformatics

“Recent studies have demonstrated that the pharyngeal microbiome comprises an abundance of bacterial species that interact with the local epithelial and immune cells, and together, they form a unique micro-ecological system.”

Skin and wounds microbiology

Screen Shot 2014-06-19 at 10.57.13 PMMicrobial profiling of combat wound infection through detection microarray and next-generation sequencing – Nicholas A. Be – Journal of Clinical Microbiology

“We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. “

Press coverage:

Screen Shot 2014-06-19 at 11.00.07 PMHealing warriors by making a census of combat wounds’ microbiota – Melissa Healy – LA Times

“New research suggests that physicians treating future U.S. troops (and perhaps those treating some of today’s wounded warriors) may be able to take a fast and thorough census of the microorganisms living in a combat wound and tailor their treatment accordingly.”

Human microbiome in the news

Screen Shot 2014-06-19 at 10.56.06 PM4 habits for a healthy gut – Martha Stewart – CNN

“Studies also suggest that diabetic and obese patients tend to lack a diversity of bacteria, and the Cleveland Clinic found that some bacteria metabolize components of egg and meat to produce a compound that aids in the clogging of arteries.”

Screen Shot 2014-06-19 at 10.44.58 PMWebinar: The Promise of the Microbiome: Function and Dysfunction in Humans and Beyond – Science Magazine, featuring David Relman, Rob Knight, and Jack Gilbert

“During this webinar, the speakers will:

  • Provide a brief introduction to microbiomes and how they may fundamentally impact our study of the natural world
  • Share their research data on human and nonhuman microbiota, including microbe-associated environmental impacts on human health
  • Discuss the role of microbiomes in obesity and malnutrition
  • Answer your questions live during the webinar!”

Bacterial detection in blood and other sites

Screen Shot 2014-06-19 at 10.58.32 PMMassive Parallel Sequencing Provides New Perspectives on Bacterial Brain Abscesses – Øyvind Kommedal – Journal of Clinical Microbiology

“Bacterial 16S rRNA genes were amplified directly from the specimens and sequenced using Ion Torrent technology, with an average of 500,000 reads per sample. The results were compared to those from culture- and Sanger sequencing-based diagnostics.”

Animal models of microbiota

Screen Shot 2014-06-19 at 10.59.25 PMDiet-Induced Alterations in Gut Microflora Contribute to Lethal Pulmonary Damage in TLR2/TLR4-Deficient Mice – Yewei Ji – Cell Reports

“Here, we show that chronic intake of a high-fat diet (HFD), not a low-fat diet, leads to severe pulmonary damage and mortality in mice deficient in Toll-like receptors 2 and 4 (DKO).”

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General microbiology and science

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Virus reactivation in sepsis, influenza mixing, and Dr. Bik’s Picks, featuring animals predicting the World Cup results, and which friends to take with you to Mars.

Infection and host response

Screen Shot 2014-06-13 at 11.39.47 PMReactivation of Multiple Viruses in Patients with Sepsis – Andrew H. Walton – PLOS ONE

“A small subgroup of septic patients had markedly elevated viral loads (>104–106 DNA copies/ml blood) for CMV, EBV, and HSV. Excluding TTV, DNAemia was uncommon in critically-ill non-septic patients and in age-matched healthy controls. Compared to septic patients without DNAemia, septic patients with viremia had increased fungal and opportunistic bacterial infections.”

 More microbes

Screen Shot 2014-06-14 at 12.30.41 AMDeadly airborne flu virus created in lab – not as bad as it sounds – Wendy Barclay – The Conversation

“Now scientists at the University of Wisconsin-Madison in the US have been criticised for recreating a very similar but distinct influenza virus by mixing together a set of genes taken from viruses of wild birds that are present in the gene pool today”

Screen Shot 2014-06-14 at 12.31.12 AMBelongs to: Circulating Avian Influenza Viruses Closely Related to the 1918 Virus Have Pandemic Potential – Tokiko Watanabe – Cell Host Microbe

Human Ancestors Got Herpes from Chimps’ Ancestors – Agata Blaszczak-Boxe – LiveScience

“Researchers found that herpes simplex virus 1 (HSV-1) infected hominids before their evolutionary split from chimpanzees 6 million years ago”

Science and Art

Franklin InstituteA Show That Really Gets Into Your Head – ‘Your Brain’ Opens at the Franklin Institute – Edward Rothstein – New York Times

“In these cases, the brain leaps ahead of what the body senses, drawing conclusions. They are sometimes wrong, sometimes subtly correct and sometimes extraordinarily imaginative.”

Dr. Bik’s Picks – Weekend Edition

CatYes, You Can Get Your Cat to Behave – Wayne Pacelle – Live Science

Animals ‘Predict’ 2014 World Cup results (video) – BBC News

“China’s panda picker Ying Mei got off to a successful start, opting for the box of food emblazoned with a Brazilian flag, before the host nation beat Croatia 3-1.”

Bedtime Procrastination: Introducing a New Area of Procrastination – Floor Kroese – Frontiers in Psychology

“Introducing a novel domain in which procrastinators experience problems, bedtime procrastination appears to be a prevalent and relevant issue that is associated with getting insufficient sleep.”

Science Blogging Versus Science Journalism – Tommaso Dorigo – Science 2.0

“Hence I tried to organize my lecture as a discussion of things that science journalist wannabes could be interested to hear, from a scientist who has been blogging for 10 years and has picked up some tricks and lessons along the way.”

Skin cancer: Sunscreen ‘not complete protection’ – Helen Briggs – BBC News

“Sunscreen alone should not be relied on to prevent malignant melanoma, a deadly form of skin cancer, research suggests.”

Longread: Forget Calories – Counting calories is misguided. The focus belongs on real food – James Hamblin – The Atlantic

“In other words, your New Year’s resolution to lose weight probably won’t last through the spring, let alone affect how you look in a swimsuit in July.”

Longread: Extroverts Don’t Belong on Mars – Olga Khazan – The Atlantic

“Extroverted friends are good for a lot of things—serving as deft and lively wingmen, spicing up book club, sparking interesting conversations at parties by wearing ostentatious leggings, etc. One thing they may be less suited for: Long voyages to faraway planets.”

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General microbiology and science, June 11

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Lots of dengue and host response today, but also biosynthetic pathways, a book review, snakes, melons, bones, and bandages for mice.

Metagenomics and gene ontology

Hao Wang atlasAtlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes – Hao Wang – PNAS

“This study demonstrates the widespread distribution of nonribosomal peptide synthetase and modular polyketide synthase biosynthetic pathways across the three domains of life, by cataloging a total of 3,339 gene clusters from 2,699 genomes. “

Microbiology general

Bacteria are godsBacteria Are Our Gods: Nicholas P. Money, a Mycologist, Has Written a Beautiful Book About the Facts of Life – Charles Mudede – The Stranger

“a beautifully written collection of linked essays called The Amoeba in the Room: Lives of the Microbes. The book is by Nicholas P. Money, a mycologist who teaches at Miami University”

Dengue

Dengue NoeckerContrasting associations of polymorphisms in FcγRIIa and DC-SIGN with the clinical presentation of dengue infection in a Mexican population – Cecilia A. Noecker – Acta Tropica

“In this study, real-time PCR was used to characterize the distribution of rs1801274 and rs4804803 in subjects with asymptomatic dengue infection (n = 145), uncomplicated dengue (n = 67), and severe dengue (n = 36) in Morelos.”

Dengue Rong Fu ChenAugmented miR-150 expression associated with depressed SOCS1 expression involved in dengue haemorrhagic fever – Rong-Fu Chen – Journal of Infection

“SOCS1 expression and lower IFN-γ level were significantly reduced in DHF patients, but not in patients with DF. Elevated SOCS1 and reduced miR-150 levels were detected 24 h after DENV-2 infection in PBMCs. “

PNASCommentary: How season and serotype determine dengue transmissibility
Neil M. Ferguson and Derek A. T. Cummings – PNAS

“The research published by Reiner et al. in PNAS (10) starts to address the last of these uncertainties by giving us a unique picture of how rates of transmission of the four dengue viruses varied in Iquitos, a small city in Peru, over a 12-y period.”

Dengue DelmelleA web-based geospatial toolkit for the monitoring of dengue fever – Eric M. Delmelle – Applied Geography

“In this paper, we present a web-based geospatial toolkit with a user-friendly interactive interface for the monitoring of dengue fever outbreaks, in space and time. “

Infection and host response

Nicholas IlottLong non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes – Nicholas E. IIott – Nature Communications

“…here we characterize the long non-coding RNA transcriptome in primary human monocytes using RNA sequencing. We identify 76 enhancer RNAs (eRNAs), 40 canonical lncRNAs, 65 antisense lncRNAs and 35 regions of bidirectional transcription (RBT) that are differentially expressed in response to bacterial lipopolysaccharide (LPS).”

Screen shot 2014-06-11 at 01.29PM, Jun 11Exploring the collaboration between antibiotics and the immune response in the treatment of acute, self-limiting infections – Peter Ankomah and Bruce R. Levin – PNAS

“We use a mathematical model and computer simulations to explore the design and evaluation of antibiotic treatment protocols for an acute, self-limiting bacterial infection. “

Beth TamburiniAntigen capture and archiving by lymphatic endothelial cells following vaccination or viral infection – Beth A. Tamburini – Nature Communications

“Antigen derived from viral infections with influenza and vesicular stomatitis virus can persist after resolution of infection. Here we show that antigen can similarly persist for weeks following viral challenge and vaccination. “

Screen Shot 2014-06-11 at 9.53.19 PMImmunologic Research has a special on Stanford Immunology, with contributions from Kari Nadeau, Robert Negrin, Christopher Contag, and many others.

Arsenic metabolism

Screen shot 2014-06-11 at 01.57PM, Jun 11Feasibility of Arsenic and Antimony NMR Spectroscopy in Solids: An Investigation of Some Group 15 Compounds – Alexandra Faucher – Solid State Nuclear Magnetic Resonance

“Results of density functional theory quantum chemistry calculations for isolated molecules using ADF and first-principles calculations using CASTEP, a gauge-including projector augmented wave method to deal with the periodic nature of solids, are compared with experiment.”

Screen shot 2014-06-11 at 02.02PM, Jun 11Role of endometrial concentrations of heavy metals (cadmium, lead, mercury and arsenic) in the aetiology of unexplained infertility – E. Tanrıkut – European Journal of Obstetrics & Gynecology and Reproductive Biology

“The concentrations of cadmium, lead, mercury and arsenic were measured in endometrial biopsy specimens using atomic absorption spectrometry.”

Screen shot 2014-06-11 at 02.06PM, Jun 11Mitigation approach of arsenic toxicity in chickpea grown in arsenic amended soil with arsenic tolerant plant growth promoting Acinetobacter sp. – Shubhi Srivastava – Electrical Engineering

“The study was undertaken with the aim of testing the effects of isolated bacterial strain nbri05 from arsenic contaminated site of West Bengal.”

Screen Shot 2014-06-11 at 10.36.36 PMNSF funds effort to market UT Arlington arsenic analyzer – University of Texas at Arlington – Phys.org

“The National Science Foundation has awarded nearly $200,000 to two University of Texas at Arlington researchers teaming with a private company to make an affordable, environmentally friendly field analyzer for arsenic levels in water.”

Science and Art

Screen Shot 2014-06-11 at 9.49.44 PMArts: The third culture – Michael John Gorman – Nature
“After months of injections with horse immunoglobulin in 2011, artist Marion Laval-Jeantet had a transfusion of horse blood in a Ljubljana art gallery. She walked around the donor animal on prosthetic hooves; then samples of her hybrid blood were freeze-dried and placed in engraved aluminium cases. “

Dr. Bik’s Picks

Screen shot 2014-06-11 at 01.27PM, Jun 11Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms – Nicholas R. Casewell – PNAS

“Venom variation observed between related snake species is therefore the result of a complex interaction between a variety of genetic and postgenomic factors acting on toxin genes. “

Shahar Cohen melonThe PH gene determines fruit acidity and contributes to the evolution of sweet melons – Shahar Cohen – Nature Communications

“We identify a family of plant-specific genes with a major effect on fruit acidity by map-based cloning of C. melo PH gene (CmPH) from melon, Cucumis melo taking advantage of the novel natural genetic variation for both high and low fruit acidity in this species”

Cow skullA Bone Collector’s Basement Of Animal Skulls Sees The Light – Lauren Sommer – NPR

“Bandar has spent 60 years building this scientific collection of animal bones. Now, many of his skulls are on view at the California Academy of Sciences in San Francisco, which has just opened an exhibit featuring his work.”

Bandage coatingBandage Coating Kills Bacteria Using Graphene And Hydrogen Peroxide – Melissae Fellet – ACS

“A bandage loaded with graphene quantum dots and a small amount of hydrogen peroxide significantly reduces the amount of bacteria in wounds on mice”

Screen Shot 2014-06-11 at 9.46.55 PMAt the start of the FIFA World Cup in Brazil, Nature has a special on South American science

Screen Shot 2014-06-11 at 10.43.30 PMQ&A: The nutrient hunter – Jascha Hoffman – Nature

“Investigative food journalist Jo Robinson has spent more than a decade scouring the literature on plant nutrition. Her demonstration garden in Washington state opens this month as her book Eating on the Wild Side (Little, Brown, 2013) emerges in paperback. She talks about eating tomatoes to protect from sunburn, why bitter is better — and how purple is the new green.”

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General microbiology and science, June 10

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Transcription in 12 different human tissues, bacteria in arterial plaques, and hairs with anticancer activity.

Infection and Host Response

Genome wideGenome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues – Zhiyun Guo – Nature Scientific Reports

“Finally, we describe TSmiR (http://bioeng.swjtu.edu.cn/TSmiR), a novel and web-searchable database that houses interaction maps of TF-TS miRNA in 12 tissues.”

IntracellularIntracellular Bacteria Interfere with Dendritic Cell Functions: Role of the Type I Interferon Pathway – Laurent Gorvel – PLOS ONE

“To analyze the mechanisms used by C. burnetiiand B. abortus to alter moDC activation, we performed microarray and found that C. burnetiiand B. abortus induced a specific signature consisting of TLR4, TLR3, STAT1 and interferon response genes.”

Screen Shot 2014-06-10 at 9.55.25 PMBacteria Present in Carotid Arterial Plaques Are Found as Biofilm Deposits Which May Contribute to Enhanced Risk of Plaque Rupture – Bernard B. Lanter – mBio

“In the current work, atherosclerotic carotid artery explants from 15 patients were all shown to test positive for the presence of eubacterial 16S rRNA genes”

Screen Shot 2014-06-10 at 10.01.00 PMRNA-seq: Impact of RNA degradation on transcript quantification – Irene Gallego Romero – BMC Biology

“We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data.”

Dengue virus

DengueSpatiotemporal Dynamics of DENV-2 Asian-American Genotype Lineages in the Americas – Daiana Mir – PLOS ONE

“Our study reveals that genetic diversity of DENV-2 AS/AM genotype circulating in the Americas mainly resulted from one single founder event and can be organized in at least four major lineages”

Phages, viruses, CRISPRs

Screen Shot 2014-06-10 at 9.53.22 PMCasposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity – Mart Krupovic – BMC Biology

“We describe a new superfamily of archaeal and bacterial mobile elements which we denote casposons because they encode Cas1 endonuclease, a key enzyme of the CRISPR-Cas adaptive immunity systems of archaea and bacteria. “

Dr. Bik’s Picks

GeckoHow do geckos climb? – Ann Le Good – BioMedCentral

“The answer, from the recent Royal Society conference on cell adhesion, is that their climbing mechanism depends on van der Waals forces (as well as friction and shear stress). “

This one is intriguing:
AnticancerAnticancer Properties of Peptide Fragments of Hair Proteins – Sergiusz Markowicz – PLOS ONE

“We found out that the mixtures of soluble peptides obtained from human hair inhibited the proliferation of human melanoma cells in vitro. Moreover, the hair-derived peptide mixtures also inhibited the proliferation of B lymphoma cells and urinary bladder cancer cells. “

EarthEarth is around 60 million years older than previously thought — and so is the moon, new research finds – Science Daily

“The timing of the giant impact between Earth’s ancestor and a planet-sized body occurred around 40 million years after the start of solar system formation. This means that the final stage of Earth’s formation is around 60 million years older than previously thought, according to new research.”

 

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More Microbiology and Science, June 6

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Natural peptides against dengue, visualizing your QIIME .biom OTU table, and exposure to cockroaches and dust to babies. And Da Picks!

 
Dengue

Screen Shot 2014-06-07 at 2.05.52 AMIdentification of natural antimicrobial agents to treat dengue infection: In vitro analysis of latarcin peptide activity against dengue virus – Rothan HA – BMC Microbiology

“The Ltc 1 peptide exhibited significant inhibitory effects against dengue NS2B-NS3pro and virus replication in the infected cells. “

Bioinformatics

Screen Shot 2014-06-07 at 1.16.46 AMVisualizing millions of DNA sequences – in your web browser! – Featuring Phinch, developed by Holly Bik in the Eisen Lab

“The idea is to take your QIIME outputs – .biom OTU table files with taxonomy and embedded metadata – directly into a data visualization framework for assessment.”

Infection, immunity, host response

Screen Shot 2014-06-07 at 2.06.31 AMA novel, nested, multiplex, real-time PCR for detection of bacteria and fungi in blood – Gosiewski, T – BMC Microbiology

“ The designed primers correctly typed the studied species as belonging to the groups of Gram-positive bacteria, Gram-negative bacteria, yeast fungi, or filamentous fungi.”

Screen Shot 2014-06-07 at 2.00.39 AMEffects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children – Susan V. Lynch – The Journal of Allergy and Clinical Immunology

“….first-year exposure to cockroach, mouse, and cat allergens was negatively associated with recurrent wheeze…. House dust microbiome composition is associated with clinical outcomes. ”

Screen Shot 2014-06-07 at 1.58.39 AMImplementation and impact of ultraviolet environmental disinfection in an acute care setting – Janet P. Haas – AJIC: American Journal of Infection Control

“During the time period UVD was in use, there was a significant decrease in overall hospital-acquired MDRO plus CD in spite of missing 24% of opportunities to disinfect contact precautions rooms. This technology was feasible to use in our acute care setting and appeared to have a beneficial effect.”

Dr. Bik’s Picks

Screen Shot 2014-06-07 at 2.39.26 AMCool video of a scientist uncovering a whale in an old painting: Whale tale: a Dutch seascape and its lost Leviathan – University of Cambridge

“When art conservators peeled back a layer of varnish on a 17th-century Dutch painting, they uncovered an image of a beached whale that had been hidden for at least 150 years. “

Screen Shot 2014-06-07 at 2.40.17 AMLooking for the best strategy? Ask a chimp – Science Daily

“If you’re trying to outwit the competition, it might be better to have been born a chimpanzee, according to a study by researchers at Caltech, which found that chimps at the Kyoto University Primate Research Institute consistently outperform humans in simple contests drawn from game theory.”

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More Microbiology and Science, June 4, 2014

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Dengue, arthritis, arsenic, two retractions, frogs singing in the gutters, and deadly sharks (but not as you know them).

Infection, sepsis, and host response

Screen Shot 2014-06-05 at 1.08.42 AMBacteria in the Adventitia of Cardiovascular Disease Patients with and without Rheumatoid Arthritis – Samuel A. Curran – PLOS ONE

“The aortic adventitia of CVD patients contains a wide range of bacterial species, and the bacterial flora is significantly less diverse in RA+CVD than CVD patients. M. oryzae may stimulate an proinflammatory response that may aggravate and perpetuate the pathological processes underlying atherosclerosis in RA patients.”

Dengue Screen Shot 2014-06-05 at 1.06.24 AM

A tetravalent alphavirus-vector based dengue vaccine provides effective immunity in an early life mouse model – Syed Muaz Khalil – Vaccine

“We report here that a single immunization with a tetravalent VRP vaccine induced NAb and T-cell responses to each serotype at a level equivalent to the monovalent vaccine components, suggesting that this vaccine modality can overcome serotype interference. “

Arsenic metabolism

Screen Shot 2014-06-05 at 1.09.38 AMSpecies- and tissue-specific bioaccumulation of arsenicals in various aquatic organisms from a highly industrialized area in the Pohang City, Korea – Seongjin Hong – Environmental Pollution

“Contamination of water and sediment with arsenic (As) in a highly industrialized area of Pohang City, Korea was investigated, with emphasis on in situ bioaccumulation of arsenicals by various aquatic organisms.”

Publishing and misconduct Screen Shot 2014-06-05 at 1.03.01 AM

Japanese scientist to retract stem cell papers – Phys.org

“Haruko Obokata, 30, would withdraw two papers at the centre of the controversy, according to a spokeswoman for Riken, the respected  that sponsored the study, marking a steep fall from grace for the young researcher.”

Dr. Bik’s Picks

SharkShark meat worse than its bite – Tony Camie – IOL Scitech

“Never mind their fearsome jaws. People are now more likely to be killed by eating shark meat rather than the other way round.”

frogUrban frogs use drains as mating megaphones – Katia Moskvitch – Nature

“Gathering in the gutter may provide a better way to seduce females.”

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