Category Archives: Metagenomics & Bioinformatics

Microbiome and general science digest, July 11

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Most recent results from American gut, a metagenomics pipeline, arsenic toxicity, polio and dengue vaccines, and pregnancy urine metabolomics to predict preterm birth.

Human gut microbiome

American GutAmerican Gut releases latest results and pipeline – Jeff Leach – American Gut

“The latest American Gut results are out and we’re very excited to share them with the American Gut community. We now have sequencing and analysis data from 3,238 participants, and as of today, this data equates to 101 million DNA sequences and 27 gigabytes of sequencing information.”

Screen shot 2014-07-11 at 04.27PM, Jul 11Place of upbringing in early childhood as related to inflammatory bowel diseases in adulthood: a population-based cohort study in Northern Europe – Signe Timm – European Journal of Epidemiology

“This study suggests a protective effect from livestock farm living in early childhood on the occurrence of IBD in adulthood, however only among subjects born after 1952. We speculate that lower microbial diversity is an explanation for the findings.”

Pregnancy and birth

Urinary pretermUrinary metabolic profiles in early pregnancy are associated with preterm birth and fetal growth restriction in the Rhea mother–child cohort study – Léa Maitre – BMC Medicine

“Here we used an exploratory metabolic profiling approach (metabolomics) to investigate the association between birth outcomes and metabolites in maternal urine collected early in pregnancy as part of the prospective mother–child cohort Rhea study. “

Metagenomics

MedusaMetagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue – Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen – PLOS Computational Biology

“Here we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. “

Proteomics

Proteomics Staph aureusGenomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine and Human-associated Staphylococcus epidermidis strains – Kirsi Savijoki – Journal of Proteome Research

“Pilot experimental infection studies indicated that while ATCC12228 was able to infect bovine host, the PM221 strain caused more severe clinical signs. “

Dengue

Demanou DengueEvidence of Dengue Virus Transmission and Factors Associated with the Presence of Anti-Dengue Virus Antibodies in Humans in Three Major Towns in Cameroon – Maurice Demanou – PLOS Neglected Tropical Diseases

“Sera were screened for anti-dengue virus IgG and IgM antibodies. Risk factors of seropositivity were tested using logistic regression methods with random effects.”

Carrasco DenguePredictive Tools for Severe Dengue Conforming to World Health Organization 2009 Criteria – Luis R. Carrasco – PLOS Neglected Tropical Diseases

“Higher risk of severe dengue (SD) was associated with female gender, lower than normal hematocrit level, abdominal distension, vomiting and fever on admission. “

Infection and host response

Screen shot 2014-07-11 at 03.35PM, Jul 11Development of Fatal Intestinal Inflammation in MyD88 Deficient Mice Co-infected with Helminth and Bacterial Enteropathogens – Libo Su – PLOS Neglected Tropical Diseases

“We found that MyD88 knockout mice co-infected with H. polygyrus and C. rodentium developed more severe intestinal inflammation and elevated mortality compared to the wild-type mice.”‘

Screen shot 2014-07-11 at 04.28PM, Jul 11Distinct Lipid A Moieties Contribute to Pathogen-Induced Site-Specific Vascular Inflammation – Connie Slocum – PLOS Pathogens

“our results point to a pivotal role for activation of the non-canonical inflammasome in P. gingivalis infection and demonstrate that P. gingivalis evades immune detection at TLR4 facilitating chronic inflammation in the vasculature. “

Dengue

Dengue vaccine lancetClinical efficacy and safety of a novel tetravalent dengue vaccine in healthy children in Asia: a phase 3, randomised, observer-masked, placebo-controlled trial – Maria Rosario Capeding – The Lancet

“Our findings show that dengue vaccine is efficacious when given as three injections at months 0, 6, and 12 to children aged 2–14 years in endemic areas in Asia, and has a good safety profile. “

Also see comment: Dengue vaccines: dawning at last? – Annelies Wilder-Smith – The Lancet

Poliovirus

Jacob John polioEffect of a single inactivated poliovirus vaccine dose on intestinal immunity against poliovirus in children previously given oral vaccine: an open-label, randomised controlled trial – Jacob John – The Lancet

“The substantial boost in intestinal immunity conferred by a supplementary dose of IPV given to children younger than 5 years who had previously received OPV shows a potential role for this vaccine in immunisation activities to accelerate eradication and prevent outbreaks of poliomyelitis.”

Also see comment: Polio endgame management: focusing on performance with or without inactivated poliovirus vaccine – Kimberly M Thompson – The Lancet

Microbes in the News

Screen shot 2014-07-11 at 04.28PM, Jul 11 1How Gross Is Your Phone? A Motherboard Science Experiment – Jason Koebler – Motherboard

“All I wanted to do was recreate a relatively simple study I had just written about. Instead, I ended up creating something vaguely dangerous, which mortified the director of a local DIY biology lab. Here’s what happens when you perform experiments on your coworkers.”

Arsenic metabolism

Screen shot 2014-07-11 at 04.29PM, Jul 11Lung tumors in mice induced by “whole-life” inorganic arsenic exposure at human-relevant doses – Michael P. Waalkes – Archives of Toxicology

“Breeder male and female CD1 mice were exposed to 0, 50, 500 or 5,000 ppb arsenic (as sodium arsenite) in the drinking water for 3 weeks prior to breeding, during pregnancy and lactation, and after weaning (at week 3) groups of male and female offspring (initial n = 40) were exposed for up to 2 years.”

Dr. Bik’s Picks

Scorpions are master architects, according to new research – Science Daily

“The burrows made by scorpions follow a very sophisticated design, beginning with a short, vertical entrance shaft that flattened out a few centimeters below the surface into a horizontal platform, new research has found.”

Beach Sand Used To Make A Battery That Lasts Three Times Longer – Douglas Main – Popular Science

“Sink your toes into this: Beach sand can be used to make lithium-ion batteries that last three times longer than current models, according to a study published in the journal Scientific Reports.”

World Now “A Safer Place”, thanks to creation of Potential Pandemic Virus – The Allium

“Yes, I get your point that they could potentially kill millions of people and hospitalise millions more, causing untold human suffering and extraordinary economic damage, but think of all the advantages to the creation of these bugs”.

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General digest, July 3

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CRISPRs, the yearly NAR Web Server issue, dengue, arsenic, and The Picks.

CRISPRs

Screen shot 2014-07-03 at 03.59PM, Jul 03 1Detection and characterization of spacer integration intermediates in type I-E CRISPR–Cas system – Zihni Arslan – Nucleic Acids Research

“We identified and characterized in Escherichia coli intermediate states of spacer integration and mapped the integration site at the chromosomal CRISPR array in vivo. “

Bioinformatics

Screen shot 2014-07-03 at 03.59PM, Jul 03Nucleic Acids Research published their yearly Web Server issue. The names of some tools alone are very entertaining (CHOPCHOP, Coffee, COGNAC, just to lists some C’s), but here are some resources that sound interesting:

Alignment-Annotator web server: rendering and annotating sequence alignments
Christoph Gille

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches – Sebastian Horwege

EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles – W. James Dittmar

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra – Felicity Allen

PIQMIe: a web server for semi-quantitative proteomics data management and analysis – Arnold Kuzniar

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data – Daogang Guan

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data – Manuel Garcia-Albornoz

deepTools: a flexible platform for exploring deep-sequencing data – Fidel Ramírez

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling – Cyrille Pauthenier

PubServer: literature searches by homology – Lukasz Jaroszewski

Arsenic metabolism

Arsenic color toolSediment color tool for targeting arsenic-safe aquifers for the installation of shallow drinking water tubewells – Mohammed Hossain – Science of the Total Environment

“Laboratory analysis of 521 groundwater samples collected from 144 wells during 2009 to 2011 indicate that As concentrations in groundwater were generally higher in the black colored sediments with an average of 239 μg/L.”

Screen shot 2014-07-03 at 03.55PM, Jul 03Arsenite stimulates glutathione export and glycolytic flux in viable primary rat brain astrocytes – Nimesha Tadepalle – Neurochemistry International

“The strong stimulation of GSH export by arsenite was prevented by MK571, an inhibitor of the multidrug resistance protein 1, suggesting that this transporter mediates the accelerated GSH export.”

Screen shot 2014-07-03 at 03.55PM, Jul 03 1Trichoderma spp. alleviate phytotoxicity in lettuce plants (Lactuca sativa L.) irrigated with arsenic-contaminated water – Antonio G. Caporale – Journal of Plant Physiology

“Plant Growth-Promoting Fungi (PGPF) of both Trichoderma species alleviated, at least in part, the phytotoxicity of As, essentially by decreasing its accumulation in the tissues and enhancing plant growth, P status and net photosynthesis rate.”

Dengue

Kwissa DengueDengue Virus Infection Induces Expansion of a CD14+CD16+ Monocyte Population that Stimulates Plasmablast Differentiation – Marcin Kwissa – Cell Host & Microbe

“Transcriptomic analysis of whole blood revealed that genes encoding proinflammatory mediators and type I interferon-related proteins were associated with high DENV levels during initial symptomatic disease. “

dengue bidetG3BP1, G3BP2 and CAPRIN1 Are Required for Translation of Interferon Stimulated mRNAs and Are Targeted by a Dengue Virus Non-coding RNA – Katell Bidet – PLOS Pathogens

“We examined three conserved host RNA-binding proteins (RBPs) G3BP1, G3BP2 and CAPRIN1 in dengue virus (DENV-2) infection and found them to be novel regulators of the interferon (IFN) response against DENV-2. “

Dengue Virus Persists in Stored Platelets and Red Blood Cells – Michael R. Sutherland – Transfusion Medicine Reviews

“…we investigated the persistence of DENV (serotypes 1-4) in stored platelet (PC) and red blood cell concentrates (RCC) under standard blood bank conditions. “

2013: Rise of the deadly dengue fever in Pakistan – Anum Wasim – Journal of Infection and Public Health

“Last year saw more than 17000 dengue cases being reported from all over the country, the highest number ever in the country’s history.”

Women in Science 

Gender: Perception differences – Nature

“Female leaders underrate how their bosses and colleagues perceive their performance, find US researchers”

Screen shot 2014-07-03 at 03.57PM, Jul 03Leader self-awareness: An examination and implications of women’s under-prediction –
Rachel E. Sturm – Journal of Organizational Behavior

“…women under-predict their bosses’ ratings of their leadership compared with men, even though they self-rate the same and are rated by their bosses similarly to men”

 

10 Words Every Girl Should Learn – Soraya Chemaly – Huffington Post

Yes! This! “A woman, speaking clearly and out loud, can say something that no one appears to hear, only to have a man repeat it minutes, maybe seconds later, to accolades and group discussion.”

Science, Publishing, and Ethics

Science Editorial: Raising the bar – Marcia McNutt – Science

“For that reason, with much help from the American Statistical Association, Science has established, effective 1 July 2014, a Statistical Board of Reviewing Editors (SBoRE), consisting of experts in various aspects of statistics and data analysis, to provide better oversight of the interpretation of observational data.”

Science ethics: Young scientists speak – Shelly Benjaminy – Science

“What is the most challenging ethical question facing young investigators in your field? How should it be addressed? In April, we asked young scientists to tell us their thoughts.“

Science and Art

Screen shot 2014-07-03 at 03.57PM, Jul 03 1Can You Guess What These Cute Pink Tiles Are Made Of? – Francie Diep – Popular Science

“These images are from research into new techniques for medical diagnoses and biometrics.”

Dr. Bik’s Picks

Screen shot 2014-07-03 at 03.51PM, Jul 03Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes – Iakes Ezkurdia – Human Molecular Genetics

“Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. “

Screen shot 2014-07-03 at 03.50PM, Jul 03With Help From Extinct Humans, Tibetans Adapted To High Altitude – Rae Ellen Bichell – NPR

“According to Nielsen and a bunch of geneticists writing in the journal Nature, the Tibetans appear to have benefited from a genetic gift from the Denisovans, an extinct human ancestor known primarily from a little girl’s tooth and pinkie bone.”

Screen shot 2014-07-03 at 03.49PM, Jul 03NSF to decide all future grant proposals by penalty shoot-out – The Allium

““We feel that this will be a much less random way of giving out funding”, said Dr. France Cordóva, Director of the NSF.”

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General microbiology and science digest, July 2

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Genome assembly, metabolomics of Salmonella infection, a brief history of women in science (but in Nature!), and Nature’s retraction of the STAP papers.

Metagenomics

Screen Shot 2014-07-02 at 10.13.28 PMBayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling – Mark Howison – PLOS ONE

“We present a Markov chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. “

Infection and host response

Screen Shot 2014-07-02 at 10.14.12 PMSalmonella Typhi and Salmonella Paratyphi – A elaborate distinct systemic metabolite signatures during enteric fever – Elin Näsström – eLife

“To investigate metabolite signals associated with enteric fever we performed two dimensional gas chromatography with time-of-flight mass spectrometry (GCxGC/TOFMS) on plasma from patients with S. Typhi and S. Paratyphi A infections and asymptomatic controls, identifying 695 individual metabolite peaks.”

and: Host-pathogen interactions: Honing in on enteric fever – Lyle R McKinnon, Quarraisha Abdool Karim – eLife

“The use of metabolomics could lead to improved diagnostics for enteric fever. “

Screen Shot 2014-07-02 at 10.14.58 PMHuman Genetic Variation and Yellow Fever Mortality during 19th Century U.S. Epidemics – Lauren E Blake, Mariano A Garcia-Blanco – mBio

“Caucasians diagnosed with YF were 6.8 times more likely to succumb than non-Caucasians with the disease. No other major causes of death during the 19th century demonstrated a similar mortality skew toward Caucasians. “

Bacterial and viral detection in clinical samples

Screen Shot 2014-07-02 at 10.15.58 PMThe Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples – A Useful Panmicrobial Diagnostic Tool – Maiken W. Rosenstierne – PLOS ONE

“We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses.”

The Sooner, The Better – Nicholette Zeliadt – The Scientist

“New approaches to diagnosing bacterial infections may one day allow the identification of pathogens and their antibiotic susceptibility in a matter of hours or minutes.”

Screen Shot 2014-07-02 at 10.16.45 PMReview: Biosensors for Whole-Cell Bacterial Detection – Asif Ahmed – Clinical Microbiology Reviews

” In this review, we discuss recent progress in the use of biosensors for the detection of whole bacterial cells for sensitive and earlier identification of bacteria without the need for sample processing.”

Screen Shot 2014-07-02 at 10.17.23 PMIsolation of Microorganisms Using Sub-Micrometer Constrictions – Nil Tandogan – PLOS ONE

“We present an automated method for isolating pure bacterial cultures from samples containing multiple species that exploits the cell’s own physiology to perform the separation.”

Phages and viruses

Screen Shot 2014-07-02 at 10.18.17 PMFour Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages – Yan D. Niu – PLOS ONE

“Comparative genomic, proteomic and phylogenetic analysis suggested that the four phages along with 17 T1-like phage genomes from database of National Center for Biotechnology Information (NCBI) can be assigned into a proposed subfamily “Tunavirinae” with further classification into five genera”

Dengue

Screen Shot 2014-07-02 at 10.18.45 PMClinical and Virological Descriptive Study in the 2011 Outbreak of Dengue in the Amazonas, Brazil – Valquiria do Carmo Alves Martins – PLOS ONE

“The aim of the study was to describe the clinical epidemiology of dengue in Manaus, the capital city of the state of the Amazonas, where all the four DENV serotypes were co-circulating simultaneously.”

Phylogeny and taxonomy

Screen Shot 2014-07-02 at 10.12.14 PMComparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups – Xiao-Yang Gao – PLOS ONE

“We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. “

Screen Shot 2014-07-02 at 10.12.46 PMLivestock-Associated MRSA Carriage in Patients without Direct Contact with Livestock – Miranda M. L. van Rijen – PLOS ONE

“Fifty-six individuals (20.7%) without animal contact carried MC398. In hospitals with high pig-densities in the adherence area, the proportion of MC398 of all MUO was higher than this proportion in hospitals without pigs in the surroundings.”

 Arsenic metabolism

Screen Shot 2014-07-02 at 10.02.56 PMMichigan’s arsenic problem is among the worst in the nation. Here’s why that matters – Rebecca Williams – Michigan Radio

“If you’re on city water, your drinking water has to comply with a federal regulation that limits the amount of arsenic in it, but if you’re on a private well, the federal and state governments do not limit the amount of arsenic in your well.”

Women in Science

Screen Shot 2014-07-02 at 9.59.45 PMWomen in science: A temporary liberation – Patricia Fara – Nature

“The First World War ushered women into laboratories and factories. In Britain, it may have won them the vote, argues Patricia Fara, but not the battle for equality.”

Science and Ethics

Nature Editorial: STAP retracted – Nature

“This week, Nature publishes retractions of two high-profile papers that claimed a major advance in the field of stem cells… We — research funders, research practitioners, institutions and journals — need to put quality assurance and laboratory professionalism ever higher on our agendas, to ensure that the money entrusted by governments is not squandered, and that citizens’ trust in science is not betrayed.”

Dr. Bik’s Picks

Screen Shot 2014-07-02 at 10.11.31 PMPLOS ONE Publishes its 100,000th Article – Damian Pattinson – PLOS Blogs

“PLOS ONE publishes its 100,000th article – a pretty major milestone for a journal that has seen its fair share of momentous events, and a perfect opportunity to reflect on this journey.”

Screen Shot 2014-07-02 at 10.08.37 PMLeprosy, Still Claiming Victims – Natalie Angier, New York Times

““I’m absolutely convinced that leprosy must be thought of as a genetic disease as well as an infectious one,” Dr. Schurr said. In the end, he added wryly, “understanding it may help cure diseases of rich people, too.””

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General microbiome digest, July 1

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Diet and gut microbiome (again), Campylobacter in chicken is not a commensal, microbiomes of fish, insects, corals, plant, and hospitals, and women in science.

Human gut microbiome

Screen shot 2014-07-01 at 06.07PM, Jul 01Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health – T Kelder – Nutrition & Diabetes

“We assessed fecal microbiota composition and host response patterns of metabolic and inflammatory markers in 10 apparently healthy men subjected to a high-fat high-caloric diet (HFHC, 1300 kcal/day extra) for 4 weeks. “

Pregnancy and birth

Screen shot 2014-07-01 at 06.08PM, Jul 01 1Gestational Age and Age at Sampling Influence Metabolic Profiles in Premature Infants
Reese H. Clark – Pediatrics

“Metabolic profiles (15 amino acids and 35 acylcarnitines) were obtained by using standard newborn techniques on infants born between 23 and 31 completed weeks of gestation.”

Screen shot 2014-07-01 at 06.08PM, Jul 01Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing – Jason M. Knight – Nature Scientific Reports

“we have developed a novel, noninvasive, molecular approach that utilizes next generation RNA sequencing on stool samples containing intact epithelial cells for the purpose of quantifying intestinal gene expression.”

Screen shot 2014-07-01 at 06.09PM, Jul 01Cesarean Section and Rate of Subsequent Stillbirth, Miscarriage, and Ectopic Pregnancy: A Danish Register-Based Cohort Study – Sinéad M. O’Neill – PLOS Medicine

“This study found that cesarean section is associated with a small increased rate of subsequent stillbirth and ectopic pregnancy.”

Bird microbiome

Screen shot 2014-07-01 at 06.10PM, Jul 01Campylobacter jejuni Is Not Merely a Commensal in Commercial Broiler Chickens and Affects Bird Welfare – Suzanne Humphrey – mBio

“Through experimental infection of four commercial breeds of broiler chickens, we show that breed has a significant effect on C. jejuni infection and the immune response of the animals, although these factors have limited impact on the number of bacteria in chicken ceca. “

Fish microbiome

Screen shot 2014-07-01 at 06.10PM, Jul 01 1Quorum quenching bacteria Bacillus sp. QSI-1 protect zebrafish (Danio rerio) from Aeromonas hydrophila infection – Weihua Chu – Nature Scientific Reports

“In this study, the effect of Bacillus sp. QSI-1 as an efficient quorum quencher on virulence factors production and biofilm formation of fish pathogen Aeromonas hydrophila was investigated. ”

Insect microbiome

Screen shot 2014-07-01 at 06.11PM, Jul 01Evolutionary origin of insect–Wolbachia nutritional mutualism – Naruo Nikoh – PNAS

“In the bedbug’s Wolbachia genome, we identified a gene cluster encoding the complete synthetic pathway for biotin (vitamin B7), which is not present in other Wolbachia genomes and is presumably acquired via lateral transfer from a coinfecting endosymbiont. “

Corals and sponges microbiome

Screen shot 2014-07-01 at 06.12PM, Jul 01Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors – Linda W. Kelly – PNAS

“The present study investigated the community structure and metabolic potential of microbes inhabiting coral reefs located across an extensive area in the central Pacific. “

Plant microbiome

Screen shot 2014-07-01 at 06.13PM, Jul 01The role of sulfur and phosphorus mobilizing bacteria in biochar induced growth promotion of Lolium perenne – A Fox – FEMS Microbiology Ecology

“16S rRNA gene based rhizobacteria community analysis revealed a significant biochar treatment effect. Abundance of nematodes feeding on bacteria was also significantly increased in the biochar treatments.”

Functional diversification within bacterial lineages promotes wide functional overlapping between taxonomic groups in a Mediterranean soil forest – J Curiel Yuste – FEMS Microbiology Ecology

“We investigated the relationship between taxonomy and functioning of soil bacterial communities in soils from a Mediterranean Holm-oak forest using a high throughput DNA pyrosequencing technique. “

Soil, sewage and sludge microbiome

Screen shot 2014-07-01 at 06.15PM, Jul 01Response of soil-associated microbial communities to intrusion of coal mine-derived acid mine drainage – Justin S Brantner and John M Senko – Environmental Science & Technology

” Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment. “

Transformation Products and Human Metabolites of Triclocarban and Triclosan in Sewage Sludge Across the United States – Benny F. G. Pycke – Environmental Science & Technology

“Here, we report on the levels of eight transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in raw and treated sewage sludge.”

Built Environment Microbiome

Screen shot 2014-07-01 at 06.14PM, Jul 01Rethinking Sterile: The Hospital Microbiome – Carrie Arnold – Environ Health Perspect

“Gilbert, an environmental microbiologist at Argonne National Laboratory, and his platoon of graduate students, postdocs, and research assistants descended on the hospital several times each day, even before it opened to the public. Armed with cotton swabs, they focused their efforts on the floors devoted to surgery and oncology. “

Bioinformatics

Screen shot 2014-07-01 at 06.15PM, Jul 01 1A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples – Samia N. Naccache – Genome Research

“Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. “

Metagenomics

Metagenomic scaffolds enable combinatorial lignin transformation
Cameron R. Strachan – PNAS

“In this study, we devised a previously unidentified biosensor responsive to lignin transformation products. We used this biosensor in a functional screen to recover metagenomic scaffolds sourced from coal bed bacterial communities. “

Arsenic metabolism

Sealing rice field boundaries in Bangladesh: a pilot study demonstrates reductions in water use, arsenic loading to field soils, and methane emissions from irrigation water – Rebecca B Neumann – Environmental Science & Technology

“Irrigation of rice fields in Bangladesh with arsenic-contaminated and methane-rich groundwater loads arsenic into field soils and releases methane into the atmosphere. We tested the water-savings potential of sealing field bunds (raised boundaries around field edges) as a way to mitigate these negative outcomes.”

Localised Flux-Maxima of Arsenic, Lead and Iron around Root Apices in Flooded Lowland Rice – Paul Nicholas Williams – Environmental Science & Technology

“Here we use new diffusive gradients in thin-film (DGT)/planar optode sandwich sensors deployed in situ on rice roots to demonstrate a new geochemical niche of greatly enhanced As, Pb and Fe(II) mobilization into solution immediately adjacent to the root tips characterized by O2 enrichment and low pH. “

Dengue

Screen shot 2014-07-01 at 06.16PM, Jul 01Baicalin, a metabolite of baicalein with antiviral activity against dengue virus – Ehsan Moghaddam – Nature Scientific Reports

“Here, we examined the anti-DENV properties of baicalin in vitro, and described the inhibitory potentials of baicalin at different steps of DENV-2 (NGC strain) replication.”

Antibiotic resistance

Review: The expression of antibiotic resistance genes in antibiotic-producing bacteria – Stefanie Mak – Molecular Microbiology

“Antibiotic-producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. “

General microbiology

Screen shot 2014-07-01 at 06.20PM, Jul 01Bacterial sugar utilization gives rise to distinct single-cell behaviors – Taliman Afroz – Molecular Microbiology

“Here, we performed single-cell analyses to probe the behavior of representative pathways in the model bacterium Escherichia coli. “

Identification of essential Alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems – Patrick D. Curtis and Yves V. Brun – Molecular Microbiology

“These results show that while essential cell functions are conserved across varying genetic distance, much of a given organism’s essential gene pool is specific to that organism.”

Science and career

Screen shot 2014-07-01 at 06.22PM, Jul 01Elite male faculty in the life sciences employ fewer women – Jason M. Sheltzer and Joan C. Smith – PNAS

“To explore the current causes of women’s underrepresentation in biology, we collected publicly accessible data from university directories and faculty websites about the composition of biology laboratories at leading academic institutions in the United States. “

Screen shot 2014-07-01 at 06.01PM, Jul 01Americans Think We Have the World’s Best Colleges. We Don’t. – Kevin Carey – New York Times

“We see K-12 schools and colleges differently because we’re looking at two different yardsticks: the academic performance of the whole population of students in one case, the research performance of a small number of institutions in the other.”

Dr. Bik’s picks

Screen shot 2014-07-01 at 06.23PM, Jul 01Herbivore diet breadth mediates the cascading effects of carnivores in food webs – Michael S. Singer – PNAS

“Accounting for phylogenetic nonindependence of herbivores and plants, we show for the first time (to our knowledge) that dietary specialization of herbivore species is associated with reduced bird predation across an herbivore phylogeny, and that dietary specialization of herbivores increases the antipredator effects of camouflage and aposematism.”

Screen shot 2014-07-01 at 06.23PM, Jul 01 1Evolution of the ribosome at atomic resolution – Anton S. Petrov – PNAS

“Comparing eukaryotic and prokaryotic ribosomes allows us to identify 3D insertion fingerprints of the expansion segments. Similar fingerprints allow us to analyze the common core and detect ancestral expansion segments within it. “

Plastic mapPlastic debris in the open ocean – Andrés Cózar – PNAS

“In this work, we synthetize data collected across the world to provide a global map and a first-order approximation of the magnitude of the plastic pollution in surface waters of the open ocean.”

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General microbiology and science, June 27

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Viruses in primate genomes, viruses altering shrimp metabolome, transposable elements and repeats, dengue, other infectious diseases in developing countries and Dr. Bik’s Picks.

Metagenomics / viruses

Screen Shot 2014-06-27 at 9.21.29 PMCute animal alert! A tarsier is a tiny primate with huge eyes.
The First Endogenous Herpesvirus, Identified in the Tarsier Genome, and Novel Sequences from Primate Rhadinoviruses and Lymphocryptoviruses – Amr Aswad, Aris Katzourakis – PLOS Genetics

“We describe the first endogenous herpesvirus from the genome of the Philippine tarsier, belonging to the Roseolovirus genus, and characterize its highly defective genome that is integrated and flanked by unambiguous host DNA. From a draft assembly of the aye-aye genome, we use bioinformatic tools to reveal over 100,000 bp of a novel rhadinovirus that is the first lemur gammaherpesvirus, closely related to Kaposi’s sarcoma-associated virus.”

 Metabolomics

Screen Shot 2014-06-27 at 9.32.37 PMAn Invertebrate Warburg Effect: A Shrimp Virus Achieves Successful Replication by Altering the Host Metabolome via the PI3K-Akt-mTOR Pathway – Mei-An Su – PLOS Pathogens

“We show that the PI3K-Akt-mTOR pathway was of central importance in triggering this WSSV-induced Warburg effect. Although dsRNA silencing of the mTORC1 activator Rheb had only a relatively minor impact on WSSV replication, in vivo chemical inhibition of Akt, mTORC1 and mTORC2 suppressed the WSSV-induced Warburg effect and reduced both WSSV gene expression and viral genome replication.”

Biofilms

Screen Shot 2014-06-27 at 9.33.21 PMFilaments in curved streamlines: rapid formation of Staphylococcus aureus biofilm streamers – Minyoung Kevin Kim – New Journal of Physics

“We discovered that S. aureus rapidly forms flow-induced, filamentous biofilm streamers, and furthermore if surfaces are coated with human blood plasma, streamers appear within minutes and clog the channels more rapidly than if the channels are uncoated. “

Chromosomal organization

Screen Shot 2014-06-27 at 9.34.04 PMDigital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats – Manisha Brahmachary – PLOS Genetics

“Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. “

Screen Shot 2014-06-27 at 9.34.37 PMLarge-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes – Jaime Iranzo – PLOS Computational Biology

“In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. “

Microbial Ecology

Screen Shot 2014-06-27 at 9.35.00 PMEx Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community – Margie Kinnersley – PLOS Genetics

“We previously showed that a population of E. coli that originated from a single clone and was cultured in the presence of a single limiting resource, evolves into a stable, three-membered community, wherein one clone excretes metabolites that the others utilize as carbon sources. To discern the genetic factors at work in producing this outcome and to illuminate the community’s physiology, we sequenced the genomes of the ancestral and evolved clones.”

Infectious diseases in developing countries

Screen Shot 2014-06-27 at 9.35.43 PMExploring the Relationship between Access to Water, Sanitation and Hygiene and Soil-Transmitted Helminth Infection: A Demonstration of Two Recursive Partitioning Tools – Katherine Gass – PLOS Neglected Tropical Diseases

“Improvements to water, sanitation and hygiene (WASH) likely provide sustained benefit, but few rigorous studies have evaluated the specific WASH components most influential in reducing infection. “

Screen Shot 2014-06-27 at 9.36.14 PMSocial Sciences Research on Infectious Diseases of Poverty: Too Little and Too Late? – José Azoh Barry – PLOS Neglected Tropical Diseases

“Besides the vicious circle these diseases maintain with dire conditions of poverty, an increased microbial resistance to some therapeutic drugs adds to the complexity of health disparities and human suffering among the socially disadvantaged, marginalized, and prejudiced against.”

Dengue

Screen Shot 2014-06-27 at 9.36.37 PMVariability in Dengue Titer Estimates from Plaque Reduction Neutralization Tests Poses a Challenge to Epidemiological Studies and Vaccine Development – Henrik Salje – PLOS Neglected Tropical Diseases

“We used repeated assays on the same two pools of serum using five different viruses (2,319 assays) to characterize the variability in the technique under identical experimental conditions. We also assessed the performance of multiple statistical models to interpolate continuous values of neutralization titer from discrete measurements from serial dilutions.”

Science and career

PLOSTen Simple Rules for Approaching a New Job – Philip E. Bourne – PLOS Computational Biology

“Thinking both as a job applicant and a job interviewer about how I have approached job situations over the years before, during, and after the interview and how those situations have turned out, I can offer the following ten simple rules as you prepare.”

A New Online Computational Biology Curriculum – David B. Searls – PLOS Computational Biology

“A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. “

Arsenic metabolism

Screen Shot 2014-06-27 at 10.00.06 PMAssociations between Arsenic Species in Exfoliated Urothelial Cells and Prevalence of Diabetes among Residents of Chihuahua, Mexico – Jenna M. Currier – Environ Health Perspect

“We measured concentrations of trivalent and pentavalent iAs, methyl-As (MAs), and dimethyl-As (DMAs) species in EUC from 374 residents of Chihuahua, Mexico, who were exposed to iAs in drinking water.”

Dr. Bik’s Picks

Screen Shot 2014-06-27 at 10.09.01 PMWith pictures and videos: Duration of urination does not change with body size – Patricia J. Yang – PNAS

“In this study, we report a mathematical model that clarifies misconceptions in urology and unifies the results from 41 independent urological and anatomical studies. The theoretical framework presented may be extended to study fluid ejection from animals, a universal phenomenon that has received little attention.”

Screen Shot 2014-06-27 at 10.01.44 PMFrom Gemstones to Arsenic: How the Development of Pigment Colored Art – Allison Meier

“A new exhibition at London’s National Gallery — Making Colour — looks at the development of color in art, from the Middle Ages to 1900. “

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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 18

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Learn about dengue at the World Cup, a deadly lake, 3D structures of genomes, OTUs and tables, musical kids, and why your iPhone headphones are always in a knot.

Dengue

Evaluation of single-round infectious, chimeric dengue type 1 virus as an antigen for dengue functional antibody assays – Atsushi Yamanaka – Vaccine

“In the present study, SRIPs of DENV-1 (D1-SRIPs) were evaluated as an antigen for functional antibody assays.”

An inhibition model of BPTI to unlinked dengue virus NS2B-NS3 protease – Hua Li – FEBS Letters

“BPTI shows strong competitive inhibitory activity (Ki = 6.5 nM) against this unlinked protease, which adopts a closed conformation.”

The role of cell proteins in dengue virus infection – Ma. Isabel Salazar – Journal of Proteomics

“This review focuses on recent reports about cellular proteins involved along the dengue virus replication cycle, in prime cellular targets during the infection of both humans and mosquito hosts and also on the proteomics and other approaches that are being used to reveal the entire orchestration and most significant processes altered during infection.”

Dengue outlook for the World Cup in Brazil – Eduardo Massad – The Lancet Infectious Diseases

Correspondence on: Dengue outlook for the World Cup in Brazil: an early warning model framework driven by real-time seasonal climate forecasts

Arsenic metabolism

43,000 die annually in Bangladesh: Study – The Daily Star

“This rate is 25 percent all over Bangladesh, said Dr Kazi Matin Ahmed, geology professor of Dhaka University. He presented the paper at a seminar titled “Arsenic Activities, Research and Outcomes” organised by the Bangladesh Medical Research Council (BMRC) in its auditorium in the capital yesterday.”

Arsenic speciation in rice-based food for adults with celiac disease – Sandra Munera-Picazo – Food Additives and Contaminants

“…the objective of this study was to analyze the occurrence of arsenic (As) in gluten-free products, basically those rice-based, intended for celiac adult consumers.”

Could This Acid Lake Hold the Elixir of Life for Cancer Patients? – Ryot.org

“The Berkeley Acid Pit is a giant hole filled with arsenic and sulfuric acid, and has a history of causing disturbing deaths… and it’s making its way into the city’s water supply, according to PitWatch.”

Chromosomal Organization

Targeted chromatin capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements – Petros Kolovos – Epigenetics &

“We applied T2C on well-known model regions, the mouse beta-globin locus and the human H19/IGF2 locus. In both cases we identified all known chromatin interactions”

A statistical approach for inferring the 3D structure of the genome – Nelle Varoquaux – Bioinformatics

“We propose a novel approach to infer a consensus 3D structure of a genome from Hi-C data. The method incorporates a statistical model of the contact counts, assuming that the counts between two loci follow a Poisson distribution whose intensity decreases with the physical distances between the loci.”

Spatial organization of interphase chromosomes and the role of chromatin fibril dynamics in the positioning of genome elements – E. S. Gushchanskaya – Molecular Biology

“In this review, we discuss the results of these projects, which allow us to explain the functional basis of nucleus multilevel compartmentalization and to identify the principles of high-level chromatin organization. “

Computational ecology

A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals – Giovanni Strona – Nature Communications

“A well-known problem in numerical ecology is how to recombine presence-absence matrices without altering row and column totals. “

Consistent, comprehensive and computationally efficient OTU definitions – Jai Ram Rideout – PeerJ PrePrints

“We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis.”

 

Bacteria in blood and sterile sites

Rapid and direct MALDI-MS identification of pathogenic bacteria from blood using ionic liquid-modified magnetic nanoparticles (Fe3O4@SiO2) – Mukesh L. Bhaisare – Journal of Materials Chemistry B

“A novel method for pathogenic bacteria identification directly from blood samples using cationic ionic liquid-modified magnetic nanoparticles (CILMS) is reported.”

Metagenomics

GroopM: An automated tool for the recovery of population genomes from related metagenomes – Michael Imelfort – PeerJ PrePrints

“Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. “

DNA-dependent RNA polymerase detects hidden giant viruses in published databanks – Vikas Sharma – Genome Biology and Evolution

“To explore the dark matter, we used viral RNAP2 and reconstructed putative ancestral RNAP2, which were significantly superior in detecting distant clades than current sequences, and we revealed two additional unknown mimiviruses, misclassified as an euryarchaeote and a oomycete plant pathogen, and detected unknown putative viral clades”

Metabolomics

Comparative Metabolomics and Structural Characterizations Illuminate Colibactin Pathway-Dependent Small Molecules – Maria I. Vizcaino – Journal of the American Chemical Society

“Here we implemented a comparative metabolomics and targeted structural network analyses approach to identify a catalog of small molecules dependent on the colibactin pathway from the meningitis isolate E. coli IHE3034 and the probiotic E. coli Nissle 1917.”

Scientific writing and publishing

Screen Shot 2014-06-18 at 11.01.34 PMColour blindness: Still too many red–green figures – S. Colby Allred – Nature

“People with red–green colour blindness cannot interpret figures in research papers that use these colours. We call for all journals to provide alternative versions of figures that are more accessible to such individuals.”

Open access: Sharing your data is easier than you think – Stephen Eglen – Nature

“Storing large volumes of raw data is costly, but many items destined for sharing are highly processed and relatively small. “

Dr. Bik’s Picks

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes – Erica M. Goss – PNAS

“We sequenced four nuclear genes in representative samples from Mexico and the South American Andes. An Andean origin of P. infestans does not receive support from detailed analyses of Andean and Mexican populations. “

Behavioral and Neural Correlates of Executive Functioning in Musicians and Non-Musicians – Jennifer Zuk – PLOS ONE

“Overall, musicians show enhanced performance on several constructs of EF, and musically trained children further show heightened brain activation in traditional EF regions during task-switching.”

There’s a scientific reason your iPhone headphones are always tangled – Fiona MacDonald – Science Alert

“But between 46 centimeters and 150 centimeters (about five feet), the probability of a knot forming rises dramatically.”

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General microbiology and science, June 17

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How to freeze and preserve communities, host response, standardized metadata for pathogens, primers for fungal detection and more. Check out Dr. Bik’s Picks for coffee in space and sticky tongues.

Infection and host response

The effect of age on the systemic inflammatory response in patients with community-acquired pneumonia – Lonneke A. van Vught – Clinical Microbiology and Infection

“Serum concentrations of pro-inflammatory (interleukin (IL)-6 and IL-8) and anti-inflammatory cytokines (IL-10 and IL-1 receptor antagonist) did not differ between age groups, although admission IL-8 levels tended to be higher in old patients (p = 0.05). “

Clinical Disease Severity of Respiratory Viral Co-Infection versus Single Viral Infection: A Systematic Review and Meta-Analysis – Sandra A. Asner – PLOS ONE

“No differences in clinical disease severity between viral co-infections and single respiratory infections were documented.”

Standardized Metadata for Human Pathogen/Vector Genomic Sequences – Vivien G. Dugan – PLOS ONE

“The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. “

Discovering Hidden Connections among Diseases, Genes and Drugs Based on Microarray Expression Profiles with Negative-Term Filtering – Jain-Shing Wu – PLOS ONE

“This study proposes a novel means of employing existing GEPs to reveal hidden relationships among diseases, genes, and drugs within a rich biomedical database, PubMed. Unlike the co-occurrence method, which considers only the appearance of keywords, the proposed method also takes into account negative relationships and non-relationships among keywords, the importance of which has been demonstrated in previous studies.”

MS spectrometry and microbiology

A simple, robust and rapid approach to detect carbapenemases in Gram negative isolates by MALDI-TOF mass spectrometry: validation with triple quadripole tandem mass spectrometry, microarray and PCR – Christelle Vogne – Clinical Microbiology and Infection

“Here, we developed a simple, easy and rapid MALDI-TOF-based assay to detect carbapenemases and compared this innovative test with 4 other diagnostic approaches on 47 clinical isolates. “

Source-Identifying Biomarker Ions between Environmental and Clinical Burkholderia pseudomallei Using Whole-Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) – Suthamat Niyompanich – PLOS ONE

“In this present study, we employed a whole-cell MALDI-TOF MS approach for assessing its potency in clustering a total of 11 different B. pseudomallei isolates (consisting of 5 environmental and 6 clinical isolates) with respect to their origins and to further investigate the source-identifying biomarker ions belonging to each bacterial group.”

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – Emilie Saussereau – Clinical Microbiology and Infection

“The demonstration that bacteriophages infect their bacterial hosts in the sputum environment, regardless of the clinical characteristics of the patients, represents a major step towards the development of bacteriophage therapy to treat chronic lung infections.”

Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing –
Jason T. Ladner – mBio

“Here, we propose five “standard” categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing.”

Dengue

Dengue Serosurvey in Sint Eustatius – Teresa Leslie – PLOS ONE

“ Few studies have investigated dengue on Sint Eustatius. Blood samples were collected to determine the prevalence of antibodies against dengue in the Sint Eustatius population.”

General microbiology

Invited Editorial: Bioterrorism: myth or reality? – Gilbert Greub and Martin P. Grobusch – Clinical Microbiology and Infection

“Interestingly, while there are no doubt many features which tell those topics apart from each other, bioterrorism, in its broad sense, in its perception by the public, strikingly shares some features with the human interest in viral hemorrhagic fevers as witnessed during the recent Zaire ebolavirus disease outbreak “

Invited Editorial: New epidemiology of Staphylococcus aureus infections – Jean-Philippe Rasigade – Clinical Microbiology and Infection

“The clinical and molecular epidemiology of S. aureus infections has changed dramatically over the past two decades with the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA).”

Sequencing and data analysis

Summarizing Specific Profiles in Illumina Sequencing from Whole-Genome Amplified DNA – Isheng J. Tsai – DNA Research

“To utilize the full potential of WGA to reveal the real biological interest, this article highlights the importance of recognizing additional sources of errors from amplified sequence reads and discusses the potential implications in downstream analyses.”

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics – Federico M. Ibarbalz – PLOS ONE

“The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge.”

HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis – Luis Santana-Quintero – PLOS ONE

“High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. “

Sample preparation, primers, PCR

Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity – Frederiek-Maarten Kerckhof – PLOS ONE

“ In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. ”

Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies – Michiel Op De Beeck – PLOS ONE

“In the current study, three selected primer pairs were tested for their suitability as fungal metabarcoding primers.”

Chromosome organization

Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes – Yongjie Huang and Jan Mrázek – DNA Research

“Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented.”

Dr. Bik’s Picks

Tongue adhesion in the horned frog Ceratophrys sp. – Thomas Kleinteich & Stanislav N. Gorb- Scientific Reports

“Here we measured for the first time adhesive forces and tongue contact areas in living individuals of a horned frog (Ceratophrys sp.) against glass. We found that Ceratophrys sp. generates adhesive forces well beyond its own body weight.”

Good news: Espresso machine in SPAAAACE. Bad news: Fuelled by URINE – Simon Sharwood – The Register

“A critical issue standing between humanity and long-term residence in space has been solved after boffins invented an espresso machine they plan to send up to the International Space Station (ISS), groan-inducingly dubbed the ISSpresso.”

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General microbiology and science, June 16

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It’s late and I got lots for you, so no pictures today. Dengue, phages, ecology, techniques, and lots more.

Antibiotic resistance

Review: Microbiological effects of sublethal levels of antibiotics – Dan I. Andersson & Diarmaid Hughes – Nature Reviews Microbiology

“In this Review, we discuss the ecology of antibiotics and the ability of subinhibitory concentrations to select for bacterial resistance. “

A Bacterial Battle  – Lisa M. Jarvis – Chemical and Engineering News

“The regulatory path to approving new antibiotics has been cleared, but work still remains to rebuild a healthy drug pipeline”

Bacteria are everywhere
How safe is your kitchen? – Lyxan Toledanes – The Daily News Online

“Despite a spacious kitchen, Parker sat on the counter next to Masters’ prep area, where she was chopping vegetables and chicken on separate cutting mats. ”

Adventures in the microbiome (part 2) – Mike Edmund

“There’s an intriguing case report that was just published in Clinical Microbiology and Infection”

Stafford students find bacteria on tainted tablets – Amanda Oglesby

“Four sixth-graders huddled over a table inside All Saints Regional Catholic School as they took turns swabbing bacteria from the surfaces of an iPhone and iPad.”

Bioslime: new sensor to detect harmful bacteria on food industry surfaces – BarfBlog

“The Biolisme project is using research from the University to develop a sensor capable of collecting and detecting Listeria monocytogenes on food industry surfaces, thereby preventing contaminated products from entering the market.”

Viruses and phages

Functional long-range RNA–RNA interactions in positive-strand RNA viruses – Beth L. Nicholson & K. Andrew White – Nature Reviews Microbiology

“In this Review, we discuss recent insights into the structure and function of these intriguing genomic features and highlight their diverse roles in the gene expression and genome replication of positive-strand RNA viruses.”

Unravelling the structural and mechanistic basis of CRISPR–Cas systems – John van der Oost – Nature Reviews Microbiology

“In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR–Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.”

The elemental composition of virus particles: implications for marine biogeochemical cycles – Luis F. Jover – Nature Reviews Microbiology

“In this Analysis article, we use a biophysical scaling model of intact virus particles that has been validated using sequence and structural information to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. “

Phage therapies for plants and people – Michael Gross – Current Biology

Dengue

NEA to explore biological control methods to tackle dengue

“One of the techniques involves the use of Aedes aegypti mosquitoes, which are infected with a certain bacteria, to control their population.”

Techniques general

Storage of Human Biospecimens: Selection of the Optimal Storage Temperature – Allison Hubel – Biopreservation and Biobanking

“The overall objective of this article is to describe the scientific basis for selecting a storage temperature for a biospecimen based on current scientific understanding. To that end, this article reviews some physical basics of the temperature, nucleation, and ice crystal growth present in biological samples stored at low temperatures (−20°C to −196°C), and our current understanding of the role of temperature on the activity of degradative molecules present in biospecimens.”

DNA polymerase hybrids derived from the family-B enzymes of Pyrococcus furiosus and Thermococcus kodakarensis: improving performance in the polymerase chain reaction – Ashraf M. Elshawadfy – Frontiers Microbiology

“The significance of this work is the observation that improvements in PCR performance are easily attainable by blending elements from closely related archaeal polymerases, an approach that may, in future, be extended by using more polymerases from these organisms.”

Metabolomics, Proteomics, Mass spectrometry

Bruker Announces Powerful New Mass Spectrometry Systems and Solutions for Life-Science Research, Clinical Research, Biopharma and Applied Markets – Wall Street Journal

“At the 62(nd) ASMS Conference on Mass Spectrometry and Allied Topics today, Bruker Corporation (NASDAQ:BRKR) today announced mass spectrometry-based product introductions for life-science research and proteomics, for clinical research, for pharma/biopharma/CRO customers, as well as for applied and industrial markets. “

Medically, Proteomics Advances Will Rival the Genetics Advances of the Last Ten Years – Genetic Engineering and Biotechnology News

“..in explaining why proteomics is likely to have such a major impact, Dr. Anderson starts with a major difference between the genetic testing common today, and the proteomic testing that is fast coming on the scene. “

Metagenomics and informatics

Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation – Yvonne L. Chan – Molecular Biology and Evolution

“Here we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage.”

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit – Jesse D. Bloom – Molecular Biology and Evolution

“Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing.”

Ecology

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning – Sascha Krause – Frontiers in Microbiology

“We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. “

The importance of the viable but non-culturable state in human bacterial pathogens – Laam Li – Frontiers in Microbiology

“The conditions that trigger the induction of the VBNC state and resuscitation from it are summarized and the mechanisms underlying these two processes are discussed. “

Deciphering microbial interactions and detecting keystone species with co-occurrence networks – David Berry – Frontiers in Microbiology

“Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation.”

Scientific writing and publishing

Sources of error in the retracted scientific literature – Arturo Casadevall, R. Grant Steen and Ferric C. Fang – The FASEB Journal

“Analysis of the retraction notices for 423 articles indexed in PubMed revealed that the most common causes of error-related retraction are laboratory errors, analytical errors, and irreproducible results.”

Dr. Bik’s Picks

Magnets: Artificial Magnetic Bacteria: Living Magnets at Room Temperature – Miguel Martín – Adv. Funct. Mater

“After grafting the magnetic nanoparticles, the artificial magnetic bacteria remain alive. In fact they are converted into living magnets at room temperature.”

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More Microbiology and Science, June 6

Posted on by

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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