General microbiology and science, June 18

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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