General digest, July 3

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


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. “


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.”


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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