General microbiology and science, June 11

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 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 –

“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.”