Tag Archives: influenza

General microbiology and science, July 9

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Transcriptomic and proteomic analysis of Dengue infection,  bacteria that can tolerate arsenate, and -shocking!- bacteria on elevator buttons.

Dengue

Monocyte-Plasmablast Crosstalk during Dengue – Angela M. Green, Eva Harris – Cell Host & Microbe

“In this issue, Kwissa et al. (2014) begin with transcriptomic analysis and then integrate studies in human clinical samples, nonhuman primates, and coculture of primary human cells to identify a role for CD14+CD16+ monocytes in generating plasmablast responses during dengue virus infection.”

Screen Shot 2014-07-09 at 10.24.23 PMBelongs to: Dengue 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.”

Screen Shot 2014-07-09 at 10.25.06 PMQuantitative proteomic analysis of Huh-7 cells infected with Dengue virus by label-free LC–MS – Victoria Pando-Robles – Journal of Proteomics

“In order to gain a better reading of the cross talk between virus and host cell proteins, we used a proteomics approach to analyze the host response to DENV infection in a hepatic cell line Huh-7.”

Dengue hemorrhagic fever: Comparison of patients with primary and secondary infections – Muhammad Khurram – Journal of Infection and Public Health

“The two Groups were compared for statistically significant association in terms of age, gender, laboratory parameter (at admission hematocrit [HCT], platelet, white blood cell [WBC] counts, alanine aminotransferase [ALT] value), severity (DHF or dengue shock syndrome), and outcome (recovered or expired).”

Comments on the clinical and laboratory characteristics of patients with dengue hemorrhagic fever manifestations and their transfusion profile – Romélia Pinheiro Gonçalves Lemes – Revista Brasileira de Hematologia e Hemoterapia

Belongs to: Clinical and laboratory characteristics of patients with dengue hemorrhagic fever manifestations and their transfusion profile – Denys Eiti Fujimoto – Revista Brasileira de Hematologia e Hemoterapia

“A retrospective descriptive study was performed to analyze the distribution of relative frequencies of clinical and laboratory variables. The study was carried out in Rio Branco with confirmed dengue fever cases.”

Viruses and phages

Viruses as new agentsViruses as new agents of organomineralization in the geological record – Muriel Pacton – Nature Communications

“Here we use contextual metagenomic data and microscopic analyses to show that viruses occur in high diversity within a modern lacustrine microbial mat, and vastly outnumber prokaryotes and other components of the microbial mat.”

Screen Shot 2014-07-09 at 10.30.33 PMReview: Exploiting gut bacteriophages for human health – Marion Dalmasso – Trends in Microbiology

“Individual phageomes vary depending on age and health, thus providing a useful biomarker of human health as well as suggesting potential interventions targeted at the gut microbiota.”

Through the looking glass: witnessing host–virus interplay in zebrafish – Jean-Pierre Levraud – Trends in Microbiology

“Besides traditional host models such as mice, the zebrafish offers an attractive cocktail of optical accessibility and genetic tractability, blended with a vertebrate-type immunity, where innate responses can easily be separated from adaptive ones.”

Antibiotics and resistance

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone – Nicholas J Croucher – BMC Biology

“Whole genome sequencing of an international collection of 189 isolates estimated that PMEN2 emerged around the late 1960s, developing resistance through multiple homologous recombinations and the acquisition of a Tn5253-type integrative and conjugative element (ICE). “

Arsenate metabolism

Screen Shot 2014-07-09 at 10.27.05 PMInfluence of an arsenate-reducing and polycyclic aromatic hydrocarbons-degrading Pseudomonas isolate on growth and arsenic accumulation in Pteris vittata L. and removal of phenanthrene – Tiancai Feng – International Biodeterioration & Biodegradation

“In this study, the effect of bacterial inoculation on plant growth and arsenic uptake by Pteris vittata and phenanthrene dissipation was investigated hydroponically using an arsenate-reducing and PAH-degrading Pseudomonas isolate. “

Screen Shot 2014-07-09 at 10.28.17 PMBrevibacillus sp. KUMAs2, a bacterial isolate for possible bioremediation of arsenic in rhizosphere – Ivy Mallick – Ecotoxicology and Environmental Safety

“As resistant property in KUMAs2 was found to be plasmid-borne, which carried both As oxidizing and reducing genes. The strain could promote chilli plant growth under As contaminated soil environment by decreasing As accumulation in plant upon successful colonization in the rhizosphere, which suggests the possibility of using this isolate for successful bioremediation of As in the crop field.”

Infection and host response

Influenza Promotes Pneumococcal Growth during Coinfection by Providing Host Sialylated Substrates as a Nutrient Source – Steven J. Siegel – Cell Host & Microbe

“We find that prior influenza infection enhances pneumococcal colonization of the murine nasopharynx, which in turn promotes bacterial spread to the lungs. “

Microbes in the news

Bacteria Could Provide A Powerful New Way To Fight Fat And Depression – Lauren F. Friedman – Business Insider

“With increased understanding of these tiny organisms, we might just be able to coax them to do our bidding, giving us unprecedented control over human health.”

Screen Shot 2014-07-09 at 10.28.38 PMHospital elevator buttons coated with more bacteria than bathroom surfaces – Helen Branswell – Canadian Press

“You might want to use an elbow to push the elevator button the next time you are in a hospital.”

Screen Shot 2014-07-09 at 10.27.35 PMBelongs to: Elevator buttons as unrecognized sources of bacterial colonization in hospitals – Christopher E Kandel – Open Medicine

“Elevator buttons had a higher prevalence of colonization than toilet surfaces (61% v. 43%, p = 0.008).”

Science and Art

Screen Shot 2014-07-09 at 10.26.17 PMIntricate bacteria sculptures painstakingly hand-cut from paper – Chris Higgins – Wired

“Among the microbes Brown studied in preparation for the undertaking, which took four months overall (one to draw, two to hand cut and one to piece them together) are proteus bacteria, Escherichia coli, salmonella, hyphae, Spirillum volutans and Vibrio cholerae.”

Science, publishing and ethics

Not all plagiarism requires a retraction – Praveen Chaddah – Nature

“The ease with which large chunks of text can be digitally scanned and compared with what has previously been published has produced a new breed of academic watchdog”

Dr. Bik’s Picks

Screen Shot 2014-07-09 at 10.35.00 PMAncient arachnid brought ‘back to life’: Video recreates 410-million-year-old animal walking – Science Daily

“Scientists have recreated the walking gait of a 410-million-year-old arachnid, one of the first predators on land, based on fossil evidence. The scientists used the fossils — thin slices of rock showing the animal’s cross-section — to work out the range of motion in the limbs of this ancient, extinct early relative of the spiders.”

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Venus, the Chimera Cat: Venus the cat appears to have 2 faces – WSAV

“The left side of Venus’ face is black with a green eye, the right side of her face has orange tabby cat markings with a striking blue eye. “

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Human and other microbiomes, July 2

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Fungi in the mouth, microbiome in celiac disease, viruses in bats, fecal microbiota of penguins, and bacteria in water and concrete.

Human oral microbiome

Screen Shot 2014-07-02 at 10.35.22 PMMolecular Analysis of Fungal Populations in Patients with Oral Candidiasis Using Internal Transcribed Spacer Region – Shinsuke Ieda – PLOS ONE

“In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions.”

Human respiratory microbiome

Screen Shot 2014-07-02 at 10.35.47 PMLetter: No Clinical Association of Live Attenuated Influenza Virus with Nasal Carriage of Bacteria or Acute Otitis Media – Kathleen L. Coelingh, Robert B. Belshe – mBio

“We write this note to clarify the article “Live Attenuated Influenza Vaccine Enhances Colonization of Streptococcus pneumoniae and Staphylococcus aureus in Mice” by Mina et al. (1) in order that patients or clinicians not misinterpret the study’s clinical relevance.”

Human gut microbiome

Review: Screen Shot 2014-07-02 at 10.16.45 PMIntestinal Microbiota and Probiotics in Celiac Disease – Luís Fernando de Sousa Moraes – Clinical Microbiology Reviews

“This review aims to discuss the characteristics of the microbiota in CD subjects and the use of probiotics as a novel therapy for CD. “

Bat microbiome

Screen Shot 2014-07-02 at 10.36.24 PMBat Distribution Size or Shape as Determinant of Viral Richness in African Bats – Gaël D. Maganga – PLOS ONE

“We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. “

Bird microbiome

Screen Shot 2014-07-02 at 10.36.58 PMInfluence of Fasting during Moult on the Faecal Microbiota of Penguins – Meagan L. Dewar – PLOS ONE

“Therefore, the present study aimed to examine the microbial composition and diversity of the GI microbiota of fasting little (Eudyptula minor) and king penguins (Aptenodytes patagonicus) penguins during early and late moult.”

Invertebrate microbiome

Screen Shot 2014-07-02 at 10.37.27 PMBacterial Community Composition in the Gut Content and Ambient Sediment of Sea Cucumber Apostichopus japonicus Revealed by 16S rRNA Gene Pyrosequencing – Fei Gao – PLOS ONE

“The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. “

Plant microbiome

Screen Shot 2014-07-02 at 10.37.55 PMSelecting Microbial Strains from Pine Tree Resin: Biotechnological Applications from a Terpene World – Cristina Vilanova – PLOS ONE

“The taxonomic and functional diversity of the cultivated, resin-tolerant fraction of the whole microbiota were unveiled by high-throughput sequencing, which resulted in the detection of more than 40 bacterial genera among the terpene-degrading microorganisms, and a range of genes involved in the degradation of different terpene families.”

Water and concrete microbiology

Screen Shot 2014-07-02 at 10.38.23 PMCoupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species – Alexander J. Probst – PLOS ONE

“Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current.”

Screen Shot 2014-07-02 at 10.38.41 PMMicrobial Quality and Phylogenetic Diversity of Fresh Rainwater and Tropical Freshwater Reservoir – Rajni Kaushik – PLOS ONE

“The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. “

Screen Shot 2014-07-02 at 10.29.38 PMBacteria and concrete-a love-hate relationship – Embriette Hyde

“Sometimes bacteria appear to harm concrete, sometimes they appear to help it.”

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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 digest, June 3, 2014

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Dengue, immunology, arsenic, and The Picks.


Immunology

Review: Ontogeny of early life immunity – David J. Dowling, Ofer Levy – Trends in Immunology

“Here, we review novel mechanistic insights into early life immunity, with an emphasis on emerging models of human immune ontogeny”

Dengue

Time-varying, serotype-specific force of infection of dengue virus – Robert C. Reiner, Jr. – PNAS

“Using a bespoke method for a 12-y longitudinal dataset of serotype-specific dengue virus (DENV) infections, we estimated time-varying, serotype-specific FoIs for all four DENV serotypes. “

Correspondence: A “microRNA-like” small RNA expressed by Dengue virus? – Rebecca L. Skalsky – PNAS

Reply to Skalsky et al.: A microRNA-like small RNA from Dengue virus – Mazhar Hussain and Sassan Asgari – PNAS


More Microbiology

Review: Tropheryma whipplei and Whipple’s disease – Florence Fenollar, Jean-Christophe Lagier, Didier Raoult – Journal of Infection

“T. whipplei seems to be an opportunistic bacterium that causes chronic infections in susceptible patients with as yet unknown predisposing factors.”

Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus
Michael Worobey – PNAS

“We infer that the virus arose via reassortment between a preexisting human H1 IAV lineage and an avian virus”

Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses – Lauren Byrd-Leotis – PNAS

“Studies using novel “shotgun glycan microarray” technology identify, for the first time to our knowledge, the endogenous receptors for influenza viruses from a natural host, the pig.”

Counties Deploying Bacteria-Sniffing Dogs To Find Failing Septic Systems – Bellamy Pailthorp – PKLU.org

“Molly, a border collie trained by Environmental Canine Services, can sniff out human fecal coliform bacteria in water samples.”

Arsenic metabolism

Arsenic in the Multi-aquifer System of the Mekong Delta, Vietnam: Analysis of Large-Scale Spatial Trends and Controlling Factors – Laura E. Erban – Environmental Science & Technology

“We relate strong trends in the distribution of contamination among well samples to explanatory variables derived from 3D ancillary physicochemical data sets using logistic regression models.”

Monitoring Arsenic Contamination in Agricultural Soils with Reflectance Spectroscopy of Rice Plants – Tiezhu Shi – Environmental Science & Technology

“The prediction of soil As contents was achieved by partial least-squares regression (PLSR) using laboratory and field spectra of rice plants, as well as linear regression employing normalized difference spectral index (NDSI) calculated from fild spectra. “

Marine Mammals

Fossil record shows whales evolved from land to sea – Steve Luckstead – UnionBulletin

“Other mammals such as seals, sea lions and walrusess spend a good part of their lives in the ocean, but they are clearly tetrapods (four-legged). But whales don’t have any leg-like appendages. So what gives?”


Science and Art

Sculpting the apples of science – Helen Fields – PNAS

“Rath’s work is based on a visit to the US Department of Agriculture’s Plant Genetic Resources Unit (PGRU) in Geneva, New York. The PGRU grows thousands of apple varieties that might otherwise disappear from orchards.”

Dr. Bik’s Picks

Evidence of bird dropping masquerading by a spider to avoid predators – Min-Hui Liu – Nature Scientific Reports

” The orb-web spider Cyclosa ginnaga has a silver body and adds a white discoid-shaped silk decoration to its web. The size, shape and colour of C. ginnaga’s body resemble, when viewed by the human eye against its decoration, a bird dropping. “

Why Have Female Hurricanes Killed More People Than Male Ones? – Ed Yong – National Geographic

“Here’s a simple fact with an uncertain explanation: historically, hurricanes with female names have, on average, killed more people than those with male ones.”

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