Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Scooped by Alice Gibbons
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Supercomputing for the parallelization of whole genome analysis

Supercomputing for the parallelization of whole genome analysis | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract

Motivation: The declining cost of generating DNA sequence is promoting an increase in whole genome sequencing, especially as applied to the human genome. Whole genome analysis requires the alignment and comparison of raw sequence data, and results in a computational bottleneck because of limited ability to analyze multiple genomes simultaneously.

Results: We now adapted a Cray XE6 supercomputer to achieve the parallelization required for concurrent multiple genome analysis. This approach not only markedly speeds computational time but also results in increased usable sequence per genome. Relying on publically available software, the Cray XE6 has the capacity to align and call variants on 240 whole genomes in approximately 50 hours. Multisample variant calling is also accelerated.

Availability and Implementation: The MegaSeq workflow is designed to harness the size and memory of the Cray XE6, housed at Argonne National Laboratory, for whole genome analysis in a platform designed to better match current and emerging sequencing volume.

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Scooped by Ian M Mackay, PhD
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How much compute power do you need for next-gen sequencing?

Chris Upton + helpers's insight:

During our next-gen course, a "student" (really a professor from Australia ;) asked me if I could provide some guidance on what computational infrastructure was necessary to handle next-gen sequencing data. While we used Amazon Web Services during the course, she was interested in finding out if they could use their local HPC, or some other dedicated compute center, to process their data.

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Suggested by Sam Hibbitts
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Clean cut genetics

Clean cut genetics | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Wellcome Trust-funded researchers are helping to show how new ‘genome editing’ techniques could be used to transform the future of genetics research. Reading sequences of genetic code has become fa...
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Scooped by C_Fleis
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Popular disinfectants do not kill HPV | Penn State University

Commonly used disinfectants do not kill human papillomavirus (HPV) that makes possible non-sexual transmission of the virus, thus creating a need for hospital policy changes, according to researchers from Penn State College of Medicine and Brigham Young University.
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Molecular detection of human rhinoviruses in respiratory samples: a comparison of Taqman probe-, SYBR green I- and BOXTO-based real-time PCR assays

Human Rhinoviruses (HRV) are major causative agents of acute respiratory tract infections in all age group and important contributing factors of childhood morbidity and mortality. Clinical presentation is poorly specific and the great antigenic and genetic variability of HRVs renders the biological diagnosis complex. Here, we have evaluated several molecular diagnostic protocols, including Taqman probe-based and intercalating agent-based RT-PCR assays.
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Scooped by Ed Rybicki
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A synchronized global sweep of the internal genes of modern avian influenza virus : Nature : Nature Publishing Group

A synchronized global sweep of the internal genes of modern avian influenza virus : Nature : Nature Publishing Group | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Zoonotic infectious diseases such as influenza continue to pose a grave threat to human health. However, the factors that mediate the emergence of RNA viruses such as influenza[thinsp]A virus (IAV) are still incompletely understood. Phylogenetic inference is crucial to reconstructing the origins and tracing the flow of IAV within and between hosts. Here we show that explicitly allowing IAV host lineages to have independent rates of molecular evolution is necessary for reliable phylogenetic inference of IAV and that methods that do not do so, including /`relaxed/' molecular clock models, can be positively misleading. A phylogenomic analysis using a host-specific local clock model recovers extremely consistent evolutionary histories across all genomic segments and demonstrates that the equine H7N7 lineage is a sister clade to strains from birds[mdash]as well as those from humans, swine and the equine H3N8 lineage[mdash]sharing an ancestor with them in the mid to late 1800s. Moreover, major western and eastern hemisphere avian influenza lineages inferred for each gene coalesce in the late 1800s. On the basis of these phylogenies and the synchrony of these key nodes, we infer that the internal genes of avian influenza virus (AIV) underwent a global selective sweep beginning in the late 1800s, a process that continued throughout the twentieth century and up to the present. The resulting western hemispheric AIV lineage subsequently contributed most of the genomic segments to the 1918 pandemic virus and, independently, the 1963 equine H3N8 panzootic lineage. This approach provides a clear resolution of evolutionary patterns and processes in IAV, including the flow of viral genes and genomes within and between host lineages.
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Scooped by Chris Upton + helpers
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Venn Diagrams Simplified

Venn Diagrams Simplified | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Not a week goes by without me having to compare multiple lists to evaluate overlap. Re-analyzing any data and comparing that with previously computed data, comparing results from multiple tools or ...
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Rescooped by Kenzibit from Host Cell & Pathogen Interactions
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CRTC2 enhances HBV transcription and replication by inducing PGC1alpha expression

Hepatitis B virus (HBV) transcription and replication are essentially restricted to hepatocytes. Based on the HBV enhancer and promoter complex that links hepatic glucose metabolism to its transcription and replication, HBV adopts a regulatory system that is unique to the hepatic gluconeogenic genes. CRTC2, the CREB-regulated transcription coactivator 2, is a critical switch modulating the gluconeogenic program in response to both hormonal and intracellular signals. However, the relationship between CRTC2 and HBV transcription and replication remains unclear.
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Scooped by Torben Barsballe
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Transmission-Blocking Antibodies against Mosquito C-Type Lectins for Dengue Prevention

Transmission-Blocking Antibodies against Mosquito C-Type Lectins for Dengue Prevention | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

 

C-type lectins are a family of proteins with carbohydrate-binding activity. Several C-type lectins in mammals or arthropods are employed as receptors or attachment factors to facilitate flavivirus invasion. We previously identified a C-type lectin in Aedes aegypti, designated as mosquito galactose specific C-type lectin-1 (mosGCTL-1), facilitating the attachment of West Nile virus (WNV) on the cell membrane. Here, we first identified that 9 A. aegypti mosGCTL genes were key susceptibility factors facilitating DENV-2 infection, of which mosGCTL-3 exhibited the most significant effect. We found that mosGCTL-3 was induced in mosquito tissues with DENV-2 infection, and that the protein interacted with DENV-2 surface envelop (E) protein and virions in vitro and in vivo. In addition, the other identified mosGCTLs interacted with the DENV-2 E protein, indicating that DENV may employ multiple mosGCTLs as ligands to promote the infection of vectors. The vectorial susceptibility factors that facilitate pathogen invasion may potentially be explored as a target to disrupt the acquisition of microbes from the vertebrate host. Indeed, membrane blood feeding of antisera against mosGCTLs dramatically reduced mosquito infective ratio. Hence, the immunization against mosGCTLs is a feasible approach for preventing dengue infection. Our study provides a future avenue for developing a transmission-blocking vaccine that interrupts the life cycle of dengue virus and reduces disease burden.

 

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Scooped by Chris Upton + helpers
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The state of modern evolutionary theory may not be what you think it is

The state of modern evolutionary theory may not be what you think it is | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
I was rather surprised yesterday to see so much negative reaction to my statement that there’s more to evolution than selection, and that random, not selective, changes dominate our history. It was in the context of what should be taught in our public schools, and I almost bought the line that we can only teach…
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Long Distance Signals Protect Brain from Viral Infections

Abstract:

WASHINGTON, DC – February 10, 2014 – The brain contains a defense system that prevents at least two unrelated viruses—and possibly many more—from invading the brain at large. The research is published online ahead of print in the Journal of Virology.
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Scooped by Chris Upton + helpers
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Scientific method: Statistical errors

Scientific method: Statistical errors | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume.
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13 people die of flu in two weeks: CDC | Society | FOCUS TAIWAN - CNA ENGLISH NEWS

Taipei, Feb. 11 (CNA) Taiwan reported 256 new flu cases within the last two weeks, including H3N2, H1N1 and type B strains, resulting in 13 fatalities, the Centers for Disease Control (CDC) said Tuesday.
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Scooped by Chris Upton + helpers
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Virology Journal | Abstract | Detection and genetic characterization of Seoul Virus from commensal brown rats in France

Hantaviruses are single-stranded RNA viruses, which are transmitted to humans primarily via inhalation of aerosolised virus in contaminated rodent urine and faeces. Whilst infected reservoir hosts are asymptomatic, human infections can lead to two clinical manifestations, haemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), with varying degrees of clinical severity. The incidence of rodent and human cases of Seoul virus (SEOV) in Europe has been considered to be low, and speculated to be driven by the sporadic introduction of infected brown rats (Rattus norvegicus) via ports.
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Rescooped by Ian M Mackay, PhD from Tools and tips for scientific tinkers and tailors
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BioCode's Notes: In the ERA of science communication, Why you need Twitter, Professional Blog and ImpactStory?

BioCode's Notes: In the ERA of science communication, Why you need Twitter, Professional Blog and ImpactStory? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Where is the information? Where are the scientifically relevant results? Where are the good ideas? Are these things (only) in journals?

Via Mel Melendrez-Vallard
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Mel Melendrez-Vallard's curator insight, February 19, 2014 2:16 PM

good blog on the importance of social networking in science

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The Untranslated Regions of Classic Swine Fever Virus RNA Trigger Apoptosis

Abstract

"Classical swine fever virus (CSFV) causes a broad range of disease in pigs, from acute symptoms including high fever and hemorrhages, to chronic disease or unapparent infection, depending on the virus strain. CSFV belongs to the genus Pestivirus of the family Flaviviridae. It carries a single-stranded positive-sense RNA genome. An internal ribosomal entry site (IRES) in the 5′ untranslated region (UTR) drives the translation of a single open reading frame encoding a 3898 amino acid long polypeptide chain. The open reading frame is followed by a 3′ UTR comprising four highly structured stem-loops. In the present study, a synthetic RNA composed of the 5′ and 3′ UTRs of the CSFV genome devoid of any viral coding sequence and separated by a luciferase gene cassette (designated 5′UTR-Luc-3′UTR) triggered apoptotic cell death as early as 4 h post-transfection."

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Rescooped by Chris Upton + helpers from Genomics and metagenomics of microbes
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Genomics and the origin of species : Nature Reviews Genetics

Genomics and the origin of species : Nature Reviews Genetics | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.


Via Bradford Condon
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Professors, we need you to do more! | Doing Good Science, Scientific American Blog Network

Professors, we need you to do more! | Doing Good Science, Scientific American Blog Network | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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On the scalability of statistical procedures: why the p-value bashers just don’t get it. Simply Statistics

On the scalability of statistical procedures: why the p-value bashers just don’t get it.   Simply Statistics | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The problem is not p-values it is a fundamental shortage of data analytic skill.
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Bacteriophage Therapy – an Alternative to Antibiotics? | microBEnet: The microbiology of the Built Environment network.

Bacteriophage Therapy – an Alternative to Antibiotics? | microBEnet: The microbiology of the Built Environment network. | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Microbiology of the Built Environment - Site for the MicroBEnet project

Via Mel Melendrez-Vallard
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Scooped by Chris Upton + helpers
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CD28 and CD3 have complementary roles in T-cell traction forces

CD28 and CD3 have complementary roles in T-cell traction forces | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Cells have the remarkable ability to sense the mechanical properties of the extracellular environment. This has been developed primarily in the context of cell interaction with extracellular matrix through integrins, but recent studies showed that T cells exhibit mechanosensing through CD3 and CD28, nonintegrin receptors that provide activation and costimulatory signals. This report demonstrates that T cells generate significant forces through the T-cell receptor (TCR) and CD28, and delineates the contributions of each in force generation. Moreover, the distribution of force generation and local assembly of active signaling intermediates suggest similarities between TCR- and integrin-based connections between the cell and substrate.

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Scooped by Torben Barsballe
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Radioactive tracers map spread of HIV analogue

Radioactive tracers map spread of HIV analogue | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Scientists have imaged an analogue of HIV as it spread through the bodies of live macaque monkeys using radioactive markers and routine radiology techniques. The researchers hope to use the method to follow lurking human infections that could otherwise evade detection.

 

Francois Villinger, a virologist at Emory University School of Medicine in Atlanta, Georgia, and his team worked with rhesus macaques (Macaca mulatta) that had been infected with simian immunodeficiency virus (SIV), the non-human-primate equivalent of HIV, for between two and six years.

 

The scientists tagged SIV antibodies, which bind to the outer envelope of the virus, with copper-64, a radioactive isotope used in experimental radiotherapy against cancer. The isotopes emit signals that can be captured using scanning techniques called positron-emission tomography (PET) and computed tomography (CT) — both widely used in modern hospitals.

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Virology Journal | Abstract | Genome characterization of Long Island tick rhabdovirus, a new virus identified in Amblyomma americanum ticks

Abstract:

Ticks are implicated as hosts to a wide range of animal and human pathogens. The full range of microbes harbored by ticks has not yet been fully explored.
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Mind-controlling virus forces parasitic wasp to put all its eggs in one basket : Not Exactly Rocket Science

Mind-controlling virus forces parasitic wasp to put all its eggs in one basket : Not Exactly Rocket Science | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Julia Paoli's insight:

so cool!

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Rescooped by Bradford Condon from Genomics and metagenomics of microbes
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Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

This special issue ofInternational Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

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