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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Virus detector harnesses ring of light in 'whispering gallery mode'

Virus detector harnesses ring of light in 'whispering gallery mode' | Virology and Bioinformatics from Virology.ca | Scoop.it
By affixing nanoscale gold spheres onto a microscopic bead of glass, researchers have created a super-sensor that can detect even single samples of the smallest known viruses.

Via Tandy Agostini
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PLoS Pathogens: ADCC Develops Over Time during Persistent Infection with Live-Attenuated SIV and Is Associated with Complete Protection against SIVmac251 Challenge

PLoS Pathogens: ADCC Develops Over Time during Persistent Infection with Live-Attenuated SIV and Is Associated with Complete Protection against SIVmac251 Challenge | Virology and Bioinformatics from Virology.ca | Scoop.it

"Here we show that live-attenuated SIV induces progressive increases in ADCC over time, and that the development of these antibodies is dependent upon the persistent replication of the vaccine strain. In two different experiments, the animals immunized with live-attenuated SIV that remained uninfected after pathogenic SIV challenge had higher measures of ADCC than those that became infected. Our results suggest that antibodies contribute to protection by live-attenuated SIV, and that persistent stimulation of antibody responses may be essential for HIV-1 vaccines to induce high ADCC activity."

 

Shit HOT results, in that they demonstrate that - as some have said repeatedly over years - that neutralising Ab are NOT necessarily the Holy Grail, and that ADCC and other mechanisms are also really important.  Good Stuff...B-)

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The DNA Learning Center from Cold Spring Harbor Laboratories - 200 educational videos

The DNA Learning Center from Cold Spring Harbor Laboratories - 200 educational videos | Virology and Bioinformatics from Virology.ca | Scoop.it

The mission of Cold Spring Harbor Laboratory's DNA Learning Center is to prepare students and families to thrive in the genomic age.


Via Dr. Stefan Gruenwald
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Oncolytic virotherapy for ovarian cancer

Oncolytic virotherapy for ovarian cancer | Virology and Bioinformatics from Virology.ca | Scoop.it

In the past two decades, more than 20 viruses with selective tropism for tumor cells have been developed as oncolytic viruses (OVs) for treatments of a variety of malignancies. Of these viruses, eleven have been tested in human ovarian cancer models in preclinical studies. So far, nine phase I or II clinical trials have been conducted or initiated using four different types of OVs in patients with recurrent ovarian cancers.

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Advantage flu virus: Scientists discover one of the ways the influenza virus disarms host cells

Scientists have discovered one of the ways the influenza virus disarms our natural defense system. The virus decreases the production of key immune regulating proteins in human cells that help fight the invader.
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Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in biopython

Ongoing innovation in phylogenetics and evolutionary biology has been accompanied by a proliferation of software tools, data formats, analytical techniques and web servers.
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3D model of the Ebola virus

3D model of the Ebola virus | Virology and Bioinformatics from Virology.ca | Scoop.it

The Ebola virus and it’s close relative the Marburg virus are members of the Filoviridae family. These viruses are the causative agents of severe hemorrhagic fever, a disease with a fatality rate of up to 90%. The Ebola virus infects mainly the capillary endothelium and several types of immune cells. The symptoms of Ebola infection include maculopapular rash, petechiae, purpura, ecchymoses, dehydration and hematomas.

 

Since Ebola was first described in 1976, there have been several epidemics of this disease. Hundreds of people have died because of Ebola infections, mainly in Zaire, Sudan, Congo and Uganda. In addition, several fatalities have occurred because of accidents in laboratories working with the virus. Currently, a number of scientists claim that terrorists may use Ebola as a biological weapon.

 

In the 3D model presented in this study, Ebola-encoded structures are shown in maroon, and structures from human cells are shown in grey. The Ebola model is based on X-ray analysis, NMR spectroscopy, and general virology data published in the last two decades. Some protein structures were predicted using computational biology techniques, such as molecular modeling.


Via Dr. Stefan Gruenwald
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PNAS: Viroid RNA redirects host DNA ligase 1 to act as an RNA ligase

PNAS: Viroid RNA redirects host DNA ligase 1 to act as an RNA ligase | Virology and Bioinformatics from Virology.ca | Scoop.it

Viroids are a unique class of noncoding RNAs: composed of only a circular, single-stranded molecule of 246–401 nt, they manage to replicate, move, circumvent host defenses, and frequently induce disease in higher plants. Viroids replicate through an RNA-to-RNA rolling-circle mechanism consisting of transcription of oligomeric viroid RNA intermediates, cleavage to unit-length strands, and circularization. Though the host RNA polymerase II (redirected to accept RNA templates) mediates RNA synthesis and a type-III RNase presumably cleavage of Potato spindle tuber viroid (PSTVd) and closely related members of the family Pospiviroidae, the host enzyme catalyzing the final circularization step, has remained elusive. In this study we propose that PSTVd subverts host DNA ligase 1, converting it to an RNA ligase, for the final step. To support this hypothesis, we show that the tomato (Solanum lycopersicum L.) DNA ligase 1 specifically and efficiently catalyzes circularization of the genuine PSTVd monomeric linear replication intermediate opened at position G95–G96 and containing 5′-phosphomonoester and 3′-hydroxyl terminal groups. Moreover, we also show a decreased PSTVd accumulation and a reduced ratio of monomeric circular to total monomeric PSTVd forms in Nicotiana benthamiana Domin plants in which the endogenous DNA ligase 1 was silenced. Thus, in a remarkable example of parasitic strategy, viroids reprogram for their replication the template and substrate specificity of a DNA-dependent RNA polymerase and a DNA ligase to act as RNA-dependent RNA polymerase and RNA ligase, respectively.

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HHMI News: Viral Genome Springs into Action to Fight the Immune System

Scientists have found that the virus vaccinia, a member of the poxvirus family, increases the size of its genome when it confronts the immune system, thereby increasing the odds of a random mutation that will improve its survival.

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CDC - Seasonal Influenza (Flu) - More H3N2v Cases Reported

CDC - Seasonal Influenza (Flu) - More H3N2v Cases Reported | Virology and Bioinformatics from Virology.ca | Scoop.it

CDC Centers for Disease Control and Prevention Influenza Flu: More H3N2v Cases Reported, Still Linked to Pig Exposure.  The Center for Disease Control and Prevention continues to monitor the situation, and reports that 71 additional cases of H3N2v are being reported, bringing the total number of such infections since July 2012 in the United States to 224. There is so much interaction between people and pigs in county and state fair settings at this time of year, and the spread and severity of illness are the main factors of concern to the CDC.


Via Dr. Mary T. Johnson, Chris Upton + helpers
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Sci Rep-Plant viruses alter insect behavior to enhance their spread

Sci Rep-Plant viruses alter insect behavior to enhance their spread | Virology and Bioinformatics from Virology.ca | Scoop.it

Pathogens and parasites can induce changes in host or vector behavior that enhance their transmission. In plant systems, such effects are largely restricted to vectors, because they are mobile and may exhibit preferences dependent upon plant host infection status. Here we report the first evidence that acquisition of a plant virus directly alters host selection behavior by its insect vector. We show that the aphid Rhopalosiphum padi, after acquiring Barley yellow dwarf virus (BYDV) during in vitro feeding, prefers noninfected wheat plants, while noninfective aphids also fed in vitro prefer BYDV-infected plants. This behavioral change should promote pathogen spread since noninfective vector preference for infected plants will promote acquisition, while infective vector preference for noninfected hosts will promote transmission. We propose the “Vector Manipulation Hypothesis” to explain the evolution of strategies in plant pathogens to enhance their spread to new hosts. Our findings have implications for disease and vector management.

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Functional Exhaustion of CD4+ T Lymphocytes during Primary Cytomegalovirus Infection

Functional Exhaustion of CD4+ T Lymphocytes during Primary Cytomegalovirus Infection | Virology and Bioinformatics from Virology.ca | Scoop.it
Human CMV establishes lifelong persistence after primary infection. Chronic CMV infection is associated with intermittent viral reactivation inducing high frequencies of CD4+ T lymphocytes with potent antiviral and helper properties. Primary CMV infection is characterized by an intense viral replication lasting for several months. The impact of this prolonged exposure to high Ag loads on the functionality of CD4+ T cells remains incompletely understood.

Via Gilbert Faure au nom de l'ASSIM
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Association between the JC Polyomavirus Infection and Male Infertility - MicrobiologyBytes

Association between the JC Polyomavirus Infection and Male Infertility - MicrobiologyBytes | Virology and Bioinformatics from Virology.ca | Scoop.it
A higher prevalence of JC virus in the semen and urine of infertile men than in matched controls suggests the virus may be responsible for male infertility.
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PLoS Pathogens: Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing

PLoS Pathogens: Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing | Virology and Bioinformatics from Virology.ca | Scoop.it

Hepatitis C virus infects as many as 170 million people worldwide. Globally, there are seven major genotypes of HCV that differ by approximately 30% in nucleotide sequence. Importantly, the natural history of HCV infection is variable, ranging from spontaneous resolution to persistent viremia and chronic disease. Factors responsible for this variability in clinical outcome are unknown but likely involve a combination of viral and host determinants. To this end, a precise molecular identification of transmitted HCV genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of plasma viral RNA to identify transmitted viral genomes and their progeny in 17 subjects with acute infection. Numbers of transmitted viruses leading to productive clinical infection ranged from 1 to 37 or more (median = 4). Surprisingly, we found evidence of high multiplicity acute-to-acute HCV transmission in 3 of 17 subjects, which suggests that clinical transmission of HCV, like that of HIV-1, may be enhanced in early infection when virus titers are highest and neutralizing antibodies are absent. These results provide novel insight into HCV transmission and early virus diversification key to our understanding of virus natural history and response to drug selection and immune pressure.

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Tracing the genetic pathway from the first Eukaryotes to Homo sapiens

Tracing the genetic pathway from the first Eukaryotes to Homo sapiens | Virology and Bioinformatics from Virology.ca | Scoop.it

www.dhushara.com/book/unraveltree/unravel.htm

 

The Tree of Life, in biological terms, has come to be identified with the evolutionary tree of biological diversity. It is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher Eukaryotes, plants, animals and fungi, but Protista, Eubacteria, and Archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself.


Via Dr. Stefan Gruenwald
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BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome

BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome | Virology and Bioinformatics from Virology.ca | Scoop.it
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Vaccination with Adenovirus Serotypes 35, 26, and 48 Elicits Higher Levels of Innate Cytokine Responses than Adenovirus Serotype 5 in Rhesus Monkeys

Vaccination with Adenovirus Serotypes 35, 26, and 48 Elicits Higher Levels of Innate Cytokine Responses than Adenovirus Serotype 5 in Rhesus Monkeys | Virology and Bioinformatics from Virology.ca | Scoop.it

"These data demonstrate that Ad35, Ad26, and Ad48, which utilize CD46 as their primary cellular receptor, induce significantly greater innate cytokine responses than Ad5, which uses the coxsackievirus and adenovirus receptor (CAR). These differences in innate triggering result in markedly different immunologic milieus for the subsequent generation of adaptive immune responses by these vaccine vectors."

 

Important news for the vectored vaccine community in general, and for HIV vaccine in particular: Ad5 was the vehicle of choice; now it looks as though it shouldn't be.

 

Adenovirus graphic courtesy of Russell Kightley Media

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Pangaea and the Out-of-Africa Model of Varicella-Zoster Virus Evolution and Phylogeography

The goal of this minireview is to provide an overview of varicella-zoster virus (VZV) phylogenetics and phylogeography when placed in the broad context of geologic time.

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A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein

A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein | Virology and Bioinformatics from Virology.ca | Scoop.it

Interleukin 18 (IL18) is a cytokine that plays an important role in inflammation as well as host defense against microbes. Mammals encode a soluble inhibitor of IL18 termed IL18 binding protein (IL18BP) that modulates IL18 activity through a negative feedback mechanism. Many poxviruses encode homologous IL18BPs, which contribute to virulence.

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The Black Death is dead (thanks to evolution)

The Black Death is dead (thanks to evolution) | Virology and Bioinformatics from Virology.ca | Scoop.it

Centuries-old DNA reveals the source of the Black Death: a bacterial strain that is now apparently extinct. Evolution explains why.


Via Luca Baptista
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geneXplain platform | GeneXplain

geneXplain platform | GeneXplain | Virology and Bioinformatics from Virology.ca | Scoop.it
The geneXplain platform is an online toolbox and workflow management system for bioinformatics and systems biology. The individual modules, or Bricks, can be flexibly put together to workflows.

Via Sandrine Palcy
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How lethal is rabies virus?

How lethal is rabies virus? | Virology and Bioinformatics from Virology.ca | Scoop.it
New evidence from humans in the Peruvian Amazon suggests that rabies virus might be less lethal than previously believed.
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Genomic Sequencing of Darwin's Finches

Genomic Sequencing of Darwin's Finches | Virology and Bioinformatics from Virology.ca | Scoop.it
Charles Darwin had first eluded to the Galapagos finches in the second edition of the Journal of Researches, published in 1845, more than 20 years before the publication of The Origin of Species: “Seeing this gradation and ...

Via Dr Richard Badge
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Genetic roulette in a new world - Research - University of Cambridge

Genetic roulette in a new world - Research - University of Cambridge | Virology and Bioinformatics from Virology.ca | Scoop.it

Dr Robin Hesketh, Senior Lecturer in the Department of Biochemistry and author of Betrayed by Nature, explains how advances in inexpensive, rapid gene sequencing and expression analysis is revolutionising cancer research and the development of new treatments.


Via Pedro Fernandes
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JGV---Application of next-generation sequencing technologies in virology

JGV---Application of next-generation sequencing technologies in virology | Virology and Bioinformatics from Virology.ca | Scoop.it

The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples.

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