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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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PLOS ONE: Pandemic H1N1 Influenza Isolated from Free-Ranging Northern Elephant Seals in 2010 off the Central California Coast

PLOS ONE: Pandemic H1N1 Influenza Isolated from Free-Ranging Northern Elephant Seals in 2010 off the Central California Coast | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract

Interspecies transmission of influenza A is an important factor in the evolution and ecology of influenza viruses. Marine mammals are in contact with a number of influenza reservoirs, including aquatic birds and humans, and this may facilitate transmission among avian and mammalian hosts. Virus isolation, whole genome sequencing, and hemagluttination inhibition assay confirmed that exposure to pandemic H1N1 influenza virus occurred among free-ranging Northern Elephant Seals (Mirounga angustirostris) in 2010. Nasal swabs were collected from 42 adult female seals in April 2010, just after the animals had returned to the central California coast from their short post-breeding migration in the northeast Pacific.

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MicroMicrobe •  Microbial image of the month This is a great...

MicroMicrobe •  Microbial image of the month This is a great... | Virology and Bioinformatics from Virology.ca | Scoop.it
 Microbial image of the month


This is a great image of a biofilm growing on a micro-fibrous material. Biofilms are aggregates of bacteria that are coated with a ‘slimy’ substance consisting of polysaccharide, DNA and proteins.
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'MERS' Makes Its Debut in a Scientific Journal - ScienceInsider

'MERS' Makes Its Debut in a Scientific Journal - ScienceInsider | Virology and Bioinformatics from Virology.ca | Scoop.it

A group of coronavirus experts has published its proposal to name a new, deadly virus after the Middle East, the region where it originates. In a short paper published online today by the Journal of Virology, the Coronavirus Study Group (CSG), along with several other scientists, recommends calling the pathogen Middle East Respiratory Syndrome Coronavirus (MERS-Cov).

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Heterogenous nuclear ribonucleoprotein Q increases protein expression from HIV-1 Rev dependent transcripts.

Heterogenous nuclear ribonucleoproteins (hnRNPs) control many processes of the gene expression machinery including mRNA transcription, splicing, export, stability and translation.
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Review: Influenza virus in pigs - Molecular Immunology

Review: Influenza virus in pigs - Molecular Immunology | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza virus disease still remains one of the major threats to human health, involving a wide range of animal species and pigs play an important role in influenza ecology. Pigs were labeled as “mixing vessels” since they are susceptible to infection with avian, human and swine influenza viruses and genetic reassortment between these viruses can occur. After the H1N1 influenza pandemic of 2009 with a swine origin virus, the most recent research in “influenzology” is directed at improving knowledge of porcine influenza virus infection. This tendency is probably due to the fact that domestic pigs are closely related to humans and represent an excellent animal model to study various microbial infectious diseases. In spite of the role of the pig in influenza virus ecology, swine immune responses against influenza viruses are not fully understood. Considering these premises, the aim of this review is to focus on the in vitro studies performed with porcine cells and influenza virus and on the immune responses of pigs against human, avian and swine influenza viruses in vivo. The increased acceptance of pigs as suitable and valuable models in the scientific community may stimulate the development of new tools to assess porcine immune responses, paving the way for their consideration as the future “gold standard” large-animal model in immunology.

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PLOS Pathogens: Mutualistic Polydnaviruses Share Essential Replication Gene Functions with Pathogenic Ancestors

PLOS Pathogens: Mutualistic Polydnaviruses Share Essential Replication Gene Functions with Pathogenic Ancestors | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract

"Viruses are usually thought to form parasitic associations with hosts, but all members of the family Polydnaviridae are obligate mutualists of insects called parasitoid wasps. Phylogenetic data founded on sequence comparisons of viral genes indicate that polydnaviruses in the genus Bracovirus (BV) are closely related to pathogenic nudiviruses and baculoviruses. However, pronounced differences in the biology of BVs and baculoviruses together with high divergence of many shared genes make it unclear whether BV homologs still retain baculovirus-like functions..."

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Human monoclonal ScFv that bind to different functional domains of M2 and inhibit H5N1 influenza virus replication

Novel effective anti-influenza agent that tolerates influenza virus antigenic variation is needed.
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BMC Bioinformatics | Abstract | Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

BMC Bioinformatics | Abstract | Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great
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The Comprehensive Antibiotic Resistance Database

The Comprehensive Antibiotic Resistance Database | Virology and Bioinformatics from Virology.ca | Scoop.it

Comprehensive Antibiotic Research Database (CARD,arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture and the environment.

 

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Adherens junction protein nectin-4 is the epithelial ... [Nature. 2011] - PubMed - NCBI

Adherens junction protein nectin-4 is the epithelial ... [Nature. 2011] - PubMed - NCBI | Virology and Bioinformatics from Virology.ca | Scoop.it
PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Immunological assessment of influenza vaccines and immune correlates of protection. Expert Rev Vaccines. 2013

Influenza vaccines remain the primary public health tool in reducing the ever-present burden of influenza and its complications. In seeking more immunogenic, more effective and more broadly cross-protective influenza vaccines, the landscape of influenza vaccines is rapidly expanding, both in near-term advances and next-generation vaccine design. Although the first influenza vaccines were licensed over 60 years ago, the hemagglutination-inhibition antibody titer is currently the only universally accepted immune correlate of protection against influenza. However, hemagglutination-inhibition titers appear to be less effective at predicting protection in populations at high risk for severe influenza disease; older adults, young children and those with certain medical conditions. The lack of knowledge and validated methods to measure alternate immune markers of protection against influenza remain a substantial barrier to the development of more immunogenic, broadly cross-reactive and effective influenza vaccines. Here, the authors review the knowledge of immune effectors of protection against influenza and discuss assessment methods for a broader range of immunological parameters that could be considered in the evaluation of traditional or new-generation influenza vaccines.

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PLOS Pathogens: A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

PLOS Pathogens: A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems | Virology and Bioinformatics from Virology.ca | Scoop.it

Plants and pathogens evolve in response to each other. This co-evolutionary arms race is fueled by genetic variation underlying the recognition of pathogen proteins by the host and the defeat of host defenses by the pathogen. Together with new mutations, genetic diversity in populations of both the host and pathogen represent a pool of possible variants to maintain adaptation via natural selection.

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Amid Heightened Concerns, New Name for Novel Coronavirus Emerges

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Ed Rybicki's comment, May 10, 2013 1:05 PM
ABSTRACT!! ANd naming it after the Middle East will go down well...B-)
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Human monoclonal ScFv that bind to different functional domains of M2 and inhibit H5N1 influenza virus replication Virol J. 2013

BACKGROUND:

Novel effective anti-influenza agent that tolerates influenza virus antigenic variation is needed. Highly conserved influenza virus M2 protein has multiple pivotal functions including ion channel activity for vRNP uncoating, anti-autophagy and virus assembly, morphogenesis and release. Thus, M2 is an attractive target of anti-influenza agents including small molecular drugs and specific antibodies.

METHODS:

Fully human monoclonal single chain antibodies (HuScFv) specific to recombinant and native M2 proteins of A/H5N1 virus were produced from huscfv-phagemid transformed E. coli clones selected from a HuScFv phage display library using recombinant M2 of clade 1 A/H5N1 as panning antigen. The HuScFv were tested for their ability to inhibit replication of A/H5N1 of both homologous and heterologous clades. M2 domains bound by HuScFv of individual E. coli clones were identified by phage mimotope searching and computerized molecular docking.

RESULTS:

HuScFv derived from four huscfv-phagemid transformed E. coli clones (no. 2, 19, 23 and 27) showed different amino acid sequences particularly at the CDRs. Cells infected with A/H5N1 influenza viruses (both adamantane sensitive and resistant) that had been exposed to the HuScFv had reduced virus release and intracellular virus. Phage peptide mimotope search and multiple alignments revealed that conformational epitopes of HuScFv2 located at the residues important for ion channel activity, anti-autophagy and M1 binding; epitopic residues of HuScFv19 located at the M2 amphipathic helix and cytoplasmic tail important for anti-autophagy, virus assembly, morphogenesis and release; epitope of HuScFv23 involved residues important for the M2 activities similar to HuScFv2 and also amphipathic helix residues for viral budding and release while HuScFv27 epitope spanned ectodomain, ion channel and anti-autophagy residues. Results of computerized homology modelling and molecular docking conformed to the epitope identification by phages.

CONCLUSIONS:

HuScFv that bound to highly conserved epitopes across influenza A subtypes and human pathogenic H5N1clades located on different functional domains of M2 were produced. The HuScFv reduced viral release and intracellular virus of infected cells. While the molecular mechanisms of the HuScFv await experimental validation, the small human antibody fragments have high potential for developing further as a safe, novel and mutation tolerable anti-influenza agent especially against drug resistant variants.

 
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PLOS ONE: Malaria Infected Mosquitoes Express Enhanced Attraction to Human Odor

PLOS ONE: Malaria Infected Mosquitoes Express Enhanced Attraction to Human Odor | Virology and Bioinformatics from Virology.ca | Scoop.it

Abstract

There is much evidence that some pathogens manipulate the behaviour of their mosquito hosts to enhance pathogen transmission. However, it is unknown whether this phenomenon exists in the interaction of Anopheles gambiae sensu stricto with the malaria parasite, Plasmodium falciparum - one of the most important interactions in the context of humanity, with malaria causing over 200 million human cases and over 770 thousand deaths each year. Here we demonstrate, for the first time, that infection with P. falciparum causes alterations in behavioural responses to host-derived olfactory stimuli in host-seeking female An. gambiae s.s. mosquitoes.

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Cloning produces human embryonic stem cells | Genes & Cells | Science News

Cloning produces human embryonic stem cells | Genes & Cells | Science News | Virology and Bioinformatics from Virology.ca | Scoop.it

For the first time, scientists have created human embryonic stem cells by transferring the nucleus of a mature cell into an egg. The cloning technique could nudge the dream of personalized medicine closer to reality, researchers suggest May 15 in Cell.

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Immunization with Biodegradable Nanoparticles Efficiently Induces Cellular Immunity and Protects against Influenza Virus Infection

Immunization with Biodegradable Nanoparticles Efficiently Induces Cellular Immunity and Protects against Influenza Virus Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

The ability of vaccines to induce T cell responses is crucial for preventing diseases caused by viruses or bacteria. Nanoparticles (NPs) are considered an efficient tool for inducing potent immune responses. In this study, we describe a novel vaccination approach with biodegradable calcium phosphate (CaP) NPs that serve as carrier of immunoactive TLR9 ligand (CpG) combined with a viral Ag from the influenza A virus hemagglutinin. Functionalized CaP NPs were efficiently taken up by dendritic cells in vivo and elicited a potent T cell–mediated immune response in immunized mice with high numbers of IFN-γ–producing CD4+ and CD8+ effector T cells. Most importantly, both i.p. and intranasal immunization with these NPs offered protection in a mouse model of influenza virus infection. This study demonstrates the great potential of CaP NPs as a novel vaccination tool that offers substantial flexibility for several infection models.

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Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics

During the 2009 H1N1 influenza pandemic, vaccines for the virus became available in large quantities only after human infections peaked. To accelerate vaccine availability for future pandemics, we developed a synthetic approach that very rapidly generated vaccine viruses from sequence data. Beginning with hemagglutinin (HA) and neuraminidase (NA) gene sequences, we combined an enzymatic, cell-free gene assembly technique with enzymatic error correction to allow rapid, accurate gene synthesis. We then used these synthetic HA and NA genes to transfect Madin-Darby canine kidney (MDCK) cells that were qualified for vaccine manufacture with viral RNA expression constructs encoding HA and NA and plasmid DNAs encoding viral backbone genes. Viruses for use in vaccines were rescued from these MDCK cells. We performed this rescue with improved vaccine virus backbones, increasing the yield of the essential vaccine antigen, HA. Generation of synthetic vaccine seeds, together with more efficient vaccine release assays, would accelerate responses to influenza pandemics through a system of instantaneous electronic data exchange followed by real-time, geographically dispersed vaccine production.

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Ed Rybicki's comment, May 16, 2013 6:11 AM
...using mammalian cells. With all of the cost disadvantages that entails.
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PLOS ONE: Potent Inhibition of Hendra Virus Infection via RNA Interference and Poly I:C Immune Activation

PLOS ONE: Potent Inhibition of Hendra Virus Infection via RNA Interference and Poly I:C Immune Activation | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract

"Hendra virus (HeV) is a highly pathogenic zoonotic paramyxovirus that causes fatal disease in a wide range of species, including humans. HeV was first described in Australia in 1994, and has continued to re-emerge with increasing frequency. HeV is of significant concern to human health due to its high mortality rate, increasing emergence, absence of vaccines and limited post exposure therapies..."

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PLOS Computational Biology: Selection for Replicases in Protocells

PLOS Computational Biology: Selection for Replicases in Protocells | Virology and Bioinformatics from Virology.ca | Scoop.it

The origin of life must have required a series of transitions building new levels of molecular interaction. However, a tension often exists between the fitness of an individual sequence and the fitness of the collective. This tension would be important for the earliest replicase enzymes (i.e., replicases), which would help other individuals replicate without helping themselves directly. The proposed solution to this problem is to essentially create small groups of interactors, either by compartmentation or a lattice-like structure. Selection among individuals in the group favors parasites, but selection at the level of the group favors groups with more replicases, thus allowing ‘altruistic’ replicases to survive.

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PLOS ONE: Protein Clustering and RNA Phylogenetic Reconstruction of the Influenza a Virus NS1 Protein Allow an Update in Classification and Identification of Motif Conservation

The non-structural protein 1 (NS1) of influenza A virus (IAV), coded by its third most diverse gene, interacts with multiple molecules within infected cells. NS1 is involved in host immune response regulation and is a potential contributor to the virus host range. Early phylogenetic analyses using 50 sequences led to the classification of NS1 gene variants into groups (alleles) A and B. We reanalyzed NS1 diversity using 14,716 complete NS IAV sequences, downloaded from public databases, without host bias. Removal of sequence redundancy and further structured clustering at 96.8% amino acid similarity produced 415 clusters that enhanced our capability to detect distinct subgroups and lineages, which were assigned a numerical nomenclature. Maximum likelihood phylogenetic reconstruction using RNA sequences indicated the previously identified deep branching separating group A from group B, with five distinct subgroups within A as well as two and five lineages within the A4 and A5 subgroups, respectively. Our classification model proposes that sequence patterns in thirteen amino acid positions are sufficient to fit >99.9% of all currently available NS1 sequences into the A subgroups/lineages or the B group. This classification reduces host and virus bias through the prioritization of NS1 RNA phylogenetics over host or virus phenetics. We found significant sequence conservation within the subgroups and lineages with characteristic patterns of functional motifs, such as the differential binding of CPSF30 and crk/crkL or the availability of a C-terminal PDZ-binding motif. To understand selection pressures and evolution acting on NS1, it is necessary to organize the available data. This updated classification may help to clarify and organize the study of NS1 interactions and pathogenic differences and allow the drawing of further functional inferences on sequences in each group, subgroup and lineage rather than on a strain-by-strain basis.

  
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Studying a poxvirus gene capture mode through recombination and reactivation

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The restriction factors of human immunodeficienc... [J Biol Chem. 2012] - PubMed - NCBI

PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity

Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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Ahead of Print - Novel Poxvirus in Big Brown Bats, Northwestern United States - Vol. 19 No. 6 - June 2013 - Emerging Infectious Disease journal - CDC

Ahead of Print - Novel Poxvirus in Big Brown Bats, Northwestern United States - Vol. 19 No. 6 - June 2013 - Emerging Infectious Disease journal - CDC | Virology and Bioinformatics from Virology.ca | Scoop.it
A wildlife hospital and rehabilitation center in northwestern United States received several big brown bats with necrosuppurative osteomyelitis in multiple joints. Wing and joint tissues were positive by PCR for poxvirus.
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