Virology and Bioinformatics from Virology.ca
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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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Chimeric hemagglutinin influenza virus vaccine constructs elicit broadly-protective stalk-specific antibodies... J Virol. 2013

We report structural characterization of the first antibody identified to cross-neutralize multiple subtypes of influenza A viruses. The crystal structure of mouse antibody C179 bound to the pandemic 1957 H2N2 hemagglutinin (HA) reveals that it targets a similar epitope on the HA stem as the recently identified human broadly neutralizing antibodies (bnAbs). C179 also inhibits the low-pH conformational change of the HA, but uses a different angle of approach and both heavy and light chains.

  
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Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein

Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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PLOS Computational Biology: Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

PLOS Computational Biology: Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
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Ed Rybicki's comment, April 12, 2013 9:31 AM
Abstract, dudes, abstract!
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Bad Science Watch | Important Issues. Sound Science. Real Change.

Bad Science Watch | Important Issues. Sound Science. Real Change. | Virology and Bioinformatics from Virology.ca | Scoop.it
Bad Science Watch is an independent non-profit activist organization dedicated to improving the lives of Canadians by countering bad science.
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BMC Bioinformatics | Abstract | Clustering evolving proteins into homologous families

Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics.
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Role of human Toll-like receptors in naturally occurring influenza A infections.

CONCLUSIONS:

Our results suggest that TLRs play an important role in early, innate viral inhibition in naturally occurring influenza. Inflammatory cytokine responses are concomitantly induced. These findings support investigation of TLR targeting as a novel intervention approach for prophylaxis against influenza.

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Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period

Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period | Virology and Bioinformatics from Virology.ca | Scoop.it
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Ian M Mackay, PhD's curator insight, October 8, 2013 7:23 PM

Our publication on an Australian community cohort - all 3 species and many HRV types circulate in one place at one time.

HRV-Bs are under-represnetd - as usual.

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Protein maintains order in the nucleus

Protein maintains order in the nucleus | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers in Freiburg identify a protein responsible for the correct arrangement of the chromosome centromeres in the nucleus.
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Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family

The family Mimiviridae belongs to the large monophyletic group of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV; proposed order Megavirales) and encompasses giant viruses infecting amoeba and probably other unicellular eukaryotes.
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Hepatitis A virus discovered to cloak itself in membranes hijacked from infected cells

Hepatitis A virus discovered to cloak itself in membranes hijacked from infected cells | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses have historically been classified into one of two types – those with an outer lipid-containing envelope and those without an envelope.
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Ed Rybicki's curator insight, April 12, 2013 9:37 AM

...and hep A steals membranes from liver cells to circulate as an enveloped particle(s) in blood. This is a fascinating find, and doubtless will be followed by similar for other viruses.

 

The commentary has some speculation as to how vaccines work, if antibodies can't see the virus - but they forget the virus has to get INTO the host in the first place, and environmental forms are non-enveloped, AND that the vaccine may well elicit some degree of cell-mediated immunity, which would target infected cells displaying degraded protein on their surfaces via MHC I-type receptors.

Gaby's curator insight, October 20, 2014 7:20 PM

Una noticia que revolucionará a los virologos!

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An open letter to my dad on the occasion of his recent anti-vax Facebook postings

An open letter to my dad on the occasion of his recent anti-vax Facebook postings | Virology and Bioinformatics from Virology.ca | Scoop.it
Dear Pa, I know you care deeply about many issues, especially social justice.
Chris Upton + helpers's insight:

From  @aetiology   Tara Smith's Blog

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Pedro Fernandes's curator insight, April 4, 2013 3:31 AM

A very didactical letter about a serious problem: the propagation of "noise" in science, worsened by popularised news sharing causes a panic over false (falsified) results. This is a socuial problem that pushed o lot of people to stop vaccinating their children, a mistake that is causing child death, new surges of disease, etc.

 

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Getting Genetics Done: Comparing Sequence Classification Algorithms for Metagenomics

Getting Genetics Done: Comparing Sequence Classification Algorithms for Metagenomics | Virology and Bioinformatics from Virology.ca | Scoop.it

Metagenomics is the study of DNA collected from environmental samples (e.g., seawater, soil, acid mine drainage, the human gut, sputum, pus, etc.). While traditional microbial genomics typically means sequencing a pure cultured isolate, metagenomics involves taking a culture-free environmental sample and sequencing a single gene (e.g. the 16S rRNA gene), multiple marker genes, or shotgun sequencing everything in the sample in order to determine what's there.

A challenge in shotgun metagenomics analysis is the sequence classification problem: i.e., given a sequence, what's it's origin? I.e., did this sequence read come from E. coli or some other enteric bacteria? Note that sequence classification does not involve genome assembly - sequence classification is done on unassembled reads. If you could perfectly classify the origin of every sequence read in your sample, you would know exactly what organisms are in your environmental sample and how abundant each one is.

The solution to this problem isn't simply BLAST'ing every sequence read that comes off your HiSeq 2500 against NCBI nt/nr. The computational cost of this BLAST search would be many times more expensive than the sequencing itself. There are many algorithms for sequence classification. This paper examines a wide range of the available algorithms and software implementations for sequence classification as applied to metagenomic data.


Via Pedro Barbosa
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Dmitry Alexeev's curator insight, March 28, 2013 2:06 AM

it feels graet when all these methods converge on composition of microbiota in your data)_

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GigaScience | Full text | Crowdsourcing genomic analyses of ash and ash dieback: power to the people

Ash dieback is a devastating fungal disease of ash trees that has swept across Europe and recently reached the UK. This emergent pathogen has received little study in the past and its effect threatens to overwhelm the ash population. In response to this we have produced some initial genomics datasets and taken the unusual step of releasing them to the scientific community for analysis without first performing our own. In this manner we hope to ‘crowdsource’ analyses and bring the expertise of the community to bear on this problem as quickly as possible

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Unintentional transfer of vaccinia virus associated with smallpox vaccines: ACAM2000 (®) compared with Dryvax (®).

Background: Routine vaccination against smallpox (variola) ceased in the US in 1976. However, in 2002 limited coverage for military personnel and some healthcare workers was reinstituted. In March 2008, ACAM2000® replaced Dryvax® as the vaccine used in the United States against smallpox. Unintentional transfer of vaccinia virus from a vaccination site by autoinoculation or contact transmission, can have significant public health implications. We summarize unintentional virus transfer AEs associated with ACAM2000® since March 2008 and compare with Dryvax®.

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Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence | Virology and Bioinformatics from Virology.ca | Scoop.it

A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi.

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Bradford Condon's curator insight, April 11, 2013 11:51 AM

Expansion of transposable elements in pathogenic compared to non-pathogenic isolates of Pyrenophora tritici-repentis.

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Mutations in hemagglutinin that affect receptor binding and pH stability increase replication of a PR8 influenza virus with H5 HA in the upper respiratory tract of ferrets and may contribute to tra...

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Ed Rybicki's comment, April 12, 2013 9:31 AM
OK, I suppose the title is long enough to be an abstract for this one...B-)
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Structure of a classical broadly neutralizing stem antibody in complex with a pandemic H2 hemagglutinin

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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Cell - The Lipid Mediator Protectin D1 Inhibits Influenza Virus Replication and Improves Severe Influenza

Cell - The Lipid Mediator Protectin D1 Inhibits Influenza Virus Replication and Improves Severe Influenza | Virology and Bioinformatics from Virology.ca | Scoop.it
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Reassortment Complements Spontaneous Mutation in Influenza A Virus NP and M1 Genes To Accelerate Adaptation to a New Host

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Galaxy LIMS for next-generation sequencing

Galaxy LIMS for next-generation sequencing | Virology and Bioinformatics from Virology.ca | Scoop.it

Summary: We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation.

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Health leaders lay out their concerns about the new bird flu

Health leaders lay out their concerns about the new bird flu | Virology and Bioinformatics from Virology.ca | Scoop.it
Three sick people. That's all it took to make scientists who study influenza edge-of-seat nervous this week over a rapidly evolving public health situation in China.
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Vaccines and the Republican War on Science

Vaccines and the Republican War on Science | Virology and Bioinformatics from Virology.ca | Scoop.it
Ever since Chris Mooney’s Republican War on Science was published in 2005, folks have been looking for a way to argue that Democrats are just as bad.
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Using cryptography, scientists have invented a new technique to decrypt eukaryotic genomes

Using cryptography, scientists have invented a new technique to decrypt eukaryotic genomes | Virology and Bioinformatics from Virology.ca | Scoop.it

The main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. Generally, promoters have been classified in two major classes, namely TATA and CpG. Nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. Accordingly, a group of scientists has now tried to find some fundamental questions: Why certain genes have an overall predisposition for higher gene expression levels than others? What causes such a predisposition? Is there a structural relationship of these sequences in different tissues? Is there a strong phylogenetic relationship between promoters of closely related species?

 

In order to gain valuable insights into different promoter regions, they obtained a series of image-based patterns allowing the identificaion of 10 generic classes of promoters. A comprehensive analysis was undertaken for promoter sequences from Arabidopsis thaliana, Drosophila melanogaster, Homo sapiensand Oryza sativa, and a more extensive analysis of tissue-specific promoters in humans. The scientists observed a clear preference for these species to use certain classes of promoters for specific biological processes. Moreover, in humans, they found that different tissues use distinct classes of promoters, reflecting an emerging promoter network. Depending on the tissue type, comparisons made between these classes of promoters reveal a complementarity between their patterns whereas some other classes of promoters have been observed to occur in competition. Furthermore, they also noticed the existence of some transitional states between these classes of promoters that may explain certain evolutionary mechanisms, which suggest a possible predisposition for specific levels of gene expression and perhaps for a different number of factors responsible for triggering gene expression. They conclusions from all this are based on comprehensive data from three different databases and a new computer model whose core is using Kappa index of coincidence.


Via Dr. Stefan Gruenwald
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