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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
Nicolas Palopoli's insight:

Besides the interesting recall of the Intelligent Systems for Molecular Biology (ISMB) annual conferences on computational biology, it offers a nice insight into current state-of-the-art methodologies and upcoming trends in the discipline.

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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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It's a group effort - the curators:

It's a group effort - the curators: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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40 reasons why you should blog about your research

40 reasons why you should blog about your research | Virology and Bioinformatics from Virology.ca | Scoop.it
It helps you become more clear about your ideas. It gives you practice at presenting your ideas for a non-specialist audience. It increases your visibility within academia. It increases your visibi...
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Performance of the Xpert HPV assay in women attending for cervical screening

Performance of the Xpert HPV assay in women attending for cervical screening | Virology and Bioinformatics from Virology.ca | Scoop.it

This is the first study to report on the performance of the Xpert HPV Assay in a screening population.

 

Xpert HPV Assay׳s performance in detecting HPV is comparable to two clinically validated HPV tests.

 

Xpert HPV Assay showed a relative sensitivity of 98.73% for CIN 2 or higher and 100% for CIN3 or higher.

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Deep sequencing of HPV16 genomes

Deep sequencing of HPV16 genomes | Virology and Bioinformatics from Virology.ca | Scoop.it

Abstract

For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current “gold standard” of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%.

Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3–222, P=0.002), and the sensitive detection of variant lineage coinfections. This method represents an innovative high-throughput, ultra-deep coverage technique for HPV genomic sequencing, which, in turn, enables the investigation of the role of genetic variation in HPV epidemiology and carcinogenesis.

  

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An Enhanced Synthetic Multiclade DNA Prime Induces Improved Cross-Clade-Reactive Functional Antibodies when Combined with an Adjuvanted Protein Boost in Nonhuman Primates

The search for an efficacious human immunodeficiency virus type 1 (HIV-1) vaccine remains a pressing need. The moderate success of the RV144 Thai clinical vaccine trial suggested that vaccine-induced HIV-1-specific antibodies can reduce the risk of HIV-1 infection. We have made several improvements to the DNA platform and have previously shown that improved DNA vaccines alone are capable of inducing both binding and neutralizing antibodies in small-animal models. In this study, we explored how an improved DNA prime and recombinant protein boost would impact HIV-specific vaccine immunogenicity in rhesus macaques (RhM). After DNA immunization with either a single HIV Env consensus sequence or multiple constructs expressing HIV subtype-specific Env consensus sequences, we detected both CD4+ and CD8+ T-cell responses to all vaccine immunogens. These T-cell responses were further increased after protein boosting to levels exceeding those of DNA-only or protein-only immunization. In addition, we observed antibodies that exhibited robust cross-clade binding and neutralizing and antibody-dependent cellular cytotoxicity (ADCC) activity after immunization with the DNA prime-protein boost regimen, with the multiple-Env formulation inducing a more robust and broader response than the single-Env formulation. The magnitude and functionality of these responses emphasize the strong priming effect improved DNA immunogens can induce, which are further expanded upon protein boost. These results support further study of an improved synthetic DNA prime together with a protein boost for enhancing anti-HIV immune responses.

 
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You have to get to the abstract to find out it's for HIV...B-)

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Alfalfa Leaf Curl Virus: an Aphid-Transmitted Geminivirus

The family Geminiviridae comprises seven genera differentiated by genome organization, sequence similarity, and insect vector. Capulavirus, an eighth genus, has been proposed to accommodate two newly discovered highly divergent geminiviruses that presently have no known vector. Alfalfa leaf curl virus, identified here as a third capulavirus, is shown to be transmitted by Aphis craccivora. This is the first report of an aphid-transmitted geminivirus.

 
Ed Rybicki's insight:

My babies...B-) Refers both to the viruses - I helped name all of the original genera and the family - and two of the authors.

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Salmon Gill Poxvirus, the Deepest Representative of the Chordopoxvirinae

Poxviruses are large DNA viruses of vertebrates and insects causing disease in many animal species, including reptiles, birds, and mammals. Although poxvirus-like particles were detected in diseased farmed koi carp, ayu, and Atlantic salmon, their genetic relationships to poxviruses were not established. Here, we provide the first genome sequence of a fish poxvirus, which was isolated from farmed Atlantic salmon. In the present study, we used quantitative PCR and immunohistochemistry to determine aspects of salmon gill poxvirus disease, which are described here. The gill was the main target organ where immature and mature poxvirus particles were detected. The particles were detected in detaching, apoptotic respiratory epithelial cells preceding clinical disease in the form of lethargy, respiratory distress, and mortality. In moribund salmon, blocking of gas exchange would likely be caused by the adherence of respiratory lamellae and epithelial proliferation obstructing respiratory surfaces. The virus was not found in healthy salmon or in control fish with gill disease without apoptotic cells, although transmission remains to be demonstrated. PCR of archival tissue confirmed virus infection in 14 cases with gill apoptosis in Norway starting from 1995. Phylogenomic analyses showed that the fish poxvirus is the deepest available branch of chordopoxviruses. The virus genome encompasses most key chordopoxvirus genes that are required for genome replication and expression, although the gene order is substantially different from that in other chordopoxviruses. Nevertheless, many highly conserved chordopoxvirus genes involved in viral membrane biogenesis or virus-host interactions are missing. Instead, the salmon poxvirus carries numerous genes encoding unknown proteins, many of which have low sequence complexity and contain simple repeats suggestive of intrinsic disorder or distinct protein structures.

 
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Large Tailed Spindle Viruses of Archaea: a New Way of Doing Viral Business

Viruses of Archaea continue to surprise us. Archaeal viruses have revealed new morphologies, protein folds, and gene content. This is especially true for large spindle viruses, which infect only Archaea. We present a comparison of particle morphologies, major coat protein structures, and gene content among the five characterized large spindle viruses to elucidate defining characteristics. Structural similarities and a core set of genes support the grouping of the large spindle viruses into a new superfamily.

 
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Researchers suggest approach to fight common virus in immunosuppressed patients

Researchers suggest approach to fight common virus in immunosuppressed patients | Virology and Bioinformatics from Virology.ca | Scoop.it
Using an animal model they developed, Saint Louis University and Utah State university researchers have identified a strategy that could keep a common group of viruses called adenoviruses from replicating and causing sickness in humans.
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Influenza B strain leaving kids temporarily unable to walk on the rise in Australia

Influenza B strain leaving kids temporarily unable to walk on the rise in Australia | Virology and Bioinformatics from Virology.ca | Scoop.it
The number of people suffering "Type B" flu is on the rise in Australia, with children among those to suffer the symptoms most severely. Professor Robert Booy, an infectious disease and vaccine expert from the University of Sydney, told SBS that the spike in cases was unusual. "This season we’ve had a real surge in [Type] B and it has surged early in the season," he said.

Via Ian M Mackay, PhD
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Expression of a single gene lets scientists easily grow hepatitis C virus in the lab | Newswire

Expression of a single gene lets scientists easily grow hepatitis C virus in the lab | Newswire | Virology and Bioinformatics from Virology.ca | Scoop.it
Worldwide, 185 million people have chronic hepatitis C. Since the late 1980s, when scientists discovered the virus that causes the infection, they have struggled to find ways to grow it in human cells in the lab — an essential part of learning how the virus works and developing new effective treatments.

In a study published in Nature on August 12, scientists led by The Rockefeller University’s Charles M. Rice, Maurice R. and Corinne P. Greenberg Professor in Virology and head of the Laboratory of Virology and Infectious Disease, report that when they overexpressed a particular gene in human liver cancer cell lines, the virus could easily replicate. This discovery allows study of naturally occurring forms of hepatitis C virus (HCV) in the lab.


A red flag: Researchers engineered cultured cells to contain a red marker that moves into the nucleus upon HCV infection. Nothing happened when normal cells were exposed to HCV (top), but when the researchers expressed the protein SEC14L2, some nuclei changed color from blue to purple (bottom).
“Being able to easily culture HCV in the lab has many important implications for basic science research,” says Rice. “There is still much we don’t understand about how the virus operates, and how it interacts with liver cells and the immune system.”

 

Hepatitis C virus graphic from Russell Kightley Media


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'Fishing expedition' nets nearly tenfold increase in number of sequenced virus genomes

'Fishing expedition' nets nearly tenfold increase in number of sequenced virus genomes | Virology and Bioinformatics from Virology.ca | Scoop.it
Using a specially designed computational tool as a lure, scientists have netted the genomic sequences of almost 12,500 previously uncharacterized viruses from public databases.

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Job interview nerves: top tips on how to keep your cool

Job interview nerves: top tips on how to keep your cool | Virology and Bioinformatics from Virology.ca | Scoop.it
If your interview nerves have cost you a job, here's some expert advice from our panel
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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary We are now in the age of big data. More than ever before, biological discoveries require powerful and flexible tools for managing large datasets, including both visual and statistical tools. Pathway-based visualization is particularly powerful since it enables one to analyze complex datasets within the context of actual biological processes and to elucidate how each change in a cell effects related processes. To facilitate such approaches, we present Escher, a web application that can be used to rapidly build pathway maps. On Escher maps, diverse datasets related to genes, reactions, and metabolites can be quickly contextualized within metabolism and, increasingly, beyond metabolism. Escher is available now for free use (under the MIT license) at https://escher.github.io .
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Potential additional benefit of a nine-valent second generation HPV vaccine

Potential additional benefit of a nine-valent second generation HPV vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
AbstractIntroduction

A second generation HPV vaccine has been developed for the prevention of anogenital cancers and precancerous lesions of the cervix, vulva, vagina, anus and of genital warts due to nine HPV types.

We estimated the annual burden of these diseases attributable to the nine HPV types compared to HPV types from first generation vaccines in women and men in Europe.

Material and methods

Incidence rates from the IARC database, cancer registries, the literature and Eurostat population data were used.

The burden attributable to the HPV types targeted by both vaccines was estimated by applying the relative contribution of the respective HPV types from epidemiological studies.

Results

In 2013, the number of new anogenital HPV-attributable cancers was 44,480 with 39,494 of these cases related to second vs. 33,285 to first generation vaccine types.

Among the 284,373 to 541,621 new HPV-attributable anogenital precancerous lesions 235,364–448,423 and 135,025–256,830 were estimated to be related to second and first generation vaccine types, respectively.

The annual number of new genital warts was 753,608–935,318, with 90% related to HPV6/11.

Conclusions

These data demonstrate how the large public health impact that was achieved by the first generation HPV vaccines could be further increased by second generation vaccines.

  
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Cloak and Dagger: Alternative Immune Evasion and Modulation Strategies of Poxviruses

Cloak and Dagger: Alternative Immune Evasion and Modulation Strategies of Poxviruses | Virology and Bioinformatics from Virology.ca | Scoop.it
As all viruses rely on cellular factors throughout their replication cycle, to be successful they must evolve strategies to evade and/or manipulate the defence mechanisms employed by the host cell. In addition to their expression of a wide array of host modulatory factors, several recent studies have suggested that poxviruses may have evolved unique mechanisms to shunt or evade host detection. These potential mechanisms include mimicry of apoptotic bodies by mature virions (MVs), the use of viral sub-structures termed lateral bodies for the packaging and delivery of host modulators, and the formation of a second, “cloaked” form of infectious extracellular virus (EVs). Here we discuss these various strategies and how they may facilitate poxvirus immune evasion. Finally we propose a model for the exploitation of the cellular exosome pathway for the formation of EVs.
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Double-Stranded RNA Is Detected by Immunofluorescence Analysis

Early biochemical studies of viral replication suggested that most viruses produce double-stranded RNA (dsRNA), which is essential for the induction of the host immune response. However, it was reported in 2006 that dsRNA could be detected by immunofluorescence antibody staining in double-stranded DNA and positive-strand RNA virus infections but not in negative-strand RNA virus infections. Other reports in the literature seemed to support these observations. This suggested that negative-strand RNA viruses produce little, if any, dsRNA or that more efficient viral countermeasures to mask dsRNA are mounted. Because of our interest in the use of dsRNA antibodies for virus discovery, particularly in pathological specimens, we wanted to determine how universal immunostaining for dsRNA might be in animal virus infections. We have detected the in situ formation of dsRNA in cells infected with vesicular stomatitis virus, measles virus, influenza A virus, and Nyamanini virus, which represent viruses from different negative-strand RNA virus families. dsRNA was also detected in cells infected with lymphocytic choriomeningitis virus, an ambisense RNA virus, and minute virus of mice (MVM), a single-stranded DNA (ssDNA) parvovirus, but not hepatitis B virus. Although dsRNA staining was primarily observed in the cytoplasm, it was also seen in the nucleus of cells infected with influenza A virus, Nyamanini virus, and MVM. Thus, it is likely that most animal virus infections produce dsRNA species that can be detected by immunofluorescence staining. The apoptosis induced in several uninfected cell lines failed to upregulate dsRNA formation.

 
Ed Rybicki's insight:

I love it when an old technique comes back: I remember hearing about use of Abs to dsRNA as far back as the early 1980s, and here it is back again - largely because of the improvement in microscopes and techniques for detecting immunoflourescence.  Nice one!  It'll have to find its way into my textbook....

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The Multiplicity of Cellular Infection Changes Depending on the Route of Cell Infection in a Plant Virus

The multiplicity of cellular infection (MOI) is the number of virus genomes of a given virus species that infect individual cells. This parameter chiefly impacts the severity of within-host population bottlenecks as well as the intensity of genetic exchange, competition, and complementation among viral genotypes. Only a few formal estimations of the MOI currently are available, and most theoretical reports have considered this parameter as constant within the infected host. Nevertheless, the colonization of a multicellular host is a complex process during which the MOI may dramatically change in different organs and at different stages of the infection. We have used both qualitative and quantitative approaches to analyze the MOI during the colonization of turnip plants by Turnip mosaic virus. Remarkably, different MOIs were observed at two phases of the systemic infection of a leaf. The MOI was very low in primary infections from virus circulating within the vasculature, generally leading to primary foci founded by a single genome. Each lineage then moved from cell to cell at a very high MOI. Despite this elevated MOI during cell-to-cell progression, coinfection of cells by lineages originating in different primary foci is severely limited by the rapid onset of a mechanism inhibiting secondary infection. Thus, our results unveil an intriguing colonization pattern where individual viral genomes initiate distinct lineages within a leaf. Kin genomes then massively coinfect cells, but coinfection by two distinct lineages is strictly limited.

 
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New Insights into the Role of the Nuclear Egress Complex of Herpesviruses

Herpesviruses are unusual among enveloped viruses because they bud twice yet acquire a single envelope. They are also the only known viruses that bud into the nuclear envelope. We discovered that the herpesvirus nuclear egress complex could bud membranes without the help of other proteins by forming a coat-like hexagonal scaffold inside the budding membrane. This finding raises the possibility that a phenotypically similar nuclear export of large RNAs is cargo driven.
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Cell type-specific manipulation with GFP-dependent Cre recombinase : Nature Neuroscience : Nature Publishing Group

Cell type-specific manipulation with GFP-dependent Cre recombinase : Nature Neuroscience : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it
GFP reporter lines are useful for labeling specific cell types. Here, the authors developed a method to convert GFP expression directly into Cre recombinase activity. GFP-dependent Cre was delivered via electroporation or AAV to neural tissues in the mouse, and could be used for optogenetic control of specific cell types.
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Bamboo mosaic virus yields its structural secrets after 75+ years

Bamboo mosaic virus yields its structural secrets after 75+ years | Virology and Bioinformatics from Virology.ca | Scoop.it
A hugely destructive plant virus so flexible that it has resisted efforts to describe its form since before World War II has finally surrendered its secrets. The discovery of what makes the bendy bug so malleable will revolutionize the efforts to stop such flexible plant viruses - and the billions in crop loss they cause every year—and may even lead to a new vehicle for delivering vaccines in humans.
Ed Rybicki's insight:

Always going to lead to vaccines...B-)  Always.  And it was always going to look like bendy TMV.

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Self-targeting blocks malaria parasite invasion

Self-targeting blocks malaria parasite invasion | Virology and Bioinformatics from Virology.ca | Scoop.it
If you missed it: Self-targeting blocks #malaria parasite invasion, #OA
by Kirk Deitsch
http://t.co/CQGexdmiXG http://t.co/zu0KgKv8hG

Via Denis Hudrisier
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If you ask different questions you get different answers – one more way science isn’t broken it is just really hard | Simply Statistics

If you ask different questions you get different answers – one more way science isn’t broken it is just really hard | Simply Statistics | Virology and Bioinformatics from Virology.ca | Scoop.it
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Team discovers the ancient origins of deadly Lassa virus

Team discovers the ancient origins of deadly Lassa virus | Virology and Bioinformatics from Virology.ca | Scoop.it
Working as part of an international team in the United States and West Africa, a researcher at The Scripps Research Institute (TSRI) has published new findings showing the ancient roots of the deadly Lassa virus, a relative of Ebola virus, and how Lassa virus has changed over time.

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BMC Genomics | BEACON: automated tool for B acterial G E nome A nnotation C omparis ON

Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs).
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