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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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Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. - J Virol Methods. 2014

The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated.

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RNA Viruses: A Case Study of the Biology of Emerging Infectious Diseases

There are 180 currently recognized species of RNA virus that can infect humans, and on average, 2 new species are added every year. RNA viruses are routinely exchanged between humans and other hosts (particularly other mammals and sometimes birds) over both epidemiological and evolutionary time: 89% of human-infective species are considered zoonotic and many of the remainder have zoonotic origins. Some viruses that have crossed the species barrier into humans have persisted and become human-adapted viruses, as exemplified by the emergence of HIV-1. Most, however, have remained as zoonoses, and a substantial number have apparently disappeared again. We still know relatively little about what determines whether a virus is able to infect, transmit from, and cause disease in humans, but there is evidence that factors such as host range, cell receptor usage, tissue tropisms, and transmission route all play a role. Although systematic surveillance for potential new human viruses in nonhuman hosts would be enormously challenging, we can reasonably aspire to much better knowledge of the diversity of mammalian and avian RNA viruses than exists at present.

Via Ed Rybicki
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Genomic and Metagenomic Approaches for Predicting Pathogen Evolution

Global climate change can alter the distribution of microbial pathogens and vectors that transmit infectious diseases, exposing humans to newly emerging or reemerging diseases. Early detection of potential pathogens and vectors in the environment can facilitate upstream interventions that limit the spread of infectious disease. Metagenomics is the analysis of DNA sequences from a population of microorganisms in a particular environment, followed by the computational reconstruction of the data to determine what organisms are present and predict their role in the environment. Defining the microbial populations associated with humans, animals, and their environment provides insight into the structure of microbial communities in any particular niche, including the abundance, diversity, and composition of the microbes and viruses present. It can also reveal the distribution of virulence genes within that niche. These data can be used to identify reservoirs of pathogens in an environment and predict environments with a high probability for evolution of new pathogens or outbreaks caused by known pathogens, thereby facilitating approaches to prevent infections of animals or humans before serious outbreaks of infectious disease.
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Molecular Genetics of Mycobacteriophages

Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond.
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How Not to Be Wrong: The Power of Mathematical Thinking eBook: Jordan Ellenberg: Amazon.ca: Kindle Store

How Not to Be Wrong: The Power of Mathematical Thinking eBook: Jordan Ellenberg: Amazon.ca: Kindle Store
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MATH and STATS in real life....   why it matters!

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Virology Journal | Abstract | Mutations within the conserved NS1 nuclear export signal lead to inhibition of influenza A virus replication

The influenza A virus NS1 protein is a virulence factor and an antagonist of host cell innate immune responses. During virus infection NS1 protein has several functions both in the nucleus and in the cytoplasm and its intracellular localization is regulated by one or two nuclear localization signals (NLS) and a nuclear export signal (NES).
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Dengue Vaccine Candidate demonstrates promising results in Phase III efficacy study | Outbreak News Today

Dengue Vaccine Candidate demonstrates promising results in Phase III efficacy study | Outbreak News Today | Virology and Bioinformatics from Virology.ca | Scoop.it
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Influenza A Virus Host Shutoff Disables Antiviral Stress-Induced Translation Arrest

Influenza A Virus Host Shutoff Disables Antiviral Stress-Induced Translation Arrest | Virology and Bioinformatics from Virology.ca | Scoop.it
by Denys A. Khaperskyy, Mohamed M. Emara, Benjamin P. Johnston, Paul Anderson, Todd F.
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Python bumps off Java as top learning language

Python bumps off Java as top learning language | Virology and Bioinformatics from Virology.ca | Scoop.it
Python's simpler syntax and ability to scale up for enterprise development have made it the preferred language choice for learning to code.
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SimFlu: A simulation tool for predicting the variation pattern of influenza A virus.

SimFlu: A simulation tool for predicting the variation pattern of influenza A virus. | Virology and Bioinformatics from Virology.ca | Scoop.it

Since the first pandemic outbreak of avian influenza A virus (H5N1 subtype) in 1997, the National Center for Biotechnology Information (NCBI) has provided a large number of influenza virus sequences with well-organized annotations. Using the time-series sequences of influenza A viruses, we developed a simulation tool for influenza virus, named SimFlu, to predict possible future variants of influenza viruses. SimFlu can create variants from a seed nucleotide sequence of influenza A virus using the codon variation parameters included in the SimFlu package. The SimFlu library provides pre-calculated codon variation parameters for the H1N1, H3N2, and H5N1 subtypes of influenza A virus isolated from 2000 to 2011, allowing the users to simulate their own nucleotide sequences by selecting their preferred parameter options. SimFlu supports three operating systems - Windows, Linux, and Mac OS X. SimFlu is publicly available at http://lcbb.snu.ac.kr/simflu.

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Google Genomics — Google Developers

Google Genomics — Google Developers | Virology and Bioinformatics from Virology.ca | Scoop.it
Gives access to Google Genomics.

Explore genetic variation interactively.Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.

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Chris Upton + helpers's curator insight, July 4, 12:42 PM

Generally...   I hate Google...

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Simple chained guide trees give high-quality protein multiple sequence alignments Boyce K, Sievers F, Higgins DG

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random.

 

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Forgotten vials of smallpox found in Bethesda, Md.

Forgotten vials of smallpox found in Bethesda, Md. | Virology and Bioinformatics from Virology.ca | Scoop.it
Forgotten vials of smallpox found in storage room
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Useful Review on Rotavirus

Rotaviruses (RV) are ubiquitous, highly infectious, segmented double-stranded RNA genome viruses of importance in public health because of the severe acute gastroenteritis they cause in young children and many animal species. They are very well adapted to their host, with symptomatic and asymptomatic reinfections being virtually universal during the first 3 years of life. Antibodies are the major arm of the immune system responsible for protecting infants from RV reinfection. The relationship between the virus and the B cells (Bc) that produce these antibodies is complex and incompletely understood: most blood-circulating Bc that express RV-specific immunoglobulin (Ig) on their surface (RV-Ig) are naive Bc and recognize the intermediate capsid viral protein VP6 with low affinity. When compared to non-antigen-specific Bc, RV-Bc are enriched in CD27+ memory Bc (mBc) that express IgM. The Ig genes used by naive RV-Bc are different than those expressed by RV-mBc, suggesting that the latter do not primarily develop from the former. Although RV predominantly infects mature villus enterocytes, an acute systemic viremia also occurs and RV-Bc can be thought of as belonging to either the intestinal or systemic immune compartments. Serotype-specific or heterotypic RV antibodies appear to mediate protection by multiple mechanisms, including intracellular and extracellular homotypic and heterotypic neutralization. Passive administration of RV-Ig can be used either prophylactically or therapeutically. A better understanding of the Bc response generated against RV will improve our capacity to identify improved correlates of protection for RV vaccines.

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Genetics of Phage Lysis

We have been witnessing an increased interest in bacteriophage studies focused on their use as antibacterial agents to fight pathogenic bacteria. This interest is a consequence of the phages' ability to lyse a bacterial host. Until recently, little was known about the mechanisms used by mycobacteriophages to induce lysis of their complex hosts. However, studies on Ms6-induced lysis have changed this scenario and provided new insights into the mechanisms of bacteriophage-induced lysis. Specific lysis protein genes have been identified in mycobacteriophage genomes, reflecting the particular mycobacterial cell envelope composition. These include enzymes that target mycolic acid–containing lipids and proteins that participate in the secretion of the phage endolysin, functioning as chaperone-like proteins. This chapter focuses on the current knowledge of mycobacteriophage-induced lysis, starting with an overview of phage lysis and basic features of the lysis players.
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Web-Based Surveillance Systems for Human, Animal, and Plant Diseases

The emergence of infectious diseases, caused by novel pathogens or the spread of existing ones to new populations and regions, represents a continuous threat to humans and other species. The early detection of emerging human, animal, and plant diseases is critical to preventing the spread of infection and protecting the health of our species and environment. Today, more than 75% of emerging infectious diseases are estimated to be zoonotic and capable of crossing species barriers and diminishing food supplies. Traditionally, surveillance of diseases has relied on a hierarchy of health professionals that can be costly to build and maintain, leading to a delay or interruption in reporting. However, Internet-based surveillance systems bring another dimension to epidemiology by utilizing technology to collect, organize, and disseminate information in a more timely manner. Partially and fully automated systems allow for earlier detection of disease outbreaks by searching for information from both formal sources (e.g., World Health Organization and government ministry reports) and informal sources (e.g., blogs, online media sources, and social networks). Web-based applications display disparate information online or disperse it through e-mail to subscribers or the general public. Web-based early warning systems, such as ProMED-mail, the Global Public Health Intelligence Network (GPHIN), and Health Map, have been able to recognize emerging infectious diseases earlier than traditional surveillance systems. These systems, which are continuing to evolve, are now widely utilized by individuals, humanitarian organizations, and government health ministries.
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Virus in Found Tubes of Smallpox Is Viable | Science Blogs | WIRED

Virus in Found Tubes of Smallpox Is Viable | Science Blogs | WIRED | Virology and Bioinformatics from Virology.ca | Scoop.it
Here’s an update on the vials found on the National Institutes of Health campus last week that were labeled smallpox, and transported earlier this week to the Centers for Disease Control and Prevention: The CDC and NIH have both confirmed that the virus in two of the tubes is viable. That is, if the vials…
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Not at all surprising

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Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon

The identification of novel giant viruses from the nucleocytoplasmic large DNA viruses group and their virophages has increased in the last decade and has helped to shed light on viral evolution. This study describe the discovery, isolation and characterization of Samba virus (SMBV), a novel giant virus belonging to the Mimivirus genus, which was isolated from the Negro River in the Brazilian Amazon. We also report the isolation of an SMBV-associated virophage named Rio Negro (RNV), which is the first Mimivirus virophage to be isolated in the Americas.
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I do wish these excitable folk would stop naming things so capriciously - although they ARE imaginative!
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Oncogenic Herpesvirus KSHV Hijacks BMP-Smad1-Id Signaling to Promote Tumorigenesis

Oncogenic Herpesvirus KSHV Hijacks BMP-Smad1-Id Signaling to Promote Tumorigenesis | Virology and Bioinformatics from Virology.ca | Scoop.it

Although KSHV exerts multiple mechanisms to promote cell survival by repressing TGF-β signaling, little is known whether KSHV manipulates BMP signaling and contributes to the pathogenesis of KSHV-induced malignancies. In the present study, we have identified Smad1 as a novel binding protein of LANA by tandem affinity purification. We demonstrated that LANA up-regulated Id transcription through BMP-Smad1-Id signaling pathway. Id proteins were significantly up-regulated in KSHV-transformed MM (KMM) cells, and were abundantly expressed in human KS lesions; therefore, they were probably relevant to the development of KS. Importantly, we have shown that Ids are required to maintain the oncogenic phenotype of KMM cells in vitro and in vivo. These findings illustrate a novel mechanism by which a tumor virus hijacks and converts a developmental pathway into an indispensable oncogenic pathway for tumorigenesis. Furthermore, we showed that BMP signaling inhibitors dramatically hampered the tumorigenicity of KMM cells in vitro and in vivo. Our results demonstrate that small inhibitors targeting BMP-Smad1-Id signaling pathway are promising candidates for the treatment of KS.

 

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A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection. - Biomed Res Int. 2014

A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection. - Biomed Res Int. 2014 | Virology and Bioinformatics from Virology.ca | Scoop.it

Rapidly mutating viruses, such as hepatitis C virus (HCV) and HIV, have adopted evolutionary strategies that allow escape from the host immune response via genomic mutations. Recent advances in high-throughput sequencing are reshaping the field of immuno-virology of viral infections, as these allow fast and cheap generation of genomic data. However, due to the large volumes of data generated, a thorough understanding of the biological and immunological significance of such information is often difficult. This paper proposes a pipeline that allows visualization and statistical analysis of viral mutations that are associated with immune escape. Taking next generation sequencing data from longitudinal analysis of HCV viral genomes during a single HCV infection, along with antigen specific T-cell responses detected from the same subject, we demonstrate the applicability of these tools in the context of primary HCV infection. We provide a statistical and visual explanation of the relationship between cooccurring mutations on the viral genome and the parallel adaptive immune response against HCV.

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Constructing Vaccines [HD Animation] - YouTube

See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/
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Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online

Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online | Virology and Bioinformatics from Virology.ca | Scoop.it
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CDC Media Statement on Newly Discovered Smallpox Samples

On July 1, 2014, the National Institutes of Health (NIH) notified the appropriate regulatory agency, the Division of Select Agents and Toxins (DSAT) of the Centers for Disease Control and Prevention (CDC), that employees discovered vials labeled ”variola,” commonly known as smallpox, in an unused portion of a storage room in a Food and Drug Administration (FDA) laboratory located on the NIH Bethesda campus.

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Evolution and Ecology of Influenza A Viruses.

Wild aquatic bird populations have long been considered the natural reservoir for influenza A viruses with virus transmission from these birds seeding other avian and mammalian hosts. While most evidence still supports this dogma, recent studies in bats have suggested other reservoir species may also exist. Extensive surveillance studies coupled with an enhanced awareness in response to H5N1 and pandemic 2009 H1N1 outbreaks is also revealing a growing list of animals susceptible to infection with influenza A viruses. Although in a relatively stable host-pathogen interaction in aquatic birds, antigenic, and genetic evolution of influenza A viruses often accompanies interspecies transmission as the virus adapts to a new host. The evolutionary changes in the new hosts result from a number of processes including mutation, reassortment, and recombination. Depending on host and virus these changes can be accompanied by disease outbreaks impacting wildlife, veterinary, and public health.

 

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Bushmeat in the Time of Ebola | VICE News

Bushmeat in the Time of Ebola | VICE News | Virology and Bioinformatics from Virology.ca | Scoop.it
VICE News went to the bushmeat markets in Liberia, where the most recent outbreak of the deadly Ebola virus is said to have originated.
Ken Yaw Agyeman-Badu's insight:

I love this documentary - Bushmeat in the Time of Ebola.

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Ed Rybicki's curator insight, July 10, 11:14 AM
Thanks, Ken!