Viruses and Bioinformatics from Virology.uvic.ca
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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Viruses and Bioinformatics from Virology.uvic.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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Viruses and Bioinformatics from Virology.uvic.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: | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
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A mouse model of paralytic myelitis caused by enterovirus D68

A mouse model of paralytic myelitis caused by enterovirus D68 | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Reports of polio-like paralysis, referred to as acute flaccid myelitis (AFM), have recently emerged in association with infections caused by enterovirus D68 (EV-D68). In the second half of 2014, 120 cases of AFM, mostly in young children, were reported during a nationwide outbreak of EV-D68 respiratory disease. The number of AFM cases has risen again in 2016. Although epidemiological evidence between EV-D68 infection and AFM is accumulating, a causal link has not been definitely established. Here we demonstrate that strains of EV-D68 recovered during the 2014 epidemic can cause a paralytic illness in mice that resembles human AFM. Evidence that EV-D68 causes paralysis in this mouse model include: (1) loss of spinal cord motor neurons innervating paralyzed limbs, (2) detection of virus in the spinal cord and, specifically, motor neurons, (3) transmission of neurological disease when injecting virus isolated from spinal cords of paralyzed mice into naïve mice, thus fulfilling Koch’s postulates, and (4) the ability to prevent AFM by pre-administering serum containing EV-D68 antibodies from previously infected mice. This experimental mouse model can be used to better understand the pathogenesis of EV-D68-induced CNS disease and to facilitate the development of potential therapies.
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(Avian flu) Jiangxi bans live poultry sales amid seven deaths

(Avian flu) Jiangxi bans live poultry sales  amid seven deaths | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Since January, at least 270 H7N9 human infections have been reported in China, with at least 87 fatalities

Via Ian M Mackay, PhD
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Identification of several high-risk HPV inhibitors and drug targets with a novel high-throughput screening assay

Identification of several high-risk HPV inhibitors and drug targets with a novel high-throughput screening assay | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Human papillomaviruses are causative agents of many different cancers; they are most commonly associated with cervical cancer which leads to about quarter of a million deaths each year. Regardless of extensive studies for decades there is no specific cure against HPV infection. During this research, we have engineered modified HPV marker genomes that express Renilla luciferase reporter gene which expression level correlates directly with viral genome copy number. We have used such modified HPV genome in high-throughput screening of NCI Diversity Set IV chemical library and have identified a number of novel high-risk HPV-specific chemical compounds and drug targets. Such Renilla-expressing marker genomes could be used in various cell systems suitable for HPV replication studies to conduct high-throughput screens and quantify viral genome copy number quickly and effectively.
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Identification and molecular characterization of a novel sugarcane streak mastrevirus and an isolate of the A-strain of maize streak virus from sugarcane in Nigeria

Identification and molecular characterization of a novel sugarcane streak mastrevirus and an isolate of the A-strain of maize streak virus from sugarcane in Nigeria | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Sugarcane and maize plants showing symptoms typical of those described for the so-called “African streak viruses” (AfSVs) were encountered during field surveys conducted from February to July 2015 to document viruses infecting both crops across the northern Guinea savannah region of Nigeria. As part of this study, two categories of complete mastrevirus-like genome sequences were obtained from nine samples (maize = 2; sugarcane = 7). In pairwise comparisons, the full-length genomes of the first sequence category (2,687 nt each; maize = 2; sugarcane = 2) shared 96 to 99% identity with global isolates of the A-strain of maize streak virus (MSV-A), indicating that sugarcane may also serve as a reservoir host to MSV-A. Analysis of the complete genomes belonging to the second sequence category (2,757 nt each; sugarcane = 5) showed that they shared 42 to 67% identity with their closest AfSV relatives, thus indicating that they represent sequences of a novel mastrevirus. Both sequence categories shared 61-62% sequence identity with each other. Further analysis revealed that the novel sugarcane-infecting virus, tentatively named as sugarcane chlorotic streak virus (SCSV), arose from a putative interspecific recombination event involving two grass-infecting mastreviruses, eragrostis streak virus and urochloa streak virus, as putative parental sequences. The results of this study add to the repertoire of diverse AfSVs present in cereal and sugarcane mixed cropping landscapes in the northern Guinea savannah region of Nigeria, with implications for disease epidemiology.

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Great piece of work! And even nicer because it cites my Top Ten viruses article B-)
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Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells

Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author Summary Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that, upon congenital infection, can cause severe neonatal birth defects. To better understand the early innate immune response to ZIKV, we compared infection of human dendritic cells (DCs) between a contemporary Puerto Rican isolate and historic isolates from Africa and Asia. Human DCs supported productive replication following infection with the contemporary strain and exhibited donor variability in viral replication, but not viral binding. While contemporary and historic Asian lineage viruses replicated similarly, the African strains displayed more rapid replication kinetics with higher infection magnitude and uniquely induced cell death. Minimal DC activation and antagonism of type I interferon (IFN) translation was observed during ZIKV infection, despite strong induction of IFNB1 transcription and translation of other antiviral effector proteins. Treatment with a RIG-I agonist potently blocked ZIKV replication in human DCs, while type I IFN treatment was significantly less effective. Mechanistically, all ZIKV strains inhibited type I IFN receptor signaling through blockade of STAT1 and STAT2 phosphorylation. Altogether, we found that while ZIKV efficiently evades type I IFN responses during infection of human DCs, RIG-I signaling remains capable of inducing a strong antiviral state.
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Identification of several high-risk HPV inhibitors and drug targets with a novel high-throughput screening assay

Identification of several high-risk HPV inhibitors and drug targets with a novel high-throughput screening assay | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Human papillomaviruses are causative agents of many different cancers; they are most commonly associated with cervical cancer which leads to about quarter of a million deaths each year. Regardless of extensive studies for decades there is no specific cure against HPV infection. During this research, we have engineered modified HPV marker genomes that express Renilla luciferase reporter gene which expression level correlates directly with viral genome copy number. We have used such modified HPV genome in high-throughput screening of NCI Diversity Set IV chemical library and have identified a number of novel high-risk HPV-specific chemical compounds and drug targets. Such Renilla-expressing marker genomes could be used in various cell systems suitable for HPV replication studies to conduct high-throughput screens and quantify viral genome copy number quickly and effectively.
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A single mutation in the envelope protein modulates flavivirus antigenicity, stability, and pathogenesis

A single mutation in the envelope protein modulates flavivirus antigenicity, stability, and pathogenesis | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Flaviviruses include emerging pathogens such as WNV, DENV, and ZIKV that threaten global health. Despite causing significant morbidity, effective vaccines or therapeutic agents to protect humans against many flaviviruses are lacking. Because of the importance of antibodies in flavivirus immunity and vaccine protection, much effort is focused on understanding the factors that modulate antibody recognition of flaviviruses. Virus breathing, which allows viruses to sample different conformations at equilibrium, has the potential to transiently expose otherwise inaccessible antibody epitopes. Here, we report the identification a single mutation in the envelope protein that alters the exposure of a poorly accessible epitope and the stability of both WNV and DENV through changes in the ensemble of structures sampled by the virus. For WNV, this change attenuated infection and pathogenesis in mice, suggesting that virus conformational dynamics have relevant consequences in vivo.
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Your travels are Written in your body - Common Science Space

Your travels are Written in your body - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Our bones, teeth and hair carry in them an encrypted GPS log of where we’ve been. If you lived in Seattle through your childhood and moved to Chicago ten years ago, that is indelibly written there. There will also be a record of what you’ve eaten recently. Advances in the science and technology of reading... Continue Reading
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Picornavirus RNA is protected from cleavage by ribonuclease during virion uncoating and transfer across  membranes

Picornavirus RNA is protected from cleavage by ribonuclease during virion uncoating and transfer across  membranes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Picornaviruses are a large family of important human and animal pathogens that include poliovirus, human rhinovirus and foot-and-mouth disease virus. Picornaviruses enter the host cell by hijacking one of the vesicle-mediated cellular entry routes. However, once the virus is internalized, the mechanism used to deliver the viral genome across the vesicle membrane and into the cytoplasm remains unclear and even controversial. Here we show that for poliovirus (a member of the enterovirus genus), viral RNA is translocated directly from the particle, across the vesicle membrane into the lumen of liposomes in a receptor-decorated liposome model, or cytoplasm during infection, without being exposed to external medium surrounding the liposomes or the lumen of the entry vesicle, respectively. Our results suggest that the interaction between the viral particle and the membrane results in a specific mechanism of viral genome delivery that not only directs but also protects the RNA so that it reaches the cytoplasm as an intact and functional molecule. Additionally, we show that this is also the case for equine rhinitis A virus, a member of the aphthovirus genus, whose genome delivery mechanism has previously been thought to differ significantly from the mechanism used by enteroviruses suggesting the possibility of a unified mechanism of RNA delivery for the entire picornavirus family.
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Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Emerging infectious diseases are often characterized by host switching events, in which a pathogen jumps from its original host to infect a novel species. However, given the ecological and genetic barriers a virus must overcome to jump species and adapt to new hosts, it might be reasonable to assume that successful cross-species transmission is a relatively rare occurrence and that viruses are instead more likely to co-diverge with their hosts. Using a comparative co-phylogenetic analysis performed at the scale of virus family we have revealed that co-divergence is relatively infrequent among 19 diverse families of RNA and DNA viruses, such that cross-species transmission plays a central role in virus evolution. Host jumping was especially common in viruses with RNA genomes, and by drawing broad-scale comparisons our analysis reveals which virus families have a greater propensity to jump species barriers and hence successfully emerge in new hosts. Finally, our data suggest that sampling more viruses increases the likelihood of detecting host jumping events.
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Cocktail of bacteria-killing viruses prevents cholera infection in animal models

Cocktail of bacteria-killing viruses prevents cholera infection in animal models | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Oral administration of a cocktail of three viruses, all of which specifically kill cholera bacteria, prevents infection and cholera-like symptoms in animal model experiments, report scientists from Tufts University School of Medicine (TUSM) and the Sackler School of Graduate Biomedical Sciences at Tufts inNature Communications on Feb. 1. The findings are the first to demonstrate the potential efficacy of bacteria-killing viruses—known as bacteriophages, or phages—as an orally administered preventive therapy against an acute gastrointestinal bacterial disease.

 

“While phage therapy has existed for decades, our study is proof-of-principle that it can be used to protect against infection and intervene in the transmission of disease,” said senior study author Andrew Camilli, Ph.D., Howard Hughes Medical Institute Investigator and professor of molecular biology and microbiology at TUSM. “We are hopeful that phages can someday be a tool in the public health arsenal that helps decrease the global burden of cholera, which affects up to four million people around the world each year.”

 

In previous work, Camilli and colleagues searched for phages that are specific for Vibrio cholerae, the bacterium that causes cholera—a potentially lethal infectious disease marked by severe diarrhea and dehydration. While phages that kill V. cholerae are abundant in nature, the team identified three strains that uniquely retained the ability to kill V. cholerae within the small intestine, the site of infection in humans. These phages function by targeting bacterial surface receptors normally involved in infectiousness, making them ideal therapeutic candidates—to develop resistance, cholera bacteria must acquire mutations in these receptors, which cause the bacteria to become less infectious.


Via Dr. Stefan Gruenwald, Kenzibit
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Ed Rybicki's curator insight, February 13, 5:08 AM
While this great, it is a modern vindication of something no less a person that the co-discoverer of phages himself, Felix d'Herelle, advocated as a cure for dysentery - and put into practice in India in the 1920s, apparently (https://rybicki.wordpress.com/2015/02/17/happy-centenary-phages/). He was also the godfather of work done at the Eliava Institute in Georgia, which really laid the foundation of phage therapy.
Ed Rybicki's comment, February 13, 5:09 AM
Thanks! Great stuff.
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Genome Sequence of the First Coleopteran Iflavirus Isolated from Western Corn Rootworm

Western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is the worst insect pest of maize in North America and is invasive in Europe (1). Management of WCR in the United States depends primarily on transgenic plants that express Bacillus thuringiensis (Bt) insecticidal toxins, but populations resistant to Bt toxins have been reported (2). Hence, novel control strategies for WCR management are needed. Small RNA viruses of insects, such as iflaviruses, have potential for insect pest management. Several iflaviruses have recently been discovered in the insect orders Hemiptera (3), Lepidoptera (4), and Hymenoptera (5–7). Here, we report the genome sequence of an iflavirus from WCR, the first identified from Coleoptera.

Ed Rybicki's insight:
Interesting because it could shed some light on evolutionary descent of these viruses - and push back the origin of picorna-like viruses by a good few million years.
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HPV 2017 - Papillomavirus Conference, Cape Town

HPV 2017 - Papillomavirus Conference, Cape Town | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The 31st International Papillomavirus Conference (HPV 2017), will take place in Cape Town, South Africa, from 28 February - 5 March, 2017.
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Ed Rybicki's curator insight, February 26, 5:25 AM
#HPV2017 to join the tweetfest!
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There is no controversy - HPV vaccines are saving lives around the world

There is no controversy - HPV vaccines are saving lives around the world | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
HPV vaccine is now used in 84 countries, including the USA, Canada, Australia and most of Western Europe.

Via Ed Rybicki
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Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses

Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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The mutation rates and mutational bias of influenza A virus

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Rabies vaccine development by expression of recombinant viral glycoprotein

Rabies vaccine development by expression of recombinant viral glycoprotein | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The rabies virus envelope glycoprotein (RVGP) is the main antigen of rabies virus and is the only viral component present in all new rabies vaccines being proposed. Many approaches have been taken since DNA recombinant technology became available to express an immunogenic recombinant rabies virus glycoprotein (rRVGP). These attempts are reviewed here, and the relevant results are discussed with respect to the general characteristics of the rRVGP, the expression system used, the expression levels achieved, the similarity of the rRVGP to the native glycoprotein, and the immunogenicity of the vaccine preparation. The most recent studies of rabies vaccine development have concentrated on in vivo expression of rRVGP by viral vector transduction, serving as the biotechnological basis for a new generation of rabies vaccines.

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Ed Rybicki's curator insight, February 20, 7:29 AM
Covers plant expression of rabies virus antigens, but then says this:
"cloned as a translational fusion product with the alpha mosaic virus (AlMV) coat protein (CP)” Alfalfa!! Idiot!
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Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication

Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Coronaviruses are long known to be particularly successful in evading host innate immune responses. This manifests in barely detectable interferon responses during the first hours of infection and greatly facilitates establishment of robust virus replication. This phenotype of early innate immune evasion is common to all coronaviruses and can have detrimental consequences particular for infections with highly pathogenic coronaviruses, such as SARS-CoV and MERS-CoV. We therefore hypothesized that there must be an evolutionary conserved viral function that has evolved to prevent sensing of coronavirus infection by infected host cells. Our study now describes this function, namely the highly conserved coronavirus endoribonuclease activity. We found that coronaviruses that lack this enzymatic activity are readily visible to infected host cells that can now mount a swift and potent host response restricting virus replication within hours. Our study provides a new paradigm of a first layer of RNA virus innate immune evasion during the early phase of infection, that takes place at the site of RNA synthesis, and is based on removal of dsRNA that would otherwise trigger the simultaneous activation of cytoplasmic host cell sensors.
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Mucosal stromal fibroblasts markedly enhance HIV infection of CD4+ T cells

Mucosal stromal fibroblasts markedly enhance HIV infection of CD4+ T cells | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary The molecular basis by which small amounts of HIV can initiate infection in the mucosa is not well understood. Here, we report that genital and rectal fibroblasts, amongst the most abundant cells of the mucosa, potently increase HIV infection of T cells. Fibroblasts are more abundant and can be more effective as infection enhancers than dendritic cells, which are thought to play a role in early HIV transmission by facilitating infection of T cells. In contrast to fibroblasts, mucosal epithelial cells, which line the mucosa, inhibit HIV infection. Our findings suggest that abrasions in the genital and rectal epithelium may increase HIV transmission in part by allowing external HIV to escape an antiviral environment to access the infection-favorable environment of the stromal fibroblasts. These studies suggest that approaches to limit fibroblast-mediated enhancement may diminish HIV transmission rates.
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Capulavirus and Grablovirus: two new genera in the family Geminiviridae

Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows. Here, we report the establishment of two new genera: Capulavirus, with four new species (Alfalfa leaf curl virus, Euphorbia caput-medusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus), and Grablovirus, with one new species (Grapevine red blotch virus). The aphid species Aphis craccivora has been shown to be a vector for Alfalfa leaf curl virus, and the treehopper species Spissistilus festinus is the likely vector of Grapevine red blotch virus. In addition, two highly divergent groups of viruses found infecting citrus and mulberry plants have been assigned to the new species Citrus chlorotic dwarf associated virus and Mulberry mosaic dwarf associated virus, respectively. These species have been left unassigned to a genus by the ICTV because their particle morphology and insect vectors are unknown.
Ed Rybicki's insight:
Man, we really started something with our mastre- and begomo- and curtoviruses, all those years ago...B-)
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Phylogenetic trees in R using ggtree

Phylogenetic trees in R using ggtree | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 packa…
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The effective rate of influenza reassortment is limited during human infection

The effective rate of influenza reassortment is limited during human infection | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary The influenza virus is an important cause of disease in the human population. During the course of an infection the virus can evolve rapidly. An important mechanism of viral evolution is reassortment, whereby different segments of the influenza genome are shuffled with other segments, producing new viral combinations. Here we study natural selection and reassortment during the course of infections occurring in human hosts. Examining viral genome sequence data from these infections, we note that genetic variants that were acquired during the growth of viruses in culture are selected against in the human host. In addition, we find evidence that the effective rate of reassortment is low. We suggest that the spatial separation between viruses in different parts of the host airway may limit the extent to which genetically distinct segments reassort with one another. Within the global population of influenza viruses, reassortment remains an important factor. However, reassortment is not so rapid as to exclude the possibility of interactions between genome segments affecting the course of influenza evolution during a single infection.
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Human immunity against EBV—lessons from the clinic

Human immunity against EBV—lessons from the clinic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The mammalian immune system has evolved over many millennia to be best equipped to protect the host from pathogen infection. In many cases, host and pathogen have coevolved, each acquiring sophisticated ways of inducing or protecting from disease. Epstein-Barr virus (EBV) is a human herpes virus that infects >90% of individuals. Despite its ubiquity, infection by EBV is often subclinical; this invariably reflects the necessity of the virus to preserve its host, balanced with sophisticated host immune mechanisms that maintain viral latency. However, EBV infection can result in various, and often fatal, clinical sequelae, including fulminant infectious mononucleosis, hemophagocytic lymphohistiocytosis, lymphoproliferative disease, organomegaly, and/or malignancy. Such clinical outcomes are typically observed in immunosuppressed individuals, with the most extreme cases being Mendelian primary immunodeficiencies (PIDs). Although these conditions are rare, they have provided critical insight into the cellular, biochemical, and molecular requirements for robust and long-lasting immunity against EBV infection. Here, we review the virology of EBV, mechanisms underlying disease pathogenesis in PIDs, and developments in immune cell–mediated therapy to treat disorders associated with or induced by EBV infection.

Via Gilbert C FAURE
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1 tip for effective data visualization in Python

1 tip for effective data visualization in Python | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Data visualization is a common way to represent tabular data in an easier to parse format. In this tutorial, you’ll learn how to make effective data visualizations in Python.
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ORCAN—a web-based meta-server for real-time detection and functional annotation of orthologs

Summary: ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1–2 percent points.
Availability and Implementation: The service is available for free at http://www.combio.pl/orcan/.
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