Viruses and Bioinformatics from Virology.uvic.ca
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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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A Human Type 5 Adenovirus–Based Tuberculosis Vaccine Induces Robust T Cell Responses in Humans Despite Preexisting Anti-Adenovirus Immunity

Abstract

There is an urgent need to develop new tuberculosis (TB) vaccines to safely and effectively boost Bacille Calmette-Guérin (BCG)–triggered T cell immunity in humans. AdHu5Ag85A is a recombinant human type 5 adenovirus (AdHu5)–based TB vaccine with demonstrated efficacy in a number of animal species, yet it remains to be translated to human applications. In this phase 1 study, we evaluated the safety and immunogenicity of AdHu5Ag85A in both BCG-naïve and previously BCG-immunized healthy adults. Intramuscular immunization of AdHu5Ag85A was safe and well tolerated in both trial volunteer groups. Moreover, although AdHu5Ag85A was immunogenic in both trial volunteer groups, it much more potently boosted polyfunctional CD4+ and CD8+ T cell immunity in previously BCG-vaccinated volunteers. Furthermore, despite prevalent preexisting anti-AdHu5 humoral immunity in most of the trial volunteers, we found little evidence that such preexisting anti-AdHu5 immunity significantly dampened the potency of AdHu5Ag85A vaccine. This study supports further clinical investigations of the AdHu5Ag85A vaccine for human applications. It also suggests that the widely perceived negative effect of preexisting anti-AdHu5 immunity may not be universally applied to all AdHu5-based vaccines against different types of human pathogens.

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Personal Genomics Firm 23andMe Patents Designer Baby System, Denies Plans to Use It - Wired Science

Personal Genomics Firm 23andMe Patents Designer Baby System, Denies Plans to Use It - Wired Science | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
As described in a patent recently granted by the United States Patent Office, consumer genomics company 23andMe has developed a system for helping prospective parents choose the traits of their offspring, from disease risk to hair color. Put another way, it’s a designer baby-making system.
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Lateral Gene Transfer from the Dead

Lateral Gene Transfer from the Dead | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria. [Gene tree reconciliation; lateral gene transfer; macroevolution; phylogeny.]

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Mel Melendrez-Vallard's curator insight, October 2, 2013 6:24 PM

sweet...and morbid...but sweet.

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PLOS Pathogens: Host Adaptation Is Contingent upon the Infection Route Taken by Pathogens

PLOS Pathogens: Host Adaptation Is Contingent upon the Infection Route Taken by Pathogens | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract

Evolution of pathogen virulence is affected by the route of infection. Also, alternate infection routes trigger different physiological responses on hosts, impinging on host adaptation and on its interaction with pathogens. Yet, how route of infection may shape adaptation to pathogens has not received much attention at the experimental level. We addressed this question through the experimental evolution of an outbred Drosophila melanogaster population infected by two different routes (oral and systemic) with Pseudomonas entomophila. The two selection regimes led to markedly different evolutionary trajectories. Adaptation to infection through one route did not protect from infection through the alternate route, indicating distinct genetic bases. Finally, relatively to the control population, evolved flies were not more resistant to bacteria other than Pseudomonas and showed higher susceptibility to viral infections. These specificities and trade-offs may contribute to the maintenance of genetic variation for resistance in natural populations. Our data shows that the infection route affects host adaptation and thus, must be considered in studies of host-pathogen interaction.

 

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PLOS Computational Biology: Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PLOS Computational Biology: Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

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Review: Determinants of virulence of influenza A virus - Online First - Springer

Review: Determinants of virulence of influenza A virus - Online First - Springer | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Influenza A viruses cause yearly seasonal epidemics and occasional global pandemics in humans. In the last century, four human influenza A virus pandemics have occurred. Occasionally, influenza A viruses that circulate in other species cross the species barrier and infect humans. Virus reassortment (i.e. mixing of gene segments of multiple viruses) and the accumulation of mutations contribute to the emergence of new influenza A virus variants. Fortunately, most of these variants do not have the ability to spread among humans and subsequently cause a pandemic. In this review, we focus on the threat of animal influenza A viruses which have shown the ability to infect humans. In addition, genetic factors which could alter the virulence of influenza A viruses are discussed. The identification and characterisation of these factors may provide insights into genetic traits which change virulence and help us to understand which genetic determinants are of importance for the pandemic potential of animal influenza A viruses.
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PATRIC Releases Multiple Analysis Tool Enhancements, New Tutorials Page, and New Genomic and Transcriptomic Data

PATRIC Releases Multiple Analysis Tool Enhancements, New Tutorials Page, and New Genomic and Transcriptomic Data | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

 

PATRIC Has Passed the 10,000 Genome Mark!

In fact, we currently have well over 12,000 genomes, and almost 3,000 of them were just added in September 2013.   This release also features USDA Brucella and Mycobacterium bovis genomes, which are available exclusively at PATRIC. 

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Divine Ndi Achiri's curator insight, October 4, 2013 9:00 AM

Open source microscopes will enhance the desire of most researchers to undertake their researches without spending much on buying expensive microscopes.....This will help researchers living in developping countries to do their researches in situ without immigrating to other countries.

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Bioinformatics and Data Analysis in Microbiology | Book

Bioinformatics and Data Analysis in Microbiology | Book | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

This book provides invaluable, up-to-date and detailed information on various aspects of bioinformatics data analysis with applications to microbiology. It describes a number of different useful bioinformatics tools, makes links to some wet-lab techniques, explains different approaches to tackle a problem, talks about current challenges and limitations, gives examples of applications of bioinformatics methods to microbiology, and discusses future trends. The chapters include topics such as genome sequencing techniques, assembly, SNP analysis, annotation, comparative genomics, microbial community profiling, metagenomics, phylogenetic microarrays, barcoding and more. Each chapter is written by scientists who are expert in the field, and is peer-reviewed.

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Coursera

Coursera | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Take free online classes from 80+ top universities and organizations.
Bioinformatics Algorithms (Part 1)Pavel Pevzner, Phillip E. C. Compeau and Nikolay Vyahhi

This course will cover some of the common algorithms underlying the following fundamental topics in bioinformatics: assembling genomes, comparing DNA and protein sequences, finding regulatory motifs, analyzing genome rearrangements, identifying proteins, and many other topics.

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PLOS ONE: Variant Callers for Next-Generation Sequencing Data: A Comparison Study

PLOS ONE: Variant Callers for Next-Generation Sequencing Data: A Comparison Study | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Next generation sequencing (NGS) has been leading the genetic study of human disease into an era of unprecedented productivity. Many bioinformatics pipelines have been developed to call variants from NGS data. The performance of these pipelines depends crucially on the variant caller used and on the calling strategies implemented. We studied the performance of four prevailing callers, SAMtools, GATK, glftools and Atlas2, using single-sample and multiple-sample variant-calling strategies. Using the same aligner, BWA, we built four single-sample and three multiple-sample calling pipelines and applied the pipelines to whole exome sequencing data taken from 20 individuals. We obtained genotypes generated by Illumina Infinium HumanExome v1.1 Beadchip for validation analysis and then used Sanger sequencing as a “gold-standard” method to resolve discrepancies for selected regions of high discordance. Finally, we compared the sensitivity of three of the single-sample calling pipelines using known simulated whole genome sequence data as a gold standard. Overall, for single-sample calling, the called variants were highly consistent across callers and the pairwise overlapping rate was about 0.9. Compared with other callers, GATK had the highest rediscovery rate (0.9969) and specificity (0.99996), and the Ti/Tv ratio out of GATK was closest to the expected value of 3.02. Multiple-sample calling increased the sensitivity. Results from the simulated data suggested that GATK outperformed SAMtools and glfSingle in sensitivity, especially for low coverage data. Further, for the selected discrepant regions evaluated by Sanger sequencing, variant genotypes called by exome sequencing versus the exome array were more accurate, although the average variant sensitivity and overall genotype consistency rate were as high as 95.87% and 99.82%, respectively. In conclusion, GATK showed several advantages over other variant callers for general purpose NGS analyses. The GATK pipelines we developed perform very well.

 
Via Mel Melendrez-Vallard
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Consed: a graphical editor for next-generation sequencing

Consed: a graphical editor for next-generation sequencing | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Summary: The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consedto reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added.

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PLOS ONE: Differential Host Response, Rather Than Early Viral Replication Efficiency, Correlates with Pathogenicity Caused by Influenza Viruses

PLOS ONE: Differential Host Response, Rather Than Early Viral Replication Efficiency, Correlates with Pathogenicity Caused by Influenza Viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Influenza viruses exhibit large, strain-dependent differences in pathogenicity in mammalian hosts. Although the characteristics of severe disease, including uncontrolled viral replication, infection of the lower airway, and highly inflammatory cytokine responses have been extensively documented, the specific virulence mechanisms that distinguish highly pathogenic strains remain elusive. In this study, we focused on the early events in influenza infection, measuring the growth rate of three strains of varying pathogenicity in the mouse airway epithelium and simultaneously examining the global host transcriptional response over the first 24 hours. Although all strains replicated equally rapidly over the first viral life-cycle, their growth rates in both lung and tracheal tissue strongly diverged at later times, resulting in nearly 10-fold differences in viral load by 24 hours following infection. We identified separate networks of genes in both the lung and tracheal tissues whose rapid up-regulation at early time points by specific strains correlated with a reduced viral replication rate of those strains. The set of early-induced genes in the lung that led to viral growth restriction is enriched for both NF-κB binding site motifs and members of the TREM1 and IL-17 signaling pathways, suggesting that rapid, NF-κB –mediated activation of these pathways may contribute to control of viral replication. Because influenza infection extending into the lung generally results in severe disease, early activation of these pathways may be one factor distinguishing high- and low-pathogenicity strains.

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PLOS Pathogens: Highly Significant Antiviral Activity of HIV-1 LTR-Specific Tre-Recombinase in Humanized Mice

PLOS Pathogens: Highly Significant Antiviral Activity of HIV-1 LTR-Specific Tre-Recombinase in Humanized Mice | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Stable integration of HIV proviral DNA into host cell chromosomes, a hallmark and essential feature of the retroviral life cycle, establishes the infection permanently. Current antiretroviral combination drug therapy cannot cure HIV infection. However, expressing an engineered HIV-1 long terminal repeat (LTR) site-specific recombinase (Tre), shown to excise integrated proviral DNA in vitro, may provide a novel and highly promising antiviral strategy. We report here the conditional expression of Tre-recombinase from an advanced lentiviral self-inactivation (SIN) vector in HIV-infected cells. We demonstrate faithful transgene expression, resulting in accurate provirus excision in the absence of cytopathic effects. Moreover, pronounced Tre-mediated antiviral effects are demonstrated in vivo, particularly in humanized Rag2−/−γc−/− mice engrafted with either Tre-transduced primary CD4+ T cells, or Tre-transduced CD34+ hematopoietic stem and progenitor cells (HSC). Taken together, our data support the use of Tre-recombinase in novel therapy strategies aiming to provide a cure for HIV.

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SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Summary: At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid.

 
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A Changing Landscape of Fungal Genomics - The Ecological Genomics of Fungi

A Changing Landscape of Fungal Genomics - The Ecological Genomics of Fungi | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Fungi play an important role in nature and the economy. Being an important source of food, medicine, and enzymes, fungi can also cause human disease, threaten agriculture, and damage buildings. Sequencing of the first fungal genome, Saccharomyces cerevisiae, led to an unprecedented development of the baker's yeast as a model organism and to the building of an entire collection of tools to explore fungal and eukaryotic biology. Large-scale genomic initiatives led to generating a critical mass of data for comparative genomics. New types and large amounts of data posed new challenges for bioinformatics but also opened doors to new applications. This chapter explores the changing landscape of fungal genomics, the challenges in experimental and computational technologies, and the transformations they lead to in biological science.

 

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The Gemini Virus

The Gemini Virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Available in: NOOK Book (eBook), Paperback, Hardcover, Audiobook. This science-based thriller from Wil Mara will chill you to your coreBob Easton thinks he has a cold. Before he dies in agony, four days later, he infects dozens of people.

Via Ed Rybicki
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Ed Rybicki's curator insight, October 1, 2013 9:28 AM

Of course, there are already geminiviruses in good standing: these infect plants rather than people, and do not make people cough, but make plants feel rather uncomfortable.

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12 Beautiful And Terrifying Photos Of Glass-Blown Pathogens

12 Beautiful And Terrifying Photos Of Glass-Blown Pathogens | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
UK-based sculptor Luke Jerram creates glass-blown models of deadly viruses, bacteria, and parasites 1,000,000 times their actual size.
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12 Experts Share Top Curation Tips

Six steps to easy content curation.

 

Curation is sometimes confusing. Everyone has a different definition and it's used in many different ways as part of content and marketing strategies.

 

I asked 10 of my favorite curation experts for their best tips, tools, their favorite curator and suggestions on innovative uses of curation. Each is a curator on Scoop.it, my favorite curation tool and channel. New and experienced curators are going to learn from their advice.


Via Jeff Domansky, Ally Greer
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Lee Wise's curator insight, October 7, 2013 10:54 PM

Some will enjoy this resource!

wanderingsalsero's curator insight, October 20, 2013 8:12 PM

I haven't read this yet but "panels" are always a good way to get a synopsis of any subject......in this case: curation.

Maria Richards's curator insight, March 29, 2014 4:51 PM

It seems so simple here!

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Genome Analysis: Current Procedures and Applications | Book

Genome Analysis: Current Procedures and Applications | Book | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

In this book, an impressive array of expert authors highlight and review current advances in genome analysis. This volume provides an invaluable, up-to-date and comprehensive overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research. The first part of the book is devoted to the methods and applications that arose from, or were significantly advanced by, NGS technologies: the identification of structural variation from DNA-seq data; whole-transcriptome analysis and discovery of small interfering RNAs (siRNAs) from RNA-seq data; motif finding in promoter regions, enhancer prediction and nucleosome sequence code discovery from ChiP-Seq data; identification of methylation patterns in cancer from MeDIP-seq data; transposon identification in NGS data; metagenomics and metatranscriptomics; NGS of viral communities; and causes and consequences of genome instabilities. The second part is devoted to the field of RNA biology with the last three chapters devoted to computational methods of RNA structure prediction including context-free grammar applications.

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Next Generation Sequencing: Current Technologies and Applications | Book

Next Generation Sequencing: Current Technologies and Applications | Book | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Explores the most recent advances in NGS instrumentation and data analysis. Includes a comprehensive description of current NGS platforms, their sequencing chemistries, instrument specifications, general workflows and procedures.
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An open source microscope

A cheap professional microscope based on open-source technologies has been developed by a group of engineers at the University of Cambridge in the United Kingdom.


Via Cesar Sanchez
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The Facts In The Case Of Dr. Andrew Wakefield

The Facts In The Case Of Dr. Andrew Wakefield | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A fifteen page story about the MMR vaccination controversy. As ever, I'm sure a few spelling errors have slipped past me. Feel free to point any out so I can correct them. The reference links for the strip are in the next blog entry.
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Labcoats Unbuttoned

Debunking some of the garbage on the internet...

Supports solid science facts...!!

 

A good read..

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H9N2 avian influenza infection altered expression pattern of Sphiogosine-1-phosphate Receptor 1 in BALB/c mice

H9N2 avian influenza infection altered expression pattern of Sphiogosine-1-phosphate Receptor 1 in BALB/c mice | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The pathological damage inflicted by virulent AIV strains is often caused by inducing a positive feedback loop of cytokines in immune cells that cause excessive inflammation.
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