Virology and Bioi...
Follow
Find
66.6K views | +0 today
Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Rescooped by Kenzibit from Host Cell & Pathogen Interactions
Scoop.it!

Herpes Simplex Virus Type 1 Single Strand DNA Binding Protein and Helicase/Primase Complex Disable Cellular ATR Signaling

Herpes Simplex Virus Type 1 Single Strand DNA Binding Protein and Helicase/Primase Complex Disable Cellular ATR Signaling | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
more...
No comment yet.
Scooped by Torben Barsballe
Scoop.it!

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

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

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.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

History: Great myths die hard

History: Great myths die hard | Virology and Bioinformatics from Virology.ca | Scoop.it
Finding that part of the story of Louis Pasteur's rabies vaccine is false, Héloïse Dufour and Sean Carroll explore how science fables are born, spread and die.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

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

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes | Virology and Bioinformatics from Virology.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.

 
more...
No comment yet.
Rescooped by Bradford Condon from Genomics and metagenomics of microbes
Scoop.it!

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

A Changing Landscape of Fungal Genomics - The Ecological Genomics of Fungi | Virology and Bioinformatics from Virology.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.

 

more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

The Gemini Virus

The Gemini Virus | Virology and Bioinformatics from Virology.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
more...
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.

Scooped by C_Fleis
Scoop.it!

12 Beautiful And Terrifying Photos Of Glass-Blown Pathogens

12 Beautiful And Terrifying Photos Of Glass-Blown Pathogens | Virology and Bioinformatics from Virology.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.
more...
No comment yet.
Rescooped by Chris Upton + helpers from Lean Content Marketing
Scoop.it!

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
more...
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!

Scooped by Chris Upton + helpers
Scoop.it!

Genome Analysis: Current Procedures and Applications | Book

Genome Analysis: Current Procedures and Applications | Book | Virology and Bioinformatics from Virology.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.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Next Generation Sequencing: Current Technologies and Applications | Book

Next Generation Sequencing: Current Technologies and Applications | Book | Virology and Bioinformatics from Virology.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.
more...
No comment yet.
Rescooped by Chris Upton + helpers from Twisted Microbiology
Scoop.it!

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
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

The Facts In The Case Of Dr. Andrew Wakefield

The Facts In The Case Of Dr. Andrew Wakefield | Virology and Bioinformatics from Virology.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.
more...
No comment yet.
Scooped by Torben Barsballe
Scoop.it!

PLOS Pathogens: APOBEC3G Polymorphism as a Selective Barrier to Cross-Species Transmission and Emergence of Pathogenic SIV and AIDS in a Primate Host

PLOS Pathogens: APOBEC3G Polymorphism as a Selective Barrier to Cross-Species Transmission and Emergence of Pathogenic SIV and AIDS in a Primate Host | Virology and Bioinformatics from Virology.ca | Scoop.it

Cellular restriction factors, which render cells intrinsically resistant to viruses, potentially impose genetic barriers to cross-species transmission and emergence of viral pathogens in nature. One such factor is APOBEC3G. To overcome APOBEC3G-mediated restriction, many lentiviruses encode Vif, a protein that targets APOBEC3G for degradation. As with many restriction factor genes, primate APOBEC3G displays strong signatures of positive selection. This is interpreted as evidence that the primate APOBEC3G locus reflects a long-term evolutionary “arms-race” between retroviruses and their primate hosts. Here, we provide direct evidence that APOBEC3G has functioned as a barrier to cross-species transmission, selecting for viral resistance during emergence of the AIDS-causing pathogen SIVmac in captive colonies of Asian macaques in the 1970s. Specifically, we found that rhesus macaques have multiple, functionally distinct APOBEC3G alleles, and that emergence of SIVmac and simian AIDS required adaptation of the virus to evade APOBEC3G-mediated restriction. Our evidence includes the first comparative analysis of APOBEC3G polymorphism and function in both a reservoir and recipient host species (sooty mangabeys and rhesus macaques, respectively), and identification of adaptations unique to Vif proteins of the SIVmac lineage that specifically antagonize rhesus APOBEC3G alleles. By demonstrating that interspecies variation in a known restriction factor selected for viral counter-adaptations in the context of a documented case of cross-species transmission, our results lend strong support to the evolutionary “arms-race” hypothesis. Importantly, our study confirms that APOBEC3G divergence can be a critical determinant of interspecies transmission and emergence of primate lentiviruses, including viruses with the potential to infect and spread in human populations.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

A comprehensive map of the influenza A virus replication cycle |BMC Systems Biology

Background

Influenza is a common infectious disease caused by influenza viruses. Annual epidemics cause severe illnesses, deaths, and economic loss around the world. To better defend against influenza viral infection, it is essential to understand its mechanisms and associated host responses. Many studies have been conducted to elucidate these mechanisms, however, the overall picture remains incompletely understood. A systematic understanding of influenza viral infection in host cells is needed to facilitate the identification of influential host response mechanisms and potential drug targets.

Description We constructed a comprehensive map of the influenza A virus ('IAV') life cycle ('FluMap') by undertaking a literature-based, manual curation approach. Based on information obtained from publicly available pathway databases, updated with literature-based information and input from expert virologists and immunologists, FluMap is currently composed of 960 factors (i.e., proteins, mRNAs etc.) and 456 reactions, and is annotated with ~500 papers and curation comments. In addition to detailing the type of molecular interactions, isolate/strain specific data are also available. The FluMap was built with the pathway editor CellDesigner in standard SBML (Systems Biology Markup Language) format and visualized as an SBGN (Systems Biology Graphical Notation) diagram. It is also available as a web service (online map) based on the iPathways+ system to enable community discussion by influenza researchers. We also demonstrate computational network analyses to identify targets using the FluMap.

Conclusion

The FluMap is a comprehensive pathway map that can serve as a graphically presented knowledge-base and as a platform to analyze functional interactions between IAV and host factors. Publicly available webtools will allow continuous updating to ensure the most reliable representation of the host-virus interaction network. The FluMap is available at http://www.influenza-x.org/flumap/.

more...
Ed Rybicki's comment, October 4, 2013 5:34 PM
Nice one!
Scooped by Alice Gibbons
Scoop.it!

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.

more...
No comment yet.
Scooped by Alice Gibbons
Scoop.it!

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 | Virology and Bioinformatics from Virology.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.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Lateral Gene Transfer from the Dead

Lateral Gene Transfer from the Dead | Virology and Bioinformatics from Virology.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.]

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

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

Scooped by C_Fleis
Scoop.it!

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 | Virology and Bioinformatics from Virology.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.

 

more...
No comment yet.
Scooped by C_Fleis
Scoop.it!

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

PLOS Computational Biology: Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs | Virology and Bioinformatics from Virology.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.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

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

Review: Determinants of virulence of influenza A virus - Online First - Springer | Virology and Bioinformatics from Virology.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.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

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 | Virology and Bioinformatics from Virology.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. 

more...
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.

Scooped by Chris Upton + helpers
Scoop.it!

Bioinformatics and Data Analysis in Microbiology | Book

Bioinformatics and Data Analysis in Microbiology | Book | Virology and Bioinformatics from Virology.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.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Coursera

Coursera | Virology and Bioinformatics from Virology.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.

more...
No comment yet.
Rescooped by Chris Upton + helpers from Bioinformatics Software: Sequence Analysis
Scoop.it!

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

PLOS ONE: Variant Callers for Next-Generation Sequencing Data: A Comparison Study | Virology and Bioinformatics from Virology.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
more...
No comment yet.