Virology and Bioinformatics from Virology.ca
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The Gemini Virus

The Gemini Virus | Virology and Bioinformatics from Virology.ca | Scoop.it

"With a nod to the movie Contagion, The Gemini Virus is a vivid (the audience will become mysophobia agoraphobic), exhilarating lethal virus thriller. Part of the fun is the reactions of people as some welcome the biblical End of Days while others blame the government. Fast-paced from the first cough and sneeze, the storyline never takes a respite as the Gemini Virus goes viral."

 

A pity that geminiviruses (the real ones) only infect plants, isn't it?

 

Geminivirus graphic courtesy of Russell Kightley Media

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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

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

get in touch if you want to help curate this topic

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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 6:13 AM
Great work. Keep it going.
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Computational clustering for viral reference proteomes

Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies.

Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt’s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs.

Availability and implementation: http://proteininformationresource.org/rps/viruses/
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Contagious cancers more common in nature than thought, can spread between species

Contagious cancers more common in nature than thought, can spread between species | Virology and Bioinformatics from Virology.ca | Scoop.it
Contagious cancers are a scary idea to begin with, but scientists have made some startling new discoveries about them – they are likely more common in nature than originally thought, and some can even spread between species.
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Nextstrain: Real-time tracking of Zika virus evolution

"Nextstrain allows to view real-time tracking of Zika virus evolution and segment it according to sample time and location"
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Virus Hacks Host Genome, Steals CRISPR to Protect Itself

Virus Hacks Host Genome, Steals CRISPR to Protect Itself | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses have often been described as the ultimate parasite, shedding all of their nonessential parts and leaving behind an extremely efficient genetic transfer apparatus. Phage viruses have evolved to infect various bacteria proficiently and hijack their replication machinery to make more viruses. Yet, this often doesn’t preclude a different virus from concomitantly infecting the same bacterium and competing with or overtaking the original phage invader.


Via Ed Rybicki, Kenzibit
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Ed Rybicki's curator insight, June 17, 6:24 AM
HATE the word "hack" in the context of infection: so lazy!
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Vineyard virus denialism compromises proactive estates’ efforts

Vineyard virus denialism compromises proactive estates’ efforts | Virology and Bioinformatics from Virology.ca | Scoop.it
THE problem of vineyard virus has been a recurring theme among serious wine writers in SA — one that the critics and commentators have taken more seriously than many of the players more directly affected by the problem. This is partly because growers would like to wish it away, and probably believe that if they hear no evil and speak no evil, there will be no evil.

Those who care about wine quality refuse to be silent about it because the fruit from virus-infected vines is palpably impaired.

The virus most prevalent in SA is leaf-roll. Once it has infected a vine, it is there for life. If it is not in the original plant material; it is spread by mealy bugs or by pruning secateurs. Once it is in a vineyard, if it is not isolated and the plant removed, everything will finally be infected. Clearly, doing nothing about it is not a great strategy: it is a bit like ignoring your HIV and hoping it will not become AIDS.

Ed Rybicki's insight:
Now for a SERIOUS virus....
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Genome assembly from synthetic long read clouds

Here, we introduce Architect, a new de novo scaffolder aimed at SLR technologies. Unlike previous assembly strategies, Architect does not require a costly subassembly step; instead it assembles genomes directly from the SLR’s underlying short reads, which we refer to as read clouds. This enables a 4- to 20-fold reduction in sequencing requirements and a 5-fold increase in assembly contiguity on both genomic and metagenomic datasets relative to state-of-the-art assembly strategies aimed directly at fully subassembled long reads.
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One Codex

One Codex | Virology and Bioinformatics from Virology.ca | Scoop.it
One Codex - Fast, portable, and scalable bioinformatics for clinical diagnostics, environmental research, and disease monitoring.
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Benchmarking the next generation of homology inference tools

Conclusion: Profile methods are superior at inferring remote homologs but the difference in accuracy between methods is relatively small. PHMMER and CSBLAST stand out with the highest accuracy, yet still at a reasonable computational cost. Additionally, we show that less than 0.1% of Swiss-Prot protein pairs considered homologous by one database are considered non-homologous by another, implying that these classifications represent equivalent underlying biological phenomena, differing mostly in coverage and granularity.
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3D Structure Of Gene Transcription Activation Identified

3D Structure Of Gene Transcription Activation Identified | Virology and Bioinformatics from Virology.ca | Scoop.it
The three-dimensional structure of a gene-specific transcription activation complex has been discovered by scientists at Rutgers University. This is the first structural and mechanistic description of the process cells use to turn on, or activate, specific genes in response to changes in cell type, developmental state and environment. Transcription is the first in a series of steps cells take to read out genetic information in DNA. Richard H. Ebright and other Rutgers scientists have shown how a transcription activator protein interacts with the enzyme (RNA polymerase) that cells use to perform transcription. They also show how the transcription activator protein
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The Role of microRNAs in the Pathogenesis of Herpesvirus Infection

The Role of microRNAs in the Pathogenesis of Herpesvirus Infection | Virology and Bioinformatics from Virology.ca | Scoop.it
MicroRNAs (miRNAs) are small non-coding RNAs important in gene regulation. They are able to regulate mRNA translation through base-pair complementarity. Cellular miRNAs have been involved in the regulation of nearly all cellular pathways, and their deregulation has been associated with several diseases such as cancer. Given the importance of microRNAs to cell homeostasis, it is no surprise that viruses have evolved to take advantage of this cellular pathway. Viruses have been reported to be able to encode and express functional viral microRNAs that target both viral and cellular transcripts. Moreover, viral inhibition of key proteins from the microRNA pathway and important changes in cellular microRNA pool have been reported upon viral infection. In addition, viruses have developed multiple mechanisms to avoid being targeted by cellular microRNAs. This complex interaction between host and viruses to control the microRNA pathway usually favors viral infection and persistence by either reducing immune detection, avoiding apoptosis, promoting cell growth, or promoting lytic or latent infection. One of the best examples of this virus-host-microRNA interplay emanates from members of the Herperviridae family, namely the herpes simplex virus type 1 and type 2 (HSV-1 and HSV-2), human cytomegalovirus (HCMV), human herpesvirus 8 (HHV-8), and the Epstein–Barr virus (EBV). In this review, we will focus on the general functions of microRNAs and the interactions between herpesviruses, human hosts, and microRNAs and will delve into the related mechanisms that contribute to infection and pathogenesis.
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An Introduction to Programming for Bioscientists: A Python-Based Primer

Contemporary biology has largely become computational biology, whether it involves applying physical principles to simulate the motion of each atom in a piece of DNA, or using machine learning algorithms to integrate and mine “omics” data across whole cells (or even entire ecosystems). The ability to design algorithms and program computers, even at a novice level, may be the most indispensable skill that a modern researcher can cultivate. As with human languages, computational fluency is developed actively, not passively. This self-contained text, structured as a hybrid primer/tutorial, introduces any biologist—from college freshman to established senior scientist—to basic computing principles (control-flow, recursion, regular expressions, etc.) and the practicalities of programming and software design. We use the Python language because it now pervades virtually every domain of the biosciences, from sequence-based bioinformatics and molecular evolution to phylogenomics, systems biology, structural biology, and beyond. To introduce both coding (in general) and Python (in particular), we guide the reader via concrete examples and exercises. We also supply, as Supplemental Chapters, a few thousand lines of heavily-annotated, freely distributed source code for personal study.
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Won Gi Yoo's curator insight, June 7, 10:05 PM
내용은 둘째치고 논문이 43장짜리..;;;
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A bird’s eye view of influenza A virus transmission: challenges with characterizing both sides of a co-evolutionary dynamic

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ORFanFinder: automated identification of taxonomically restricted orphan genes

Motivation: Orphan genes, also known as ORFans, are newly evolved genes in a genome that enable the organism to adapt to specific living environment. The gene content of every sequenced genome can be classified into different age groups, based on how widely/narrowly a gene’s homologs are distributed in the context of species taxonomy. Those having homologs restricted to organisms of particular taxonomic ranks are classified as taxonomically restricted ORFans.

Results: Implementing this idea, we have developed an open source program named ORFanFinder and a free web server to allow automated classification of a genome’s gene content and identification of ORFans at different taxonomic ranks. ORFanFinder and its web server will contribute to the comparative genomics field by facilitating the study of the origin of new genes and the emergence of lineage-specific traits in both prokaryotes and eukaryotes.

Availability and implementation: http://cys.bios.niu.edu/orfanfinder

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GenVisR: Genomic Visualizations in R

Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.

Availability and Implementation: GenVisR is an R package available via Bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website.
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Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics: Cell Reports

Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics: Cell Reports | Virology and Bioinformatics from Virology.ca | Scoop.it
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Assemblytics: a web analytics tool for the detection of variants from an assembly. - PubMed - NCBI

Assemblytics is a web app for detecting and analyzing variants from a de novo genome assembly aligned to a reference genome. It incorporates a unique anchor filtering approach to increase robustness to repetitive elements, and identifies six classes of variants based on their distinct alignment signatures. Assemblytics can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species. Multiple interactive visualizations enable in-depth explorations of the genomic distributions of variants.
AVAILABILITY AND IMPLEMENTATION:
http://assemblytics.com, https://github.com/marianattestad/assemblytics ;

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Sandia researchers discover mechanism for Rift Valley fever virus infection - Scienmag

Sandia researchers discover mechanism for Rift Valley fever virus infection - Scienmag | Virology and Bioinformatics from Virology.ca | Scoop.it
LIVERMORE, Calif. -- Viruses can't live without us -- literally. As obligate parasites, viruses need a host cell to survive and grow. Scientists are exploiting this characteristic by developing t..
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fqtools: an efficient software suite for modern FASTQ file manipulation

Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (e.g. searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines.

Availability and implementation: fqtools is open source and is available at: https://github.com/alastair-droop/fqtools.
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Viral Pathogenesis: Tracing the steps of Zika virus 

Epidemiological data have linked the infection of pregnant women with Zika virus (ZIKV) to microcephaly of their babies, and ZIKV was detected in brain tissue and amniotic fluid of microcephalic fetuses; however, direct experimental evidence of a causal link was scarce. Now, for the first time, three studies in pregnant mice show pathological changes in unborn mice following infection with ZIKV.
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Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers

Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression.
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Recombinant Sheep Pox Virus Proteins Elicit Neutralizing Antibodies

The aim of this work was to evaluate the immunogenicity and neutralizing activity of sheep pox virus (SPPV; genus Capripoxvirus, family Poxviridae) structural proteins as candidate subunit vaccines to control sheep pox disease. SPPV structural proteins were identified by sequence homology with proteins of vaccinia virus (VACV) strain Copenhagen. Four SPPV proteins (SPPV-ORF 060, SPPV-ORF 095, SPPV-ORF 117, and SPPV-ORF 122), orthologs of immunodominant L1, A4, A27, and A33 VACV proteins, respectively, were produced in Escherichia coli. Western blot analysis revealed the antigenic and immunogenic properties of SPPV-060, SPPV-095, SPPV-117 and SPPV-122 proteins when injected with adjuvant into experimental rabbits. Virus-neutralizing activity against SPPV in lamb kidney cell culture was detected for polyclonal antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins. To our knowledge, this is the first report demonstrating the virus-neutralizing activities of antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins.
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Quantifying influenza virus diversity and transmission in humans. - PubMed - NCBI

Nat Genet. 2016 Feb;48(2):195-200. doi: 10.1038/ng.3479. Epub 2016 Jan 4. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
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Evaluation of potentially achievable vaccination coverage with simultaneous administration of vaccines among children in the United States

Evaluation of potentially achievable vaccination coverage with simultaneous administration of vaccines among children in the United States | Virology and Bioinformatics from Virology.ca | Scoop.it
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