Viruses and Bioinformatics from Virology.uvic.ca
84.7K views | +10 today
Follow
 
Scooped by Chris Upton + helpers
onto Viruses and Bioinformatics from Virology.uvic.ca
Scoop.it!

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.

more...
No comment yet.
Viruses and Bioinformatics from Virology.uvic.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...
Scooped by Chris Upton + helpers
Scoop.it!

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

more...
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.
Scooped by Cindy
Scoop.it!

Viral phylogeny in court: the unusual case of the Valencian anesthetist

A large and complex outbreak of hepatitis C virus in Valencia, Spain that began 25 years ago led to the prosecution and conviction of an anesthetist who was accused of infecting hundreds of his patients. Evolutionary analyses of viral gene sequences were presented as evidence in the trial, and these are now described in detail by González-Candelas and colleagues in a paper published in BMC Biology. Their study illustrates the challenges and opportunities that arise from the use of phylogenetic inference in criminal trials concerning virus transmission.

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

The ancestors are not among us

The ancestors are not among us | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
>>Terms like 'basal', 'early-diverging', and 'first-branching' reflect persistent misconceptions about evolution and phylogenies
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

SWORD—a highly efficient protein database search

Motivation: Protein database search is one of the fundamental problems in bioinformatics. For decades, it has been explored and solved using different exact and heuristic approaches. However, exponential growth of data in recent years has brought significant challenges in improving already existing algorithms. BLAST has been the most successful tool for protein database search, but is also becoming a bottleneck in many applications. Due to that, many different approaches have been developed to complement or replace it. In this article, we present SWORD, an efficient protein database search implementation that runs 8–16 times faster than BLAST in the sensitive mode and up to 68 times faster in the fast and less accurate mode. It is designed to be used in nearly all database search environments, but is especially suitable for large databases. Its sensitivity exceeds that of BLAST for majority of input datasets and provides guaranteed optimal alignments.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Life Expectancy I: How Far We've Come - Common Science Space

Life Expectancy I: How Far We've Come - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
In 2006 the World Health Organisation coined a new term: “the Glasgow Effect”. It resulted from an analysis of life expectancy data in two neighbourhoods in Glasgow, Scotland. One, a prosperous upper-middle-class village outside the central city, Lenzie, had a life expectancy for a male child at birth of 82, up there with the highest... Continue Reading
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Assessing Student Learning

Assessing Student Learning | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
For those of us involved in curriculum redesign, the University of Leicester Learning Institute has put together a useful page o
more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

Science fiction: Boldly going for 50 years

Science fiction: Boldly going for 50 years | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Sidney Perkowitz scans the impacts of Star Trek on science, technology and society.

Via Ed Rybicki
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Phage community in the gut

The gut microbiome has an important role in human health, but the role of phages in maintaining the structure and function of the gut microbial community is unclear. Manrique et al. analysed phages that are associated with the gut microbiome of healthy individuals and identified 23 phages that were common in more than half of the individuals. This set of gut microbiome phages was less prevalent in individuals with gastrointestinal disease, which suggests that they have a role in human health. Next, the authors investigated the structure of the phage community using a network analysis tool. They identified 44 phage groups, of which nine were shared across more than 50% of healthy individuals. On the basis of their results, the authors propose the existence of a healthy gut phageome (HGP) that comprises a core, a common and a low overlap group. Future studies are required to elucidate the role of the phageome in health and disease.

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

HIV uses a 'molecular iris' to control capsid access

HIV uses a 'molecular iris' to control capsid access | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
HIV hides its genome inside a proteinaceous shell formed by capsid hexamers to evade detection and degradation in the cytosol of host cells; however, the capsid also hinders access of substrates that are essential for reverse transcription, such as deoxynucleoside triphosphates (dNTPs). Thus far, it was unclear how HIV imported dNTPs into the capsid. Jacques et al. now show that a dynamic pore exists in the centre of each capsid hexamer that enables the entry of dNTPs and thereby supports reverse transcription inside the capsid.

The HIV capsid is a conical structure that is formed by a single protein, the capsid protein. Capsid monomers are arranged into a symmetrical hexamer around a central axis and the authors hypothesized that a pore might exist along this axis. However, there was no evidence for such a pore from previous hexamer structures. In fact, previous structures showed that the amino-terminal β-hairpins of each capsid monomer blocked the opening of such a potential pore. When the authors examined this region more closely, including in structures of capsid monomers, they noticed that the β-hairpin is flexible and can assume different conformations by tilting up to 15 Å away from the axis of symmetry. Indeed, when reconstructing a capsid hexamer based on monomer structures with this 'open' β-hairpin conformation, a central pore is formed. The conformational change is likely to depend on the protonation status of a histidine residue at the base of the β-hairpin. This is supported by the observation that structures that were obtained at a high crystallisation pH adopted a closed conformation, whereas structures that were obtained at a low pH adopted an open conformation. Interestingly, at physiological pH, the β-hairpin assumes an intermediate position, indicating high flexibility. Thus, the β-hairpin functions as a 'molecular iris' that controls entry to a central pore in the capsid.

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

Dengue vaccine could make things worse: ‘We should be careful in considering where and how to use this vaccine’ | Outbreak News Today

Dengue vaccine could make things worse: ‘We should be careful in considering where and how to use this vaccine’ | Outbreak News Today | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Rescooped by Chris Upton + helpers from Funding, Careers and Communication in Science Research
Scoop.it!

Why women leave academia and why universities should be worried

Why women leave academia and why universities should be worried | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A recent report reveals that only 12% of third year female PhD students want a career in academia. Curt Rice looks at the reasons why and warns that universities' survival is at risk

Via Ian M Mackay, PhD
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

The debt we owe to retroviruses

The debt we owe to retroviruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
It was already known that genes inherited from ancient retroviruses are essential to the formation of the placenta in mammals. Now it appears that genes with retrovirus origins may also be responsible for the more developed muscle mass seen in males. Retroviruses carry proteins on their surface that are able to mediate fusion of their…
more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Trimming adapter sequences - is it necessary?

Trimming adapter sequences - is it necessary? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
This post discusses whether you can skip the adapter removal step in NGS data analysis
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Quantifying influenza virus diversity and transmission in humans

Influenza A virus is characterized by high genetic diversity1, 2, 3. However, most of what is known about influenza evolution has come from consensus sequences sampled at the epidemiological scale4 that only represent the dominant virus lineage within each infected host. Less is known about the extent of within-host virus diversity and what proportion of this diversity is transmitted between individuals5. To characterize virus variants that achieve sustainable transmission in new hosts, we examined within-host virus genetic diversity in household donor-recipient pairs from the first wave of the 2009 H1N1 pandemic when seasonal H3N2 was co-circulating. Although the same variants were found in multiple members of the community, the relative frequencies of variants fluctuated, with patterns of genetic variation more similar within than between households. We estimated the effective population size of influenza A virus across donor-recipient pairs to be approximately 100–200 contributing members, which enabled the transmission of multiple lineages, including antigenic variants.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Software citation principles

Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.
more...
No comment yet.
Scooped by Vern Paetkau
Scoop.it!

Life Expectancy II: It's in the Genes - Common Science Space

Life Expectancy II: It's in the Genes - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
(Microscopic image of C. elegans with Nomarski DIC optics: by permission, Prof. Sander van den Heuvel, Developmental Biology, Universiteit Utrecht. About 200x lifesize.) How long can we expect to live in the future? The longest recorded human life is that of a French woman, Jeanne Calment, who died aged 122 and a half, in 1997.... Continue Reading
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Genomoviridae: a new family of widespread single-stranded DNA viruses

Genomoviridae: a new family of widespread single-stranded DNA viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Here, we introduce a new family of eukaryote-infecting single-stranded (ss) DNA viruses that was created recently by the International Committee on Taxonomy of Viruses (ICTV). The family, named Genomoviridae, contains a single genus, Gemycircularvirus, which currently has one recognized virus species, Sclerotinia gemycircularvirus 1. Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) is currently the sole representative isolate of the family; however, a great number of SsHADV-1-like ssDNA virus genomes has been sequenced from various environmental, plant- and animal-associated samples, indicating that members of family Genomoviridae are widespread and abundant in the environment.

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

Background to Ebola's 40th: The Discovery of Filoviruses

Background to Ebola's 40th: The Discovery of Filoviruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Ebola is 40 today! The discovery of filoviruses: Marburg and Ebola Marburg virus In 1967, the world was introduced to a new virus: thirty-one people in Marburg and Frankfurt in Germany, and Belgrade in the then Yugoslavia, became infected in a linked outbreak with a novel haemorrhagic fever agent. Twenty-five of them were laboratory workers associated…

Via Ed Rybicki
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

A gateway protein for norovirus

The host factors that noroviruses rely on for invasion, replication and pathogenesis, and that consequently determine the species tropism of the virus, are largely unidentified. Virgin and colleagues used CRISPR–Cas9 to perform a genome-wide screen for host factors that are required for the infection of mouse cells by murine norovirus (MNoV). Four loss-of-function mutations in a single gene (Cd300lf) were identified that enabled mouse cells to survive infection by MNoV. Additional experiments in cell lines, primary cells and in vivo confirmed that Cd300lf is specifically required for the binding and replication of MNoV, and that Cd300lf is the primary receptor for MNoV infection. Expressing murine Cd300lf in HeLa cells made these human cells permissive for infection by MNoV, thus removing the species tropism barrier of MNoV infection. Finally, structural analysis of Cd300lf, which is a cell-surface immunoglobulin domain-containing protein, revealed a putative ligand binding site in its ectodomain.

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Reconstruction of Zika Virus Introduction in Brazil

Reconstruction of Zika Virus Introduction in Brazil | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
We estimated the speed of Zika virus introduction in Brazil by using confirmed cases at the municipal level. Our models indicate a southward pattern of introduction starting from the northeastern coast and a pattern of movement toward the western border with an average speed of spread of 42 km/day or 15,367 km/year.
more...
No comment yet.
Suggested by Gilbert C FAURE
Scoop.it!

Identification of small-molecule inhibitors of Zika virus infection and induced neural cell death

Identification of small-molecule inhibitors of Zika virus infection and induced neural cell death | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A high-throughput screen of preclinical, investigational and FDA-approved drugs identifies compounds that possess antiviral and neuroprotective effects against Zika virus infection in human neural progenitor cells and astrocytes.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

A Scientist's Guide To Social Media

A Scientist's Guide To Social Media | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Social networking sites like Facebook, LinkedIn, and Twitter can be intimidating for introverted scientists—all that interaction, 24/7. But actually, online communities are perfect for people who want to cogitate before they comment. Social networks also give extroverts a channel for real-time global intercommunication. No matter your personality type, career advisors recommend that postdocs use online networking tools to make connections, exchange scientific ideas, and advance a career.
more...
No comment yet.