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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Diversity of large DNA viruses of invertebrates

In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for invertebrates. We present their taxonomical classification and describe the evolutionary relationships among various groups of invertebrate-infecting viruses. We also indicate the relationships of the invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of the most important viruses in these families and indicate, which orders of invertebrates are susceptible to these pathogens.
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A Random Name Picker for Your Classroom

A Random Name Picker for Your Classroom | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Name Picker Ninja  is free tool for quickly randomly selecting a name from a list. Using Name Picker Ninja is a simple matter of pasting o
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Points of Significance : Statistics for Biologists

Points of Significance : Statistics for Biologists | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A collection of articles from the publisher of Nature that discusses statistical issues biologists should be aware of and provides practical advice to improve the statistical rigor and reproducibility of their work.
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How to Record Video Notes With MoocNote

MoocNote is a free tool for taking notes while watching a YouTube or Vimeo video. All of your notes are timestamped and all of your note
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Nanoparticle vaccines against dengue fever?

Nanoparticle vaccines against dengue fever? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Every year more than 350 million people in over 120 countries contact dengue fever, which can cause symptoms ranging from aching muscles and a skin rash to life-threatening haemorrhagic fever. Researchers have struggled to create effective vaccines against dengue virus, in part because four distinct serotypes of the virus cause dengue fever and a vaccine…
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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…
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How to read and understand a scientific paper: a guide for non-scientists

How to read and understand a scientific paper: a guide for non-scientists | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Update (8/30/14): I've written a shorter version of this guide for teachers to hand out to their classes. If you'd like a PDF, shoot me an email: jenniferraff (at) utexas (dot) edu. Last week's post (The truth about vaccinations: Your physician knows more than the University of Google) sparked a very lively discussion, with comments…
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Compound found to trigger innate immunity against viruses

Compound found to trigger innate immunity against viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A drug-like molecule can activate innate immunity and induce genes to control infection in a range of RNA viruses, including West Nile, dengue, hepatitis C, influenza A, respiratory syncytial, Nipah, Lassa and Ebola, according to new research.
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Points of Significance : Statistics for Biologists

Points of Significance : Statistics for Biologists | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A collection of articles from the publisher of Nature that discusses statistical issues biologists should be aware of and provides practical advice to improve the statistical rigor and reproducibility of their work.
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How To Detect ANY Virus In A Patient's Blood

How To Detect ANY Virus In A Patient's Blood | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Better diagnosis leads to better treatment – that’s well-known. Easier said than done, of course, since that’s not always possible when tests for diseases or infections take time to generate results, for example, or are inaccurate or insensitive. Take viruses: There is an abundance out there capable of causing disease, many of which can present similar symptoms or, perhaps worse, none at all. Detection can, therefore, be a bit of a nightmare, sometimes demanding a labor-intensive and costly suite of tests to get to the bottom of a case.


What if there was a universal, one-size-fits-all-test that could pick up any known virus in a sample, eliminating this time-consuming detective work? That might sound quite out of our clutches, but researchers at Washington University School of Medicine might just have achieved this long-awaited, eyebrow-raising feat.


“With this test, you don’t have to know what you’re looking for,” senior author Gregory Storch said in a statement. “It casts a broad net and can efficiently detect viruses that are present at very low levels. We think the test will be especially useful in situations where a diagnosis remains elusive after standard testing or in situations in which the cause of a disease outbreak is unknown.”


Describing their work in Genome Research, the results are pretty impressive. To make their “ViroCap,” the researchers began by creating a broad panel of sequences to be targeted by the test, which they generated using unique stretches of DNA or RNA found in viruses across 34 different human- and animal-infecting families. This resulted in millions of stretches of nucleic acid that can be used to capture matching strands in a sample, should they be present.


But the broad spectrum of this test is not its only remarkable quality: It’s so sensitive that it can even pick up slight variations in sequences, meaning that a virus’ subtype can also be identified – a feature not possible with many traditional tests. Although that wouldn’t necessarily change the way a patient is treated, it could aid disease surveillance.


To demonstrate its capabilities, the researchers took samples from a small group of patients at St. Louis Children’s Hospital and compared the results to those obtained from standard tests. While traditional sequencing managed to find viruses in the majority of the children, ViroCap also managed to pick up some common viruses that it had failed to detect. These included a flu virus and the virus responsible for chickenpox. In a second test run on a different group of children displaying fevers, the new test found an additional seven viruses to the 11 that the traditional testing managed to detect.  


All of this sounds great on paper, but of course it is not yet ready to be used in the clinic. Further trials are required first to check its accuracy on larger groups of people, as so far only a limited number of patients have been screened. But when the time comes, the team plans to make it widely available, which would be welcome in the face of outbreaks like Ebola. Furthermore, the team ultimately hopes to tweak it so that it can detect genetic material from other microbes, like bacteria. If that’s possible, we could have a seriously useful machine on our hands that could change diagnostic medicine for the better. 


Via Dr. Stefan Gruenwald
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Scientists Unearth a Trove of New Bacteria-Killing Viruses

Scientists Unearth a Trove of New Bacteria-Killing Viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Bacteria prey on humans, but the bugs have to beware of their own predators, too: a special class of viruses called phages.
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Rakesh Yashroy's curator insight, September 4, 2015 11:49 AM

Every living organism has an enemy threatening its existence. What is  the threat to bacteriophages? Any reply!#@?

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How Canadian researchers reconstituted an extinct poxvirus for $100,000 using mail-order DNA

How Canadian researchers reconstituted an extinct poxvirus for $100,000 using mail-order DNA | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A study that brought horsepox back to life is triggering a new debate about the risks and power of synthetic biology
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Academic Writing (#AcWri) – Raul Pacheco-Vega, PhD

This page is dedicated to suggestions I provide to improve scholars, professors and students’ writing. These tips have worked for me, and I hope they will work for you! My Top 10 Tips to Improve Your Academic Writing
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A global perspective on bioinformatics training needs

Abstract In the last decade, life-science research has become increasingly data-intensive and computational. Nevertheless, basic bioinformatics and data stewardship are still only rarely taught in life-science degree programmes, creating a widening skills gap that spans educational levels and career roles. To better understand this situation, we ran surveys to determine how the skills dearth is affecting the need for bioinformatics training worldwide. Perhaps unsurprisingly, we found that respondents wanted more short courses to help boost their expertise and confidence in data analysis and interpretation. However, it was evident that most respondents appreciated their need for training only after designing their experiments and collecting their data. This is clearly rather late in the research workflow, and suboptimal from a training perspective, as skills acquired to address a specific need at a particular time are seldom retained, engendering a cycle of low confidence in trainees. To ensure that such skill gaps do not continue to create barriers to the progress of research, we argue that universities should strive to bring their life-science curricula into the digital-data era. Meanwhile, the demand for point-of-need training in bioinformatics and data stewardship will grow. While this situation persists, international groups like GOBLET are increasing their efforts to enlarge the community of trainers and quench the global thirst for bioinformatics training.

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A Multicomponent Animal Virus Isolated from Mosquitoes

A Multicomponent Animal Virus Isolated from Mosquitoes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Multicomponent viruses, which separately package different genome segments, were thought
to be restricted to plant and fungal hosts. Ladner et al. characterize a multicomponent
mosquito virus and describe an evolutionarily related, segmented virus in a nonhuman
primate. These findings provide evidence for multicomponent animal viruses and suggest
relevance to animal health.
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Cells fight back against virus factories

Cells fight back against virus factories | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
This week I've been talking to first year students about cell biology, discussing how much the environment of the cell varies from one site to another within the cell. Viruses "know" this and much virus replication is localized at particular sites within the cell, not just occurring haphazardly. The first example of this is to…
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Newly discovered multicomponent virus is the first of its kind to infect animals

Newly discovered multicomponent virus is the first of its kind to infect animals | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A story about Science from Phys.org, as featured in Newsfusion's Science News app.
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Colorado Arts & Sciences Magazine » An evolutionary arms race between Ebola virus, bats

Colorado Arts & Sciences Magazine records the news in the College of Arts and Sciences at CU-Boulder.
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Oncolytic Virotherapy - Where Are We Going?

Oncolytic Virotherapy - Where Are We Going? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The last few years have seen an increased interest in immunotherapy in the treatment of malignant disease. In particular, there has been significant enthusiasm for oncolytic virotherapy, with a large amount of pre-clinical data showing promise in animal models in a wide range of tumour types. How do we move forward into the clinical setting and translate something which has such potential into meaningful clinical outcomes? This article reviews how the field of oncolytic virotherapy has developed so far and what the future may hold.
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Influenza Virus Reassortment Is Enhanced by Semi-infectious Particles but Can Be Suppressed by Defective Interfering Particles

Influenza Virus Reassortment Is Enhanced by Semi-infectious Particles but Can Be Suppressed by Defective Interfering Particles | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author Summary Since the genome of an influenza A virus has eight non-contiguous segments, two influenza A viruses can exchange genes readily when they infect the same cell. This process of reassortment is important to the evolution of the virus and is one reason why this pathogen is constantly changing. It has long been known that a large proportion of the virus particles that influenza and many other RNA viruses produce are not fully infectious, but the biological significance of these part
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PLOS Pathogens: RNA Virus Reassortment: An Evolutionary Mechanism for Host Jumps and Immune Evasion

PLOS Pathogens: RNA Virus Reassortment: An Evolutionary Mechanism for Host Jumps and Immune Evasion | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Reassortment is an evolutionary mechanism of segmented RNA viruses that plays an important but ill-defined role in virus emergence and interspecies transmission. Recent experimental studies have greatly enhanced our understanding of the cellular mechanisms of reassortment within a host cell. Our purpose here is to offer a brief introduction on the role of reassortment in segmented RNA virus evolution, explain the host cellular mechanisms of reassortment, and provide a synthesis of recent experimental findings and methodological developments. While we focus our discussion on influenza viruses, wherein most of the studies on reassortment have been carried out, the concepts presented are broadly applicable to other multipartite genomes.

 
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