Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Viruses, Immunology & Bioinformatics from Virology.uvic.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: | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 2017 12:46 PM
Thank You.
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Widespread position-specific conservation of synonymous rare codons within coding sequences

Widespread position-specific conservation of synonymous rare codons within coding sequences | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Proteins are long linear polymers that must fold into complex three-dimensional shapes in order to carry out their cellular functions. Every protein is synthesized by the ribosome, which decodes each trinucleotide codon in an mRNA coding sequence in order to select the amino acid residue that will occupy each position in the protein sequence. Most amino acids can be encoded by more than one codon, but these synonymous codons are not used with equal frequency. Rare codons are associated with generally slower rates for protein synthesis, and for this reason have traditionally been considered mildly deleterious for efficient protein production. However, because synonymous codon substitutions do not change the sequence of the encoded protein, the majority view is that they merely reflect genomic ‘background noise’. To the contrary, here we show that the positions of many synonymous rare codons are conserved in mRNA sequences that encode structurally similar proteins from a diverse range of organisms. These results suggest that rare codons have a functional role related to the production of functional proteins, potentially to regulate the rate of protein synthesis and the earliest steps of protein folding, while synthesis is still underway.
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Microbes catch a ride on fog, but change during the trip

Microbes catch a ride on fog, but change during the trip | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
You may think fog is beautiful or eerie, but it also transports microbes long distances to new environments and could help spread dangerous pathogens.
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In vitro thermotherapy-based methods for plant virus eradication | Plant Methods | Full Text

In vitro thermotherapy-based methods for plant virus eradication | Plant Methods | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In vitro thermotherapy-based methods for plant virus eradication

Min-Rui Wang†, Zhen-Hua Cui†, Jing-Wei Li, Xin-Yi Hao, Lei ZhaoEmail author and Qiao-Chun WangEmail authorView ORCID ID profile

†Contributed equally
Plant Methods201814:87

https://doi.org/10.1186/s13007-018-0355-y

© The Author(s) 2018

Received: 10 September 2018Accepted: 3 October 2018Published: 6 October 2018

Abstract

Production of virus-free plants is necessary to control viral diseases, import novel cultivars from other countries, exchange breeding materials between countries or regions and preserve plant germplasm. In vitro techniques represent the most successful approaches for virus eradication. In vitro thermotherapy-based methods, including combining thermotherapy with shoot tip culture, chemotherapy, micrografting or shoot tip cryotherapy, have been successfully established for efficient eradication of various viruses from almost all of the most economically important crops. The present study reviewed recent advances in in vitro thermotherapy-based methods for virus eradication since the twenty-first century. Mechanisms as to why thermotherapy-based methods could efficiently eradicate viruses were discussed. Finally, future prospects were proposed to direct further studies.
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Molecular and Genome Evolution by Dan Graur

Molecular and Genome Evolution by Dan Graur | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Over the last two weeks, I have been reading Dan Graur’s book titled “Molecular and Genome Evolution”. This is a fantastic book that everyone should read before starting to work on any genome-related project. For the benefit of our readers, I will share some comments in this short post. If time permits, I will later follow up with a longer post on the book.
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What ‘data thugs’ really need

What ‘data thugs’ really need | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In 2006, when Kevin and I started to examine Potti’s data on genetic signatures of cancer, both of us had tenure and resources to devote to the work. (We were funded to provide statistical support to faculty members and could easily argue that they would want to implement techniques Potti described.) Once we established (at least to our own satisfaction) that the results were simply wrong, it was harder to justify our work, but we couldn’t stop: patients were being enrolled in useless trials that would expose them to toxic agents.
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canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit | Bioinformatics | Oxford Academic

canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, f
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Gold medal for UCT Vaccinology Research Chair | UCT News

Gold medal for UCT Vaccinology Research Chair | UCT News | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
UCT Vaccinology Research Chair Professor Anna-Lise Williamson has been honoured with a gold medal from the SA Medical Research Council for her seminal scientific contributions.

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EU is desperately looking for an ASF vaccine - Euromeatnews.com

EU is desperately looking for an ASF vaccine - Euromeatnews.com | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Meantime, stricter measures have been implemented in order to stop the spreading of the disease.

Via Ed Rybicki
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Ed Rybicki's curator insight, September 21, 8:39 AM
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The Popularity Contest of Human Genes

The Popularity Contest of Human Genes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Since 2003, several researchers have noticed that scientists tend to study genes that are already well studied, and the genes that become popular aren’t necessarily the most biologically interesting ones. Even among genes, it seems, the rich get richer. This trend hasn’t changed in the past two decades, according to a new study from Thomas Stoeger from Northwestern University. Through a massive analysis of existing biomedical data, he found that he can predict how intensely a given gene is studied based on a small number of basic biochemical traits. Most of these, he says, reflect how easy a gene was to investigate in the 1980s and 1990s, rather than how important it is.

“People said that knowing all the genes was going to change everything,” says Luis Amaral, who led the new study. But the 16 percent of genes that were known in 1991 still accounted for half of all biomedical papers in 2015. By contrast, more recently discovered genes are more poorly known, and a quarter (27 percent) have never been the focus of a scientific paper. Based on current trends, Stoeger estimates that it would take at least five decades before every gene was characterized at the most basic level, let alone fully understood. “There’s a chance that we are missing out on a lot of interesting biology,” he says.

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Faster, Cheaper, Better: A New Way to Synthesize DNA

In what could address a critical bottleneck in biology research, Berkeley Lab researchers announced they have pioneered a new way to synthesize DNA sequences through a creative use of enzymes that promises to be faster, cheaper, and more accurate.
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Inspired by nature, reaching across disciplines

Inspired by nature, reaching across disciplines | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Inspired by the architectures of different organisms, MIT PhD student Zijay Tang is developing a living material that can sense and filter water contaminants.

Via Gerd Moe-Behrens
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Biology of viral satellites and their role in pathogenesis - ScienceDirect

Biology of viral satellites and their role in pathogenesis - ScienceDirect | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Extraviral components that can influence the accumulation and pathogenesis of their associated helper viruses are known as ‘satellites’. The maintenan…
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Putting Natural Killer Cells to the Test in Cancer Immunotherapy

Putting Natural Killer Cells to the Test in Cancer Immunotherapy | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
NK cells are “first responders” that rapidly detect and attack virus-infected cells and tumor cells, and can also help prevent metastasis.

Via Gilbert C FAURE
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Ten simple rules for developing good reading habits during graduate school and beyond

Ten simple rules for developing good reading habits during graduate school and beyond | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Honey bee‐assisted surveillance for early plant virus detection - Roberts - - Annals of Applied Biology - Wiley Online Library

Honey bee‐assisted surveillance for early plant virus detection - Roberts - - Annals of Applied Biology - Wiley Online Library | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
oney bee‐assisted surveillance for early plant virus detection
John M. K. Roberts
Kylie B. Ireland
Wee T. Tay
Dean Paini
First published: 02 October 2018
https://doi.org/10.1111/aab.12461

Funding information Commonwealth Scientific and Industrial Research Organisation, Grant/Award Number: R‐8681‐1; AgriFutures Australia, Grant/Award Number: PRJ‐8540
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Abstract

Incursions of plant viral pathogens are a primary concern for horticulture as they can significantly impact crop yields and require expensive management. Early detection of plant viruses is critical for effective plant biosecurity because it enables growers to respond quickly and limit their spread. However, current surveillance methods relying on enzyme‐linked immunosorbent assay and PCR testing of plant material can only operate at a limited scale. It quickly becomes unfeasible to test a large number of samples for area‐wide surveillance of multiple viruses and ineffective in novel virus discovery. Advances in high‐throughput sequencing (HTS) platforms have greatly improved our surveillance capability and its value demonstrated for screening plant material for viral pathogens. However, while HTS can improve detection, it does not necessarily address the issue of sampling effort needed to achieve early detection. The solution is to couple HTS with a method of constant surveillance and sampling from potentially infected plants. We propose that when managed honey bee (Apis mellifera) hives are brought to flowering crops to deliver essential pollination services, they can also provide valuable surveillance by effectively “sampling” entire crops as they collect pollen and nectar. Combining the ability of honey bees to create a representative sample from a large number of plants with the sensitivity of HTS offers a powerful system for early detection of plant viruses. We describe a novel approach to plant biosecurity where HTS virus detection in honey bees was found to provide earlier detection of plant virus incursions in Australia than current surveillance programmes. In 2013–2014, a national virus survey of honey bees was conducted, which used HTS screening of pooled honey bee samples across Australia. This HTS data simultaneously identified multiple plant viruses in these samples and showed the presence of cucumber green mottle mosaic virus in several states of Australia before its subsequent detection from diseased plant material.
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10 surprises from sequencing 25 new species –

10 surprises from sequencing 25 new species – | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Sequencing human genomes is now routine at the Sanger Institute. Bacteria, yeast, worms, malaria, and other pathogens are also all regularly sequenced in their thousands. Our people are pretty well known for sequencing the human genome, but we’ve also contributed to the first sequencing of many others including the mouse, rat, zebrafish, pig and gorilla too.

The 25 genomes project is an entirely different beast. It’s posing some new, and frankly very odd, challenges. The diversity of the new species means we’ve had a steep learning curve. Here’s a peek at some of the weird and wonderful things we’ve discovered so far:
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Ten simple rules for scientists: Improving your writing productivity

Box 1. Hurdles to writing that all scientists can face
Types of Writing Resistance

Evaluation: “This draft stinks.”
Inspiration: “I don’t have a good idea yet.”
Motivation: “I just don’t feel like it.”
Optimization: “I need to make this sentence perfect.”
Procrastination: “I will start working on it tomorrow.”
Separation: “I need a lot of time in a quiet place to write.”
Temptation: “My lab bench is really disorganized; it needs to be cleaned now.”
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Chromebook Data Science - a free online data science program for anyone with a web browser.

Chromebook Data Science - a free online data science program for anyone with a web browser. | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Today I’m excited to announce the first part of our new system, a new set of massive online open courses called Chromebook Data Science. These MOOCs are for anyone from high schoolers on up to get into data science. If you can read and follow instructions you can learn data science from these courses!

The reason they are called Chromebook Data Science is because philosophically our goal was that anyone with a Chromebook could do the courses. All you need is a web browser and an internet connection. The courses all take advantage of RStudio Cloud so that all course work can be completed entirely in a web browser. No need to install software or have the latest MacBook Computer.
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De novo genome assembly - T.Seemann - IMB winter school 2016

Introduction to de novo genome assembly (2016 edition)
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Monkeypox contacts: a puzzling problem

Monkeypox contacts: a puzzling problem | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
When it emerged that two people infected with monkeypox had travelled by plane through one of the world's busiest airports, a media storm arose, with irresponsible headlines and exaggerations of risks for others in the UK and across the globe. The two patients—currently recovering in specialist units in London and Liverpool, UK—probably contracted the infection, which produces symptoms such as fever, headache, malaise, and the typical smallpox-like vesicular rash, from animals in Nigeria, where there is an ongoing outbreak of the virus. The Nigeria Centre for Disease Control has recorded 262 suspected cases of monkeypox since the outbreak began in September, 2017, including 113 confirmed cases and seven deaths. The Nigerian outbreak is likely to be the result of a local zoonotic spillover event from the virus' natural hosts—rodents. The disease, caused by a virus of the Orthopox genus, is usually self-limiting—although it has a mortality rate of 1–10%.

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Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows | Bioinformatics | Oxford Academic

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Nidhi Shah, Michael G Nute, Tandy Warnow, Mihai Pop; Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, Bioinformatics,
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The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections

The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In 2009, the co-circulation of H5N1 and H1N1pdm09 raised concerns that a reassortment event may lead to highly pathogenic influenza strains. H1N1pdm09 and H5N1 are able to infect the same target cells of the lower respiratory tract.
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Baloxavir: A New, Single-Dose Antiviral 

Baloxavir: A New, Single-Dose Antiviral  | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A 64-year-old otherwise healthy virology professor comes to your office complaining of flu symptoms. She has had fever, cough, and sore throat for the last day or so that she attributes to one of her students. She has been furiously sanitizing her hands and comes to the office wearing a face mask. Being the savvy patient, she brings reverse transcriptase–polymerase chain reaction (RT-PCR) results that confirm she has influenza A virus (as does the student). She is febrile but hemodynamically stable with no signs of lower respiratory tract infection. She asks about available treatment options, explaining that she will be presenting at a conference tomorrow. How would you proceed? In this week’s NEJM, Hayden and colleagues report the results of two double-blind, randomized-controlled trials comparing single-dose baloxavir versus placebo or oseltamivir in patients with uncomplicated influenza in Japan and the United States during the 2015–2017 flu seasons. Baloxavir marboxil (Xofluza) is an important new addition to the armamentarium against flu because it represents a new class of antiviral drugs that target a different process than the other two classes available (amadantanes and neuraminidase inhibitors), and has antiviral activity against strains resistant to those agents. Baloxavir also has the advantage of requiring a single dose, as compared to 5 days of twice daily oseltamivir (Tamiflu). Baloxavir is a cap-dependent endonuclease inhibitor that blocks viral replication by blocking the initiation of mRNA synthesis (read more here). In the phase 3 trial (CAPSTONE-1), the investigators randomized 1436 patients (age range, 12–64 years) with uncomplicated flu to receive a single dose of baloxavir (40 mg), oseltamivir (75 mg twice daily for 5 days), or matching placebos (with those aged 12-19 assigned only to baloxavir or placebo). Uncomplicated flu was defined as fever ≥38.0°C, at least one systemic symptom and one respiratory symptom, and presentation with 48 hours of symptom onset. Pregnant women and those requiring hospitalization were excluded. The primary endpoint was the time until flu symptoms became absent or mild for at least 21.5 hours. The intention-to-treat infected population included only RT-PCR-positive patients. Roughly 85% of patients in the three treatment groups were infected with influenza A (H3N2) and most (77%) were recruited in Japan. The time to alleviation of symptoms was significantly shorter (by 26.5 hours) in the baloxavir group, when compared with the placebo group (median, 53.7 vs. 80.2 hours), and similar to the oseltamivir group (53.5 vs. 53.8 hours). Baloxavir was associated with significantly more rapid decline in potentially infectious viral load as compared to both oseltamivir and placebo. The rate of adverse events was similar in the three groups. Emergence of mutations conferring reduced baloxavir susceptibility occurred in fewer than 10% of baloxavir recipients, which prolonged time to resolution of symptoms by about 13 hours. Per CDC recommendations, only individuals with acute influenza who are at high risk of related complications (e.g., in a chronic care facility, pregnant, age ≥65 years) should receive antiviral treatment. Hence, the results of this trial are not likely to affect current practice or treatment of the professor described above. The importance of this study lies in the demonstration of the safety and efficacy of baloxavir for treatment of uncomplicated acute influenza in otherwise healthy patients. These encouraging results will form the basis for future study of baloxavir in higher risk populations, where its utility and future clinical indications may lie. Browse more From Pages to Practice »  Tenzing T. Lama, MD, MScRes, is a resident physician in the Department of Anesthesiology and Pain Medicine at the University of Washington and a Fellow at the Ethics and Transformative Values Center at the Massachusetts Institute of Technology. He graduated from Harvard Medical School and Oxford.

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The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections

The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In 2009, the co-circulation of H5N1 and H1N1pdm09 raised concerns that a reassortment event may lead to highly pathogenic influenza strains. H1N1pdm09 and H5N1 are able to infect the same target cells of the lower respiratory tract. To investigate the capacity of the emergence of reassortant viruses, we characterized viruses obtained from the co-infection of cells with H5N1 (A/Turkey/13/2006) and H1N1pdm09 (A/Lyon/969/2009 H1N1). In our analysis, all the screened reassortants possessed the PB2, HA, and NP segments from H5N1 and acquired one or two of the H1N1pdm09 segments. Moreover, the in vivo infections showed that the acquisition of the NS segment from H1N1pdm09 increased the virulence of H5N1 in mice. We conclude, therefore, that reassortment can occur between these two viruses, even if this process has never been detected in nature.
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Mini viral RNAs act as innate immune agonists during influenza virus infection | Nature Microbiology

The molecular processes that determine the outcome of influ- enza virus infection in humans are multifactorial and involve a complex interplay between host, viral and bacterial fac- tors 1 . However, it is generally accepted that a strong innate immune dysregulation known as ‘cytokine storm’ contributes to the pathology of infections with the 1918 H1N1 pandemic or the highly pathogenic avian influenza viruses of the H5N1 subtype 2–4 . The RNA sensor retinoic acid-inducible gene I (RIG-I) plays an important role in sensing viral infection and initiating a signalling cascade that leads to interferon expres- sion 5 . Here, we show that short aberrant RNAs (mini viral RNAs (mvRNAs)), produced by the viral RNA polymerase during the replication of the viral RNA genome, bind to and activate RIG-I and lead to the expression of interferon-β . We find that erroneous polymerase activity, dysregulation of viral RNA replication or the presence of avian-specific amino acids underlie mvRNA generation and cytokine expression in mam- malian cells. By deep sequencing RNA samples from the lungs of ferrets infected with influenza viruses, we show that mvR- NAs are generated during infection in vivo. We propose that mvRNAs act as the main agonists of RIG-I during influenza virus infection.
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