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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Targeted Prostaglandin E2 Inhibition Enhances Antiviral Immunity through Induction of Type I Interferon and Apoptosis in Macrophages: Immunity

Targeted Prostaglandin E2 Inhibition Enhances Antiviral Immunity through Induction of Type I Interferon and Apoptosis in Macrophages: Immunity | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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Whooping cough bounces back | Science News

Whooping cough bounces back | Science News | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A new type of pertussis vaccine introduced in the late 1990s may have led to the return of a disease that was nearly eradicated 40 years ago. Public opposition to vaccination hasn’t helped matters.
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Bananageddon: Millions face hunger as deadly fungus Panama disease decimates global banana crop

Bananageddon: Millions face hunger as deadly fungus Panama disease decimates global banana crop | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Scientists have warned that the world’s banana crop, worth £26 billion and a crucial part of the diet of more than 400 million people, is facing “disaster” from virulent diseases immune to pesticides or other forms of control.
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Will omics help to cure the flu?

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Ed Rybicki's comment, April 14, 2014 6:51 AM
Nah. Just like it won't help cure HIV, HCV, HBV....
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Antiviral strategies against influenza virus: towards new therapeutic approaches - Online First - Springer

Antiviral strategies against influenza virus: towards new therapeutic approaches - Online First - Springer | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Influenza viruses are major human pathogens responsible for respiratory diseases affecting millions of people worldwide and characterized by high morbidity and significant mortality. Influenza infections can be controlled by vaccination and antiviral drugs. However, vaccines need annual updating and give limited protection. Only two classes of drugs are currently approved for the treatment of influenza: M2 ion channel blockers and neuraminidase inhibitors. However, they are often associated with limited efficacy and adverse side effects. In addition, the currently available drugs suffer from rapid and extensive emergence of drug resistance. All this highlights the urgent need for developing new antiviral strategies with novel mechanisms of action and with reduced drug resistance potential. Several new classes of antiviral agents targeting viral replication mechanisms or cellular proteins/processes are under development. This review gives an overview of novel strategies targeting the virus and/or the host cell for counteracting influenza virus infection.

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Inferring Influenza Infection Attack Rate from Seroprevalence Data

Inferring Influenza Infection Attack Rate from Seroprevalence Data | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Seroprevalence survey is the most practical method for accurately estimating infection attack rate (IAR) in an epidemic such as influenza. These studies typically entail selecting an arbitrary titer threshold for seropositivity (e.g. microneutralization [MN] 1:40) and assuming the probability of seropositivity given infection (infection-seropositivity probability, ISP) is 100% or similar to that among clinical cases. We hypothesize that such conventions are not necessarily robust because different thresholds may result in different IAR estimates and serologic responses of clinical cases may not be representative. To illustrate our hypothesis, we used an age-structured transmission model to fully characterize the transmission dynamics and seroprevalence rises of 2009 influenza pandemic A/H1N1 (pdmH1N1) during its first wave in Hong Kong. We estimated that while 99% of pdmH1N1 infections became MN1:20 seropositive, only 72%, 62%, 58% and 34% of infections among age 3–12, 13–19, 20–29, 30–59 became MN1:40 seropositive, which was much lower than the 90%–100% observed among clinical cases. The fitted model was consistent with prevailing consensus on pdmH1N1 transmission characteristics (e.g. initial reproductive number of 1.28 and mean generation time of 2.4 days which were within the consensus range), hence our ISP estimates were consistent with the transmission dynamics and temporal buildup of population-level immunity. IAR estimates in influenza seroprevalence studies are sensitive to seropositivity thresholds and ISP adjustments which in current practice are mostly chosen based on conventions instead of systematic criteria. Our results thus highlighted the need for reexamining conventional practice to develop standards for analyzing influenza serologic data (e.g. real-time assessment of bias in ISP adjustments by evaluating the consistency of IAR across multiple thresholds and with mixture models), especially in the context of pandemics when robustness and comparability of IAR estimates are most needed for informing situational awareness and risk assessment. The same principles are broadly applicable for seroprevalence studies of other infectious disease outbreaks.

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West Nile virus may have met its match: tobacco

West Nile virus may have met its match: tobacco | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Some people think of tobacco as a drug, whereas others think of it as a therapy — or both. But for the most part, it's hard to find people who think of the tobacco plant in terms of its medical...
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Retroviruses R us

Retroviruses R us | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
About eight percent of human DNA is viral. Most are considered to be junk DNA but some of them provide important functions.
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The arable ecosystem as battleground for emergence of new human pathogens

The arable ecosystem as battleground for emergence of new human pathogens | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.

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Evidence for subclinical H5N1 avian influenza infections among Nigerian poultry workers.

In recent years Nigeria has experienced sporadic incursions of highly pathogenic H5N1 avian influenza among poultry. In 2008, 316 poultry-exposed agricultural workers, and 54 age-group matched non-poultry exposed adults living in the Enugu or Ebonyi States of Nigeria were enrolled and then contacted monthly for 24 months to identify acute influenza-like-illnesses. Annual follow-up sera and questionnaire data were collected at 12 and 24 months. Participants reporting influenza-like illness completed additional questionnaires, and provided nasal and pharyngeal swabs and acute and convalescent sera. Swab and sera specimens were studied for evidence of influenza A virus infection. Sera were examined for elevated antibodies against 12 avian influenza viruses by microneutralization and 3 human viruses by hemagglutination inhibition.

Chris Upton + helpers's insight:

Could be worrisome...

 

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Tamiflu-resistant influenza: parsing the genome for the culprits

Tamiflu-resistant influenza: parsing the genome for the culprits | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Abstract

"Tamiflu is one of the few available treatments for those who come down with the flu. But the virus quickly develops resistance; multiplying at a rate of several generations a day, these tiny pathogens rapidly accumulate genetic mutations. Because of this, they have a good chance of developing counterattacks to the antiviral. How can these infinitesimal variations be identified within the immensity of the virus’ genetic code? EPFL researchers have created a computer tool that can shed light on the flu virus’ formidable adaptability. They were able to find mutations that conferred resistance that had up to this point not yet been identified. Their software has been made freely available to researchers everywhere, and is the subject of an article published in the journal PLOS Genetics. "

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Slime mold microfluidic logical gates

Abstract

"We demonstrate how logical operations can be implemented in ensembles of protoplasmic tubes of acellular slime mold Physarum polycephalum. The tactile response of the protoplasmic tubes is used to actuate analogs of two- and four-input logical gates and memory devices. The slime mold tube logical gates display results of logical operations by blocking flow in mechanically stimulated tube fragments and redirecting the flow to output tube fragments. We demonstrate how XOR and NOR gates are constructed. We also exemplify circuits of hybrid gates and a memory device. The slime mold based gates are non-electronic, simple and inexpensive, and several gates can be realized simultaneously at sites where protoplasmic tubes merge."

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Scientists Generate 3D Structure for the Malaria Parasite Genome

Scientists Generate 3D Structure for the Malaria Parasite Genome | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Abstract - "A research team led by a cell biologist at the University of California, Riverside has generated a 3D model of the human malaria parasite genome at three different stages in the parasite’s life cycle — the first time such 3D architecture has been generated during the progression of the life cycle of a parasite ."

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Activation of the Interferon Induction Cascade by Influenza A Viruses Requires Viral RNA Synthesis and Nuclear Export


Via Mel Melendrez-Vallard, Kenzibit
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Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.

We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on thede novo analysis of the repetitive content, estimated to encompass 82% of the genome.

In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.


Via Francis Martin
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IFITM3 Restricts Influenza A Virus Entry by Blocking the Formation of Fusion Pores following Virus-Endosome Hemifusion - PLoS Pathog. 2014

Influenza viruses are major human pathogens responsible for respiratory diseases affecting millions of people worldwide and characterized by high morbidity and significant mortality. Influenza infections can be controlled by vaccination and antiviral drugs. However, vaccines need annual updating and give limited protection. Only two classes of drugs are currently approved for the treatment of influenza: M2 ion channel blockers and neuraminidase inhibitors. However, they are often associated with limited efficacy and adverse side effects. In addition, the currently available drugs suffer from rapid and extensive emergence of drug resistance. All this highlights the urgent need for developing new antiviral strategies with novel mechanisms of action and with reduced drug resistance potential. Several new classes of antiviral agents targeting viral replication mechanisms or cellular proteins/processes are under development. This review gives an overview of novel strategies targeting the virus and/or the host cell for counteracting influenza virus infection.

A

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The 2010 Cholera Outbreak in Haiti: How Science Solved a Controversy

The 2010 Cholera Outbreak in Haiti: How Science Solved a Controversy | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

On January 12, 2010, a catastrophic 7.0 magnitude earthquake struck Haiti, affecting 3,500,000 people [1], [2]. This severely damaged an already marginal public sanitation system, creating ideal conditions for outbreaks of major infectious diseases. In October 2010, nine months after the earthquake, an outbreak of cholera started, which quickly spread all across the country [3]. As of January 7, 2014, 8,534 deaths and 697,256 cholera cases have been reported by the Haitian Ministry of Public Health and Population [4]. Prior to 2010, there was no reported history of cholera in Haiti, despite devastating outbreaks in the Caribbean region in the 19th century [5]. Many wondered where the cholera in Haiti came from. Two hypotheses as to its origin were presented. The climatic hypothesis argued that nonpathogenic Vibrio cholerae, indigenous in the coastal waters of Haiti, was given the right environmental circumstances and evolved into a pathogenic strain [6]. On the other hand, the human transmission hypothesis suggested that cholera was introduced to Haiti by individuals infected in a foreign country.

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Rotavirus Activates Lymphocytes from Non-Obese Diabetic Mice by Triggering Toll-Like Receptor 7 Signaling and Interferon Production in Plasmacytoid Dendritic Cells

Rotavirus Activates Lymphocytes from Non-Obese Diabetic Mice by Triggering Toll-Like Receptor 7 Signaling and Interferon Production in Plasmacytoid Dendritic Cells | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
From molecules to physiology
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US doctors' group says patients should have option not to know their DNA

US doctors' group says patients should have option not to know their DNA | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
New genome-sequencing recommendation will enable patients to opt out of testing.
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Plant peptides in defense and signaling

Plant peptides in defense and signaling | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

This review focuses on plant peptides involved in defense against pathogen infection and those involved in the regulation of growth and development. Defense peptides, defensins, cyclotides and anti-microbial peptides are compared and contrasted. Signaling peptides are classified according to their major sites of activity. Finally, a network approach to creating an interactomic peptide map is described.


Via Jean-Michel Ané
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The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR.Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors.Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.
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Bioafrica.net - News: PhD and/or MSc Scholarship available - Computer Science

Bioafrica.net - News: PhD and/or MSc Scholarship available - Computer Science | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The causes and consequences of HIV transmission and drug resistance - Computer Science PhD and MSc studentships available at UKZN/CSIR Meraka Centre for Artificial Intelligence Research (CAIR) for the MRC Flagship research project.
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Nano-paper filter removes viruses - Uppsala University, Sweden

Nano-paper filter removes viruses - Uppsala University, Sweden | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Researchers at the Division of Nanotechnology and Functional Materials, Uppsala University have developed a paper filter, which can remove virus particles with the efficiency matching that of the best industrial virus filters. The paper filter consists of 100 percent high purity cellulose nanofibers, directly derived from nature.
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