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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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Roadblocks to translational challenges on viral pathogenesis

burkesquires's insight:

"Distinct roadblocks prevent translating basic findings in viral pathogenesis into therapies and implementing potential solutions in the clinic. An ongoing partnership between the Volkswagen Foundation and Nature Medicine resulted in an interactive meeting in 2012, as part of the “Herrenhausen Symposia” series. Current challenges for various fields of viral research were recognized and discussed with a goal in mind—to identify solutions and propose an agenda to address the translational barriers. Here, some of the researchers who participated at the meeting provide a concise outlook at the most pressing unmet research and clinical needs, identifying these key obstacles is a necessary step towards the prevention and cure of human viral diseases."

  http://www.nature.com/nm/journal/v19/n1/full/nm.3050.html
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Promising compound restores memory loss and reverses symptoms of Alzheimer’s Disease

Promising compound restores memory loss and reverses symptoms of Alzheimer’s Disease | Virology and Bioinformatics from Virology.ca | Scoop.it

New research in the FASEB Journal by NIH scientists suggests that a small molecule called TFP5 rescues plaques and tangles by blocking an overactive brain signal, thereby restoring memory in mice with Alzheimer’s — without obvious toxic side effects.

 

“We hope that clinical trial studies in AD patients yield an extended and a better quality of life, as observed in mice upon TFP5 treatment,” said Harish C. Pant, Ph.D., a senior researcher involved in the work from the Laboratory of Neurochemistry at the National Institute of Neurological Disorders at Stroke at the National Institutes of Health.

 

“We suggest that TFP5 should be an effective therapeutic compound.”

To make this discovery, Pant and colleagues used mice with a disease considered the equivalent of Alzheimer’s. One set of these mice were injected with the small molecule TFP5, while the other was injected with saline as placebo. The mice, after a series of intraperitoneal injections of TFP5, displayed a substantial reduction in the various disease symptoms along with restoration of memory loss.

 

In addition, the mice receiving TFP5 injections experienced no weight loss, neurological stress (anxiety) or signs of toxicity. The disease in the placebo mice, however, progressed normally as expected.

 

TFP5 was derived from the regulator of a key brain enzyme, called Cdk5. Over-activation of Cdk5 is implicated in the formation of plaques and tangles, the major hallmark of Alzheimer’s disease.


Via Dr. Stefan Gruenwald
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pdeppisch's comment, January 8, 2013 3:40 PM
That would be nice as both my parents died from Alzheimer's as best I could tell.
Audrey's comment, January 8, 2013 5:20 PM
If this is true, then it would be fantastic.
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The Norovirus: A Study in Puked Perfection – Phenomena: The Loom

The Norovirus: A Study in Puked Perfection – Phenomena: The Loom | Virology and Bioinformatics from Virology.ca | Scoop.it
Nicolas Palopoli's insight:

"(The Guardian) report that an outbreak of norovirus in Britain this winter has struck more than 1.1 million people with vomiting and diarrhea.

That’s right: 1.1 million. In Britain alone.

What is this fearsome bug, you may be asking, and why isn’t it the subject of a Hollywood horror movie?"

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Visualizing viral assemblies in a nanoscale biosphere - Lab on a Chip (RSC Publishing)

We present a novel microfluidic platform to examine biological assemblies at high-resolution.
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Quantitative prediction of integrase inhibitor resistance from genotype through consensus linear regression modeling

Integrase inhibitors (INI) form a new drug class in the treatment of HIV-1 patients.

We did the development of the RAL linear regression model in two stages, employing a genetic algorithm (GA) to select integrase mutations by consensus. First, we ran multiple GAs to generate first order linear regression models (GA models) that were stochastically optimized to reach a goal R2 accuracy, and consisted of a fixed-length subset of integrase mutations to estimate INI resistance. Secondly, we derived a consensus linear regression model in a forward stepwise regression procedure, considering integrase mutations or mutation pairs by descending prevalence in the GA models."

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Virology Journal | Abstract | Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits

Virology Journal | Abstract | Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits | Virology and Bioinformatics from Virology.ca | Scoop.it
Background
Human papillomavirus (HPV) is the aetiological agent for cervical cancer and genital warts. Concurrent HPV and HIV infection in the South African population is high. HIV positive (+) women are often infected with multiple, rare and undetermined HPV types. Data on HPV incidence and genotype distribution are based on commercial HPV detection kits, but these kits may not detect all HPV types in HIV + women. The objectives of this study were to (i) identify the HPV types not detected by commercial genotyping kits present in a cervical specimen from an HIV positive South African woman using next generation sequencing, and (ii) determine if these types were prevalent in a cohort of HIV-infected South African women.

Methods
Total DNA was isolated from 109 cervical specimens from South African HIV + women. A specimen within this cohort representing a complex multiple HPV infection, with 12 HPV genotypes detected by the Roche Linear Array HPV genotyping (LA) kit, was selected for next generation sequencing analysis. All HPV types present in this cervical specimen were identified by Illumina sequencing of the extracted DNA following rolling circle amplification. The prevalence of the HPV types identified by sequencing, but not included in the Roche LA, was then determined in the 109 HIV positive South African women by type-specific PCR.

Results
Illumina sequencing identified a total of 16 HPV genotypes in the selected specimen, with four genotypes (HPV-30, 74, 86 and 90) not included in the commercial kit. The prevalence's of HPV-30, 74, 86 and 90 in 109 HIV positive South African women were found to be 14.6 %, 12.8 %, 4.6 % and 8.3 % respectively.

Conclusions
Our results indicate that there are HPV types, with substantial prevalence, in HIV positive women not being detected in molecular epidemiology studies using commercial kits. The significance of these types in relation to cervical disease remains to be investigated.

 

Papillomavirus graphic by Russell Kightley Media

 


Via Ed Rybicki
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Welcome to VIPERdb

Welcome to VIPERdb | Virology and Bioinformatics from Virology.ca | Scoop.it

Descriptions of various icosahedral virus capsid structures in terms of their complete
capsids, along with detailed structural and computational analysis

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HealthMap | Global Health, Local Knowledge

HealthMap | Global Health, Local Knowledge | Virology and Bioinformatics from Virology.ca | Scoop.it
Loiret David's insight:

"HealthMap, is an established global leader in utilizing online informal sources for disease outbreak monitoring and real-time surveillance of emerging public health threats. The freely available Web site 'healthmap.org' and mobile app 'Outbreaks Near Me' deliver real-time intelligence on a broad range of emerging infectious diseases for a diverse audience including libraries, local health departments, governments, and international travelers."

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BMC Infectious Diseases | Abstract | Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lim...

The impact of extended use of ART in developing countries has been enormous. A thorough understanding of all factors contributing to the success of antiretroviral therapy is required.
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Humans have alu, cows have BovB. Why is a quarter of the cow genome similar to that of snakes?

Humans have alu, cows have BovB. Why is a quarter of the cow genome similar to that of snakes? | Virology and Bioinformatics from Virology.ca | Scoop.it

Genomes are often described as recipe books for living things. If that’s the case, many of them badly need an editor. For example, around half of the human genome has bits and pieces of DNA sprinkled around that have copied themselves throughout the genome and jumped around seemingly randomly, creating vast tracts of repetitive sequences, so called "alu" sequences - a name derived from a restriction site "Alu I" right in the middle of the repetitive part. The same is true for the cow genome, where one particular piece of DNA, known as BovB, has run amok. It’s there in its thousands. Around a quarter of a cow’s DNA is made of BovB sequences or their descendants.

 

BovB isn’t restricted to cows. If you look for it in other animals, as Ali Morton Walsh from the University of Adelaide did, you’ll find it in elephants, horses, and platypuses. It lurks among the DNA of skinks and geckos, pythons and seasnakes. It’s there in purple sea urchin, the silkworm and the zebrafish.

 

The obvious interpretation is that BovB was present in the ancestor of all of these animals, and stayed in their genomes as they diversified. If that’s the case, then closely related species should have more similar versions of BovB. The cow version should be very similar to that in sheep, slightly less similar to those in elephants and platypuses, and much less similar to those in snakes and lizards.

 

But not so. If you draw BovB’s family tree, it looks like you’ve entered a bizarre parallel universe where cows are more closely related to snakes than to elephants, and where one gecko is more closely related to horses than to other lizards.

 

This is because BovB isn’t neatly passed down from parent to offspring, as most pieces of animal DNA are. This jumping gene not only hops around genomes, but between them. 

 

This type of “horizontal gene transfer” (HGT) is an everyday event for bacteria, which can quickly pick up important abilities from each other by swapping DNA. Such trades are supposedly much rarer among more complex living things, but every passing year brings new examples of HGT among animals. For example, in 2008, Cedric Feschotte (now at the University of Utah) discovered a group of sequences that have jumped between several mammals, an anole lizard, and a frog. He called them Space Invaders.

 

The Space Invaders belong to a group of jumping genes called DNA transposons. They jump around by cutting themselves out of their surrounding DNA, and pasting themselves in somewhere new. They’re also relatively rare—they make up just 2 to 3 percent of our genome. BovB belongs to a different class of jumping genes called retrotransposons. They move through a copy-and-paste system rather than a cut-and-paste one, so that every jump produces in a new copy of the gene. For that reason, they spread like wildfire.


Via Dr. Stefan Gruenwald
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A universal problem : Nature Medicine : Nature Publishing Group

Recent headlines have promised that a 'universal flu vaccine' may be within reach, pointing to antibodies that offer broad protection in animal studies.
burkesquires's insight:

"Influenza is the Lady Gaga of viruses: it reinvents itself each year, often in unexpected ways."

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PLOS Pathogens: The Roles of Competition and Mutation in Shaping Antigenic and Genetic Diversity in Influenza

PLOS Pathogens: The Roles of Competition and Mutation in Shaping Antigenic and Genetic Diversity in Influenza | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
burkesquires's insight:

Influenza A (H3N2) offers a well-studied, yet not fully understood, disease in terms of the interactions between pathogen population dynamics, epidemiology and genetics. A major open question is why the virus population is globally dominated by a single and very recently diverged (2–8 years) lineage. Classically, this has been modeled by limiting the generation of new successful antigenic variants, such that only a small subset of progeny acquire the necessary mutations to evade host immunity. An alternative approach was recently suggested by Recker et al. in which a limited number of antigenic variants are continuously generated, but most of these are suppressed by pre-existing host population immunity. Here we develop a framework spanning the regimes described above to explore the impact of rates of mutation and levels of competition on phylodynamic patterns. We find that the evolutionary dynamics of the subtype H3N2 influenza is most easily generated within this framework when it is mutation limited as well as being under strong immune selection at a number of epitope regions of limited diversity.

 
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Did Bacteria Fuel World's Worst Extinction?

Did Bacteria Fuel World's Worst Extinction? | Virology and Bioinformatics from Virology.ca | Scoop.it
The "murderous microbes" would've sped up the Great Dying by releasing gobs of methane into the skies. (@luftbahuhn siehe http://t.co/urdS8nRD Kavaliersdelikt ist es keines, nope.

Via Franc Viktor Nekrep
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Flu? Malaria? Disease forecasters look to sky

Flu? Malaria? Disease forecasters look to sky | Virology and Bioinformatics from Virology.ca | Scoop.it
Only a 10 percent chance of showers today, but a 70 percent chance of flu next month.Thats the kind of forecasting health scientists are trying to move toward, as they increasingly include weather data in their attempts to predict disease outbreaks.
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What is the best way for a virus to build itself?

By simulating how viruses are capable of constructing their own protective protein coats, researchers reveal that linking several larger segments together may be better than building them piece-by-piece.
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A virus that creates electricity

A virus that creates electricity | Virology and Bioinformatics from Virology.ca | Scoop.it
A virus called simply M13 has the power (literally) to change the world. A team of scientists at the Berkeley Lab have genetically engineered M13 viruses to emit enough electricity to power a small LED screen.
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Virus Pathogen Database and Analysis Resource (ViPR) - Genome database with visualization and analysis tools

Searchable database of virus genomes with visualization and analysis tools.
Loiret David's insight:

"ViPR: an open bioinformatics database and analysis
resource for virology research." See article: http://nar.oxfordjournals.org/content/40/D1/D593.full-text-lowres.pdf

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Chris Upton + helpers's comment, January 7, 2013 6:05 PM
For better tools, try www.virology.ca (their mine, yes, I'm biased)
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A fast and accurate SNP detection algorithm for next-generation sequencing data

burkesquires's insight:

"Various methods have been developed for calling single-nucleotide polymorphisms from next-generation sequencing data. However, for satisfactory performance, most of these methods require expensive high-depth sequencing. Here, we propose a fast and accurate single-nucleotide polymorphism detection program that uses a binomial distribution-based algorithm and a mutation probability. We extensively assess this program on normal and cancer next-generation sequencing data from The Cancer Genome Atlas project and pooled data from the 1,000 Genomes Project. We also compare the performance of several state-of-the-art programs for single-nucleotide polymorphism calling and evaluate their pros and cons. We demonstrate that our program is a fast and highly accurate single-nucleotide polymorphism detection method, particularly when the sequence depth is low. The program can finish single-nucleotide polymorphism calling within four hours for 10-fold human genome next-generation sequencing data (30 gigabases) on a standard desktop computer."

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CIDRAP // Center for Infectious Disease Research and Policy

Loiret David's insight:

"The Center for Infectious Disease Research and Policy (CIDRAP), founded in 2001, is a global leader in addressing public health preparedness and emerging infectious disease response. Part of the Academic Health Center at the University of Minnesota, CIDRAP is led by Michael Osterholm, PhD, MPH, director and professor..."

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BioBlender

BioBlender | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Loiret David
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Loiret David's curator insight, January 4, 2013 3:18 PM

"BioBlender is a software package built on the open-source 3D modeling software Blender.

 

With BioBlender users can handle proteins in the 3D space, displaying their surface in a photorealistic way, and elaborate protein movements on the basis of known conformations".

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Visualizing viral assemblies in a nanoscale biosphere - Lab on a Chip (RSC Publishing)

We present a novel microfluidic platform to examine biological assemblies at high-resolution.
burkesquires's insight:

"We present a novel microfluidic platform to examine biological assemblies at high-resolution. We have engineered a functionalized chamber that serves as a “nanoscale biosphere” to capture and maintain rotavirus double-layered particles (DLPs) in a liquid environment. The chamber can be inserted into the column of a transmission electron microscope while being completely isolated from the vacuum system. This configuration allowed us to determine the structure of biological complexes at nanometer-resolution within a self-contained vessel. Images of DLPs were used to calculate the first 3D view of macromolecules in solution. We refer to this new fluidic visualization technology as in situ molecular microscopy."

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