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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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Human Vaccines and Their Importance to Public Health

Few medical interventions compete with vaccines for their cumulative impact on health and well-being of entire populations. Routine immunization of children in the United States now targets 16 vaccine-preventable diseases; and vaccines are now routinely given across the lifespan. Immunization efforts achieved the global eradication of smallpox, as well as the elimination of polio, measles, and rubella from the Americas. The childhood vaccine series including DTP, polio, MMR, Hib, hepatitis B, and varicella vaccines is estimated to prevent 14 million infections, avoid 33,000 premature deaths, and save $9.9 billion in direct medical costs as well as $33 billion in indirect costs for each U.S. birth cohort fully vaccinated. Newer vaccines such as pneumococcal conjugate, rotavirus, and hepatitis A vaccines have also reduced illness and hospitalizations among the target populations but also have amplified benefits beyond their direct effects through reduced transmission from those immunized to other groups. Although for most of the 20th century there was a substantial delay between a vaccine's introduction in developed countries and its broad use in poor countries, newer global public–private partnerships and advocacy are leading to accelerated uptake of new and underutilized vaccines. Since the Measles Initiative was established in 2001, more than 700 million children worldwide have received a measles vaccination and an estimated 4.3 million childhood measles deaths have been averted. The full impact of increasing routine immunization further and implementing new vaccines against pneumonia and diarrhea agents in the poorest countries could prevent more than 2 million additional childhood deaths each year.

 

Thanks @MicrobeTweets!


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A Virus That Saves Itself By Preventing Bacterial Suicide | 80beats | Discover Magazine

A Virus That Saves Itself By Preventing Bacterial Suicide | 80beats | Discover Magazine | Virology and Bioinformatics from Virology.ca | Scoop.it

"Bacteria sometimes commit suicide for the good of the group. When a virus infects a bacterium, the cell kills itself rather than allow the virus to replicate inside it and spread to the surrounding bacteria.
The way this works is that when viruses aren’t around, the bacteria manufacture both a bacterial cyanide pill—a toxin molecule they could use to wipe themselves out if they come under attack—and an antitoxin molecule that keeps the toxin in check. When a virus infects the bacterium, the toxin is released, kills the bacterial cell, and prevents the virus from spreading to other cells. It’s bad for the individual bacterial cell but good for the community—and certainly bad for the infecting virus. Now researchers have found a virus that manipulates this mechanism for its own means, saving itself by keeping its host bacteria from cellular suicide."

 

Clever little things, viruses...B-)

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Egyptian #H5N1 #Influenza Viruses—Cause for Concern?

Highly pathogenic avian H5N1 influenza viruses are now enzootic in parts of Southeast Asia and the Middle East. Occasionally, these viruses transmit to humans and cause severe respiratory disease and fatalities. Currently, these viruses are not efficiently transmitted from person to person, although limited human-to-human transmission may have occurred [1]–[4]. A major determinant of influenza virus host range is the viral hemagglutinin (HA) protein: avian virus HA binds preferentially to sialic acid linked to the penultimate galactose residue by an α2,3-linkage (Siaα2,3Gal) [5]–[7], as found for sialic acid–containing receptors of the epithelial cells in duck intestine [8], the site of avian influenza virus replication. By contrast, human virus HA has higher affinity for Siaα2,6Gal [5]–[7], the main sialyloligosaccharide on the epithelial cells of the human upper respiratory tract [9], [10].

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Pirates of the Caudovirales

Pirates of the Caudovirales | Virology and Bioinformatics from Virology.ca | Scoop.it

Molecular piracy is a biological phenomenon in which one replicon (the pirate) uses the structural proteins encoded by another replicon (the helper) to package its own genome and thus allow its propagation and spread. Such piracy is dependent on a complex web of interactions between the helper and the pirate that occur at several levels, from transcriptional control to macromolecular assembly. The best characterized examples of molecular piracy are from the E. coli P2/P4 system and the S. aureus SaPI pathogenicity island/helper system. In both of these cases, the pirate element is mobilized and packaged into phage-like transducing particles assembled from proteins supplied by a helper phage that belongs to the Caudovirales order of viruses (tailed, dsDNA bacteriophages).

This review summarizes and compares the processes that are involved in molecular piracy in these two systems.

 

Blogged by Alan Cann

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List of diseases spread by deer tick grows, including malaria-like problems and potentially fatal encephalitis

List of diseases spread by deer tick grows, including malaria-like problems and potentially fatal encephalitis | Virology and Bioinformatics from Virology.ca | Scoop.it
An emerging tick-borne disease that causes symptoms similar to malaria is expanding its range in areas of the northeast where it has become well-established, according to new research.
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High Diversity of RNA Viruses in Rodents, Ethiopia - - Emerging Infectious Disease journal - CDC

High Diversity of RNA Viruses in Rodents, Ethiopia - - Emerging Infectious Disease journal - CDC | Virology and Bioinformatics from Virology.ca | Scoop.it
We investigated synanthropic small mammals in the Ethiopian Highlands as potential reservoirs for human pathogens and found that 2 rodent species, the Ethiopian white-footed mouse and Awash multimammate mouse, are carriers of novel Mobala virus...
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#Rwanda: #HIV Infection At 51 Percent Among #Sex Workers (Page 1 of 2)

At least 51 percent of sex workers in Rwanda are infected with HIV, according to the latest report by the Rwanda Biomedical Centre (RBC).

The research was carried out in all provinces of the country at the different sex workers' hot spots, according to Dr Sabin Nsanzimana, the coordinator of HIV and STIs Care and Treatment department.

The research was the first of its kind conducted by Rwanda Biomedical Centre, according to Dr Nsanzimana.


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Scientists Use Super-Strong Bacteria to Produce 24K Gold

Scientists Use Super-Strong Bacteria to Produce 24K Gold | Virology and Bioinformatics from Virology.ca | Scoop.it
A team of Michigan State University researchers have discovered a bacterium that has the ability to withstand incredible amounts of toxicity and create 24-karat gold.i...

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Minia: implementation of the "Space-efficient and exact de Bruijn graph representation based on a Bloom filter" article

Minia: implementation of the "Space-efficient and exact de Bruijn graph representation based on a Bloom filter" article | Virology and Bioinformatics from Virology.ca | Scoop.it

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Minia assembler is now open-source.

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Isolation of a novel herpesvirus from a Pacific white-sided dolphin - Online First - Springer

Isolation of a novel herpesvirus from a Pacific white-sided dolphin - Online First - Springer | Virology and Bioinformatics from Virology.ca | Scoop.it

During establishment of primary cell culture from the kidney of a dead Pacific white-sided dolphin (Lagenorhynchus obliquidens), a cytopathic effect was observed. Polymerase chain reaction with a set of herpesvirus consensus primers yielded a fragment of the expected size. Nucleotide sequencing of the product indicated that the isolated virus was closely related to an alphaherpesvirus detected in a bottlenose dolphin in the United States, but the sequence identity at the protein level was low (86.6 %). Phylogenetic analysis of the encoded sequence confirmed that the new isolate belonged to the subfamily Alphaherpesvirinae and clustered together with other cetacean alphaherpesviruses. The complete gene encoding glycoprotein B (2,757 bp) was amplified from the novel isolate; the encoded protein was compared with the corresponding protein of other herpesviruses, revealing that this virus belongs to the genus Varicellovirus. Taken together, these results suggest that this virus corresponds to a novel herpesvirus capable of infecting Pacific white-sided dolphins.

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TWiV 206: Viral turducken

TWiV 206: Viral turducken | Virology and Bioinformatics from Virology.ca | Scoop.it
How the innate immune response to viral infection influences the production of pluripotent stem cells, and the diverse mobilome of giant viruses.
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Scientists discover new method of gene identification

Scientists discover new method of gene identification | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists studying the genes and proteins of human cells infected with a common cold virus have identified a new gene identification technique that could increase the genetic information we hold on animals by around 70 to 80 per cent.
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Bioinformatics Voyage (blog): Full NGS

Bioinformatics Voyage (blog): Full NGS | Virology and Bioinformatics from Virology.ca | Scoop.it

Even if you know all about sequencing technologies or to get more clear about it, this video would be very highly recommended. A long one but very nicely delivered by Elaine Mardis of the Genome Institute at Washington University. It is like 101 in how sequencing works.

 

From the Bioinformatics Voyage Blog

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Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism

Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism | Virology and Bioinformatics from Virology.ca | Scoop.it

Abortive infection, during which an infected bacterial cell commits altruistic suicide to destroy the replicating bacteriophage and protect the clonal population, can be mediated by toxin-antitoxin systems such as the Type III protein–RNA toxin-antitoxin system, ToxIN. A flagellum-dependent bacteriophage of the Myoviridae, ΦTE, evolved rare mutants that “escaped” ToxIN-mediated abortive infection within Pectobacterium atrosepticum. Wild-type ΦTE encoded a short sequence similar to the repetitive nucleotide sequence of the RNA antitoxin, ToxI, from ToxIN. The ΦTE escape mutants had expanded the number of these “pseudo-ToxI” genetic repeats and, in one case, an escape phage had “hijacked” ToxI from the plasmid-borne toxIN locus, through recombination. Expression of the pseudo-ToxI repeats during ΦTE infection allowed the phage to replicate, unaffected by ToxIN, through RNA–based molecular mimicry. This is the first example of a non-coding RNA encoded by a phage that evolves by selective expansion and recombination to enable viral suppression of a defensive bacterial suicide system. Furthermore, the ΦTE escape phages had evolved enhanced capacity to transduce replicons expressing ToxIN, demonstrating virus-mediated horizontal transfer of genetic altruism.

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BMC Bioinformatics | Full text | PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

BMC Bioinformatics | Full text | PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods | Virology and Bioinformatics from Virology.ca | Scoop.it
With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance.
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#Bioinformatics A gene expression atlas of the domestic #pig

This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome.
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What’s the answer? (network visualization) | The OpenHelix Blog

What’s the answer? (network visualization) | The OpenHelix Blog | Virology and Bioinformatics from Virology.ca | Scoop.it
BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful.
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Toll-like receptor 3 gene polymorphisms and severity of pandemic A/H1N1/2009 influenza in otherwise healthy children

Toll-like receptors (TLRs) form an essential part of the innate immune system, which plays a fundamental role in rapidly and effectively controlling infections and initiating adaptive immunity.
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A look at molecules that replicate the HIV virus genome

A look at molecules that replicate the HIV virus genome. I created this animation for display on a planetarium dome at the 2012 Biophysical Society meeting i...
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Paul Stamets: 6 ways #mushrooms can save the world

http://www.ted.com Mycologist Paul Stamets studies the mycelium -- and lists 6 ways that this astonishing fungus can help save the world. TEDTalks is a daily...

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VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data | Virology and Bioinformatics from Virology.ca | Scoop.it

There is an immediate need for tools to both analyse and visualize in real-time single-nucleotide polymorphisms, insertions and deletions, and other structural variants from new sequence file formats.

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BMC Bioinformatics | Oculus: faster sequence alignment by streaming read compression

Despite significant advancement in alignment algorithms, the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis.
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Phylogenetics, likelihood, evolution and complexity

Phylogenetics, likelihood, evolution and complexity | Virology and Bioinformatics from Virology.ca | Scoop.it

Summary: Phylogenetics, likelihood, evolution and complexity (PLEX) is a flexible and fast Bayesian Markov chain Monte Carlo software program for large-scale analysis of nucleotide and amino acid data using complex evolutionary models in a phylogenetic framework. The program gains large speed improvements over standard approaches by implementing ‘partial sampling of substitution histories’, a data augmentation approach that can reduce data analysis times from months to minutes on large comparative datasets.

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In Search of Spanish Flu 2 of 2 - BBC Science Documentary

In Search of Spanish Flu 2 of 2 - BBC Science Documentary, recorded 03.04.2009 Documentary in which a team of top UK virologists exhume the body of statesman...

 

And again: Ken Yaw Agyeman Badu, many thanks!


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Abbott hepatitis C drugs bring high cure rates in trial

(Reuters) - A trio of oral medicines from Abbott Laboratories Inc to treat hepatitis C produced unprecedented cure rates in patients who had failed to benefit from standard treatment, as well as very high...
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