PLOS Computational Biology is an open-access
Join Scoop.it for Free
Share ideas that matter on the social web and experience
the benefits of curating the world's best content.
I don't have a Facebook, a Twitter or a LinkedIn account
Already have an account: Login
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Curated by
Chris Upton + helpers
|
Scooped by Nicolas Palopoli onto Virology and Bioinformatics from Virology.ca |
Scoop.it!
No comment yet.
Sign up to comment
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
 Your new post is loading...
Scoop.it!
|
|
Scooped by Chad Smithson |
Scoop.it!
By adding fundamentals of biology to their computer science training, more than a few native computer scientists are contributing—and preparing themselves to contribute—to the advancement of the life sciences (among other fields), laying foundations for new branches of study. It is indeed a promising approach, but there is still much work to be done—satisfying work, one pioneer says.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chad Smithson |
Scoop.it!
For many pathogens, the initial point of entry into the host is the mucosal epithelium, and the host immune system deploys several defence mechanisms at this surface, including the mucus itself. Now, Barr et al. show that phages might constitute an additional antibacterial defence mechanism at host mucosal surfaces.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
Scooped by Chris Upton + helpers |
Scoop.it!
Patients in Vietnam and other locations with central nervous system infections may well be suffering from the effects of a newly discovered virus. Researchers have detected a virus they're calling CyCV-VN in spinal fluid from 4% of 642 patients with central nervous system infections of unknown cause, and in an average of 58% of fecal samples from pigs and poultry, suggesting animals may serve as reservoirs for transmission to humans. The virus belongs to the Cyclovirus genus, a group that has never before been implicated in human or animal disease.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chad Smithson |
Scoop.it!
It’s not been a great year for the HPV vaccine. First we learned that the completion rates in the US remain alarmingly low, and now the Japanese health ministry
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
Armed with new methods, researchers are interrogating the DNA of centuries-old pathogens extracted from the bones and teeth of victims.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Rescooped by Chris Upton + helpers from Virology News |
Scoop.it!
The Global Health Program at the Council on Foreign Relations has been tracking news reports since 2008 to produce an interactive map that plots global outbreaks of diseases that are easily prevented by inexpensive and effective vaccines.
Via Ed Rybicki
Ed Rybicki's curator insight,
June 17, 7:52 AM
BRILLIANT piece of work - and you kow, the UK comes over like some developing country, in terms of vaccine-preventable disease incidence? Frightening!
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chad Smithson |
Scoop.it!
Vaccinia virus (VACV) strain TianTan was used for much of China's modern history to vaccinate against smallpox, however the only genome sequence contains errors. We have sequenced additional examples of TianTan to obtain a better picture of this important virus.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high memory hardware (>48GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is 4-5 times faster than BWA+GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
Reassortment is fundamental to the evolution of influenza viruses and plays a key role in the generation of epidemiologically significant strains. Previous studies indicate that reassortment is restricted by segment mismatch, arising from functional incompatibilities among components of two viruses. Additional factors that dictate the efficiency of reassortment remain poorly characterized. Thus, it is unclear what conditions are favorable for reassortment and therefore under what circumstances novel influenza A viruses might arise in nature. Herein, we describe a system for studying reassortment in the absence of segment mismatch and exploit this system to determine the baseline efficiency of reassortment and the effects of infection dose and timing.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
One of the most celebrated achievements of immunology and modern medicine is the eradication of the dreaded plague smallpox. From the introduction of smallpox vaccination by Edward Jenner, to its popularization by Louis Pasteur, to the eradication effort led by Donald Henderson, this story has many lessons for us today, including the characteristics of the disease and vaccine that permitted its eradication, and the obviousness of the vaccine as a vector for other intractable Infectious diseases. The disease itself, interpreted in the light of modern molecular immunology, is an obvious immunopathological disease, which occurs after a latent interval of 1-2 weeks, and manifests as a systemic cell-mediated delayed type hypersensitivity (DTH) syndrome.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Rescooped by Chris Upton + helpers from Virology News |
Scoop.it!
The results of the phylogenomic analysis of the virophages and related genetic elements are compatible with the concept of network-like evolution of the virus world and emphasize multiple evolutionary connections between bona fide viruses and other classes of capsid-less mobile elements.
Altogether, virophages, polintons, a distinct Tetrahymena transposable element Tlr1, transpovirons, adenoviruses, and some bacteriophages form a network of evolutionary relationships that is held together by overlapping sets of shared genes and appears to represent a distinct module in the vast total network of viruses and mobile elements.
Via Chad Smithson, Ed Rybicki
Ed Rybicki's curator insight,
May 24, 9:26 AM
Blow your MINDS, virologists...deep relationships between phages, human viruses, satellite viruses and big DNA viruses - as well as with diverse mobile elements within genomes.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
Few microorganisms match the impact that the oomycetes have had on mankind. This distinct lineage of eukaryotes is well-known for its most notorious member, Phytophthora infestans, the agent of the nineteenth century Irish potato famine, and several other devastating pathogens of cultivated and wild plants [1]. Indeed, more than 60% of oomycete species infect plants [2]. Less known is the fact that many oomycetes are parasitic on animals, from freshwater fish and crustaceans to mammals, such as livestock, pets, and humans [3]. Animal parasitic oomycetes have received much less attention than their plant pathogenic kin, and our understanding of their virulence mechanisms is rudimentary. However, research momentum is poised to accelerate with the first report of the genome of an animal parasitic oomycete. In this issue of PLOS Genetics, Jiang et al. [4] describe the 63 Mbp genome sequence of the fish pathogen Saprolegnia parasitica and highlight a distinct repertoire of candidate virulence genes.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
Scooped by Ed Rybicki |
Scoop.it!
IMPORTANCE Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology frequently remains unknown, which hampers development of therapeutic or preventive strategies. Hence, identification of novel pathogens is essential and is facilitated by current next-generation sequencing-based methods. Using such technology, we identified and characterized the full genome of a novel cyclovirus in cerebrospinal fluid (CSF) specimens from two Vietnamese patients with CNS infections of unknown etiology, which was subsequently detected in none of 122 CSF specimens from patients with noninfectious neurological disorders but 4% of 642 CSF specimens from Vietnamese patients with suspected or confirmed CNS infections. Similar detection rates in feces from healthy children suggested food-borne or orofecal transmission routes, while frequent detection in feces from Vietnamese pigs and poultry (average, 58%) suggested the existence of animal reservoirs for such transmission. Further studies are needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.
Ed Rybicki's insight:
This is potentially a big deal: a new DNA virus potentially causing an acute CNS infection?? I can see PCR primers being made across the globe....
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
He’s ready for a tsunami of criticism with his latest foray into debunking popular wisdom – “Do You Believe in Magic?: The Sense and Nonsense of Alternative Medicine” in which he takes on the vitamin and herbal supplements industry, alternative medicine of all kinds, Congress and celebrity doctors who peddle their own products. It hits the shelves on Tuesday.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chad Smithson |
Scoop.it!
Serum from mice that received a single intramuscular AAV injection efficiently neutralized all H1, H2 and H5 influenza strains tested. Notably, even immunodeficient and older mice were protected by this method. If translated to humans, this prophylactic approach may be uniquely capable of protecting immunocompromised or elderly patient populations not reliably protected by existing vaccines.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
Scooped by Ken Yaw Agyeman-Badu |
Scoop.it!
JC polyomavirus is a bit of a mystery. Many people are infected with it, but few become ill as a result. This virus bides its time.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Rescooped by Chris Upton + helpers from Virology News |
Scoop.it!
Survival of infection with Ebola virus (EBOV) depends on the ability of the host to mount early and strong immune responses [1], [2]. However, given that EBOV cases are associated with 40%–90% human mortality, EBOV has developed intricate solutions to human immunological defenses. Enveloped viruses, like EBOV, must deposit their genetic material within a cell to ensure their propagation. The roles of viral envelope glycoproteins in mediating virus attachment to host cells and catalyzing the subsequent fusion of the viral and host plasma membranes have been well described (reviewed in [3]). Given the limited number of genes in EBOV and other viruses, it stands to reason that these conformationally labile glycoproteins are also involved in more than just the initial steps of a productive infection. There is strong evidence that viral entry glycoproteins (GP) are modulators of host antiviral defenses (Table 1). In this article, we discuss our current structural understanding of the functions of envelope entry glycoproteins in immune evasion using EBOV as our example.
Via Ed Rybicki
Ed Rybicki's curator insight,
May 20, 4:18 AM
Nice review on a very interesting and important topic - and highlights how viral entry proteins double as immune evasion agents.
Chris Upton + helpers's comment,
June 17, 4:11 PM
"EBOV has developed intricate solutions to human immunological defenses." Since ebola didn't evolve in humans, this must be accidental. Similar activities may exist in the natural host but not with such high mortality consequences.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
Introduction to Translational Bioinformatics Collection
Chapter 1: Biomedical Knowledge Integration
Chapter 2: Data-Driven View of Disease Biology
Chapter 3: Small Molecules and Disease
Chapter 4: Protein Interactions and Disease
Chapter 5: Network Biology Approach to Complex Diseases
Chapter 6: Structural Variation and Medical Genomics
Chapter 7: Pharmacogenomics
Chapter 8: Biological Knowledge Assembly and Interpretation
Chapter 9: Analyses Using Disease Ontologies
Chapter 10: Mining Genome-Wide Genetic Markers
Chapter 11: Genome-Wide Association Studies
Chapter 12: Human Microbiome Analysis
Chapter 13: Mining Electronic Health Records in the Genomics Era
Chapter 14: Cancer Genome Analysis
Chapter 15: Disease Gene Prioritization
Chapter 16: Text Mining for Translational Bioinformatics
Chapter 17: Bioimage Informatics for Systems Pharmacology
PLOS Computational Biology: published 25 Apr 2013 | info:doi/10.1371/journal.pcbi.1003043
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
Scientists have developed a simple color sensor principle which facilitates the detection of residual medications, trace metals from industrial process waters, and many other substances.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
When a virus infects a plant, a slient war rages, fought with RNA weapons.
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Rescooped by Chris Upton + helpers from Virology News |
Scoop.it!
The current status of phage therapy approaches is reviewed and possible hurdles to a practical medical application of bacteriophages in Western countries are identified as discussed at a recent EMBO meeting on “Viruses of Microbes” in Brussels. In view of the growing antibiotic resistance crisis, a coordinated effort by the public health sector is needed to evaluate the potential of phage therapy as an adjunct to antibiotics.
T4 coliphage picture by Russell Kightley Media
Via Ed Rybicki
Ed Rybicki's curator insight,
May 29, 10:45 AM
I missed this first time around - but it is one of the most-downloaded papers from Virology, so probably well worth a read.Or getting into the field...?
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
|
|
Scooped by Chris Upton + helpers |
Scoop.it!
Any use in the bioinformatics arena???
Delete the scoop?
Are you sure you want to delete this scoop?
Yes
Besides the interesting recall of the Intelligent Systems for Molecular Biology (ISMB) annual conferences on computational biology, it offers a nice insight into current state-of-the-art methodologies and upcoming trends in the discipline.