Virology and Bioinformatics from Virology.ca
82.6K views | +25 today
Follow
Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Ed Rybicki
Scoop.it!

Catching the bug: Researchers developing virus-detection technology

Catching the bug: Researchers developing virus-detection technology | Virology and Bioinformatics from Virology.ca | Scoop.it
A new flu virus makes its first appearance in the United States on a restroom doorknob at an international airport in January.

 

Sound familiar? Indeed, we have come to expect this scenario every year and call it an outbreak, or pessimistically, the "flu season." And in spite of living in an age when the text of the entire King James Bible can be transmitted by a mobile telephone in roughly one second, there is no reliable way to directly detect the oldest of all biological threats to human life—the virus.


Read more at: http://phys.org/news/2013-09-bug-virus-detection-technology.html#jCp

Ed Rybicki's insight:

Love the hype!  But using physics and nanotech to detect viruses by resonanace - very cool.

more...
No comment yet.
Scooped by Torben Barsballe
Scoop.it!

Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection

Animal cells harbour multiple innate effector mechanisms that inhibit virus replication. For the pathogenic retrovirus human immunodeficiency virus type 1 (HIV-1), these include widely expressed restriction factors1, such as APOBEC3 proteins2, TRIM5-α3, BST2 (refs 4, 5) and SAMHD1 (refs 6, 7), as well as additional factors that are stimulated by type 1 interferon (IFN)8, 9, 10, 11, 12, 13, 14. Here we use both ectopic expression and gene-silencing experiments to define the human dynamin-like, IFN-induced myxovirus resistance 2 (MX2, also known as MXB) protein as a potent inhibitor of HIV-1 infection and as a key effector of IFN-α-mediated resistance to HIV-1 infection. MX2 suppresses infection by all HIV-1 strains tested, has equivalent or reduced effects on divergent simian immunodeficiency viruses, and does not inhibit other retroviruses such as murine leukaemia virus. The Capsid region of the viral Gag protein dictates susceptibility to MX2, and the block to infection occurs at a late post-entry step, with both the nuclear accumulation and chromosomal integration of nascent viral complementary DNA suppressed. Finally, human MX1 (also known as MXA), a closely related protein that has long been recognized as a broadly acting inhibitor of RNA and DNA viruses, including the orthomyxovirus influenza A virus15, 16, does not affect HIV-1, whereas MX2 is ineffective against influenza virus. MX2 is therefore a cell-autonomous, anti-HIV-1 resistance factor whose purposeful mobilization may represent a new therapeutic approach for the treatment of HIV/AIDS.

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Avian-like H1N2 swine flu generated by reassortment of circulating avian-like H1N1 and H3N2 subtypes in Denmark

Avian-like H1N2 swine flu generated by reassortment of circulating avian-like H1N1 and H3N2 subtypes in Denmark | Virology and Bioinformatics from Virology.ca | Scoop.it

The "avian-like" H1N2 subtype, which has been established in the Danish pig population at least since 2003, is a reassortant between circulating swine "avian-like" H1N1 and H3N2. The Danish H1N2 has an "avian-like" H1 and differs from most other reported H1N2 viruses in Europe and North America/Asia, which have H1-genes of human or "classical-swine" origin, respectively. The variant seems, however, also to be circulating in countries like Sweden and Italy. The infection dynamics of the reassorted "avian-like" H1N2 is similar to the older "avian-like" H1N1 subtype.

 

Swine flu reassortment graphic courtesy of Russell Kightley Media

 

Ed Rybicki's insight:

Seeing as I am IN Sweden...this is rather close to (temporary) home!  Just shows: pigs are the melting pot for The Big One.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Should we say no to nosodes?

Should we say no to nosodes? | Virology and Bioinformatics from Virology.ca | Scoop.it
A growing number of medical professionals are asking why homeopathic vaccines are being sold
more...
Ed Rybicki's comment, September 19, 2013 4:13 PM
...or why, in the case of UCT Medical School, why a homeopath should be allowed to facilitate PBL....
Chris Upton + helpers's comment, September 19, 2013 4:27 PM
... aarrggghhh
Scooped by Chris Upton + helpers
Scoop.it!

SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules

Functional modules within protein sequences are often extracted by consensus sequence patterns representing a linear motif; however, other functional regions may only be described by combined features such as amino acid composition, profiles of amino acid properties and randomly distributed short sequence motifs. If only a small number of functional examples are well characterized, the researcher needs a tool to extract similar sequences for further investigation.

Availability and Implementation: We provide the web application ‘SAPA tool’, which allows the user to search with combined properties, ranks the extracted target regions by an integrated score, estimates false discovery rates by using decoy sequences and provides them as a sequence file or spreadsheet. Source code, user manual and the web application implemented in Perl, HTML, CSS and JavaScript and running on Apache are freely available at http://sapa-tool.uio.no/sapa/

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Exploring the role of human miRNAs in virus–host interactions using systematic overlap analysis

Motivation: Human miRNAs have recently been found to have important roles in viral replication. Understanding the patterns and details of human miRNA interactions during virus–host interactions may help uncover novel antiviral therapies. Based on the abundance of knowledge available regarding protein–protein interactions (PPI), virus–host protein interactions, experimentally validated human miRNA-target pairs and transcriptional regulation of human miRNAs, it is possible to explore the complex regulatory network that exists between viral proteins and human miRNAs at the system level.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Graphite Web: web tool for gene set analysis exploiting pathway topology

Graphite web is a novel web tool for pathway analyses and network visualization for gene expression data of both microarray and RNA-seq experiments. Several pathway analyses have been proposed either in the univariate or in the global and multivariate context to tackle the complexity and the interpretation of expression results. These methods can be further divided into ‘topological’ and ‘non-topological’ methods according to their ability to gain power from pathway topology. Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges. To this day, the most used approaches are non-topological and univariate although they miss the relationship among genes.

more...
No comment yet.
Scooped by Alice Gibbons
Scoop.it!

Breaking the code: The potential of the $100 genome

Breaking the code: The potential of the $100 genome | Virology and Bioinformatics from Virology.ca | Scoop.it
The ability to sequence a genome quickly and cheaply is the gateway to understanding the underlying molecular pathways for disease. Are we there yet?
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Steven Salzberg at #bog13: Assembling 22Gb Conifer Genome - Homologus

Steven Salzberg at #bog13: Assembling 22Gb Conifer Genome - Homologus | Virology and Bioinformatics from Virology.ca | Scoop.it

Steven Salzberg’s group at John’s Hopkins university is working on assembling the genome of a tree that is as tall as his publication list. He was kind enough to share the slides of his talk at the Biology of Genome 2013 conference taking place in Cold Spring Harbor Lab.

Few highlights of the talk based on his slides, private email exchanges and incredibly informative twitter updates from @leonidkruglyak, @ewanbirney and other #bog13 attendees:

Gymnosperms are way out in the phylogenetic tree of plants, and the other two out-branches in the following figure are fern and moss. JGI already sequenced fern and moss genomes. Gymnosperm genome will help biologist understand genetic diversity of higher plants.
more...
No comment yet.
Rescooped by Chris Upton + helpers from Science-Videos
Scoop.it!

Enzymes That Are Not Proteins: The Discovery of Ribozymes | HHMI's BioInteractive

Enzymes That Are Not Proteins: The Discovery of Ribozymes | HHMI's BioInteractive | Virology and Bioinformatics from Virology.ca | Scoop.it
Listen to HHMI President Dr. Thomas Cech discussing his Nobel Prize-winning discovery of RNA's catalytic properties.

Via Dr. Stefan Gruenwald
more...
Ed Rybicki's comment, September 19, 2013 4:14 PM
Heard him as newly-minted Nobel in Keystone in 1991: inspirational!
Scooped by C_Fleis
Scoop.it!

New HIV-1 Replication Pathway Discovered by NYU College of Dentistry Researchers

New HIV-1 Replication Pathway Discovered by NYU College of Dentistry Researchers | Virology and Bioinformatics from Virology.ca | Scoop.it
more...
No comment yet.
Rescooped by Chris Upton + helpers from Bioinformatics Training
Scoop.it!

Wow of the week: With a little bioengineering, E. coli becomes a pathogen-fighting superhero

Wow of the week: With a little bioengineering, E. coli becomes a pathogen-fighting superhero | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers may have found a way to turn E. coli bacteria into a way to fight hospital-acquired infections like pneumonia and bloodstream infections.

Via Gerd Moe-Behrens, Pedro Fernandes
more...
Scooped by Ed Rybicki
Scoop.it!

UCLA researchers' smartphone 'microscope' can detect a single virus

UCLA researchers' smartphone 'microscope' can detect a single virus | Virology and Bioinformatics from Virology.ca | Scoop.it
UCLA researchers' smartphone 'microscope' can detect a single virus, nanoparticles / UCLA Newsroom
Ed Rybicki's insight:

You thought your new iPhone was cool...B-)

more...
No comment yet.
Scooped by Torben Barsballe
Scoop.it!

Virology Journal | Full text | Prevalence of avian paramyxovirus type 1 in Mallards during autumn migration in the western Baltic Sea region

Newcastle disease virus (NDV) is the causative agent of the Newcastle disease, a severe disease in birds associated with substantial economic losses to the poultry industry worldwide. Sweden is situated along the Western European waterfowl flyway and applies a non-vaccination policy combined with directives of immediate euthanisation of NDV infected flocks. During the last decades there have been several outbreaks with NDV in poultry in Sweden. However, less is known about the virus prevalence in the wild bird population including waterfowl, a well-established reservoir of avian paramyxovirus type 1 (APMV-1), the paramyxovirus serotype that include pathogenic NDV.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study : The Lancet

BackgroundSince June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin.MethodsFull genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85—95%, and four 30—50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done.FindingsThree distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction.InterpretationWe present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed.
more...
No comment yet.
Scooped by Kenzibit
Scoop.it!

Researchers Create Molecule That Can Trick HIV into Destroying Itself

Researchers Create Molecule That Can Trick HIV into Destroying Itself | Virology and Bioinformatics from Virology.ca | Scoop.it
Philadelphia, PA (Scicasts) – Pinning down an effective way to combat the spread of the human immunodeficiency virus, the viral precursor to AIDS, has long been challenge task for scientists and physicians, because the virus is an elusive one that...
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Data processing and analysis of genetic variation using next-gen sequencing (2012)

Copyright Broad Institute, 2013. All rights reserved. The Primer on Medical and Population Genetics is a series of informal weekly discussions of basic genet...
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

nhmmer: DNA homology search with profile HMMs

Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Sequential Reassortments Underlie Diverse Influenza H7N9 Genotypes in China

Initial genetic characterizations have suggested that the influenza A (H7N9) viruses responsible for the current outbreak in China are novel reassortants. However, little is known about the pathways of their evolution and, in particular, the generation of diverse viral genotypes. Here we report an in-depth evolutionary analysis of whole-genome sequence data of 45 H7N9 and 42 H9N2 viruses isolated from humans, poultry, and wild birds during recent influenza surveillance efforts in China. Our analysis shows that the H7N9 viruses were generated by at least two steps of sequential reassortments involving distinct H9N2 donor viruses in different hosts. The first reassortment likely occurred in wild birds and the second in domestic birds in east China in early 2012. Our study identifies the pathways for the generation of diverse H7N9 genotypes in China and highlights the importance of monitoring multiple sources for effective surveillance of potential influenza outbreaks.

more...
No comment yet.
Scooped by Alice Gibbons
Scoop.it!

PLOS ONE: Mice Infected with Low-Virulence Strains of Toxoplasma gondii Lose Their Innate Aversion to Cat Urine, Even after Extensive Parasite Clearance

PLOS ONE: Mice Infected with Low-Virulence Strains of Toxoplasma gondii Lose Their Innate Aversion to Cat Urine, Even after Extensive Parasite Clearance | Virology and Bioinformatics from Virology.ca | Scoop.it

Toxoplasma gondii chronic infection in rodent secondary hosts has been reported to lead to a loss of innate, hard-wired fear toward cats, its primary host. However the generality of this response across T. gondii strains and the underlying mechanism for this pathogen-mediated behavioral change remain unknown. To begin exploring these questions, we evaluated the effects of infection with two previously uninvestigated isolates from the three major North American clonal lineages of T. gondii, Type III and an attenuated strain of Type I. Using an hour-long open field activity assay optimized for this purpose, we measured mouse aversion toward predator and non-predator urines. We show that loss of innate aversion of cat urine is a general trait caused by infection with any of the three major clonal lineages of parasite. Surprisingly, we found that infection with the attenuated Type I parasite results in sustained loss of aversion at times post infection when neither parasite nor ongoing brain inflammation were detectable. This suggests that T. gondii-mediated interruption of mouse innate aversion toward cat urine may occur during early acute infection in a permanent manner, not requiring persistence of parasite cysts or continuing brain inflammation.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Handbook of Biological Statistics: Introduction

Handbook of Biological Statistics: Introduction | Virology and Bioinformatics from Virology.ca | Scoop.it
Chris Upton + helpers's insight:

Welcome to the Handbook of Biological Statistics! This online textbook evolved from a set of notes for my Biological Data Analysis class at the University of Delaware. My main goal in that class is to teach biology students how to choose the appropriate statistical test for a particular experiment, then apply that test and interpret the results. I spend relatively little time on the mathematical basis of the tests; for most biologists, statistics is just a useful tool, like a microscope, and knowing the detailed mathematical basis of a statistical test is as unimportant to most biologists as knowing which kinds of glass were used to make a microscope lens. Biologists in very statistics-intensive fields, such as ecology, epidemiology, and systematics, may find this handbook to be a bit superficial for their needs, just as a microscopist using the latest techniques in 4-D, 3-photon confocal microscopy needs to know more about their microscope than someone who's just counting the hairs on a fly's back.

more...
No comment yet.
Rescooped by Chris Upton + helpers from Plant Pathogenomics
Scoop.it!

PeerJ: Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology (2013)

PeerJ: Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology (2013) | Virology and Bioinformatics from Virology.ca | Scoop.it

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology.

 

This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols.

 

The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed http://toolshed.g2.bx.psu.edu


Via Kamoun Lab @ TSL
more...
julien levy's curator insight, September 23, 2013 12:24 PM

Iplant or Galaxy webbased ?

 

Scooped by C_Fleis
Scoop.it!

Media Availability: NIH Clinical Study Establishes Human Model of Influenza Pathogenesis

"NIH Clinical Study Establishes Human Model of Influenza PathogenesisFindings Lay Foundation for More Efficient Flu Vaccine, Drug Trials"

 

"A National Institutes of Health (NIH) clinical study of healthy adult volunteers who consented to be infected with the 2009 H1N1 influenza virus under carefully controlled conditions has provided researchers with concrete information about the minimum dose of virus needed to produce mild-to-moderate illness. The study also gives a clearer picture of how much time elapses between a known time of infection, the start of viral shedding (a signal of contagiousness), the development of an immune response, and the onset and duration of influenza symptoms. The data obtained from this study provide a basis for more rapid, cost-effective clinical trials to evaluate new influenza drugs or to determine the efficacy of candidate vaccines for both seasonal and pandemic influenza."

more...
No comment yet.
Rescooped by Chris Upton + helpers from bioinformatics-databases
Scoop.it!

Proteome Database System

Proteome Database System | Virology and Bioinformatics from Virology.ca | Scoop.it

The publicly available Proteome Database System for Microbial Research 2D-PAGE has been established at the Max Planck Institute for Infection Biology and serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. The database system is centrally administrated, and investigators without specific bioinformatics competence in database construction can submit their data. The system comprises four heterogeneous but interconnected databases: (i) 2D-PAGE database for 2-D gel electrophoresis and mass spectrometry data, (ii) Isotope Coded Affinity Tag (ICAT)-LC/MS database, (iii) FUNC_CLASS database for functional classification of proteins, (iv) DIFF database for presentation of differentially regulated proteins detected by quantitative gel image analysis. The database system is hyperlinked with public databases such as SWISS-PROT; NCBI; PEDANT and KEGG. The current public release (May, 2004) contains proteomic information on 11 microorganisms such as Mycobacterium tuberculosis, Helicobacter pylori, Chlamydophila pneumoniae, Borrelia garinii, Francisella tularensis, Mycoplasma pneumoniae and information on Jurkat T-cells and mouse mammary gland. Proteomic data are presented in 18 two-dimensional gels with 2572 identified protein spots. For 254 of these spots peptide mass fingerprints are available. More than 1000 identified spots of further miroorganisms such asMycobacterium bovis BCG, Salmonella SL-1344, Vibrio cholerae are stored in the internal release of 2D-PAGE which will be publicly accessible after paper submission. The annotated proteome data such as protein name, molecular weight Mr, isoelectric point pI, gene name, ORF, NCBI accession number, identification method, sequence coverage, protein spot number, class (antigen, gastric carcinoma associated antigen etc.) can be retrieved either by clicking on protein spots or by formulating complex queries. Specific data such as pI, Mr-values or codon usage for proteins can be visualized and analyzed on the fly using the statistical software environment R (http://www.r-project.org/) or can be downloaded as spread sheet files. The Proteome Database System for Microbial Research can be accessed from http://www.mpiib-berlin.mpg.de/2D-PAGE.


Via Dr. Stefan Gruenwald
more...
No comment yet.
Rescooped by Kenzibit from Mucosal Immunity
Scoop.it!

Oral Vaccine for HIV Immunization-Emory University - iBridge Network

Oral Vaccine for HIV Immunization-Emory University - iBridge Network | Virology and Bioinformatics from Virology.ca | Scoop.it
While the preferred route of administration of a mucosal immunity vaccine would be by mouth, an orally delivered vaccine must be able to survive the high acidity in the stomach in order to elicit an immune response in the ...

Via Gilbert C FAURE
more...
No comment yet.