Viruses and Bioinformatics from Virology.uvic.ca
87.9K views | +20 today
Follow
Viruses and Bioinformatics from Virology.uvic.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 Chris Upton + helpers
Scoop.it!

Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface : Nature : Nature Publishing Group

Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface : Nature : Nature Publishing Group | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The isolation of human monoclonal antibodies is providing important insights into the specificities that underlie broad neutralization of HIV-1 (reviewed in ref. 1). Here we report a broad and extremely potent HIV-specific monoclonal antibody, termed 35O22, which binds a novel HIV-1 envelope glycoprotein (Env) epitope. 35O22 neutralized 62% of 181 pseudoviruses with a half-maximum inhibitory concentration (IC50) <50 [mgr]g ml-1. The median IC50 of neutralized viruses was 0.033 [mgr]g ml-1, among the most potent thus far described. 35O22 did not bind monomeric forms of Env tested, but did bind the trimeric BG505 SOSIP.664. Mutagenesis and a reconstruction by negative-stain electron microscopy of the Fab in complex with trimer revealed that it bound to a conserved epitope, which stretched across gp120 and gp41. The specificity of 35O22 represents a novel site of vulnerability on HIV Env, which serum analysis indicates to be commonly elicited by natural infection. Binding to this new site of vulnerability may thus be an important complement to current monoclonal-antibody-based approaches to immunotherapies, prophylaxis and vaccine design.
more...
No comment yet.
Rescooped by Chris Upton + helpers from Amazing Science
Scoop.it!

Herpes simplex virus type 1 and Alzheimer’s disease: Increasing evidence for a major role of the virus

Herpes simplex virus type 1 and Alzheimer’s disease: Increasing evidence for a major role of the virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The concept of a viral role in Alzheimer’s disease (AD), specifically of herpes simplex virus type 1 (HSV1), was first proposed several decades ago (Ball, 1982; Gannicliffe et al., 1986). Legitimizing the concept clearly depended on a positive answer to a number of test questions, the first of which was whether or not HSV1 is ever present in human brain. The subsequent discovery that HSV1 DNA resides in a high proportion of brains of elderly people in latent form (Jamieson et al., 1991)—both normals and AD patients—immediately made the concept more credible, but raised associated questions such as whether or not the virus is ever active in brain or is merely a passive resident there; whether on its own it is a causative factor in AD or it acts thus only with another factor, perhaps genetic; if active, what causes its activity; whether there is any link with the characteristic abnormal features of AD brains or their components, and whether, if indeed implicated in AD, antiviral agents would be useful for treating the disease. These questions were posed in a previous review (Wozniak and Itzhaki, 2010)—and strong evidence was presented that permitted the answer to each question to be “yes” or, very likely to be “yes”. The present review briefly summarizes the earlier evidence, and provides an update, which is especially timely in view of the subsequent steady increase in number of relevant publications.


Herpes simplex virus type 1 (HSV1), when present in brain of carriers of the type 4 allele of the apolipoprotein E gene (APOE), has been implicated as a major factor in Alzheimer’s disease (AD). It is proposed that virus is normally latent in many elderly brains but reactivates periodically (as in the peripheral nervous system) under certain conditions, for example stress, immunosuppression, and peripheral infection, causing cumulative damage and eventually development of AD.


Diverse approaches have provided data that explicitly support, directly or indirectly, these concepts. Several have confirmed HSV1 DNA presence in human brains, and the HSV1-APOE-ε4 association in AD. Further, studies on HSV1-infected APOE-transgenic mice have shown that APOE-e4 animals display a greater potential for viral damage. Reactivated HSV1 can cause direct and inflammatory damage, probably involving increased formation of beta amyloid (Aβ) and of AD-like tau (P-tau)—changes found to occur in HSV1-infected cell cultures.


Implicating HSV1 further in AD is the discovery that HSV1 DNA is specifically localized in amyloid plaques in AD. Other relevant, harmful effects of infection include the following: dynamic interactions between HSV1 and amyloid precursor protein (APP), which would affect both viral and APP transport; induction of toll-like receptors (TLRs) in HSV1-infected astrocyte cultures, which has been linked to the likely effects of reactivation of the virus in brain.


Several epidemiological studies have now shown, using serological data, an association between systemic infections and cognitive decline, with HSV1 particularly implicated. Genetic studies too have linked various pathways in AD with those occurring on HSV1 infection. In relation to the potential usage of antivirals to treat AD patients, acyclovir (ACV) is effective in reducing HSV1-induced AD-like changes in cell cultures, and valacyclovir, the bioactive form of ACV, might be most effective if combined with an antiviral that acts by a different mechanism, such as intravenous immunoglobulin (IVIG).


Via Dr. Stefan Gruenwald
more...
Krishan Maggon 's curator insight, September 2, 2014 6:48 PM

Thanks Dr. Gruenwald.

Scooped by burkesquires
Scoop.it!

VirVarSeq: a low frequency Virus Variant detection pipeline for Illumina Sequencing using adaptive base-calling accuracy filtering. Bioinformatics. 2014

MOTIVATION:

In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1 and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores that are useful for differentiating errors from the real low-frequency mutations.

RESULTS:

A variant calling tool, Q-cpileup, is proposed, which exploits the quality scores of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical samples we show that Q-cpileup is able to reduce the number of false positives. The filtering strategy is adaptive and provides an optimized threshold for individual samples in each sequencing run. Additionally, linkage information is kept between single nucleotide polymorphisms as variants are called at codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their anti-viral drug responses. A comparison with existing SNP-callers tools reveals that calling variants at codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%. Availability: The VirVarSeq is available, together with a users guide and test data at sourceforge: http://sourceforge.net/projects/virtools/?source=directory CONTACT: bie.verbist@ugent.be.

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

Rebecca Schuman: The decline and fall of higher education

Rebecca Schuman: The decline and fall of higher education | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
When the helicopter generation entered university, suddenly everyone needed A’s, and everyone needed to know exactly what needed to be done to get one.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

BMC Bioinformatics | Abstract | jvenn: an interactive Venn diagram viewer

Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability.
more...
No comment yet.
Rescooped by Bradford Condon from Genomics and metagenomics of microbes
Scoop.it!

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
First pass methods based on BLAST match are commonly used as an initial step to separate the different phylogenetic histories of genes in microbial genomes, and target putative horizontal gene transfer (HGT) events. This will continue to be necessary given the rapid growth of genomic data and the technical difficulties in conducting large-scale explicit phylogenetic analyses. However, these methods often produce misleading results due to their inability to resolve indirect phylogenetic links and their vulnerability to stochastic events.
more...
No comment yet.
Scooped by Kenzibit
Scoop.it!

Influenza polymerase encoding mRNAs utilize atypical mRNA nuclear export

Influenza is a segmented negative strand RNA virus. Each RNA segment is encapsulated by influenza nucleoprotein and bound by the viral RNA dependent RNA polymerase (RdRP) to form viral ribonucleoproteins responsible for RNA synthesis in the nucleus of the host cell. Influenza transcription results in spliced mRNAs (M2 and NS2), intron-containing mRNAs (M1 and NS1), and intron-less mRNAs (HA, NA, NP, PB1, PB2, and PA), all of which undergo nuclear export into the cytoplasm for translation. Most cellular mRNA nuclear export is Nxf1-mediated, while select mRNAs utilize Crm1.
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Epitope-based approaches to a universal influenza vaccine - J Autoimmun. 2014

Epitope-based approaches to a universal influenza vaccine - J Autoimmun. 2014 | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The development of vaccines has been one of the most important contributions of immunology to public health to date. Although several infectious diseases have all but vanished thanks to effective vaccines, the most common infectious disease, influenza, still represents a major threat to public health. This is more concerning than ever before in light of potentially virulent avian pandemic strains which have emerged in the last decade and infected human hosts, causing high morbidity and mortality. Despite considerable efforts to improve production of influenza vaccines and vaccinate large portions of the population annually, the currently available influenza vaccines are strain-specific and not effective enough. Considering the vulnerability of infants and elderly to seasonal influenza-related complications and the ever present public health threat of a deadly influenza pandemic, there is urgent need for a new kind of influenza vaccine. Ideally, such a vaccine should provide enhanced long term, multi-strain protection without compromising safety and in this way, dramatically improve global protection against seasonal and pandemic influenza viruses. This review highlights one approach to developing a universal influenza vaccine, which is based on highly conserved viral sequences, 'epitopes', that specifically activate humoral and/or cellular immune responses. This approach to vaccinology was pioneered by Prof Arnon, who initiated development of an epitope-based universal vaccine called Multimeric-001 (M-001), which has already been validated in clinical trials to induce broad immunity against A and B-Type, seasonal and pandemic strains.

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

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2,000x coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from Middle African lineages ~2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Since many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.

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

Scientists found the origins of the Ebola outbreak — by tracking its mutations

Scientists found the origins of the Ebola outbreak — by tracking its mutations | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Genetic sequences of dozens of Ebola virus samples will provide much needed information for fighting the disease.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Scientific method: Statistical errors

Scientific method: Statistical errors | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume.
Chris Upton + helpers's insight:

Worth repeating...

more...
No comment yet.
Rescooped by Chris Upton + helpers from Amazing Science
Scoop.it!

Parasitic Plant Strangleweed Injects Host With Over 9,000 RNA Transcripts

Parasitic Plant Strangleweed Injects Host With Over 9,000 RNA Transcripts | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Virginia Tech professor and Fralin Life Institute affiliate Jim Westwood has made a discovery about plant-to-plant communication: enormous amounts of genetic messages in the form of mRNA transcripts are transmitted from the parasitic plant Cuscuta (known more commonly as dodder and strangleweed) to its hosts.

 

Using Illumina next generation sequencing technologies to sequence the tissues of the host and an attached parasite, the team found that the number of genes that gets passed into the host depends on the identity of the host.  The tomato plant received 347 of the strangleweed’s mRNAs, whereas the Arabidopsis received an astonishing 9514 mRNAs.  When Arabidopsis plant receives this many mRNAs, the total genetic material of tissues in contact with the strangleweed is about 45% from the parasite.

 

The new quantitative result builds on Professor Westwood’s prior discovery of RNA transfer between the parasitic plant and its host plants.  In the prior study, Westwood found that when the strangleweed uses its haustorium (piercing appendage) to penetrate the stems of its host plants, it passes on its own RNA to the host, though only tens of mRNAs were identified.  The discovery challenged our understanding that mRNAs are mainly kept within cells.

 

But now the research team has quantified the extent to which the messages are passed.  mRNA stands for “messenger RNA” and are the snippets of genetic information that are created from DNA.  Typically an mRNA molecule is “read” by a molecule machine known as a ribosome and turned into a protein which carries out particular functions in the cell.  And usually, more mRNAs means more protein.  Therefore, the conversion from DNA to mRNA is one way to amplify or control the activation of a gene.

 

It is not yet clear what are the functions of the transmitted genes but bioinformatic analysis shows that hydrolase activity, metabolism and response to stimulus gene groups were among the most represented in those that crossed the species bridge.

 

Westwood has determined that the host plant may be receiving orders of a kind from the parasitic plant, such as lowering its natural defense system so that the strangleweed can more easily attack them.

 

The findings by Westwood, Professor of weed science, plant pathology and physiology at the College of Agriculture and Life Sciences, is even more surprising when considered against prior thought that mRNA is unstable, short-lived and fragile.

 

The discoveries also opens new avenues in the research of the eradication of parasitic plants such as broomrape and witchweed, two plants that pose serious threats to legumes and other crops.  This also has intriguing implications for increasing efficiency of yields.

 

Future plans include expansion of such research to other organismal domains, such as fungi and bacteria, also exchange the mRNA.  But the meaning and the outcome of the transmitted messages remain yet unclear and work must be done to find out what the plants are saying to each other.


Via Dr. Stefan Gruenwald
Chris Upton + helpers's insight:

Pretty freaky....

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

Whole genome analysis of sierra nevada virus, a novel mononegavirus in the family nyamiviridae. Am J Trop Med Hyg. 2014

A novel mononegavirus was isolated in 1975 from ticks (Ornithodoros coriaceus) collected during investigation of an outbreak of epizootic bovine abortion (EBA) in northern California. It was originally designated "bovine abortion-tick virus" (BA-T virus). The EBA is now known to be associated with a deltaproteobacterium infection, and not a virus. The BA-T virus had remained uncharacterized until now. We have determined by electron microscopy, serology, and genome sequencing that the BA-T virus is a fourth member of the newly proposed family Nyamiviridae, and we have renamed it Sierra Nevada virus (SNVV). Although antigenically distinct, phylogenetically SNVV is basal to Nyamanini virus (NYMV) and Midway virus (MIDWV), two other tick-borne agents. Although NYMV was found to infect land birds, and MIDWV seabirds, it is presently unknown whether SNVV naturally infects birds or mammals.

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

Buying in to bioinformatics: an introduction to commercial sequence analysis software

Buying in to bioinformatics: an introduction to commercial sequence analysis software | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

BMC Bioinformatics | Abstract | AliGROOVE -- visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support

Masking of multiple sequence alignment blocks has become a powerful method to enhance the
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Genomic Characterization of a Circovirus Associated with Fatal Hemorrhagic Enteritis in Dog, Italy

Genomic Characterization of a Circovirus Associated with Fatal Hemorrhagic Enteritis in Dog, Italy | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Dog circovirus (DogCV) was identified in an outbreak of enteritis in pups in Italy. The disease was observed in 6 young dachshunds pups of a litter from a breeding kennel and caused the death of 2 dogs. Upon full-genome analysis, the virus detected in one of the dead pups (strain Bari/411–13) was closely related to DogCVs that have been recently isolated in the USA. The present study, if corroborated by further reports, could represent a useful contribution to the knowledge of the pathogenic potential of DogCV and its association with enteritis in dogs.

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

Improved reproducibility by assuring confidence in measurements in biomedical research : Nature Methods

'Irreproducibility' is symptomatic of a broader challenge in measurement in biomedical research. From the US National Institute of Standards and Technology (NIST) perspective of rigorous metrology, reproducibility is only one aspect of establishing confidence in measurements. Appropriate controls, reference materials, statistics and informatics are required for a robust measurement process. Research is required to establish these tools for biological measurements, which will lead to greater confidence in research results.
more...
No comment yet.
Scooped by Kenzibit
Scoop.it!

Ebola Outbreak Strains Sequenced | The Scientist Magazine®

Ebola Outbreak Strains Sequenced | The Scientist Magazine® | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Ninety-nine publicly available genomes could help researchers working to develop diagnostics, vaccines, and therapies. 
more...
Ed Rybicki's curator insight, August 31, 2014 11:05 AM

99 Ebola genomes, out in cyberspace

99 Ebola genomes, out in cyberspace

And if one Ebola genome

Should accidentally mutate

There'd be...potentially one very frightening Ebola!

Scooped by Julia Paoli
Scoop.it!

Seals May Have Carried Tuberculosis To The New World – Phenomena: Not Exactly Rocket Science

Seals May Have Carried Tuberculosis To The New World – Phenomena: Not Exactly Rocket Science | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Very few people suspected the seals. Kirsten Bos from the University of Tubingen certainly didn’t when she and her colleagues started studying three Peruvian skeletons. They were just trying to und...
more...
No comment yet.
Scooped by Jung Choi
Scoop.it!

Genomes reveal start of Ebola outbreak

Jung Choi's insight:

An invaluable resource that cost the lives of 5 of the authors of the paper.

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

Microbial impacts on insect evolutionary diversification: from patterns to mechanisms

Microbial impacts on insect evolutionary diversification: from patterns to mechanisms | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Rescooped by Chris Upton + helpers from Immunology Diagnosis
Scoop.it!

Immuno-PCR: molecular and Immunological techniques combined in DNA amplification

Immuno-PCR: molecular and Immunological techniques combined in DNA amplification | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Introduction Since the first immunoassays were developed in the 1950's the variety of assay formats has increased dramatically.

Via Alfredo Corell
more...
Alfredo Corell's curator insight, September 22, 2013 2:29 PM

This new method, termed immuno-polymerase chain reaction (immuno-PCR), benefits from the specificity of antibodies and the sensitivity of PCR. Several independent studies undertaken since the publication of this seminal paper have consistently demonstrated the advantages of this technique over traditional ELISA, some achieving more than a 50,000 fold increase in sensitivity over the equivalent immunoassay [2]. Furthermore, immuno-PCR can be used in a multiplex format and offers accurate quantitation.