Viruses, Immunology & Bioinformatics from 4Virology.net
111.8K views | +2 today
Follow
Viruses, Immunology & Bioinformatics from 4Virology.net
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!

It's a group effort - the curators:

It's a group effort - the curators: | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it

get in touch if you want to help curate this topic

more...
Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 2017 12:46 PM
Thank You.
Scooped by Rob Gifford
Scoop.it!

�� DR Congo Ebola: Over 66,000 vaccinated l Al Jazeera English

It has been six months since the start of the latest Ebola epidemic in the Democratic Republic of Congo. The World Health Organization (WHO) says more than 4...
more...
No comment yet.
Rescooped by Kenzibit from Amazing Science
Scoop.it!

The First Virus Communication Signals Emerge

The First Virus Communication Signals Emerge | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it

Phage peptides used for the communication system involve six amino acids. Various phages make their own small peptide as a signal to other viruses.This peptide system hasthree genes—aimP makes the signal peptide; aimR makes the receptor for the peptide; and aimX a regulator molecule that can slow down the process if too many bacteria are being killed. This system allows the phage to know how many infections have occurred to determine whether to kill or go quiet.

 

Previous studies of Lambda phage for E. coli showed that this decision appeared to be related to the amount of food available and the number of phages present. Bacteria usually use peptides as signals for their quorum sensing.

 

Other details of the mechanism include the fact that aimP is secreted from the cell into the extra cellular space with two combining into a dimer there. AimR as a dimer then stimulates AimX.

In bacteria, the peptide binds to a receptor that alters the genetic behavior of the cell. The phage system works when the three peptides are produced: AimR becomes a dimer and then stimulates more AimX. AimX blocks blocks the genetic pathway to insert the DNA into the bacteria and instead produces the kill cycle in as yet unknown mechanism. AimP stays in the extra cellular space as a dimer. When a new phage enters a bacteria, some of the peptides are taken in with it by a transporter. Inside the cell these bind to AimR receptor, which goes from a dimer to a monomer becoming inactive. This stops the AimX inhibition of lysogeny (quiet insertion) and produces the quiet state.
Via Dr. Stefan Gruenwald
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Controversial experiments that could make bird flu more risky poised to resume

Controversial experiments that could make bird flu more risky poised to resume | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
In 2011, Fouchier and Kawaoka alarmed the world by revealing they had separately modified the deadly avian H5N1 influenza virus so that it spread between ferrets. Advocates of such gain of function (GOF) studies say they can help public health experts better understand how viruses might spread and plan for pandemics. But by enabling the bird virus to more easily spread among mammals, the experiments also raised fears that the pathogen could jump to humans. And critics of the work worried that such a souped-up virus could spark a pandemic if it escaped from a lab or was intentionally released by a bioterrorist. After extensive discussion about whether the two studies should even be published (they ultimately were) and a voluntary moratorium by the two labs, the experiments resumed in 2013 under new U.S. oversight rules.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

BioJava 5: A community driven open-source bioinformatics library

BioJava 5: A community driven open-source bioinformatics library | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
BioJava is an open-source project that provides a Java library for processing biological data. The project aims to simplify bioinformatic analyses by implementing parsers, data structures, and algorithms for common tasks in genomics, structural biology, ontologies, phylogenetics, and more. Since 2012, we have released two major versions of the library (4 and 5) that include many new features to tackle challenges with increasingly complex macromolecular structure data. BioJava requires Java 8 or higher and is freely available under the LGPL 2.1 license. The project is hosted on GitHub at https://github.com/biojava/biojava. More information and documentation can be found online on the BioJava website (http://www.biojava.org) and tutorial (https://github.com/biojava/biojava-tutorial). All inquiries should be directed to the GitHub page or the BioJava mailing list (http://lists.open-bio.org/mailman/listinfo/biojava-l).
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia

Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural ‘experiments’ in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event may reflect a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Apollo: Democratizing genome annotation

Apollo: Democratizing genome annotation | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, we present Apollo, an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform. Some of Apollo’s newer user interface features include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Best RNA-Seq aligner: A comparison of mapping tools

Best RNA-Seq aligner: A comparison of mapping tools | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
What software tools should be used for the alignment of RNA sequencing reads from NGS.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

The AC4 protein of a cassava geminivirus is required for virus infection.

Geminiviruses (family Geminiviridae) are among the most devastating plant viruses worldwide, causing severe damage in crops of economic and subsistence importan...
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Codon clusters with biased synonymous codon usage represent hidden functional domains in protein-coding DNA sequences

Protein-coding DNA sequences are thought to primarily affect phenotypes via the peptides they encode. Yet, emerging data suggest that, although they do not affect protein sequences, synonymous mutations can cause phenotypic changes. Previously, we have shown that signatures of selection on gene-specific codons usage bias are common in genomes of diverse eukaryotic species. Thus, synonymous codon usage, just as amino acid usage pattern, is likely a regular target of natural selection. Consequently, here we propose the hypothesis that at least for some protein-coding genes, codon clusters with biased synonymous codon usage patterns might represent "hidden" nucleic-acid-level functional domains that affect the action of the corresponding proteins via diverse hypothetical mechanisms. To test our hypothesis, we used computational approaches to identify over 3,000 putatively functional codon clusters (PFCCs) with biased usage patterns in about 1,500 protein-coding genes in the Drosophila melanogaster genome . Specifically, our data suggest that these PFCCs are likely associated with specific categories of gene function, including enrichment in genes that encode membrane-bound and secreted proteins. Yet, the majority of the PFCCs that we have identified are not associated with previously annotated functional protein domains. Although the specific functional significance of the majority of the PFCCs we have identified remains unknown, we show that in the highly conserved family of voltage-gated sodium channels, the existence of rare-codon cluster(s) in the nucleic-acid region that encodes the cytoplasmic loop that constitutes inactivation gate is conserved across paralogs as well as orthologs across distant animal species. Together, our findings suggest that codon clusters with biased usage patterns likely represent "hidden" nucleic-acid-level functional domains that cannot be simply predicted from the amino acid sequences they encode. Therefore, it is likely that on the evolutionary timescale, protein-coding DNA sequences are shaped by both amino-acid-dependent and codon-usage-dependent selective forces.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Ten Simple Rules for avoiding and resolving conflicts with your colleagues

Ten Simple Rules for avoiding and resolving conflicts with your colleagues | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
more...
No comment yet.
Scooped by Rob Gifford
Scoop.it!

Hunting Ebola’s Origins

Hunting Ebola’s Origins | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The outbreak of Ebola that started in 2013 in West Africa, infecting nearly 30,000 people and killing 11,000 before it ended in 2016, has long left scientists puzzling over a key question: where did the virus originate?
more...
No comment yet.
Scooped by Rob Gifford
Scoop.it!

Ebola outbreak reaches 800 cases

Ebola outbreak reaches 800 cases | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
In an update on the Ebola Virus Disease (EVD) outbreak in the North Kivu and Ituri provinces of the Democratic Republic of the Congo (DRC), the health ministry reported (computer translated) two new confirmed cases, bringing the total outbreak cases (confirmed and probable) to 800.
more...
No comment yet.
Rescooped by Kenzibit from Viruses, Immunology & Bioinformatics from 4Virology.net
Scoop.it!

Controversial experiments that could make bird flu more risky poised to resume

Controversial experiments that could make bird flu more risky poised to resume | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
In 2011, Fouchier and Kawaoka alarmed the world by revealing they had separately modified the deadly avian H5N1 influenza virus so that it spread between ferrets. Advocates of such gain of function (GOF) studies say they can help public health experts better understand how viruses might spread and plan for pandemics. But by enabling the bird virus to more easily spread among mammals, the experiments also raised fears that the pathogen could jump to humans. And critics of the work worried that such a souped-up virus could spark a pandemic if it escaped from a lab or was intentionally released by a bioterrorist. After extensive discussion about whether the two studies should even be published (they ultimately were) and a voluntary moratorium by the two labs, the experiments resumed in 2013 under new U.S. oversight rules.

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

Lab Culture Ep. 17: Exploring bioinformatics: From fellow to full time in Virginia

Lab Culture Ep. 17: Exploring bioinformatics: From fellow to full time in Virginia | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Kevin Libuit went from the APHL-CDC Bioinformatics Fellowship to a contractor to working full-time as a bioinformatician at the Virginia state lab (VA Division of Consolidated Laboratory Services (DCLS)). First he talks about when he discovered bioinformatics as a field and how the fellowship propelled his career. Then Kevin takes the mic and interviews Dr.…
more...
No comment yet.
Scooped by Cindy
Scoop.it!

The pseudoknots region of the 5′ untranslated region is a determinant of viral tropism and virulence of foot-and-mouth disease virus

The pseudoknots region of the 5′ untranslated region is a determinant of viral tropism and virulence of foot-and-mouth disease virus | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
This study demonstrates that the deletion in PKs region occurred naturally in FMDV genome. The isolated O/ME-SA/PanAsia lineage FMDV with an 86-nt deletion in PKs region showed a pig-adapted characteristic that could only cause clinical signs in swine but not bovines. Compared with the wildtype FMDV strain which possessed full infection capacity in both swine and bovines, deletion of the 86-nt in the PKs region resulted in the deficiency of the recombinant virus to cause disease in bovines. Deletion of the previously reported 43-nt in the PKs region also led to significantly decreased pathogenicity of FMDV in bovines. This study indicates that the PKs region is a novel determinant of viral tropism and virulence of FMDV.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R | Bioinformatics | Oxford Academic

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractSummary. After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Why It Took So Long to Eliminate Measles

Why It Took So Long to Eliminate Measles | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Scientists had to overcome problems with the vaccine’s safety, then public health officials had to take on complacency about the disease.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

NCBI to correct existing taxonomic information on public GenBank records with average nucleotide identity analysis

To ensure that taxonomic information on genome assemblies is as accurate as possible, NCBI will use average nucleotide identity (ANI) analysis to correct existing public records in GenBank.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

A crash course in sequencing for a microbiologist

A crash course in sequencing for a microbiologist | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
This review will discuss applications of high-throughput methods to study bacteria in a much broader context than simply their genomes. The major goal of next-generation sequencing for a microbiologist is not really resolving another circular genomic sequence. NGS started its infancy from basic structural and functional genomics, to mature into the molecular taxonomy, phylogenetic and advanced comparative genomics. Today, the use of NGS expended capabilities of diagnostic microbiology and epidemiology. The use of RNA sequencing techniques allows studying in detail the complex regulatory processes in the bacterial cells. Finally, NGS is a key technique to study the organization of the bacterial life—from complex communities to single cells. The major challenge in understanding genomic and transcriptomic data lies today in combining it with other sources of global data such as proteome and metabolome, which hopefully will lead to the reconstruction of regulatory networks within bacterial cells that allow communicating with the environment (signalome and interactome) and virtual cell reconstruction.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Ultrafast search of all deposited bacterial and viral genomic data

Ultrafast search of all deposited bacterial and viral genomic data | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it

At first sight, BLAST and its successor algorithms seem to enable these searches, performing alignment of query sequences against large databases. There are two reasons why these tools do not suffice. First, they would not scale to databases the size of the ENA or beyond. Second, they require assembled genomes as input; if applied to raw sequence data they would only find matches completely contained within a single read. However, assembly is fundamentally lossy when the input data contain multiple strains, and the highly heterogeneous historical data in the ENA would result in very variable assemblies, particularly of plasmids.

1
more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

Monkey Fever in Shivamogga: Kyasanur’s ticking time bomb

Monkey Fever in Shivamogga: Kyasanur’s ticking time bomb | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Reckless human forays into eco-sensitive forest areas and lax public health monitoring have led to a deadly outbreak of Kyasanur Forest Disease, or Monkey Fever, in Karnataka’s Shivamogga district, disrupting normal life and the local plantation economy.

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

Genome comparison of African swine fever virus China/2018/AnhuiXCGQ strain and related European p72 Genotype II strains. - PubMed - NCBI

Genome comparison of African swine fever virus China/2018/AnhuiXCGQ strain and related European p72 Genotype II strains. - PubMed - NCBI | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Transbound Emerg Dis. 2019 Jan 13. doi: 10.1111/tbed.13124. [Epub ahead of print]
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Understanding humans - the key to African swine fever control

Understanding humans - the key to African swine fever control | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
For more than ten years African swine fever (ASF) has been spreading in Eurasia, currently expanding its territory both west- and eastwards. The disease affects domestic pigs and wild boar: animals usually die within three to ten days after infection and the case fatality rate can be almost 100%. Disease impacts are enormous, relating to the welfare of domestic pigs and wild boar, and negative economic consequences for individual pig farmers, the pig industry, the hunting sector, regions, nations and common trade areas. A review published in Porcine Health and Management presents recent developments in the epidemiological understanding of African swine fever, based on the current epidemic in Europe and Asia.
more...
No comment yet.