Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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▶ Ebola virus explained in 60 seconds (video)

Here's our 60 look at why Ebola is so deadly. The World Health Organization (WHO) has called for "drastic action" to contain an Ebola outbreak in West Africa that has killed nearly 500 people. 
It is the world's largest outbreak in terms of cases, deaths and geographical spread.


Via Ed Rybicki
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A more intuitive approach to computerized clustering

A more intuitive approach to computerized clustering | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Clustering algorithms help parse large amounts of data, find correlations within subsets of the data, and assess similarity among elements within these subsets. They have become a hot field in recent years, as they have applications in astronomy, bioinformatics, and pattern recognition. Now there's a new entrant in the arena, which clusters by fast search and then finds density peaks. It clusters data based on distance to a cluster center (as in K-means), but also detects non-spherical clusters (DBSCAN).

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High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (~14 Ma old) and the most oligotrophic subsurface sediments of the world’s oceans (South Pacific Gyre (SPG)). The numbers of viruses (104–109 cm−3, counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.

 
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Networks of lexical borrowing and lateral gene transfer in language and genome evolution

Networks of lexical borrowing and lateral gene transfer in language and genome evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

For a long time, both biologists and linguists have been using family trees to model how species and languages evolve. But in contrast to biology – where the tree model is generally accepted to be the most realistic way to model how eukaryotic species (species with nucleated cells, such as animals and plants) evolve – linguists have always treated language trees with a certain suspicion. They have emphasized that – given the important role that horizontal transmission plays in language history – such trees can only capture vertical aspects of language evolution, while horizontal aspects (which linguists traditionally model as “waves” that spread out in circles around a center in geographic space) are ignored.

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Implications of finding poliovirus in sewers of Brazil and Israel

Implications of finding poliovirus in sewers of Brazil and Israel | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Why has wild poliovirus been detected in the sewers of Brazil and Israel, and what are the implications for the eradication effort?

Via Ed Rybicki
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Ed Rybicki's curator insight, July 2, 2014 5:12 AM

Not unexpectedly, a calm and thorough analysis of the potential problem from the "virology blog"!

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Two completely synthetic defective mastrevirus genomes recombine to produce viable virus

Two completely synthetic defective mastrevirus genomes recombine to produce viable virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary amongst these is the disruption of favourable co-evolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped either by compensatory mutations or secondary-recombination events. Here, we used a Maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption, and the capacity of secondary-recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesised two of the most extreme conceivable MSV chimaeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimaeras were severely defective and apparently non-infectious, neither had individual movement, encapsidation or replication associated genome regions that were on their own 'lethally recombinant'. Surprisingly, mixed inoculations of the chimaeras yielded symptomatic infections containing viruses with secondary-recombination events. These recombinants had only two to six breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments and were obviously far fitter than their synthetic parents. It is clearly evident therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to a full recovery, small numbers of secondary-recombination events can still yield tremendous fitness gains.

 

Ed Rybicki's insight:

Too ridiculously complicated for words, and I TOLD them just ONE synthetic genome would be worth publishing, but nooooo - they had to do it the difficult way.  A tour de force.  My function was just to try to make them to keep it simple(r).  Kudos Aderito et al.!

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Viruses: unlocking the greatest biodiversity on Earth.

There are about 10 times as many viruses in the oceans as there are bacteria and about 1000-fold less protists than bacteria. In fact, in a litre of coastal seawater there are more viruses than there are people on the planet. If one takes a drop of seawater and adds a nucleic-acid stain such as Yo-Pro, SYBR Green, or SYBR Gold and looks at it under a microscope, there are a myriad of tiny fluorescent dots that are reminiscent of a clear night sky (Fig. 1). Most of these dots are virus particles. If aliens randomly sampled Earth they would see a planet dominated by microbial life, most of which would be viruses. On average, there are about 10 million viruses and a mil- lion bacteria per litre of seawater or freshwater. If we compare the number of viruses in the oceans to the number of stars in the universe, there are about 1023 stars in the universe. In contrast, there are about 10 million-fold more viruses in the ocean than there are stars in the universe. If we took the 1030 viruses in the oceans and stretched them end-to-end, how far would they go? Assuming, the average length of a virus is about 100 nm, the viruses would stretch 1023 m, which is 1020 km. If converted to light years, by dividing by 1013 km, we end up with 10 million light years. The nearest star is Proxima Centauri, about 4.2 light years away; the Crab Supernova is 1000 light years away; our own gal- axy, the Milky Way, is about 150 000 light years across. In fact, all the viruses in the ocean end-to-end would stretch further than the nearest 60 galaxies. This may seem like a trivial calculation, but it is important on a number of levels. For one reason, these viruses are responsible for about Avogadro’s number, about 1024 infec- tions per second in the ocean. Each one of these events is an opportunity for lateral transfer of genes. Most of the genetic information on Earth probably resides within viruses. 

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Ed Rybicki's comment, July 2, 2014 4:25 AM
Viva Suttle!!
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Life Cycle of the HIV virus

Life Cycle of the HIV virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Produced
by Hybrid Medical Animation.

This 3D interactive scene explains the puzzle of the HIV virus, its life cycle, and how it reproduces itself in the host cell.
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Plant genomes enclose footprints of past infections by giant virus relatives

Plant genomes enclose footprints of past infections by giant virus relatives | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Nucleocytoplasmic large DNA viruses (NCLDVs) are eukaryotic viruses with large genomes (100 kb–2.5 Mb), which include giant Mimivirus, Megavirus and Pandoravirus. NCLDVs are known to infect animals, protists and phytoplankton but were never described as pathogens of land plants. Here, we show that the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii have open reading frames (ORFs) with high phylogenetic affinities to NCLDV homologues. The P. patens genes are clustered in DNA stretches (up to 13 kb) containing up to 16 NCLDV-like ORFs. Molecular evolution analysis suggests that the NCLDV-like regions were acquired by horizontal gene transfer from distinct but closely related viruses that possibly define a new family of NCLDVs. Transcriptomics and DNA methylation data indicate that the NCLDV-like regions are transcriptionally inactive and are highly cytosine methylated through a mechanism not relying on small RNAs. Altogether, our data show that members of NCLDV have infected land plants.

  

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Ed Rybicki's curator insight, June 30, 2014 7:29 AM

They're everywhere....including in moss and other genomes, apparently.

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FDA approves new antibiotic

FDA approves new antibiotic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A second new drug to treat methicillin-resistant Staphylococcus aureus (MRSA) has been approved under the U.S. Food and Drug Administration's (FDA) new fast-track incentive program.
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In the Shadow of Hemagglutinin: A Growing Interest in Influenza Viral Neuraminidase and Its Role as a Vaccine Antigen | Viruses

In the Shadow of Hemagglutinin: A Growing Interest in Influenza Viral Neuraminidase and Its Role as a Vaccine Antigen | Viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Despite the availability of vaccine prophylaxis and antiviral therapeutics, the influenza virus continues to have a significant, annual impact on the morbidity and mortality of human beings, highlighting the continued need for research in the field. Current vaccine strategies predominantly focus on raising a humoral response against hemagglutinin (HA)—the more abundant, immunodominant glycoprotein on the surface of the influenza virus. In fact, anti-HA antibodies are often neutralizing, and are used routinely to assess vaccine immunogenicity. Neuraminidase (NA), the other major glycoprotein on the surface of the influenza virus, has historically served as the target for antiviral drug therapy and is much less studied in the context of humoral immunity. Yet, the quest to discern the exact importance of NA-based protection is decades old. Also, while antibodies against the NA glycoprotein fail to prevent infection of the influenza virus, anti-NA immunity has been shown to lessen the severity of disease, decrease viral lung titers in animal models, and reduce viral shedding. Growing evidence is intimating the possible gains of including the NA antigen in vaccine design, such as expanded strain coverage and increased overall immunogenicity of the vaccine. After giving a tour of general influenza virology, this review aims to discuss the influenza A virus neuraminidase while focusing on both the historical and present literature on the use of NA as a possible vaccine antigen.
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US National Science Foundation (NSF) Discoveries - Computing a cure for HIV - Nine ways NSF-supported supercomputers help scientists understand and treat the disease

US National Science Foundation (NSF) Discoveries - Computing a cure for HIV - Nine ways NSF-supported supercomputers help scientists understand and treat the disease | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

HIV/AIDS has caused an estimated 36 million deaths, according to the World Health Organization, and remains a major menace worldwide. Today, approximately 35 million people are living with the human immunodeficiency virus (HIV), including more than a million individuals in the United States. The tendency of HIV to mutate and resist drugs has made it particularly difficult to eradicate. Some treatments have shown progress in slowing or even stopping the progress of the virus, but no cure or vaccine has been discovered that can truly stamp out the disease.

In the last decade, scientists have begun using a new weapon in the fight against HIV: supercomputers.

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I caught Ebola in Guinea and survived

I caught Ebola in Guinea and survived | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The number of people who have contracted the Ebola virus in Guinea, according to the World Health Organization, has risen to 208 - and 136 of them have died. About half of these cases have been confirmed in a laboratory - earlier cases were not tested.

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Scientist who discovered Ebola: ‘This is unprecedented’

Scientist who discovered Ebola: ‘This is unprecedented’ | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
By Mick Krever, CNN

The scientist who discovered the Ebola virus said that a current outbreak of the deadly bug in West Africa, in which 467 people have died, is “unprecedented.”

“One, [this is] the first time in West Africa that we have such an outbreak,” Dr.
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Dr. Peter Piot discovered Ebola 40 years ago. His 3 reasons why this outbreak is different

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Identity and Access Management's Role in Secure Cloud Collaboration - eSecurity Planet

Identity and Access Management's Role in Secure Cloud Collaboration - eSecurity Planet | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
As enterprises demand more secure cloud-based externalization, companies like Exostar are answering the call with IAM solutions.
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Motifs tree: a new method for predicting post-translational modifications

Motifs tree: a new method for predicting post-translational modifications | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Post-translational modifications (PTMs) are important steps in the maturation of proteins. Several models exist to predict specific PTMs, from manually detected patterns to machine learning methods. On one hand, the manual detection of patterns does not provide the most efficient classifiers and requires an important workload, and on the other hand, models built by machine learning methods are hard to interpret and do not increase biological knowledge.

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Associate Director Bioinformatic Solutions - QIAGEN

Position Description 

- Identify and evaluate new trends in development for clinical use of bioinformatics
- Define innovative bioinformatic software solutions and products for clinical use
- Develop new / enhance existing software products based on market/customer needs
- Establish long standing business relationships with academic institutes and KOLs

Position Requirements 

- MSc or PhD in bioinformatic, biology or other related sciences
- Minimum of 3 years relevant business experience including the lead of a bioinformatic team within the clinical or laboratory sector
- Know-how in requirement management and leading an assignment with dead-lines and restricted budget are an advantage
- Experience in handling regulatory processes (IVD, FDA) in medical engineering would be an advantage

Personal Requirements 

- Independent and efficient work approach 
- Ability to communicate and work interdisciplinary with internal and external customers as well as working with decentralized international teams
- Assertive demeanor with very good communication skills
- Fluent English skills
- Willingness to travel up to 30%

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Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.

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Rakesh Yashroy's curator insight, July 3, 2014 4:38 PM

As such, host-pathogen signaling is fast becoming the field of immense interest @ https://en.wikipedia.org/wiki/Membrane_vesicle_trafficking

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Substitution Rates of the Internal Genes in the Novel Avian H7N9 Influenza Virus

Substitution Rates of the Internal Genes in the Novel Avian H7N9 Influenza Virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

TO THE EDITOR—As of 30 May 2013, the novel avian influenza A(H7N9) virus has caused 132 laboratory-confirmed infections, with 37 fatal cases [1]. As the temperature went up, the reported number of infections naturally declined, with only 3 cases reported in May 2013.

As of 4 June 2013, 36 genome sequences of the novel H7N9 viruses have been deposited in the GISAID database (Global Initiative on Sharing All Influenza Data; www.gisaid.org). Using all of the 36 genome sequences, we calculated the nucleotide substitution rates for each of the 8 gene segments with the single likelihood ancestral counting method [2]. Surprisingly, the substitution rates of the internal genes (except for PB2) were very high, with a similar magnitude to those of surface protein coding genes HA and NA (Figure 1A). In particular, the substitution rates of the M2 and NP genes were even higher than those of HA and NA.

 
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A field guide to whole-genome sequencing, assembly and annotation - Ekblom - 2014 - Evolutionary Applications - Wiley Online Library

Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.

 
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BMC Microbiology | Abstract | Characterization of bacteriophage communities and CRISPR profiles from dental plaque

Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.
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Chimaeric viruses blur the borders between the major groups of eukaryotic ssDNA viruses

Chimaeric viruses blur the borders between the major groups of eukaryotic ssDNA viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Metagenomic studies have uncovered an astonishing diversity of ssDNA viruses encoding replication proteins (Reps) related to those of eukaryotic Circoviridae, Geminiviridae orNanoviridae; however, exact evolutionary relationships among these viruses remain obscure. Recently, a unique chimeric virus (CHIV) genome, which has apparently emerged via recombination between ssRNA and ssDNA viruses, has been discovered. Here we report on the assembly of 13 new CHIV genomes recovered from various environments. Our results indicate a single event of capsid protein (CP) gene capture from an RNA virus in the history of this virus group. The domestication of the CP gene was followed by an unprecedented recurrent replacement of the Rep genes in CHIVs with distant counterparts from diverse ssDNA viruses. We suggest that parasitic and symbiotic interactions between unicellular eukaryotes were central for the emergence of CHIVs and that such turbulent evolution was primarily dictated by incongruence between the CP and Rep proteins.

  

Ed Rybicki's insight:

...and we are about to look for some of these in a big way in seawater

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Decoding long nanopore sequencing reads of natural DNA : Nature Biotechnology :

Decoding long nanopore sequencing reads of natural DNA : Nature Biotechnology : | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Laszlo et al. demonstrate sequence alignment, and proof-of-concept organism identification, genome assembly and polymorphism detection from nanopore analysis of natural DNA.
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Nathan Watson-Haigh's curator insight, June 29, 2014 6:22 PM

Nice use of a de Bruijn sequence to enable the meauserment of all possible 4bp (the number they determined as contributing to the the unique current levels) combinations as they pass through the pore. That's B(4,4) = 256 http://www.hakank.org/comb/debruijn.cgi?k=4&n=4&submit=Ok

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Researchers map genomic differences in yellow fever, malaria mosquitoes

Researchers map genomic differences in yellow fever, malaria mosquitoes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

VIRGINIA Tech entomologists have developed a chromosome map for about half of the genome of the mosquito Aedes agypti, the major carrier of dengue fever and yellow fever. With the map, researchers can compare the chromosome organization and evolution between this mosquito and the major carrier of malaria, the Anopheles gambiae mosquito, to find ways to prevent diseases.

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A Shocking Fish Tale Surprises Evolutionary Biologists

A Shocking Fish Tale Surprises Evolutionary Biologists | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Unrelated lineages of electric fish all use the same small set of genes to create their voltage, a genetic search shows. Maybe the same genes could one day power pacemakers, bioengineers suggest.
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