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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Russian Doll Genetics - MicrobiologyBytes

Russian Doll Genetics - MicrobiologyBytes | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses within viruses - the curious world of bacteriophage genetics.
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Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes

Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes | Virology and Bioinformatics from Virology.ca | Scoop.it
The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts. A comprehensive genome comparison and maximum-likelihood reconstruction of the NCLDV evolution revealed a set of approximately 50 conserved, core genes that could be mapped to the genome of the common ancestor of this class of eukaryotic viruses.

Results
We performed a detailed phylogenetic analysis of these core NCLDV genes and applied the constrained tree approach to show that the majority of the core genes are unlikely to be monophyletic. Several of the core genes have been independently acquired from different sources by different NCLDV lineages whereas for the majority of these genes displacement by homologs from cellular organisms in one or more groups of the NCLDV was demonstrated.

Conclusions
A detailed study of the evolution of the genomic core of the NCLDV reveals substantial complexity and diversity of evolutionary scenarios that was largely unsuspected previously. The phylogenetic coherence between the core genes is sufficient to validate the hypothesis on the evolution of all NCLDV from a common ancestral virus although the set of ancestral genes might be smaller than previously inferred from patterns of gene presence-absence.

 

Interesting stuff!  Strengthens my contention that  "...a virus is an infectious acellular entity composed of compatible genomic components derived from a pool of genetic elements" - http://rybicki.wordpress.com/2012/07/10/a-feeling-for-the-molechism-revisited/

 

Mimivirus image courtesy Russell Kightley Media

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Rule of 6ix: A bat virus that can't fight your immune system

Rule of 6ix: A bat virus that can't fight your immune system | Virology and Bioinformatics from Virology.ca | Scoop.it

have been too busy to go into this in much detail but I'm wondering whether anyone had any ideas as to why this virus (cedar virus - a newly discovered bat RNA virus) appears not to be able to combat the human innate immune system, specifically: HeLa cell secretion of beta interferon in cell culture.

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PLoS Pathogens: Host Defense and Tolerance: Unique Challenges in the Placenta

PLoS Pathogens: Host Defense and Tolerance: Unique Challenges in the Placenta | Virology and Bioinformatics from Virology.ca | Scoop.it

Host Defense and Tolerance: Unique Challenges in the Placenta

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Virus causes peacocks to go spinning to their graves

Virus causes peacocks to go spinning to their graves | Virology and Bioinformatics from Virology.ca | Scoop.it
Virus causes peacocks to go spinning to their graves, ISLAMABAD -- The peacocks of Pakistan were dying in droves. Was the government covering it up?

 

I love it: "spinning peacock disease"...which turns out to be the reasonably prosaic Newcastle disease virus.  But it's not often you get prose like this associated with viruses:

"...peacocks whirling themselves to death in mad dances that appeared to have no earthly explanation".


Via Ed Rybicki
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Nature Genetics: Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses (2012)

Nature Genetics: Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses (2012) | Virology and Bioinformatics from Virology.ca | Scoop.it

Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.


Via Kamoun Lab @ TSL
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小楠's comment, August 20, 2012 4:49 AM
炭疽大牛都发NG了。。。
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Hyperthermia Stimulates HIV-1 Replication

Hyperthermia Stimulates HIV-1 Replication | Virology and Bioinformatics from Virology.ca | Scoop.it
HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42–45°C) and Heat Shock Proteins (HSPs) modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38–40°C) on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C) increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.
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Disassociation of the SV40 Genome from Capsid Proteins Prior to Nuclear Entry

"Previously, we demonstrated that input SV40 particles undergo a partial disassembly in the endoplasmic reticulum, which exposes internal capsid proteins VP2 and VP3 to immunostaining. Then, in the cytoplasm, disassembly progresses further to also make the genomic DNA accessible to immune detection, as well as to detection by an ethynyl-2-deoxyuridine (EdU)-based chemical reaction. The cytoplasmic partially disassembled SV40 particles retain some of the SV40 capsid proteins, VP1, VP2, and VP3, in addition to the viral genome. Findings: In the current study, we asked where in the cell the SV40 genome might disassociate from capsid components. We observed partially disassembled input SV40 particles around the nucleus and, beginning at 12 hours post-infection, 5-Bromo-2-deoxyuridine (BrdU)-labeled parental SV40 DNA in the nucleus, as detected using anti-BrdU antibodies. However, among the more than 1500 cells examined, we never detected input VP2/VP3 in the nucleus. Upon translocation of the BrdU-labeled SV40 genomes into nuclei, they were transcribed and, thus, are representative of productive infection

Our findings imply that the SV40 genome disassociates from the capsid proteins before or at the point of entry into the nucleus, and then enters the nucleus devoid of VP2/3."

 

Nice stuff!  We are still learning so much about viruses that we have known about for many years.

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MicrobeWorld - TWiP 42: The tick keeps on ticking

MicrobeWorld - TWiP 42: The tick keeps on ticking | Virology and Bioinformatics from Virology.ca | Scoop.it
Vincent and Dickson answer listener emails about Leishmania, dual infection of vectors, tapeworms, liver flukes, toxoplasmosis, and much more.
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Synthetic Biology Applications Inventory

Synthetic Biology Applications Inventory | Virology and Bioinformatics from Virology.ca | Scoop.it
This new inventory begins to track the impact of synthetic biology on a wide range of applications, from energy and pharmaceuticals to chemicals and food ingredients.

Via Socrates Logos, Pedro Fernandes
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Drosophila melanogaster as a Model Organism for Bluetongue Virus Replication and Tropism

"Bluetongue virus (BTV) is the etiological agent of bluetongue (BT), a hemorrhagic disease of ruminants that can cause high levels of morbidity and mortality. BTV is an arbovirus transmitted between its ruminant hosts by Culicoides biting midges (Diptera: Ceratopogonidae). Recently, Europe has experienced some of the largest BT outbreaks ever recorded, including areas with no known history of the disease, leading to unprecedented economic and animal welfare issues. The current lack of genomic resources and genetic tools for Culicoides restricts any detailed study of the mechanisms involved in the virus-insect interactions. In contrast, the genome of the fruit fly (Drosophila melanogaster) has been successfully sequenced, and it is used extensively as a model of molecular pathways due to the existence of powerful genetic technology. In this study, D. melanogaster is investigated as a model for the replication and tropism of BTV. Using reverse genetics, a modified BTV-1 that expresses the fluorescent mCherry protein fused to the viral nonstructural protein NS3 (BTV-1/NS3mCherry) was generated. We demonstrate that BTV-1/NS3mCherry is not only replication competent as it retains many characteristics of the wild-type virus but also replicates efficiently in D. melanogaster after removal of the bacterial endosymbiont Wolbachia pipientis by antibiotic treatment. Furthermore, confocal microscopy shows that the tissue tropism of BTV-1/NS3mCherry in D. melanogaster resembles that described previously for BTV in Culicoides. Overall, the data presented in this study demonstrate the feasibility of using D. melanogaster as a genetic model to investigate BTV-insect interactions that cannot be otherwise addressed in vector species."

 

Not only is this a big deal for working on BTV - which is far more important in Africa than in Europe, BTW - but it also throws up interesting ways for working on other orbiviruses in particular (like African horsesickness), and other arboviruses in general.

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CDC confirms 145 cases of swine flu

CDC confirms 145 cases of swine flu | Virology and Bioinformatics from Virology.ca | Scoop.it
Swine flu is spreading in Indiana, with human cases rising tenfold in a week, state public health officials said on Wednesday, confirming 113 people are infected and saying they expect to see more (◈ CDC confirms 145 cases of swine flu: Despite an...
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Ion Torrent PGM, Miseq, PacBio RS Comparison | EdgeBio

EdgeBio:

As a provider of next generation sequencing services, our laboratory and bioinformatics teams must keep abreast of a rapidly expanding range of new technologies. From the latest library prep protocls and capture kits, to emerging sequencing platforms and latest analysis software, we need to be able to provide technological expertise to our clients. As we continue to monitor the latest developments, we are always interested in hearing from other groups about their experiences with technology comparison and development.

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U.S. Medics Support Botswana HIV Prevention Efforts

U.S. Medics Support Botswana HIV Prevention Efforts | Virology and Bioinformatics from Virology.ca | Scoop.it

"Today, 17.6 percent of the general population is infected with HIV, and the rate continues to climb by 2.2 percent per year, Maj. Mooketsi Ditsela, the Botswana Defense Force’s HIV coordinator, told American Forces Press Service. Men ages 30 to 45 suffer the highest infection rates, topping 40 percent, according to Health Ministry statistics."

 

17.6 percent of the whole Botswana population is HIV positive: that is HORRIFYING.  But possibly not as bad as Swaziland....


Via Ed Rybicki
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Comparison of next-generation sequencing... [J Biomed Biotechnol. 2012] - PubMed - NCBI

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

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AtlasT4SS: A curated database for type IV secretion systems

The type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions.
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Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes

The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts.
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Lethal snake viruses identified

Lethal snake viruses identified | Virology and Bioinformatics from Virology.ca | Scoop.it
The cause of a fatal illness that affects captive snakes has been identified, according to research published today.
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Gene Variation within a Tree | The Scientist

Gene Variation within a Tree | The Scientist | Virology and Bioinformatics from Virology.ca | Scoop.it
Gene Variation within a Tree |...

 

A clone is a clone...isn't??

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Chinese villagers infected with anthrax | BioPrepWatch.com

Chinese villagers infected with anthrax | BioPrepWatch.com | Virology and Bioinformatics from Virology.ca | Scoop.it
Two villagers from eastern China’s Jiangsu Province are being treated at a local hospital for anthrax infection.
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Immunization with recombinant enterovirus 71 viral capsid protein 1 fragment stimulated antibody responses in hamsters

Enterovirus 71 (EV71) causes severe neurological diseases resulting in high mortality in young children worldwide. Development of an effective vaccine against EV71 infection is hampered by the lack of appropriate animal models for efficacy testing of candidate vaccines.
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Ed Rybicki's comment, August 12, 2012 12:44 PM
Putting a brave face on it: in other words, despite a cool model system (=hamsters) for a nasty human virus, their vaccine model does not work.. B-(
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PLoS Pathogens: The Ebola Virus Interferon Antagonist VP24 Directly Binds STAT1 and Has a Novel, Pyramidal Fold

PLoS Pathogens: The Ebola Virus Interferon Antagonist VP24 Directly Binds STAT1 and Has a Novel, Pyramidal Fold | Virology and Bioinformatics from Virology.ca | Scoop.it

Ebolaviruses cause hemorrhagic fever with up to 90% lethality and in fatal cases, are characterized by early suppression of the host innate immune system. One of the proteins likely responsible for this effect is VP24. VP24 is known to antagonize interferon signaling by binding host karyopherin α proteins, thereby preventing them from transporting the tyrosine-phosphorylated transcription factor STAT1 to the nucleus.

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Bioinformatics as a Hobby | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future

Bioinformatics as a Hobby | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future | Virology and Bioinformatics from Virology.ca | Scoop.it

Bioinformatics is the study of data generated from biological experiments. With the advent of high-throughput sequencing and many other rapidly improving technologies Biologists are often producing far more data than they can properly analyze. With data being so easy to produce we have massive amounts of data, much of it publicly available – which could hold the keys to new medicines, cures, of breakthroughs. This data just needs someone to look through it. Using data mining software bioinformaticians look though data to find interesting patterns or to find answers to questions. But just like DIY Biology, bioinformatics isn’t restricted to professionals. Given that all you need to do bioinformatics is a computer and some spare time, anyone can do it.


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Adaptive Changes in Alphavirus mRNA Translation Allowed Colonization of Vertebrate Hosts

"Genetic, phylogenetic, and biochemical data presented here support an evolutionary scenario for the natural history of alphaviruses, in which the acquisition of DLP structure in their mRNAs probably allowed the colonization of vertebrate host and the consequent geographic expansion of some of these viruses worldwide."

 

I have taught for some time now that the evolution of many mammalian viruses must have involved adaptation of originally (and sometimes still) insect-infecting agents - given that insects crawled out onto dry land quite a long time before vertebrates did.  This is a nice illustration of that.  Pity I don't teach anymore B-(

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The Tree of Life: Wow - Google Scholar "Updates" a big step forward in sifting through the scientific literature

The Tree of Life: Wow - Google Scholar "Updates" a big step forward in sifting through the scientific literature | Virology and Bioinformatics from Virology.ca | Scoop.it

Wow - Google Scholar "Updates" a big step forward in sifting through the scientific literature
By Jonathan Eisen ..

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