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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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Guelph Scientists Develop First Vaccine to Help Control Autism-Associated Bacteria | University of Guelph

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The Great Bacterial Bake Off!

If you’re a microbiologist and enjoy baking, then you’re going to love what the Bioscience department (@ICaMB_NCL) at Newcastle University did yesterday. Forget The Great British Bake Off, it’s all about The Great Bacterial Bake Off now!
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Deletion of immunomodulator C6 from vaccinia virus strain Western Reserve enhances virus immunogenicity and vaccine efficacy

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A mobile genetic element with unknown function found in distantly related viruses

The genetic element s2m seems to represent one of very few examples of mobile genetic elements in viruses. The function remains obscure and a scattered taxonomical distribution has been reported by numerous groups.
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Ed Rybicki's comment, April 29, 2013 6:24 AM
In plant and other RNA viruses, no less!! VERY interesting!
Ken Yaw Agyeman-Badu's comment, April 29, 2013 8:04 AM
Yeah Ed....a fine read.
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Viruses | Free Full-Text | Animal Models of Dengue Virus Infection

The development of animal models of dengue virus (DENV) infection and disease has been challenging, as epidemic DENV does not naturally infect non-human species.
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Alberto Castellanos's curator insight, April 8, 2:15 PM

Articulo para revisar

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Role of Tissue Protection in Lethal Respiratory Viral-Bacterial Coinfection

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Mendel: The Swiss Army Knife of Genetic Analysis Programs - Bioinformatics

SUMMARY: Mendel is one of the few statistical genetics packages that provides a full spectrum of gene mapping methods, ranging from parametric linkage in large pedigrees to GWAS with rare variants. Our latest additions to Mendel anticipate and respond to the needs of the genetics community. Compared with earlier versions, Mendel is faster and easier to use and has a wider range of applications. Supported platforms include Linux, MacOS, and Windows. AVAILABILITY: Free from www.genetics.ucla.edu/software/mendel CONTACT: klange@ucla.edu

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Virology Journal | Abstract | Development of a transmission model for dengue virus

Dengue virus (DENV) research has historically been hampered by the lack of a susceptible vertebrate transmission model.
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Receptor binding by a ferret-transmissible H5 avian influenza virus : Nature : Nature Publishing Group

Receptor binding by a ferret-transmissible H5 avian influenza virus : Nature : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it

Cell-surface-receptor binding by influenza viruses is a key determinant of their transmissibility, both from avian and animal species to humans as well as from human to human. Highly pathogenic avian H5N1 viruses that are a threat to public health have been observed to acquire affinity for human receptors, and transmissible-mutant-selection experiments have identified a virus that is transmissible in ferrets1, 2, 3, the generally accepted experimental model for influenza in humans. Here, our quantitative biophysical measurements of the receptor-binding properties of haemagglutinin (HA) from the transmissible mutant indicate a small increase in affinity for human receptor and a marked decrease in affinity for avian receptor. From analysis of virus and HA binding data we have derived an algorithm that predicts virus avidity from the affinity of individual HA–receptor interactions. It reveals that the transmissible-mutant virus has a 200-fold preference for binding human over avian receptors. The crystal structure of the transmissible-mutant HA in complex with receptor analogues shows that it has acquired the ability to bind human receptor in the same folded-back conformation as seen for HA from the 1918, 1957 (ref. 4), 1968 (ref. 5) and 2009 (ref. 6) pandemic viruses. This binding mode is substantially different from that by which non-transmissible wild-type H5 virus HA binds human receptor. The structure of the complex also explains how the change in preference from avian to human receptors arises from the Gln226Leu substitution, which facilitates binding to human receptor but restricts binding to avian receptor. Both features probably contribute to the acquisition of transmissibility by this mutant virus.

 
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BMC Genomics: Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors (2013)

BMC Genomics: Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors (2013) | Virology and Bioinformatics from Virology.ca | Scoop.it

Background - Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity. In particular, the characterisation of the structure, function and evolutionary dynamics of secreted effector proteins that are detected by host immune receptors can help guide and prioritize breeding efforts. However, to date, our knowledge of the effector repertoire of cereal rust pathogens is limited.

 

Results - We re-sequenced genomes of four PST isolates from the US and UK to identify effector candidates and relate them to their distinct virulence profiles. First, we assessed SNP frequencies between all isolates, with heterokaryotic SNPs being over tenfold more frequent (5.29 +/- 2.23 SNPs/kb) than homokaryotic SNPs (0.41 +/- 0.28 SNPs/kb). Next, we implemented a bioinformatics pipeline to integrate genomics, transcriptomics, and effector-focused annotations to identify and classify effector candidates in PST. RNAseq analysis highlighted transcripts encoding secreted proteins that were significantly enriched in haustoria compared to infected tissue. The expression of 22 candidate effector genes was characterised using qRT-PCR, revealing distinct temporal expression patterns during infection in wheat. Lastly, we identified proteins that displayed non-synonymous substitutions specifically between the two UK isolates PST-87/7 and PST-08/21, which differ in virulence to two wheat varieties. By focusing on polymorphic variants enriched in haustoria, we identified five polymorphic effector candidates between PST-87/7 and PST-08/21 among 2,999 secreted proteins. These allelic variants are now a priority for functional validation as virulence/avirulence effectors in the corresponding wheat varieties.

 

Conclusions - Integration of genomics, transcriptomics, and effector-directed annotation of PST isolates has enabled us to move beyond the single isolate-directed catalogues of effector proteins and develop a framework for mining effector proteins in closely related isolates and relate these back to their defined virulence profiles. This should ultimately lead to more comprehensive understanding of the PST pathogenesis system, an important first step towards developing more effective surveillance and management strategies for one of the most devastating pathogens of wheat.


Via Kamoun Lab @ TSL, Bradford Condon
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Mapping the H7N9 avian flu outbreaks

Mapping the H7N9 avian flu outbreaks | Virology and Bioinformatics from Virology.ca | Scoop.it
Where are the 104 human cases reported so far and where might the virus go next?
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How Does Sendai Virus Reprogram Cells?

Learn more at http://www.lifetechnologies.com/cytotune This video demonstrates how Sendai virus, found in the Cytotune®-iPS Sendai Reprogramming Kit, reprogr...
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World Immunisation Week: The fight against TB

This week is ‘World Immunisation Week’, which aims to promote vaccinations, particularly amongst the 22 million infants which are not protected with routine immunisations.
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Computer Scientists Suggest New Spin on Origins of Evolvability

Computer Scientists Suggest New Spin on Origins of Evolvability | Virology and Bioinformatics from Virology.ca | Scoop.it
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BMC Bioinformatics | Full text | The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics

User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites.
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Free Webinar: Introduction to Python for Scientists

In "Introduction to Python for Scientists," trainees will learn the basics of python programming, enabling them to build simple python scripts and be ready for the "Introduction to BioPython for Scientists" follow-up session.

 

 Introduction to Python for Scientists Join us for a Webinar on May 2  Space is limited.
Reserve your Webinar seat now at:
https://www4.gotomeeting.com/register/664205623 In "Introduction to Python for Scientists," trainees will learn the basics of python programming, enabling them to build simple python scripts and be ready for the "Introduction to BioPython for Scientists" follow-up session. Examples will focus on activities relevant to biologists.Title:Introduction to Python for ScientistsDate:Thursday, May 2, 2013Time:10:00 AM - 11:00 AM EDTAfter registering you will receive a confirmation email containing information about joining the Webinar.System Requirements
PC-based attendees
Required: Windows® 7, Vista, XP or 2003 Server Mac®-based attendees
Required: Mac OS® X 10.6 or newer Mobile attendees
Required: iPhone®, iPad®, Android™ phone or Android tablet   
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I will be teaching a webinar this Thursday on "Introduction to Python for Scientists"

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Use of immuno-dominant epitope derived from genotype 4 as a diagnostic reagent for detecting the antibodies against Hepatitis E Virus

Despite the genotype 4 has become the dominant cause of hepatitis E disease in China, none antigen derived from genotype 4 of hepatitis E virus (HEV) was used in current commercial anti-HEV immunoassay, and the serological reactivity of antigen...
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Virology Journal | Abstract | Development of a transmission model for dengue virus

Dengue virus (DENV) research has historically been hampered by the lack of a susceptible vertebrate transmission model.
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Adaptation of avian influenza A virus polymerase in mammals to overcome the host species barrier.

Avian influenza A viruses, such as the highly pathogenic avian H5N1 viruses, sporadically enter into the human population but often do not transmit between individuals. In rare cases, however, they establish a new virus lineage in humans. In addition to well-characterized barriers to cell entry, one major hurdle which avian viruses must overcome is their poor polymerase activity in human cells. There is compelling evidence that these viruses overcome this obstacle by acquiring adaptive mutations in the polymerase subunits PB1, PB2 and PA and the nucleoprotein NP, as well as in the novel polymerase co-factor NEP. Recent findings suggest that synthesis of the viral genome may represent the major defect of avian polymerases in human cells. While the precise mechanisms remain to be unveiled, it appears that a broad spectrum of polymerase adaptive mutations can act collectively to overcome this defect. Thus, identification and monitoring of emerging adaptive mutations that further increase polymerase activity in human cells is critical to estimate the pandemic potential of avian viruses.

 
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PLOS ONE: MHC Class I-Presented T Cell Epitopes Identified by Immunoproteomics Analysis Are Targets for a Cross Reactive Influenza-Specific T Cell Response

PLOS ONE: MHC Class I-Presented T Cell Epitopes Identified by Immunoproteomics Analysis Are Targets for a Cross Reactive Influenza-Specific T Cell Response | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza virus infection and the resulting complications are a significant global public health problem. Improving humoral immunity to influenza is the target of current conventional influenza vaccines, however, these are generally not cross-protective. On the contrary, cell-mediated immunity generated by primary influenza infection provides substantial protection against serologically distinct viruses due to recognition of cross-reactive T cell epitopes, often from internal viral proteins conserved between viral subtypes. Efforts are underway to develop a universal flu vaccine that would stimulate both the humoral and cellular immune responses leading to long-lived memory. Such a universal vaccine should target conserved influenza virus antibody and T cell epitopes that do not vary from strain to strain. In the last decade, immunoproteomics, or the direct identification of HLA class I presented epitopes, has emerged as an alternative to the motif prediction method for the identification of T cell epitopes. In this study, we used this method to uncover several cross-specific MHC class I specific T cell epitopes naturally presented by influenza A-infected cells. These conserved T cell epitopes, when combined with a cross-reactive antibody epitope from the ectodomain of influenza M2, generate cross-strain specific cell mediated and humoral immunity. Overall, we have demonstrated that conserved epitope-specific CTLs could recognize multiple influenza strain infected target cells and, when combined with a universal antibody epitope, could generate virus specific humoral and T cell responses, a step toward a universal vaccine concept. These epitopes also have potential as new tools to characterize T cell immunity in influenza infection, and may serve as part of a universal vaccine candidate complementary to current vaccines.

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A small molecule screen in yeast identifies inhibitors targeting protein-protein interactions within the vaccinia virus replication complex.

Genetic and biochemical data have identified at least four viral proteins essential for vaccinia virus (VACV) DNA synthesis: the DNA polymerase E9, its processivity factor (the heterodimer A20/D4) and the primase/helicase D5. These proteins are part of the VACV replication complex in which A20 is a central subunit interacting with E9, D4 and D5. We hypothesised that molecules able to modulate protein-protein interactions within the replication complex may represent a new class of compounds with anti-orthopoxvirus activities.

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The first imported human infection with avian influenza A(H7N9) confirmed in Taiwan;

The first imported human infection with avian influenza A(H7N9) confirmed in Taiwan; | Virology and Bioinformatics from Virology.ca | Scoop.it

Centers for Disease Control,R.O.C.(Taiwan).

In the late afternoon of April 24, 2013, the Central Epidemic Command Center (CECC) confirmed the first imported case of H7N9 avian influenza in a 53-year-old male Taiwanese citizen who worked in Suzhou, Jiangsu Province, China prior to illness onset.  He developed his illness three days after returning to Taiwan.  Infection with avian influenza A (H7N9) was confirmed on April 24, 2013.  The patient is currently in a severe condition and being treated in a negative-pressure isolation room.

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Cell-based genomic screening: elucidating virus–host interactions - Current Opinion in Virology

Viruses rely on host cell machinery for successful infection, while at the same time evading the host immune response. Characterization of these processes has revealed insights both into fundamental cellular processes as well as the nuances of viral replication. The recent advent of cell-based screening coupled with RNAi technology, has greatly facilitated studies focused on characterizing the virus–host interface and has expanded our understanding of cellular factors that impact viral infection. These findings have led to the discovery of potential therapeutic targets, but there is certainly more to be discovered. In this article we will review the recent progress in this arena and discuss the challenges and future of this emerging field.

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A guide for the lonely bioinformatician

This may be a uniquely UK centric blog post but I suspect not.  Let me start with a brief story.  Sat with a coffee in our canteen a few weeks ago, I overheard a conversation between a few PIs abou...
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Holy Virus Treasure Trove, Batman!

Holy Virus Treasure Trove, Batman! | Virology and Bioinformatics from Virology.ca | Scoop.it
Think about the type of animal that would make an ideal host for a virus. It would gather …
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