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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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bioinformatics-databases

bioinformatics-databases | Virology and Bioinformatics from Virology.ca | Scoop.it
Bioinformatics - Databases...
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This TOPIC is a community effort:

This TOPIC is a community effort: | Virology and Bioinformatics from Virology.ca | Scoop.it

 

 

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How infectious disease may have shaped human origins

How infectious disease may have shaped human origins | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists suggest that inactivation of two specific genes related to the immune system may have conferred selected ancestors of modern humans with improved protection from some pathogenic bacterial strains, such as Escherichia coli K1 and Group B...
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Differential assembly of Hepatitis B Virus core protein on single- and double-stranded nucleic acid suggest the dsDNA-filled core is spring-loaded

Differential assembly of Hepatitis B Virus core protein on single- and double-stranded nucleic acid suggest the dsDNA-filled core is spring-loaded | Virology and Bioinformatics from Virology.ca | Scoop.it

"Hepatitis B Virus (HBV) cores assemble on viral RNA, which is reverse transcribed within the core to the partially dsDNA genome of mature HBV. However, constraining dsDNA, a stiff polymer, within a core necessarily requires far greater capsid stability than constraining ssRNA. We hypothesized that, unlike ssRNA, dsDNA would be a poor substrate for assembly. We examined titrations of ssDNA and dsDNA with purified HBV core protein, Cp183, by EMSA, EM, DLS, and etheno-DNA fluorescence. Cp183 bound ssDNA with high affinity to form virus-like capsids. However, Cp183 bound dsDNA poorly, forming a mixture of irregular complexes. Nonetheless, we observed some normal cores in dsDNA assembly reactions, indicating that the energy required to bend DNA could be similar to the protein–protein association energy. This similarity of energies suggests that dsDNA stresses mature HBV cores, in agreement with calculation, which may be the basis for the virus maturation signal and DNA release."

 

A great paper - and one which harks back to an age where many studies on viruses were biophysical, because the molecular biological techniques we use now had simply not been invented.  I note frequent reference to Bancroft, 1970 - to a paper on self-assembly of plant viruses.  I also like the concept of HBV cores as a Jack-in-a-box: ready to pop open to deliver the goodies.

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Depopulation Vaccine Pattern

Talks about the link between mass vaccinations and the spread of man made viruses.

 

What utter and complete garbage...but there's a LOT of this crap out there.  Get active in refuting it, people!!

 

More [frightening] because these idiots think it's real.

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PLoS Pathogens: A New Evolutionary Model for Hepatitis C Virus Chronic Infection

PLoS Pathogens: A New Evolutionary Model for Hepatitis C Virus Chronic Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

"Hepatitis C virus (HCV) infects an estimated 3% of humanity [1] and is a leading global cause of liver disease and liver cancer [2]. Intervention is currently limited by the lack of a vaccine and of universally successful drug treatments. Although several next-generation drugs (e.g., direct-acting protease-inhibitors) are already improving outcomes, a number of factors will affect overall treatment success [3]. Among these, viral genetic variation and the emergence of drug resistance are of major importance."

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Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3

Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3 | Virology and Bioinformatics from Virology.ca | Scoop.it

"The flagellotropic phage 7-7-1 infects motile cells of Agrobacterium sp H13-3 by attaching to and traveling along the rotating flagellar filament to the secondary receptor at the base, where it injects its DNA into the host cell."

 

This is an interesting paper, because it describes a phage infecting Agrobacterium - and touches on a subject that has intrigued me for years, which is: How does a phage which attaches to a flagellum, get its genome inside the cell?  This throws some mud onto a previous model, which suggested a passive mode of transport like a well-oiled nut moving towards the head of a bolt, as in this case that would result in transport the other way.  Expect more on this topic!

 

Image sourced from the paper

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PLoS Neglected Tropical Diseases: A Model of DENV-3 Infection That Recapitulates Severe Disease and Highlights the Importance of IFN-γ in Host Resistance to Infection

PLoS Neglected Tropical Diseases: A Model of DENV-3 Infection That Recapitulates Severe Disease and Highlights the Importance of IFN-γ in Host Resistance to Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

"There are few animal models of dengue infection, especially in immunocompetent mice. Here, we describe alterations found in adult immunocompetent mice inoculated with an adapted Dengue virus (DENV-3) strain. Infection of mice with the adapted DENV-3 caused inoculum-dependent lethality that was preceded by several hematological and biochemical changes and increased virus dissemination, features consistent with severe disease manifestation in humans. IFN-γ expression increased after DENV-3 infection of WT mice and this was preceded by increase in expression of IL-12 and IL-18. In DENV-3-inoculated IFN-γ−/− mice, there was enhanced lethality, which was preceded by severe disease manifestation and virus replication. Lack of IFN-γ production was associated with diminished NO-synthase 2 (NOS2) expression and higher susceptibility of NOS2−/− mice to DENV-3 infection. Therefore, mechanisms of protection to DENV-3 infection rely on IFN-γ-NOS2-NO-dependent control of viral replication and of disease severity, a pathway showed to be relevant for resistance to DENV infection in other experimental and clinical settings. Thus, the model of DENV-3 infection in immunocompetent mice described here represents a significant advance in animal models of severe dengue disease and may provide an important tool to the elucidation of immunopathogenesis of disease and of protective mechanisms associated with infection."

 

This is an important development, for a very important disease: mosquito-borne dengue fever occurs around the world in the tropics, and has great potential to spread north and south with climate change.  It can also cause severe disease in humans, and having a good model system will go a long way to helping us understand how to control this.

 

Flavivirus image courtesy of Russell Kightley Media

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Tomato genome sequence bears fruit

Tomato genome sequence bears fruit | Virology and Bioinformatics from Virology.ca | Scoop.it
Work paves way for high-yield crops with good flavour.
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T cells 'hunt' parasites like animal predators seek prey, a new study reveals

T cells 'hunt' parasites like animal predators seek prey, a new study reveals | Virology and Bioinformatics from Virology.ca | Scoop.it
By pairing an intimate knowledge of immune-system function with a deep understanding of statistical physics, a cross-disciplinary team has arrived at a surprising finding: T cells use a movement strategy to track down parasites that is similar to...
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New HIV-inhibiting protein identified

New HIV-inhibiting protein identified | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists have identified a new HIV-suppressing protein in the blood of people infected with the virus. In laboratory studies, the protein, called CXCL4 or PF-4, binds to HIV such that it cannot attach to or enter a human cell.
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Launch in Rwanda of Africa's first national rotavirus vaccination ...

Merck (MSD outside the United States and Canada) said it welcomed the launch in Rwanda of Africa's first national rotavirus vaccination program with ROTATEQ (rotavirus vaccine, live, oral, pentavalent).

Via anarchic_teapot
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Schoolboy cracks age-old maths problem

Schoolboy cracks age-old maths problem | Virology and Bioinformatics from Virology.ca | Scoop.it

Shouryya Ray, who moved to Germany from India with his family at the age of 12, has baffled scientists and mathematicians by solving two fundamental particle dynamics problems posed by Sir Isaac Newton over 350 years ago.


Via Luca Baptista
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ScienceDirect.com - Advances in Virus Research - Chapter 1 - The Coevolution of Plants and Viruses: Resistance and Pathogenicity

ScienceDirect.com - Advances in Virus Research - Chapter 1 - The Coevolution of Plants and Viruses: Resistance and Pathogenicity | Virology and Bioinformatics from Virology.ca | Scoop.it
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16th-century Korean mummy provides clue to hepatitis B virus genetic code

16th-century Korean mummy provides clue to hepatitis B virus genetic code | Virology and Bioinformatics from Virology.ca | Scoop.it
The discovery of a mummified Korean child with relatively preserved organs enabled an Israeli-South Korean scientific team to conduct a genetic analysis on a liver biopsy which revealed a unique hepatitis B virus (HBV) genotype C2 sequence common...
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Application of next-generation sequencing techno... [J Gen Virol. 2012] - PubMed - NCBI

"The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture, and PCR, next generation sequencing is one of these methodologies that is now changing the way we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination, and to some extent, by their cost, which has restricted their use to a relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health."

 

And I'm going to do viruses of seawater and desert sands...B-)  Thanks @AJCann!

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ScienceDirect.com - Virology - Endogenous RNA viruses of plants in insect genomes

ScienceDirect.com - Virology - Endogenous RNA viruses of plants in insect genomes | Virology and Bioinformatics from Virology.ca | Scoop.it
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CDC - CMV: Homepage

CDC - CMV: Homepage | Virology and Bioinformatics from Virology.ca | Scoop.it
Cytomegalovirus (CMV) and Congenital CMV Infection...
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Hong Kong sees first human bird flu case in 18 months - AFP

Hong Kong sees first human bird flu case in 18 months - AFP | Virology and Bioinformatics from Virology.ca | Scoop.it
AFPHong Kong sees first human bird flu case in 18 monthsAFPBut we still need to go through the whole process of analysing the origin and channel of the infection and have to study the virology of the virus." The H5N1 strain has killed more than 350...
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PLoS Neglected Tropical Diseases: Surveillance of Dengue Fever Virus: A Review of Epidemiological Models and Early Warning Systems

PLoS Neglected Tropical Diseases: Surveillance of Dengue Fever Virus: A Review of Epidemiological Models and Early Warning Systems | Virology and Bioinformatics from Virology.ca | Scoop.it

"Dengue fever affects over a 100 million people annually hence is one of the world's most important vector-borne diseases. The transmission area of this disease continues to expand due to many direct and indirect factors linked to urban sprawl, increased travel and global warming. Current preventative measures include mosquito control programs, yet due to the complex nature of the disease and the increased importation risk along with the lack of efficient prophylactic measures, successful disease control and elimination is not realistic in the foreseeable future. Epidemiological models attempt to predict future outbreaks using information on the risk factors of the disease. Through a systematic literature review, this paper aims at analyzing the different modeling methods and their outputs in terms of acting as an early warning system. We found that many previous studies have not sufficiently accounted for the spatio-temporal features of the disease in the modeling process. Yet with advances in technology, the ability to incorporate such information as well as the socio-environmental aspect allowed for its use as an early warning system, albeit limited geographically to a local scale."

 

Useful paper on modelling virus spread

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ScienceDirect.com - Current Opinion in Virology - Rotavirus–host cell interactions: an arms race

ScienceDirect.com - Current Opinion in Virology - Rotavirus–host cell interactions: an arms race | Virology and Bioinformatics from Virology.ca | Scoop.it

► Rotavirus shuts off the translation of cellular transcripts by at least three different mechanisms.

► The formation of stress granules is prevented in rotavirus-infected cells.

► Rotavirus infection elicits and modulates the unfolded protein response of the cell.

► The innate immune response of the cells is controlled during rotavirus infection.

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Viruses Attack Mitochondria to Travel and Spread Within the Nervous System

Viruses Attack Mitochondria to Travel and Spread Within the Nervous System | Virology and Bioinformatics from Virology.ca | Scoop.it
Observed for the first time in neurons, biologists from Princeton University documented common strains of the herpes virus indirectly taking control of a cell's mitochondria.
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16th-Century Korean Mummy Provides Clue to Hepatitis B Virus Genetic Code - Science Daily (press release)

16th-Century Korean Mummy Provides Clue to Hepatitis B Virus Genetic Code - Science Daily (press release) | Virology and Bioinformatics from Virology.ca | Scoop.it
ScienceBlog.com16th-Century Korean Mummy Provides Clue to Hepatitis B Virus Genetic CodeScience Daily (press release)... Seok Ju Seon Memorial Museum; Dr.
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Comparative analysis of microarray data in Arabidopsis transcriptome during compatible interactions with plant viruses

Background
At the moment, there are a number of publications describing gene expression profiling in virus-infected plants. Most of the data are limited to specific host-pathogen interactions involving a given virus and a model host plant - usually Arabidopsis thaliana. Even though several summarizing attempts have been made, a general picture of gene expression changes in susceptible virus-host interactions is lacking.

Methods
To analyze transcriptome response to virus infection, we have assembled currently available microarray data on changes in gene expression levels in compatible Arabidopsis-virus interactions. We used the mean r (Pearson's correlation coefficient) for neighboring pairs to estimate pairwise local similarity in expression in the Arabidopsis genome.

Results
Here we provide a functional classification of genes with altered expression levels. We also demonstrate that responsive genes may be grouped or clustered based on their co-expression pattern and chromosomal location.

Conclusions
In summary, we found that there is a greater variety of upregulated genes in the course of viral pathogenesis as compared to repressed genes. Distribution of the responsive genes in combined viral databases differed from that of the whole Arabidopsis genome, thus underlining a role of the specific biological processes in common mechanisms of general resistance against viruses and in physiological/cellular changes caused by infection. Using integrative platforms for the analysis of gene expression data and functional profiling, we identified overrepresented functional groups among activated and repressed genes. Each virus-host interaction is unique in terms of the genes with altered expression levels and the number of shared genes affected by all viruses is very limited. At the same time, common genes can participate in virus-, fungi- and bacteria-host interaction. According to our data, non-homologous genes that are located in close proximity to each other on the chromosomes, and whose expression profiles are modified as a result of the viral infection, occupy 12% of the genome. Among them 5% form co-expressed and co-regulated clusters.

 

This is quite a big deal as a plant virus-host interaction paper: comparative analysis of transcriptome responses to different viruses should result in some very interesting observations.

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Crop Circles - Mystery Solved

Crop Circles - Mystery Solved | Virology and Bioinformatics from Virology.ca | Scoop.it
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