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Rescooped by Ken Yaw Agyeman-Badu from Host Cell & Pathogen Interactions
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The potential role of microfilaments in host cells for infection with infectious spleen and kidney necrosis virus infection

Infectious spleen and kidney necrosis virus (ISKNV) belongs to the genus Megalocytivirus from the family Iridoviridae.
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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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It's a group effort - the curators:

It's a group effort - the curators: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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Rescooped by Chris Upton + helpers from immunology
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Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access (#PLOSCompBio: Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes http://t.co/nw7bx47t8B)...

Via Gilbert Faure au nom de l'ASSIM
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Rescooped by Chris Upton + helpers from Python Resources for Bioinformatics
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Free eBook: Python for Biologists

Free eBook: Python for Biologists | Virology and Bioinformatics from Virology.ca | Scoop.it

Via burkesquires
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Rescooped by Chris Upton + helpers from Influenza
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Phospholipase D facilitates efficient entry of influenza virus allowing escape from innate mmune inhibition

Role of phospholipase D in influenza from VICB members HA Brown, CW Lindsley, JS Daniels. #chemicalbiology http://t.co/u1xs7g7GxO

Via Mel Melendrez-Vallard
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Rescooped by Ken Yaw Agyeman-Badu from Host Cell & Pathogen Interactions
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Effects of two amino acid substitutions in the capsid proteins on the interaction of two cell-adapted PanAsia-1 strains of foot-and-mouth disease virus serotype O with...

Some cell-adapted strains of foot-and-mouth disease virus (FMDV) can utilize heparan sulfate (HS) as a receptor to facilitate viral infection in cultured cells. A number of independent sites on the capsid that might be involved in FMDV-HS interaction have been studied. However, the previously reported residues do not adequately explain HS-dependent infection of two cell-adapted PanAsia-1 strains (O/Tibet/CHA/6/99tc and O/Fujian/CHA/9/99tc) of FMDV serotype O.
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The Importance of Biological Safety

The Importance of Biological Safety | Virology and Bioinformatics from Virology.ca | Scoop.it
Biological safety is about ensuring that individuals, products and the environment as a whole are all kept as safe as possible from hazardous biological materials. Not only are more
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Avian Influenza Virus Transmissio... [Curr Top Microbiol Immunol. 2014] - PubMed - NCBI

Avian Influenza Virus Transmissio... [Curr Top Microbiol Immunol. 2014] - PubMed - NCBI | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza A viruses cause yearly epidemics and occasional pandemics. In addition, zoonotic influenza A viruses sporadically infect humans and may cause severe respiratory disease and fatalities. Fortunately, most of these viruses do not have the ability to be efficiently spread among humans via aerosols or respiratory droplets (airborne transmission) and to subsequently cause a pandemic. However, adaptation of these zoonotic viruses to humans by mutation or reassortment with human influenza A viruses may result in airborne transmissible viruses with pandemic potential. Although our knowledge of factors that affect mammalian adaptation and transmissibility of influenza viruses is still limited, we are beginning to understand some of the biological traits that drive airborne transmission of influenza viruses among mammals. Increased understanding of the determinants and mechanisms of airborne transmission may aid in assessing the risks posed by avian influenza viruses to human health, and preparedness for such risks. This chapter summarizes recent discoveries on the genetic and phenotypic traits required for avian influenza viruses to become airborne transmissible between mammals.

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The virus detective who discovered Ebola

The virus detective who discovered Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
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Scooped by Ken Yaw Agyeman-Badu
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Why Has This Really Common Virus Only Just Been Discovered? – Phenomena: Not Exactly Rocket Science

Why Has This Really Common Virus Only Just Been Discovered? – Phenomena: Not Exactly Rocket Science | Virology and Bioinformatics from Virology.ca | Scoop.it
The most common viruses in your body don’t make you ill. Instead, they infect the legions of microbes that live in your gut. These bacteriophages, or phages for short, number in their trillions. An...
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Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm

Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm | Virology and Bioinformatics from Virology.ca | Scoop.it

Abstract

The HMT3522 progression series of human breast cells have been used to discover how tissue architecture, microenvironment and signaling molecules affect breast cell growth and behaviors. However, much remains to be elucidated about malignant and phenotypic reversion behaviors of the HMT3522-T4-2 cells of this series. We employed a “pan-cell-state” strategy, and analyzed jointly microarray profiles obtained from different state-specific cell populations from this progression and reversion model of the breast cells using a tree-lineage multi-network inference algorithm, Treegl. We found that different breast cell states contain distinct gene networks. The network specific to non-malignant HMT3522-S1 cells is dominated by genes involved in normal processes, whereas the T4-2-specific network is enriched with cancer-related genes. The networks specific to various conditions of the reverted T4-2 cells are enriched with pathways suggestive of compensatory effects, consistent with clinical data showing patient resistance to anticancer drugs. We validated the findings using an external dataset, and showed that aberrant expression values of certain hubs in the identified networks are associated with poor clinical outcomes. Thus, analysis of various reversion conditions (including non-reverted) of HMT3522 cells using Treegl can be a good model system to study drug effects on breast cancer.

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Accelerating Genomic Analysis | Algorithmic Trading Opinions & Financial Insight | Automated Trader

Accelerating Genomic Analysis | Algorithmic Trading Opinions & Financial Insight | Automated Trader | Virology and Bioinformatics from Virology.ca | Scoop.it
One of the biggest catchphrases in modern science is Human Genome-the DNA coding that largely pre-determines who we are and many of our medical outcomes. By mapping and analyzing the structure of the human genetic code, scientists and doctors h...
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Globe-Trotting Virus Hides Inside People's Gut Bacteria

Globe-Trotting Virus Hides Inside People's Gut Bacteria | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists have discovered what may be the most common virus in people worldwide. The tiny critter doesn't make us sick but may be involved in obesity and diabetes.
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Why are emerging viruses here – and why now?

Why are emerging viruses here – and why now? | Virology and Bioinformatics from Virology.ca | Scoop.it
The US is on the brink of a new virus epidemic; a virus that wasn’t there ten years ago but which is now worrying officials. Chikungunya, which causes an incapacitating fever, is spread via Aedes mosquitoes…
Chris Upton + helpers's insight:

R0 is influenced by multiple issues

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Lecture Slides | HRP214 | Stanford - Writing in the Sciences

Lecture Slides | HRP214 | Stanford - Writing in the Sciences | Virology and Bioinformatics from Virology.ca | Scoop.it
Chris Upton + helpers's insight:

Excellent!!!!!

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Rescooped by Chris Upton + helpers from Viral Modeling and Simulation
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Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China

Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China | Virology and Bioinformatics from Virology.ca | Scoop.it
by Kaifa Wei, Yanhui Chen, Yina Lin, Yutian Pan
The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically.

Via burkesquires
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#Chikungunya virus in the #US (@CDCgov, July 27 2014, edited)

#Chikungunya virus in the #US (@CDCgov, July 27 2014, edited) | Virology and Bioinformatics from Virology.ca | Scoop.it
[Source: US Centers for Disease Control and Prevention (CDC), full page: (LINK).]
Chikungunya virus in the United States [      ]
Updates of chikungunya case counts are publically released every Tuesday evening (MT).

Via Mel Melendrez-Vallard
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Rescooped by Chris Upton + helpers from Plants and Microbes
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PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014)

PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014) | Virology and Bioinformatics from Virology.ca | Scoop.it

Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.


Via Kamoun Lab @ TSL
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Rescooped by Ken Yaw Agyeman-Badu from Host Cell & Pathogen Interactions
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The CD8 Antiviral Factor (CAF) can suppress HIV-1 transcription from the Long Terminal Repeat (LTR) promoter in the absence of elements upstream of the CATATAA box

The CD8 Antiviral Factor (CAF) suppresses viral transcription from the HIV-1 Long Terminal Repeat (LTR) promoter in a non-cytolytic manner. However, the region on the LTR upon which CAF acts is unknown. Our objective was to determine the region on the LTR upon which CAF acts to suppress HIV-1 transcription.
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Viruses101 | Learn Science at Scitable

Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses 101 will delve into the world of microscopic killers. Each post will explore a new virus ? its components, effects on victims, and its impact on the global community.
Julia Paoli's insight:

Two residents in Florida are the first in the U.S. to contract chikungunya locally.

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Astrology can aid healthcare - MP (UK)

Astrology can aid healthcare - MP (UK) | Virology and Bioinformatics from Virology.ca | Scoop.it

A Conservative MP has spoken of his belief in astrology and his desire to incorporate it into medicine.

David Tredinnick said he had spent 20 years studying astrology and healthcare and was convinced it could work.

The MP for Bosworth, a member of the health committee and the science and technology committee, said he was not afraid of ridicule or abuse.

"There is no logic in attacking something that has a proven track record," he told BBC News.

He said he had studied the Indian astrological system Iahiri and the way it was used by that country's government and recalled how Chris Patten, Britain's last governor of Hong Kong, had an official astrologer, whom Mr Tredinnick had consulted while on a parliamentary delegation there.

 
Chris Upton + helpers's insight:

WTF!  

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Sierra Leone's chief Ebola doctor contracts the virus | Top News | Reuters

Sierra Leone's chief Ebola doctor contracts the virus | Top News | Reuters | Virology and Bioinformatics from Virology.ca | Scoop.it
FREETOWN (Reuters) - The head doctor fighting the deadly tropical virus Ebola in Sierra Leone has himself caught the disease, the government said.
The 39-year-old Sheik Umar Khan, hailed as a national
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Mel Melendrez-Vallard's curator insight, July 25, 7:33 AM

Just a really sad reality of those on the front lines of defense against diseases like Ebola.

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Why an Ebola epidemic is spinning out of control

Why an Ebola epidemic is spinning out of control | Virology and Bioinformatics from Virology.ca | Scoop.it
Laurie Garrett says poor governance, ignorance and hysteria are worsening the Ebola epidemic in Sierra Leone, Guinea and Liberia.
Chris Upton + helpers's insight:

Where are those homeopathy "we can cure anything with our magic water" nuts when you need one?

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Virology Journal | Abstract | Defining viral species: making taxonomy useful

Virus taxonomy at present is best characterized as a categorization of convenience, without a firm basis in the principles of evolutionary biology. Specifically, virus species definitions appear to depend more on tradition and popular opinion among virologists than on firm, quantitative biological evidence. I suggest a series of changes to underlying species concepts that would shift the field from one that simply files viruses away in taxonomic boxes to one that can learn important biological lessons from its taxonomy.
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Viruses Throughout Life & Time: Friends, Foes, Change Agents

Viruses Throughout Life & Time: Friends, Foes, Change Agents | Virology and Bioinformatics from Virology.ca | Scoop.it
"Viruses Throughout Life & Time: Friends, Foes, Change Agents" aims to increase awareness of the viral world by examining the role of viruses in biological systems and as major drivers of evolution.

Via Mya Breitbart
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Suffix tree searcher: exploration of common substrings in large DNA sequence sets

Suffix tree searcher: exploration of common substrings in large DNA sequence sets | Virology and Bioinformatics from Virology.ca | Scoop.it

BACKGROUND:

Large DNA sequence data sets require special bioinformatics tools to search and compare them. Such tools should be easy to use so that the data can be easily accessed by a wide array of researchers. In the past, the use of suffix trees for searching DNA sequences has been limited by a practical need to keep the trees in RAM. Newer algorithms solve this problem by using disk-based approaches. However, none of the fastest suffix tree algorithms have been implemented with a graphical user interface, preventing their incorporation into a feasible laboratory workflow.

RESULTS:

Suffix Tree Searcher (STS) is designed as an easy-to-use tool to index, search, and analyze very large DNA sequence datasets. The program accommodates very large numbers of very large sequences, with aggregate size reaching tens of billions of nucleotides. The program makes use of pre-sorted persistent "building blocks" to reduce the time required to construct new trees. STS is comprised of a graphical user interface written in Java, and four C modules. All components are automatically downloaded when a web link is clicked. The underlying suffix tree data structure permits extremely fast searching for specific nucleotide strings, with wild cards or mismatches allowed. Complete tree traversals for detecting common substrings are also very fast. The graphical user interface allows the user to transition seamlessly between building, traversing, and searching the dataset.

CONCLUSIONS:

Thus, STS provides a new resource for the detection of substrings common to multiple DNA sequences or within a single sequence, for truly huge data sets. The re-searching of sequence hits, allowing wild card positions or mismatched nucleotides, together with the ability to rapidly retrieve large numbers of sequence hits from the DNA sequence files, provides the user with an efficient method of evaluating the similarity between nucleotide sequences by multiple alignment or use of Logos. The ability to re-use existing suffix tree pieces considerably shortens index generation time. The graphical user interface enables quick mastery of the analysis functions, easy access to the generated data, and seamless workflow integration.

Chris Upton + helpers's insight:

If he won't put it up, I will...B-) This the 100th, Chris??

Actually #101, but I should discount the crappy one that should have been withdrawn!

This one took many years to get published....  the software is cool, but only the comp sci folks understand the Math.

 

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BMC Research Notes | Abstract | Suffix tree searcher: exploration of common substrings in large DNA sequence sets

Large DNA sequence data sets require special bioinformatics tools to search and compare them. Such tools should be easy to use so that the data can be easily accessed by a wide array of researchers. In the past, the use of suffix trees for searching DNA sequences has been limited by a practical need to keep the trees in RAM. Newer algorithms solve this problem by using disk-based approaches. However, none of the fastest suffix tree algorithms have been implemented with a graphical user interface, preventing their incorporation into a feasible laboratory workflow.
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