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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
Nicolas Palopoli's insight:

Besides the interesting recall of the Intelligent Systems for Molecular Biology (ISMB) annual conferences on computational biology, it offers a nice insight into current state-of-the-art methodologies and upcoming trends in the discipline.

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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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We Have Nothing: The Human Cost Of Ebola

We Have Nothing: The Human Cost Of Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
Harrowing personal stories reveal the catastrophic impact of the deadly virus on one of the world's poorest regions.
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Footage From 1976 Documents Discovery of Ebola Virus

Footage From 1976 Documents Discovery of Ebola Virus | Virology and Bioinformatics from Virology.ca | Scoop.it
In 1976, a group of health workers took a pair of film cameras to what was then known as Zaire and documented their discovery of a new, deadly virus. Today we know that virus as Ebola.
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On the Quarantine Period for Ebola Virus

On the Quarantine Period for Ebola Virus | Virology and Bioinformatics from Virology.ca | Scoop.it

Background:
21 days has been regarded as the appropriate quarantine period for holding individuals potentially exposed to Ebola Virus (EV) to reduce risk of contagion. There does not appear to be a systematic discussion of the basis for this period.

Methods:
The prior estimates for incubation time to EV were examined, along with data on the first 9 months of the current outbreak. These provided estimates of the distribution of incubation times.

Results:
A 21 day period for quarantine may result in the release of individuals with a 0.2 – 12% risk of release prior to full opportunity for the incubation to proceed. It is suggested that a detailed cost-benefit assessment, including considering full transmission risks, needs to occur in order to determine the appropriate quarantine period for potentially exposed individuals.

Ed Rybicki's insight:

Oops...of course, it was never a figure set in stone - but a 12% risk is significant!

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LRB · Paul Farmer · Diary: Ebola

LRB · Paul Farmer · Diary: Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
I have just returned from Liberia with a group of physicians and health activists. We are heading back in a few days. The country is in the midst of the largest ever epidemic of Ebola haemorrhagic fever. It’s an acute and brutal affliction. Ebola is a zoonosis – it leaps from animal . . .
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A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus

A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus | Virology and Bioinformatics from Virology.ca | Scoop.it
by Xiaoyun Yang, Lennert Steukers, Katrien Forier, Ranhua Xiong, Kevin Braeckmans, Kristien Van Reeth, Hans Nauwynck Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement...

Via Gilbert Faure au nom de l'ASSIM
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Study suggests 21-day Ebola quarantine period is not enough

Study suggests 21-day Ebola quarantine period is not enough | Virology and Bioinformatics from Virology.ca | Scoop.it
A new study has suggested that the standard 21-day quarantine period that’s currenty being used for cases of Ebola might not be enough.
Hannah Davis's insight:

No need to panic: quarantine period just needs to be extended a bit. The main problem in the current outbreak is not that people aren't being quarantined for long enough, but that they're not being quarantined at all.

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How the immune system spots tumors

How the immune system spots tumors | Virology and Bioinformatics from Virology.ca | Scoop.it
The receptor protein Dectin-1 recognizes structures found on cancerous cells, and then triggers an anti-tumor immune response.
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Rescooped by burkesquires from Tools and tips for scientific tinkers and tailors
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Virus entry at a glance

Virus entry at a glance | Virology and Bioinformatics from Virology.ca | Scoop.it
I'm not normally very keen on infographics - but I like this one:

Source: Yamauchi, Y., and Helenius, A. (2013) Virus entry at a glance. Journal of Cell Science, 126(6): 1289-1295.

Via Mel Melendrez-Vallard
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A comprehensive collection of systems biology data characterizing the host response to viral infection

A comprehensive collection of systems biology data characterizing the host response to viral infection | Virology and Bioinformatics from Virology.ca | Scoop.it

The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.

 
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Why Ebola may pose a greater threat in the ICU

Why Ebola may pose a greater threat in the ICU | Virology and Bioinformatics from Virology.ca | Scoop.it
The nature of the Ebola virus makes it a grave threat to those who have the most intimate contact with patients' bodies -- health care workers, family caregivers and grave diggers.
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Mechanisms of Virus Membrane Fusion Proteins - Annual Review of Virology, 1(1):171

Enveloped viruses infect host cells by a membrane fusion reaction that takes place at the cell surface or in intracellular compartments following virus uptake. Fusion is mediated by the membrane interactions and conformational changes of specialized virus envelope proteins termed membrane fusion proteins. This article discusses the structures and refolding reactions of specific fusion proteins and the methods for their study and highlights outstanding questions in the field.

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How quickly Ebola spreads compared to other diseases

How quickly Ebola spreads compared to other diseases | Virology and Bioinformatics from Virology.ca | Scoop.it
Compared to other infectious diseases, Ebola spreads slowly and to relatively few people. But it is extremely deadly: Thousands have been killed this year in West Africa, and more are falling ill every day.
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This Is What The Ebola Virus Really Looks Like -- And How It Works

This Is What The Ebola Virus Really Looks Like -- And How It Works | Virology and Bioinformatics from Virology.ca | Scoop.it
We're guessing that by now, you're pretty familiar with this little squiggle. But if you want to know what Ebola really looks like -- and how it hijacks cells to wreak havoc inside the human body -- you need a detailed diagram of an Ebola virus parti...
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Viruses | Free Full-Text | Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing

Viruses | Free Full-Text | Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing | Virology and Bioinformatics from Virology.ca | Scoop.it
The complete genome of human cytomegalovirus (HCMV) was elucidated almost 25 years ago using a traditional cloning and Sanger sequencing approach. Analysis of the genetic content of additional laboratory and clinical isolates has lead to a better, albeit still incomplete, definition of the coding potential and diversity of wild-type HCMV strains. The introduction of a new generation of massively parallel sequencing technologies, collectively called next-generation sequencing, has profoundly increased the throughput and resolution of the genomics field. These increased possibilities are already leading to a better understanding of the circulating diversity of HCMV clinical isolates. The higher resolution of next-generation sequencing provides new opportunities in the study of intrahost viral population structures. Furthermore, deep sequencing enables novel diagnostic applications for sensitive drug resistance mutation detection. RNA-seq applications have changed the picture of the HCMV transcriptome, which resulted in proof of a vast amount of splicing events and alternative transcripts. This review discusses the application of next-generation sequencing technologies, which has provided a clearer picture of the intricate nature of the HCMV genome. The continuing development and application of novel sequencing technologies will further augment our understanding of this ubiquitous, but elusive, herpesvirus.
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Ebola data on DataMarket

Ebola data on DataMarket | Virology and Bioinformatics from Virology.ca | Scoop.it
The outbreak of the Ebola virus disease (EVD) in western Africa that started in March this year is the deadliest outbreak of EVD to date. In August the World Health Organization declared the epidem...
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A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus

A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus | Virology and Bioinformatics from Virology.ca | Scoop.it

Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. Sialic acids present on the epithelial surface have long been considered to be determinants of influenza virus tropism. However, mucus which is also rich in sialic acids may serve as the first barrier of selection. It was investigated how influenza virus interacts with the mucus to infect epithelial cells. Two techniques were applied to track SIV H1N1 in porcine mucus. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. Furthermore, the effects of neuraminidase on SIV getting through or binding to the mucus were studied by using zanamivir, a neuraminidase inhibitor (NAI), and Arthrobacter ureafaciensneuraminidase. The distribution of the diffusion coefficient shows that 70% of SIV particles were entrapped, while the rest diffused freely in the mucus. Additionally, SIV penetrated the porcine mucus with time, reaching a depth of 65 µm at 30 min post virus addition, 2 fold of that at 2 min. Both the microscopic diffusion and macroscopic penetration were largely diminished by NAI, while were clearly increased by the effect of exogenous neuraminidase. Moreover, the exogenous neuraminidase sufficiently prevented the binding of SIV to mucus which was reversely enhanced by effect of NAI. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract.

 
Ed Rybicki's insight:

Good stuff!  I especially like their "virus in-capsule-mucus penetration system".  Amazing this hasn't been looked at in this sort of detail previously.

 
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Antiviral drug discovery: broad-spectrum drugs from nature - Natural Product Reports (RSC Publishing)

Covering: up to April 2014The development of drugs with broad-spectrum antiviral activities is a long pursued goal in drug discovery. It has been shown that blocking co-opted host-factors abrogates the replication of many viruses, yet the development of such host-targeting drugs has been met with scepticism mainly
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Five Fast Facts About Ebola | Viruses101 | Learn Science at Scitable

Five Fast Facts About Ebola | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Can cats or dogs become infected with Ebola? Which country has the highest number of Ebola cases? These and other interesting questions about the 2014 Ebola Outbreak are answered.
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Live Attenuated and Inactivated Viral Vaccine Formulation and Nasal Delivery: Potential and Challenges

Live Attenuated and Inactivated Viral Vaccine Formulation and Nasal Delivery: Potential and Challenges | Virology and Bioinformatics from Virology.ca | Scoop.it
Vaccines are cost-effective for the prevention of infectious diseases and have significantly reduced mortality and morbidity. Novel approaches are needed to develop safe and effective vaccines against disease. Major challenges in vaccine development include stability in a suitable dosage form, and effective modes of delivery. Many live attenuated vaccines are capable of eliciting both humoral and cell mediated immune responses if physicochemically stable in an appropriate delivery vehicle. Knowing primary stresses that impart instability provide a general rationale for formulation development and mode of delivery. Since most pathogens enter the body through the mucosal route, live-attenuated vaccines have the advantage of mimicking natural immunization via non-invasive delivery. This presentation will examine aspects of formulation design, types of robust dosage forms to consider, effective routes of delivery (invasive and noninvasive), and distinctions between live attenuated or inactivated vaccines.
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Ebola by the numbers: The size, spread and cost of an outbreak

Ebola by the numbers: The size, spread and cost of an outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
As the virus continues to rampage in West Africa, Nature’s graphic offers a guide to the figures that matter.
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Crossroads (iii) – a New Direction for Bioinformatics with Twelve Fundamental Problems « Homolog.us – Bioinformatics

Crossroads (iii) – a New Direction for Bioinformatics with Twelve Fundamental Problems « Homolog.us – Bioinformatics | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Wei Shen
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Computation | Free Full-Text | Incongruencies in Vaccinia Virus Phylogenetic Trees

Over the years, as more complete poxvirus genomes have been sequenced, phylogenetic studies of these viruses have become more prevalent. In general, the results show similar relationships between the poxvirus species; however, some inconsistencies are notable. Previous analyses of the viral genomes contained within the vaccinia virus (VACV)-Dryvax vaccine revealed that their phylogenetic relationships were sometimes clouded by low bootstrapping confidence. To analyze the VACV-Dryvax genomes in detail, a new tool-set was developed and integrated into the Base-By-Base bioinformatics software package. Analyses showed that fewer unique positions were present in each VACV-Dryvax genome than expected. A series of patterns, each containing several single nucleotide polymorphisms (SNPs) were identified that were counter to the results of the phylogenetic analysis. The VACV genomes were found to contain short DNA sequence blocks that matched more distantly related clades. Additionally, similar non-conforming SNP patterns were observed in (1) the variola virus clade; (2) some cowpox clades; and (3) VACV-CVA, the direct ancestor of VACV-MVA. Thus, traces of past recombination events are common in the various orthopoxvirus clades, including those associated with smallpox and cowpox viruses.
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New Methods in Tissue Engineering: Improved Models for Viral Infection - Annual Review of Virology, 1(1):475

New insights in the study of virus and host biology in the context of viral infection are made possible by the development of model systems that faithfully recapitulate the in vivo viral life cycle. Standard tissue culture models lack critical emergent properties driven by cellular organization and in vivo–like function, whereas animal models suffer from limited susceptibility to relevant human viruses and make it difficult to perform detailed molecular manipulation and analysis. Tissue engineering techniques may enable virologists to create infection models that combine the facile manipulation and readouts of tissue culture with the virus-relevant complexity of animal models. Here, we review the state of the art in tissue engineering and describe how tissue engineering techniques may alleviate some common shortcomings of existing models of viral infection, with a particular emphasis on hepatotropic viruses. We then discuss possible future applications of tissue engineering to virology, including current challenges and potential solutions.

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Loss of long term protection with the inclusion of HIV pol to a DNA vaccine encoding gag

Loss of long term protection with the inclusion of HIV pol to a DNA vaccine encoding gag | Virology and Bioinformatics from Virology.ca | Scoop.it

Traditional vaccine strategies that induce antibody responses have failed to protect against HIV infection in clinical trials, and thus cell-mediated immunity is now an additional criterion. Recent clinical trials that aimed to induce strong T cell responses failed to do so. Therefore, to enhance induction of protective T cell responses, it is crucial that the optimum antigen combination is chosen. Limited research has been performed into the number of antigens selected for an HIV vaccine. This study aimed to compare DNA vaccines encoding either a single HIV antigen or a combination of two antigens, using intradermal vaccination of C57BL/6 mice. Immune assays were performed on splenocytes, and in vivo protection was examined by challenge with a chimeric virus, EcoHIV, able to infect mouse but not human leukocytes, at 10 days (short term) and 60 days (long term) post final vaccination. At 60 days there was significantly lower frequency of induced antigen-specific CD8+ T cells in the spleens of pCMVgag–pol-vaccinated mice compared with mice which received pCMVgag only. Most importantly, short term viral control of EcoHIV was similar for pCMVgag and pCMVgag–pol-vaccinated mice at day 10, but only the pCMVgag-vaccinated significantly controlled EcoHIV at day 60 compared with pCMV-vaccinated mice, showing that control was reduced with the inclusion of the HIV pol gene.

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Blog about it! Getting students closer to science | Science in School

Blog about it! Getting students closer to science | Science in School | Virology and Bioinformatics from Virology.ca | Scoop.it
Julia Paoli's insight:

Yeah, so excited to be featured in Science in School!

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