Virology and Bioinformatics from Virology.ca
82.5K views | +28 today
Follow
Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Chad Smithson
Scoop.it!

How Many Microbes Are Hiding Among Us?

How Many Microbes Are Hiding Among Us? | Virology and Bioinformatics from Virology.ca | Scoop.it

Microbes are everywhere—even inside us. But because so many of these bugs won't grow in the lab, scientists have had a tough time figuring out just who they are and how they live. That may soon change. By sequencing the DNA in individual cells, researchers have gotten to know 200 new microbes—and they may be able to characterize many more.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

UberCloud Experiment now open to bioinformatics and ...

Now the UberCloud Experiment is open also to organizations focusing on bioinformatics and computational biology. The UberCloud Experiment started in mid-2012 with the aim of exploring the end-to-end process employed ...
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

10 truths a supervisor will never tell you

10 truths a supervisor will never tell you | Virology and Bioinformatics from Virology.ca | Scoop.it
There are some important dos and don’ts to bear in mind when choosing someone to oversee your doctoral thesis, advises Tara Brabazon
Chris Upton + helpers's insight:

Title is a bit misleading, but it's useful advice.

more...
Mel Melendrez-Vallard's curator insight, July 12, 2013 7:20 AM

Per Chris Upton--title a bit misleading but actually has some nice insight that I never considered when looking at PhD programs.

Scooped by Torben Barsballe
Scoop.it!

Bacteriology: Toxins in tandem

Bacteriology: Toxins in tandem | Virology and Bioinformatics from Virology.ca | Scoop.it

During the complex process of infection, nothing is more fascinating than the interplay between host immunity and pathogen virulence — particularly in asymptomatic carriers, who seem to be in perfect health while normally life-threatening organisms replicate within them. The most infamous such carrier was 'Typhoid Mary', a cook in the United States who infected more than 50 people with typhoid fever by passing on the causative bacterium Salmonella Typhi (Fig. 1). Another perplexing feature of these bacteria is the existence of the closely related Salmonella Typhimurium, which does not cause life-threatening infections despite having apparently similar virulence properties to S. Typhi. A paper by Song et al.1, published on Nature's website today, places several key pieces in this puzzle.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

ABC's The View: Just Say No to adding Jenny McCarthy to The View. Petition that supports vaccination.

ABC's The View: Just Say No to adding Jenny McCarthy to The View

more...
No comment yet.
Rescooped by Chris Upton + helpers from Synthetic Biology
Scoop.it!

Synthetic yeast could make beer cheaper and stronger

Synthetic yeast could make beer cheaper and stronger | Virology and Bioinformatics from Virology.ca | Scoop.it

 

The synthetic yeast project, also known as Sc2.0, will draw together expertise from around the world.

One of the aims of the project is to develop this yeast strain as a vehicle that you can put in new chemical pathways and directly manipulate it in a way that is not possible at the moment.Making more alcohol resistant strains will be very useful for that industry in terms of cost value. Also, strains that are metabolically more optimal and don't require as much energy will be useful.

 


Via Marko Dolinar
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

The largest viral genome from a human

The largest viral genome from a human | Virology and Bioinformatics from Virology.ca | Scoop.it
A new Mimivirus has now been isolated from a human patient with pneumonia.
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Pathogenesis and transmission of avian influenza A (H7N9) virus in ferrets and mice

On 29 March 2013, the Chinese Center for Disease Control and Prevention confirmed the first reported case of human infection with an avian influenza A(H7N9) virus1. The recent human infections with H7N9 virus, totalling over 130 cases with 39 fatalities to date, have been characterized by severe pulmonary disease and acute respiratory distress syndrome (ARDS)2. This is concerning because H7 viruses have typically been associated with ocular disease in humans, rather than severe respiratory disease3. This recent outbreak underscores the need to better understand the pathogenesis and transmission of these viruses in mammals. Here we assess the ability of A/Anhui/1/2013 and A/Shanghai/1/2013 (H7N9) viruses, isolated from fatal human cases, to cause disease in mice and ferrets and to transmit to naive animals. Both H7N9 viruses replicated to higher titre in human airway epithelial cells and in the respiratory tract of ferrets compared to a seasonal H3N2 virus. Moreover, the H7N9 viruses showed greater infectivity and lethality in mice compared to genetically related H7N9 and H9N2 viruses. The H7N9 viruses were readily transmitted to naive ferrets through direct contact but, unlike the seasonal H3N2 virus, did not transmit readily by respiratory droplets. The lack of efficient respiratory droplet transmission was corroborated by low receptor-binding specificity for human-like α2,6-linked sialosides. Our results indicate that H7N9 viruses have the capacity for efficient replication in mammals and human airway cells and highlight the need for continued public health surveillance of this emerging virus.

  
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Molecular Biology and Epidemiology of Dianthoviruses

Molecular Biology and Epidemiology of Dianthoviruses | Virology and Bioinformatics from Virology.ca | Scoop.it

The genus Dianthovirus is one of eight genera in the family Tombusviridae. All the genera have monopartite positive-stranded RNA genomes, except the dianthoviruses which have bipartite genomes. The dianthoviruses are distributed worldwide. Although they share common structural features with the otherTombusviridae viruses in their virions and the terminal structure of the genomic RNAs, the bipartite nature of the dianthovirus genome offers an ideal experimental system with which to study basic issues of virology. The two genomic RNAs seem to use distinct strategies to regulate their translation, transcription, genome replication, genome packaging, and cell-to-cell movement during infection. This review summarizes the current state of our knowledge of the dianthoviruses, with its main emphasis on the molecular biology of the virus, including the viral and host factors required for its infection of host plants. The epidemiology of the virus and the possible viral impacts on agriculture and the environment are also discussed.

more...
Mel Melendrez-Vallard's curator insight, July 10, 2013 3:24 PM

I am posting this because I have never heard of Dianthoviruses and this work is actually pretty cool, I love basic science.

Scooped by C_Fleis
Scoop.it!

PLOS ONE: Towards the Conservation of Endangered Avian Species: A Recombinant West Nile Virus Vaccine Results in Increased Humoral and Cellular Immune Responses in Japanese Quail (Coturnix japonica)

PLOS ONE: Towards the Conservation of Endangered Avian Species: A Recombinant West Nile Virus Vaccine Results in Increased Humoral and Cellular Immune Responses in Japanese Quail (Coturnix japonica) | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract

West Nile Virus (WNV) arrived in North America in 1999 and is now endemic. Many families of birds, especially corvids, are highly susceptible to WNV and infection often results in fatality. Avian species susceptible to WNV infection also include endangered species, such as the Greater Sage-Grouse (Centrocercus uropbasianuts) and the Eastern Loggerhead Shrike (Lanius ludovicianus migrans). The virus has been shown to contribute towards the likelihood of their extinction. Although a clear and present threat, there exists no avian WNV vaccine available to combat this lethal menace. As a first step in establishing an avian model for testing candidate WNV vaccines, avian antibody based reagents were assessed for cross-reactivity with Japanese quail (Coturnix japonica) T cell markers CD4 and CD8; the most reactive were found to be the anti-duck CD8 antibody, clone Du-CD8-1, and the anti-chicken/turkey CD4 antibody, clone CT4. These reagents were then used to assess vaccine performance as well as to establish T cell populations in quail, with a novel population of CD4/CD8 double positive T cells being identified in Japanese quail. Concurrently, non-replicating recombinant adenoviruses, expressing either the WNV envelope or NS3 ‘genes’ were constructed and assessed for effectiveness as avian vaccines...

 

more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites

Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites | Virology and Bioinformatics from Virology.ca | Scoop.it

Understanding and controlling the interaction of graphene-based materials with cell membranes is key to the development of graphene-enabled biomedical technologies and to the management of graphene health and safety issues. Very little is known about the fundamental behavior of cell membranes exposed to ultrathin 2D synthetic materials. Here we investigate the interactions of graphene with cells membranes.

more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Bacterial molecules may prevent inflammatory bowel disease

Bacterial molecules may prevent inflammatory bowel disease | Virology and Bioinformatics from Virology.ca | Scoop.it

Common molecules made by bacteria in the gut may act as chill pills for the immune system. Molecules secreted by intestinal bacteria work to prevent misplaced immune attacks in inflammatory bowel diseases like colitis, a new study finds.

more...
No comment yet.
Scooped by Kenzibit
Scoop.it!

A quantitative infection assay for human type I, II, and III interferon antiviral activities

Upon virus infection, cells secrete a diverse group of antiviral molecules that signal proximal cells to enter into an antiviral state, slowing or preventing viral spread.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Bioinformatics for Beginners – File Formats Part 3. – Alignments ...

Bioinformatics for Beginners – File Formats Part 3. – Alignments ... | Virology and Bioinformatics from Virology.ca | Scoop.it
The generally used file formats for sequence based alignments are the SAM and BAM formats. These files can contain information about mapped and unmapped reads, the contigs of the reference sequence that was used ...
more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Gene therapy treats children with rare diseases

Gene therapy treats children with rare diseases | Virology and Bioinformatics from Virology.ca | Scoop.it

A virus derived from HIV can safely fix broken immune systems and correct genetic diseases, suggest two new studies involving children with rare conditions.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Jonathan Kay: Canadian doctors explain why so many of us die badly

Jonathan Kay: Canadian doctors explain why so many of us die badly | Virology and Bioinformatics from Virology.ca | Scoop.it
Often, it's not doctors who are pushing dying patients into aggressive, futile end-of-life medical treatments, but guilt-ridden relatives who can't bear the idea of 'pulling the plug'
more...
No comment yet.
Scooped by Torben Barsballe
Scoop.it!

Characterization of H7N9 influenza A viruses isolated from humans

Characterization of H7N9 influenza A viruses isolated from humans | Virology and Bioinformatics from Virology.ca | Scoop.it

Avian influenza A viruses rarely infect humans; however, when human infection and subsequent human-to-human transmission occurs, worldwide outbreaks (pandemics) can result. The recent sporadic infections of humans in China with a previously unrecognized avian influenza A virus of the H7N9 subtype (A(H7N9)) have caused concern owing to the appreciable case fatality rate associated with these infections (more than 25%), potential instances of human-to-human transmission1, and the lack of pre-existing immunity among humans to viruses of this subtype. Here we characterize two early human A(H7N9) isolates, A/Anhui/1/2013 (H7N9) and A/Shanghai/1/2013 (H7N9); hereafter referred to as Anhui/1 and Shanghai/1, respectively. In mice, Anhui/1 and Shanghai/1 were more pathogenic than a control avian H7N9 virus (A/duck/Gunma/466/2011 (H7N9); Dk/GM466) and a representative pandemic 2009 H1N1 virus (A/California/4/2009 (H1N1pdm09); CA04). Anhui/1, Shanghai/1 and Dk/GM466 replicated well in the nasal turbinates of ferrets. In nonhuman primates, Anhui/1 and Dk/GM466 replicated efficiently in the upper and lower respiratory tracts, whereas the replicative ability of conventional human influenza viruses is typically restricted to the upper respiratory tract of infected primates. By contrast, Anhui/1 did not replicate well in miniature pigs after intranasal inoculation. Critically, Anhui/1 transmitted through respiratory droplets in one of three pairs of ferrets. Glycan arrays showed that Anhui/1, Shanghai/1 and A/Hangzhou/1/2013 (H7N9) (a third human A(H7N9) virus tested in this assay) bind to human virus-type receptors, a property that may be critical for virus transmissibility in ferrets. Anhui/1 was found to be less sensitive in mice to neuraminidase inhibitors than a pandemic H1N1 2009 virus, although both viruses were equally susceptible to an experimental antiviral polymerase inhibitor. The robust replicative ability in mice, ferrets and nonhuman primates and the limited transmissibility in ferrets of Anhui/1 suggest that A(H7N9) viruses have pandemic potential.

more...
No comment yet.
Rescooped by Chris Upton + helpers from Modern Life Science: of computers and men
Scoop.it!

Largest cancer database launched

Largest cancer database launched | Virology and Bioinformatics from Virology.ca | Scoop.it
The world's largest database of cancer patients is being set up in England in an attempt to revolutionise care, Public Health England has announced.

Via Sandrine Palcy
more...
Sandrine Palcy's curator insight, June 14, 2013 8:08 AM

UK at forefront of personalised medicine.

Scooped by burkesquires
Scoop.it!

Towards multiscale modeling of influenza infection

Aided by recent advances in computational power, algorithms, and higher fidelity data, increasingly detailed theoretical models of infection with influenza A virus are being developed. We review single scale models as they describe influenza infection from intracellular to global scales, and, in particular, we consider those models that capture details specific to influenza and can be used to link different scales. We discuss the few multiscale models of influenza infection that have been developed in this emerging field. In addition to discussing modeling approaches, we also survey biological data on influenza infection and transmission that is relevant for constructing influenza infection models. We envision that, in the future, multiscale models that capitalize on technical advances in experimental biology and high performance computing could be used to describe the large spatial scale epidemiology of influenza infection, evolution of the virus, and transmission between hosts more accurately.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales

Past influenza pandemics appear to be characterized by multiple waves of incidence, but the mechanisms that account for this phenomenon remain unclear. We propose a simple epidemic model, which incorporates three factors that might contribute to the generation of multiple waves: (i) schools opening and closing, (ii) temperature changes during the outbreak, and (iii) changes in human behaviour in response to the outbreak. We fit this model to the reported influenza mortality during the 1918 pandemic in 334 UK administrative units and estimate the epidemiological parameters. We then use information criteria to evaluate how well these three factors explain the observed patterns of mortality. Our results indicate that all three factors are important but that behavioural responses had the largest effect. The parameter values that produce the best fit are biologically reasonable and yield epidemiological dynamics that match the observed data well.

 
more...
No comment yet.
Rescooped by Chris Upton + helpers from Synthetic Biology
Scoop.it!

Synthetic Life: Dr Dan Gibson Discusses the Science of Big DNA

Synthetic Life: Dr Dan Gibson Discusses the Science of Big DNA | Virology and Bioinformatics from Virology.ca | Scoop.it

Approaches for Assembling Synthetic, Genome-Sized DNA


Via Integrated DNA Technologies
more...
No comment yet.
Rescooped by Chris Upton + helpers from Synthetic Biology
Scoop.it!

Bioengineers look beyond patents - Nature.com

Bioengineers look beyond patents - Nature.com | Virology and Bioinformatics from Virology.ca | Scoop.it

Last month, DNA2.0 deposited gene sequences encoding three of its fluorescent proteins into an open-access collection of recipes for DNA ‘parts’, molecular building blocks used to engineer organisms to carry out specific functions. The company vows not to pursue its patent rights against anyone using the sequences. Such moves are unusual among larger biotechnology companies, which tend to guard patents fiercely, but for DNA2.0 the choice was strategic.


Via Marko Dolinar
more...
No comment yet.
Scooped by C_Fleis
Scoop.it!

Exosomes mediate the cell-to-cell transmission of IFN-α-induced antiviral activity

Abstract

The cell-to-cell transmission of viral resistance is a potential mechanism for amplifying the interferon-induced antiviral response. In this study, we report that interferon-α (IFN-α) induced the transfer of resistance to hepatitis B virus (HBV) from nonpermissive liver nonparenchymal cells (LNPCs) to permissive hepatocytes via exosomes. Exosomes from IFN-α-treated LNPCs were rich in molecules with antiviral activity. Moreover, exosomes from LNPCs were internalized by hepatocytes, which mediated the intercellular transfer of antiviral molecules. Finally, we found that exosomes also contributed to the antiviral response of IFN-α to mouse hepatitis virus A59 and adenovirus in mice. Thus, we propose an antiviral mechanism of IFN-α activity that involves the induction and intercellular transfer of antiviral molecules via exosomes.

more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Solution to Vaccine Mystery Starts to Crystallize

Solution to Vaccine Mystery Starts to Crystallize | Virology and Bioinformatics from Virology.ca | Scoop.it

More than 80 years ago, manufacturers started spiking vaccines with alum, an additive, termed an adjuvant, that spurs a stronger reaction from the immune system. Yet scientists have struggled to explain exactly how alum, a catch-all term for several types of aluminum-containing adjuvants, does this. Recently, researchers have floated at least three possible mechanisms.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

A Systems Analysis Identifies a Feedforward Inflammatory Circuit Leading to Lethal Influenza Infection

A Systems Analysis Identifies a Feedforward Inflammatory Circuit Leading to Lethal Influenza Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

For acutely lethal influenza infections, the relative pathogenic contributions of direct viral damage to lung epithelium versus dysregulated immunity remain unresolved. Here, we take a top-down systems approach to this question. Multigene transcriptional signatures from infected lungs suggested that elevated activation of inflammatory signaling networks distinguished lethal from sublethal infections. Flow cytometry and gene expression analysis involving isolated cell subpopulations from infected lungs showed that neutrophil influx largely accounted for the predictive transcriptional signature. Automated imaging analysis, together with these gene expression and flow data, identified a chemokine-driven feedforward circuit involving proinflammatory neutrophils potently driven by poorly contained lethal viruses. Consistent with these data, attenuation, but not ablation, of the neutrophil-driven response increased survival without changing viral spread. These findings establish the primacy of damaging innate inflammation in at least some forms of influenza-induced lethality and provide a roadmap for the systematic dissection of infection-associated pathology.

more...
No comment yet.