Sunday, 27 April 2014

porter take 1

Doing science all day and talking about science in this blog can get a bit repetitive. But luckily I have a hobby to rest my mind, which takes the form of homebrewing beer (only on extract at the minute). I dabbled a bit before and am now continuing to dabble after my move to Glasgow. My first 'new' homebrew experience is making a porter-like beer (maybe on the 'robust' side), which in my head was a 'less-smooth' stout. You can read the exact description here. This was actually brewed for a friend of mine's birthday in April..

Below is the recipe I followed: and results.

Virology, science, scicomm and life


Vincent Racaniello posts an intrigueing question over at Virology blog and debate ensures. What are your thoughts? why do some viruses have a segmented genome? measles versus influenza

A recent study published in the lancet looked at what viruses might be causing CNS disease in African malaria-endemic regions not big surprise that mumps virus appeared to be a big cause (also lethal) - no mumps vaccination there. But major result of this paper is that in >2/3s patients we have no idea what caused disease. Unknown viruses anyone?

": For those interested in innate immunity, read this article: " and virus! This paper looked at what RNA sequences were being recognised in measles virus-infected cells. Showed bias towards A/U-rich regions of the L gene mRNA.

PLoS published a nice short look at RSV pathogenesis and potential for vaccine design highlighting many of the issues with RSV regions but also showed where research could lead to, including new vaccines.

GAVI outlined their plans to expand impact of vaccines by 2020

More infographics. Measles infographics. I like these but think asymptomatic cases change it  I wouldlike more complicated infographics..

China and the SARS Epidemic, what was learned in ten years? Applicable to SA and MERS situation  An important history lesson if the Saudi Health Ministry are reading. But then there are also science issues: Why can't we predict evolution of MERS? Poor understanding of virus fitness. What constraints are acting?

'Don’t worry, I’m not contagious' – and other microbiological delusions are discussed in this insightful piece

it's about the little things - new virology blog. I follow the author but can't remember who... Help?  Turns out it was Mike Nicholl. Go read it. It's very good. 

For some reason I got interested n fruit bats and the Niger river in west Africa... Fruit bat annual migrations in west Africa re seasons  What links west Africa? The Niger River of course.

Other science

The Independant reported How a genetic disease was cured in an adult for the first time thi was using CRISPR/Cas9 technology. This was also done using adult MICE and high-powered injections.


The varieties of peer review: by via  . Where do you want to fit in?

Defectivebrayne did a video summary of the last paper about the designer synthetic yeast chromosome: . This is very good and informative and capturesmany of the points that were discussed at that session. 

life in general

Finally made it to Glasgow brewdog. Working my way down the list  - and then went again that week. Some great beers on showcase there.

Wednesday, 16 April 2014

Negatively regulating cell tropism modulates viral pathogenesis

I seem to keep saying this but it's good to have in mind: viruses are obligate intracellular parasites. They infect cells and this is what allows them to replicate and persist (and evolve) in the environment. What cells these viruses infect helps dictate how they infect and importantly, how they cause disease. The process of causing disease is known as pathogenesis and is the subject of this post. Knowing what cells a virus infects - and how they infect the cells - provides an understanding of basic virus biology and may influence the development of new antiviral treatments and vaccine design and implementation. Of course this isn't the only factor influencing viral infection, pathogenesis and transmission but it's a pretty major one and it's one factor that I have articulated interest in during and after my formative PhD years. 
a reconstruction of prototypical alphavirus particle (Sindbis virus)

I have always felt (probably simplistically) that a virus actively chooses what cells to infect. Viruses evolve and adapt to particular host factors that allow it to enter, replicate in and assemble new infectious particles, which carry on the infectious cycle. On the scale of a human body, a virus might have adapted to infect epithelial cells lining your respiratory tract to allow initial infection, it might infect lymphocytes allowing modulation of systemic immunity, which may also provide the virus with access to tissues around the body that can lead to a large boost in replication facilitating virus excretion and transmission. Each one of these steps,in my head, the virus has chosen to infect. But what if a virus chooses not to infect a certain cell type, or at least limit replication. This is something I have not considered before. That was until I read this paper out recently. Not open access sadly:

RNA viruses can hijack vertebrate microRNAs to suppress innate immunity

To recap the paper, which has a particular pop. Sci title, (which I don't particularly like) but it's an interesting enough paper anyway. This group was interested in what stopped their favourite positive-sense RNA virus (North American eastern equine encephalitis virus, or EEEV, an rare infection limited to North America) from replicating in one certain cell type, myeloid dendritic cells. These cells are very important for antiviral immunity and act to coordinate our antiviral response to pathogens. Thus their biology affects protection from infection, disease progression and ultimately survival. They do this by sensing components of viruses or their replication and signalling to other cells that they have found an intruder. This signalling takes the form of an increase in interferon production and likely secretion of pro inflammatory proteins, designed to promote anti pathogen responses following infection. As myeloid dendritic cells pose a significant barrier to infection viruses have evolved multiple strategies to interact with and manipulate this cell type. Many viruses infect this cell type (for one example see this) and from within the cell influence it's behaviour but what EEEV does is a bit different. It simply avoids ever entering these cell types. And how it achieves this was the aim of this paper. 
electron micrograph of EEEV virus particles (red) inside host cells 

What they found was that EEEV harbours sequences that are recognised by myeloid specific miRNAs, in particular miR-142-3p. This miRNA bound to viral genomes and prevented critical translation and subsequent replication and infection. Deletion of the region within the viral genome alleviated this restriction in replication in culture and addition of the region to other RNAs restricted their expression. There is also a mouse model for EEEV pathogenesis and when mice were infected with wild type or miR-142-3p binding region-deleted viruses they noticed a striking difference on infection and pathogenesis. Deletion of miR binding led to a decrease in virulence associated with increased replication in lymph nodes (as you might expect from a virus with little myeloid restriction) and secretion if interferons. 

Now this is cool but it's not all simple. This region is also required for replication in mosquitoes (the vector species for EEEV). This is not thought to be mediated by a miR-142-3p interaction, presumably because it is not present in the insect genome. What is also difficult about this work is that they base their conclusions on whole-sale deletion of the miR-binding region and not targeted nucleotide substitutions, which could rule out any other functions this region might have, for example in RNA secondary structure or protein-RNA interactions. Until these experiments are done I think that the complete role of this region in the EEEV genome will not be cleared up. However, the interaction of miR-142-3p and the virus genome appears solid and with some interesting consequences.

These data show that EEEV contains an RNA sequence within its genome that directly limits its replication in these important cells in order to influence pathogenesis by physically interacting with host miRNAs. And, importantly, the virus doesn't really care - it actually likes it that way. It actively uses this 'negative tropism' to modulate the hosts immune response towards it, favouring its own replication and immune subversion. Uncovering secrets of viruses like this is fascinating and can have an impact on human health. Importantly it may lead to engineered vaccines for viruses, especially EEEV. Imagine an EEEV that replicated in myeloid cells, triggering an antiviral response in infected hosts that would limit disease but produce long-term protection? This work is put in context when you consider than influenza viruses that cannot express their genes in myeloid cells (antigen presenting cells specifically) by engineering of miR-142 into its genome (in the tenOever lab) do not stimulate an antiviral IFN response.  Taken together with this work on EEEV, the myeloid cell/miR-142/pathogen axis looks like an interesting target when considering the link between infection, disease and rational vaccine design. But like any gene product that is involved in lots of aspects of host biology like miR-142 be wary when extrapolating from cell cultures and mice.