Tuesday, 19 February 2008

The bioinformatics of the 'flu

What was the most lethal epidemic of infectious disease in modern times? AIDS perhaps? You might think so, but you would be wrong. Between the beginning of the epidemic and the end of 2007, AIDS killed people 25 million; the influenza epidemic of 1918 killed 40 million. This vast figure is also about double the number who died in the First World War, which ended the same year. Furthermore, a high proportion of those deaths were of healthy individuals in the prime of life. Yet most of the time we think of influenza as little more than a very nasty nuisance...

However, there has recently been a renewed interest in past influenza epidemics as a result of the result of the virulent strain of influenza currently sweeping through populations of wild and domestic birds worldwide. The influenza virus is endemic in birds, and strains tend to spread periodically from them to mammalian hosts: pigs as well as humans. Mapping genetic changes in the influenza virus, and how these affect its spread, is an important research area. Richard Goldstein of the National Institute for Medical Research, based in Mill Hill, London, gave a fascinating Monday seminar on this topic yesterday, looking into the past to see how genetic changes could have led to the lethal 1918 epidemic.

Influenza viruses contain two proteins on their spherical surfaces: a neuraminidase and a hemagglutinin. These proteins come in various forms: 16 different hemagglutinins are known, and 9 different neuraminidases. Any influenza virus can be characterised by these variants - for example, the most common type of influenza currently afflicting humans is H3N2, and the feared bird flu H5N1. Recent flu epidemics appear to have been caused by reassortment events, where the genomes of different viral subtypes combine to form an entirely new one that will not be recognised by human immune systems. An epidemic in 1957, for instance, coincided with a shift from influenza H1N1 (which had been circulating since 1918) to H2N2.

Influenza virus hemagglutinin and neuraminidase are both mainly-beta proteins, and their structures are described further on this page of PPS section 5.

So, what happened in, or before, 1918 to cause the epidemic of H1N1 flu? Molecular geneticists, such as Goldstein, study this by reconstructing phylogenetic trees showing the evolutionary distance between viral isolates taken in different places at different times. Yet most of these calculations can only show evolutionary distance, not the direction of change - in the jargon of phylogeny, they produce unrooted, rather than rooted, trees (there is no known "top"). The research was at rather an impasse until postdoc Mario dos Reis (a Birkbeck Ph.D.) noticed that the GC content of viruses infecting humans, but not of those infecting birds, decreased over time. This enabled the group to add an evolutionary "clock" to the phylogenetic tree for each of the influenza virus' 11 genes. This showed that some of the genes had entered the human population at different times, indicating that the variant that caused the 1918 flu had arisen from several recombination events. Interestingly, only one gene (neither H nor N) could have made the jump in 1918; most viral proteins were present in the human population in their 1918 forms well before that year. M1, like some other proteins, appears to have made the shift in 1899.

So, what did happen in 1918? There do appear to have been changes to the H gene then. But it may also be possible that the world population was so debilitated, and susceptible, after four years of war that a variant that had already been around for a few years was, unusually, able to cause such an epidemic...

Monday, 11 February 2008

Function of vFLIP - a protein from the virus associated with Kaposi's sarcoma

Today's Monday seminar was given by Professor Mary Collins from the Division of Infection and Immunity at University College London's medical school. She described some of her studies of the function and mechanism of vFLIP, a protein from the human herpesvirus 8 (HHV8). This is a cancer-causing (oncogenic) virus and is responsible for the AIDS-associated tumour, Kaposi's sarcoma.

While very many people - about 10-15% of blood donors in London, for example - have been exposed to, and have antibodies for, this virus, it only causes problems in people with defective immune systems. In these people, however, it can cause lymphoma or multicentric Castleman's disease as well as Kaposi's sarcoma. This, however, is now - thanks to HIV and AIDS - one of the commonest cancers worldwide, in fact the commonest in some African countries. AIDS-related Kaposi's sarcoma is fairly rapidly fatal if untreated; however, it can now be controlled very well (although not completely cured) with anti-retroviral therapy.

HHV8 is a large (by viral standards!) double-stranded DNA virus. The protein vFLIP is one of a cluster of proteins expressed while the virus is latent. It binds to a protein called i-kappa kinase gamma in virus-infected cells. This causes the kinase to phosphorylate inhibitors of the cytokine NF-kappa B, leading to the release of NF-kappa B from inhibitor complexes and ultimately the degradation of the inhibitors. This leads to a cascade of gene expression that is essential for the prevention of apoptosis; in contrast, knockdown of vFLIP levels by siRNA will lead to induction of apoptosis. vFLIP is therefore implicated in the survival of virally infected cells.

Endothelial cells that have been infected by HHV8 adopt a characteristic "spindle cell" phenotype. Microarrays have shown that the virus induces complex re-programming of gene transcription in these cells, which is likely to induce this dramatic change in their morphology. Future work will elucidate the precise role of the signal transduction cascade induced by vFLIP in this "morphological reprogramming".

There is no structure available for vFLIP, but there are a large number of kinase structures known. From the UniProt database, the closest to i-kappa kinase is the intracellular Ser/Thr protein kinase domain of Mycobacterium tuberculosis PknB (PDB entry 1MRU).

Tuesday, 5 February 2008

Seminar by Prof Armitage, Oxford

This weeks Monday seminar was by Prof Judy Armitage from Oxford (http://www.bioch.ox.ac.uk/aspsite/research/brochure/Armitage/) . Do go to her website as it will help you to see some of the pictures. She was interesting to us as a biologist (microbial physiologist) heading up a Systems Biology centre. Systems Biology is a trendy phrase but has almost as many meanings as there are centres. Systems Biology is really putting biology on a quantitative basis by developing mathematical models that accurately predict experiments. This can be at various scales, whole organisms, individual organs, whole cells or just a particular pathway. Prof Armitage has been studying the photosynthetic bacteria Rhodobacter sphaeroides for many years. It has now become more significant as Craig Ventner has found that a close relation is the most abundant organism in sea water and therefore central to photosynthesis in the sea.
However what Judy is currently studying is the chemotactic response where these bacteria swim towards their food source. In contrast to the well studied E.coli system where there is only one set of proteins, there are 4 operons in R.spheroides. Although in vitro the proteins were able to cross react and phosphorylate, they did not compensate for each other when deleted.
Her group showed by attaching fluorescent proteins (GFP/CFP) etc to the various components that unlike E.coli where the chemotactic proteins were all at the pole of the cell, there were two systems in R.spheroides, one at the pole but the other in the mid cell. One to sense the internal "happiness" of the cell- ie was it well fed and the other to go and find new food sources when it was not. She pointed out the importance of a number of their experimental details. Firstly they add the fluorescent protein in frame with the protein of interest in the genome so as to get natural abundance not overexpression. Secondly they only pay attention to those mutants where the pathway still functions as the fusions can sometimes disrupt the true localisation and give a false result, but when this happens the pathway does not work. The group has also done work on the flagellae that drive the bacteria and using a special fluorescent microscope were able to count the numbers of the subunits that drive the motor- 22 per complex.
Her take home message was that you cannot assume that all things work the same as E.coli!

Saturday, 2 February 2008

Dear Dr. Clare;

Thank you for inviting us to this blog. It should be a interesting experience! Take care, bye!

Best regards,
Dr. Nadia