Monday, May 26, 2008

Arginase and ageing - rethinking SAM

Age-Related Alteration of Arginase Activity Impacts on Severity of Leishmaniasis
is a very exciting paper, so convincing in fact that it makes me question whether my hypothesis on SAM is of any use at all to explain susceptibility to leishmaniasis. Arginase activity has been shown time and time again to be crucial to parasite proliferation, but I always wondered whether there was some proverbial elephant standing in the room that no-one mentioned. The SAM story was meant to complement and expand the arginase part and I still believe that with its dual role in polyamine synthesis and regulation of gene expression amongst others, SAM might still be shown to play a role in this experimental system.

At first, I thought that by changes in DNA methylation SOCS expression would be altered affecting cell signalling and arginase activity in host macrophages. This may still be the case, but maybe it would be better to focus on the polyamine synthesis aspect at first. If antimony treatment should deplete SAM levels this could be investigated by incubating macrophage cultures with antimony and measure polyamine levels by thin layer chromatography as carried out by Modolell and colleagues.

Friday, May 09, 2008

Letting go - now back to Leishmania

Letting go is hard to do, especially when you have fought tooth and nail to get your point across and went through some crazy times. I recently attended the "God Be in My Head" event at the Dana Centre, where a panel chaired by Colin Blakemore discussed the possibility of so-called "God spots" in the brain, and although epilepsy and schizzophrenia were mentioned as possible links to abstract thinking, creativity and spiritual experience, I was surprised to observe that no-one at the event mentioned mania, which seems to me to lie at the intersection between the two other states of mind. One of the best suggestions of the evening was the idea to analyse the brain activity of problem-solving scientists using functional MRI and to try to compare the results to the brain scans of nuns praying or monks meditating. I like it even though I am getting a bit tired of functional MRI papers, but somehow I don't see that experiment being carried out any time soon, the eureka experience and phenomena such as calculation-induced halucinations are science's dirty little secrets and I doubt whether scientists really are prepared to address these issues.

At any rate, I'm digressing, whilst it is fun to rejoin the scientific debate and to watch my representation of the genetic code climb the "google charts", I have to let go of certain ideas and redirect my focus on my PhD. Consequently, I find myself thinking more and more about Leishmania these days. Given that S-adenosyl methionine (SAM) is involved in a number of different cellular processes possibly affecting the replication of intracellular parasites, how would it be possible to differentiate the effects of the individual processes? The ones I am particularly interested in are polyamine synthesis and DNA methylation. Would it be enough to add radiolabelled SAM to infected cells and to try to see where the marked methyl group might end up? Is there radiolabelled SAM available in which the non-methyl carbon atoms are 14C, making the substance useful in tracking polyamines? Whilst I would try to focus on in vitro experiments at first keeping things as simple as possible, I also wonder what in vivo experiments might look like. What effect might adding or depleting SAM have in vivo? What about methylthioadenosine (MTA), a product of the SAM catabolism that arises after the polyamine synthesis step? How could the effect of SAM derivatives be untangled from possible changes to cytokine production?

Too many questions for me to answer...

Friday, May 02, 2008

Nearly there...

Finally, the "Journal of Theoretical Biology" accepted my manuscript for publication as a letter to the editor. The unedited version of the article can be found ahead of print online at

What a relief. I know it's just one little paper and the impact factor of the journal could be higher, but for some reason this paper is incredibly important to me. I don't know if I have made a huge fool of myself or not, but it's too late anyway. I tried to keep the article as short as possible and did not include any acknowledgements, but of course I would not have been able to persevere in this ridiculous struggle had I not had the support of some incredible people along the way. I don't know whether mRNA-tRNA interaction occurs in a 2-1-2-3 way, but I find the sheer oddness of a language that starts with the middle instead of the beginning of an information unit exciting and cannot get the picture of tRNA-precursor molecules forming aggregates with the second codon base acting as an anchor out of my head. Imagine the message
being translated as "thetaskisnotsomuchtoseewhatnoonehasyetseenbuttothinkwhatnoonehasyetthoughtaboutthatwhicheverybodysees." and finally for the information to "fold" into the beautiful quote: "The task is not so much to see what no one has yet seen but to think what no one has yet thought, about that which everybody sees."

Of course if the interaction between mRNA and tRNA occurred in a 1-2-3-way, the importance of the second base might be explained by a longer interval spent reading the base, so the order would roughly be 1-2-2-3. If the binding of codon and anticodon happened in such a way that all three bases bound simultaneously, then the base in the middle might spend the longest time bound to its cognate because the bases 5' and 3' of it would act as a sort of buffer (like velcro, the middle bit usually the hardest to get off first).

With possible closure on the rearrangement of the genetic code in sight, I wonder if somebody else might pick up on the methionine story. Perhaps one group might try to engineer an organism that uses an initiator-tRNA charged with isoleucine, valine, threonine or homocysteine instead of methionine and report on what the resulting phenotype might be...

But all of this has merely been a side project, the biggest reward for me would be if my initial hypothesis about the involvement of S-adenosylmethionine in determining resistance or susceptibility in experimental leishmaniasis, might prove to be useful.