Freedom of speech within science

Not so much research but a rant. As you may have heard the chief advisor to the government about drugs policy Prof Nutt was told to resign recently after he gave a lecture stating his views on cannabis classification in the UK and how the government (former Home Secretary Jackie Smith) did not listen to their advice on the matter and increased its classification and punishment for taking it. I do not care about the drug’s classification to be honest. I don’t take it and never have but the current Home Secretary (Alan Johnson, tipped to be future Labour leader, among a couple of others) has had a disagreement with the scientist and dismissed him after he gave a lecture stating his opinion. The reason given was he had crossed the boundary between science and politics. What? A scientist who is an unpaid advisor states his opinion based on evidence then states the government didn’t listen to them when deciding policy is crossing the line?! It sounds like he was starting a debate, using his freedom of speech to discuss topics. The government has decided no, if you don’t agree with us and you are helping us then sod off. Whether you agree with Prof Nutt or not I don’t think it matters. What matters is whether advisors are allowed to criticise the government’s policy when they are not listened to. They believe not. Alan Johnson said: ‘he was not dismissed because of the work of the council but because of his failure to recognise that... his role is to advise rather than criticise’. My PM Gordon Brown said: ‘Prof Nutt had repeatedly undermined Labour's drug message.’ I think it is ridiculous to suggest a scientist cannot talk about such things in public and suggests to me the government is being hypersensitive over these matters. Perhaps because they cannot handle anymore bad press and people going against them. After all the chances of them winning the next election are slim to none.

So far Lord Drayson (a businessman) who determines science policy in the government’s Business department and coordinates with the research councils was strongly against this when he first heard it. Lord Winston FRS, a respected scientist in the public eye and Labour peer, is against the dismissal and Prof John Beddington FRS (who recently recovered an honorary degree from York University in the Summer 2009 graduation ceremony) has spoken the most sense on the matter (http://news.bbc.co.uk/1/hi/sci/tech/8340318.stm). He is the chief advisor to the government on all things sciencey. He points out most scientific committees do not have a problem with the government. This is reassuring but and the send of an email the Home Secretary (with no background what so ever in science) has dismissed an advisor and caused two to quit in sympathy because they don’t think they can work with a government that a) doesn’t listen to them and b) forces out the head of the committee for no good reason. I think this is unacceptable from the government hence I have written to the Home Secretary and feel I should email my local MP as well. Hopefully my next post will contain more science and less ranting. It’s being planned, just need to get some pretty photos.

Ig Nobels 2009

For a few years now that I have been following the Ig Nobels as they are awarded. To continue the tradition, here is a post with the list of this year's winners:

VETERINARY MEDICINE PRIZE
Catherine Douglas and Peter Rowlinson of Newcastle University, Newcastle-Upon-Tyne, UK, for showing that cows who have names give more milk than cows that are nameless.
"Exploring Stock Managers' Perceptions of the Human-Animal Relationship on Dairy Farms and an Association with Milk Production," Catherine Bertenshaw [Douglas] and Peter Rowlinson, Anthrozoos, vol. 22, no. 1, March 2009, pp. 59-69.

PEACE PRIZE
Stephan Bolliger, Steffen Ross, Lars Oesterhelweg, Michael Thali and Beat Kneubuehl of the University of Bern, Switzerland, for determining — by experiment — whether it is better to be smashed over the head with a full bottle of beer or with an empty bottle.
"Are Full or Empty Beer Bottles Sturdier and Does Their Fracture-Threshold Suffice to Break the Human Skull?" Stephan A. Bolliger, Steffen Ross, Lars Oesterhelweg, Michael J. Thali and Beat P. Kneubuehl, Journal of Forensic and Legal Medicine, vol. 16, no. 3, April 2009, pp. 138-42.

ECONOMICS PRIZE
The directors, executives, and auditors of four Icelandic banks — Kaupthing Bank, Landsbanki, Glitnir Bank, and Central Bank of Iceland — for demonstrating that tiny banks can be rapidly transformed into huge banks, and vice versa — and for demonstrating that similar things can be done to an entire national economy.

CHEMISTRY PRIZE
Javier Morales, Miguel Apátiga, and Victor M. Castaño of Universidad Nacional Autónoma de México, for creating diamonds from liquid — specifically from tequila.
"Growth of Diamond Films from Tequila," Javier Morales, Miguel Apatiga and Victor M. Castano, 2008, arXiv:0806.1485.

MEDICINE PRIZE
Donald L. Unger, of Thousand Oaks, California, USA, for investigating a possible cause of arthritis of the fingers, by diligently cracking the knuckles of his left hand — but never cracking the knuckles of his right hand — every day for more than sixty (60) years.
"Does Knuckle Cracking Lead to Arthritis of the Fingers?", Donald L. Unger, Arthritis and Rheumatism, vol. 41, no. 5, 1998, pp. 949-50.

PHYSICS PRIZE
Katherine K. Whitcome of the University of Cincinnati, USA, Daniel E. Lieberman of Harvard University, USA, and Liza J. Shapiro of the University of Texas, USA, for analytically determining why pregnant women don't tip over.
"Fetal Load and the Evolution of Lumbar Lordosis in Bipedal Hominins," Katherine K. Whitcome, Liza J. Shapiro & Daniel E. Lieberman, Nature, vol. 450, 1075-1078 (December 13, 2007). DOI:10.1038/nature06342.

LITERATURE PRIZE
Ireland's police service (An Garda Siochana), for writing and presenting more than fifty traffic tickets to the most frequent driving offender in the country — Prawo Jazdy — whose name in Polish means "Driving License".

PUBLIC HEALTH PRIZE
Elena N. Bodnar, Raphael C. Lee, and Sandra Marijan of Chicago, Illinois, USA, for inventing a brassiere that, in an emergency, can be quickly converted into a pair of protective face masks, one for the brassiere wearer and one to be given to some needy bystander.
U.S. patent # 7255627, granted August 14, 2007 for a “Garment Device Convertible to One or More Facemasks.”

MATHEMATICS PRIZE
Gideon Gono, governor of Zimbabwe’s Reserve Bank, for giving people a simple, everyday way to cope with a wide range of numbers — from very small to very big — by having his bank print bank notes with denominations ranging from one cent ($.01) to one hundred trillion dollars ($100,000,000,000,000).
Zimbabwe's Casino Economy — Extraordinary Measures for Extraordinary Challenges, Gideon Gono, ZPH Publishers, Harare, 2008, ISBN 978-079-743-679-4.

BIOLOGY PRIZE:
Fumiaki Taguchi, Song Guofu, and Zhang Guanglei of Kitasato University Graduate School of Medical Sciences in Sagamihara, Japan, for demonstrating that kitchen refuse can be reduced more than 90% in mass by using bacteria extracted from the feces of giant pandas.
"Microbial Treatment of Kitchen Refuse With Enzyme-Producing Thermophilic Bacteria From Giant Panda Feces," Fumiaki Taguchia, Song Guofua, and Zhang Guanglei, Seibutsu-kogaku Kaishi, vol. 79, no 12, 2001, pp. 463-9. [and abstracted in Journal of Bioscience and Bioengineering, vol. 92, no. 6, 2001, p. 602.]

Looking for some science on swine flu

As a medical association in Spain has recently communicated to the press, more than anything there seems to be an epidemic of fear going on. As I am currently living in Portugal, I do not know what the situation is in other countries, but I can tell you how the situation is here. Every news bulletin starts with more news about the flu, even though no one has died here yet. It then finishes with a previously recorded warning on how one should wash hands frequently and keep 1m away from other people while talking to them, quite an ordeal in a country where the common greeting is a couple of kisses in the cheek. In addition, we have ambulances going around with the paramedics dressed as in the photo, right out of films like ‘Outbreak’. Now, most people seem to assume that because I have just graduated with a Biology degree that I should know everything there is to know about the current flu. Besides the generic question ‘So, what do you think about this flu thing?’, I have had some more specific questions, from ‘I heard that it is impossible for this combination of genes to happen in nature, surely this must have been created by evil scientists with corporative interests?’ to ‘This virus is called H1N1, the 1918 pandemic virus was also H1N1, are we all going to die of Spanish flu?’. I try to explain people that at uni we are taught how to get informed about things, rather than becoming specialist on every single biological problems; and that frankly I am so fed up of hearing about this flu that I couldn’t be bothered to look it up. However, I think the hysteria might be affecting me, probably because I’ve just read the book Blindness (if you have read it/watched the film you will know why). So I decided to interrupt my holidays-away-from-science to read a bit about this topic, and thought I would tell you some of my findings.

My first port of call was the website of the World Health Organisation, usually a reliable source for information. I was pleasantly surprised by the lack of over-dramatic information. There is of course a whole section dedicated to this flu, right in the home page, but the answers given in the FAQs seem quite sensible. It tells us that 2009 A(H1N1) is spread as the normal flu, and that the current worries as based on the fact that being a virus which never circulated in humans before, there is no, or very little, immunity. In addition, as stated in their website, the virus is spreading fast in young people (10-45), from a majority of mild cases to some serious illnesses, the majority of which in patients with underlying conditions. The recommendations of the WHO are to take pain killers and drink loads of fluids if you have the flu. And only contact the medical services if you have serious symptoms like shortness of breath, or if the fever lasts for longer than 3 days. Quite unlike what recently happened in Portugal. When a man who had travelled to Britain was diagnosed with this flu, he saw his house invaded by doctors who quickly took him away to a hospital and confined the whole family to their house. Without telling them what to do or when they could leave.

Anyway, I then thought it would be a good idea to read some information from journals, a bit more scientific and hopefully less dramatic source of news. However, as you know, I am currently unable to access most papers, as I am in between universities and am yet to be provided with a username in my new institution. So what follows is based on a couple of papers I could access, and is by no means comprehensive.

As an introduction, some information from the Virology handouts we were given last October. Influenza viruses are RNA viruses that have a segmented genome (8 segments/genome). The glycoprotein spikes, haemagglutinin (HA) and neuraminidase (NA) are important in the entrance of the virus in the host cells. There are 15 known HA and 9 NA serotypes, and their combination provides the name that we see for the viruses such as H1N1. Birds and pigs are important reservoirs for genetic and antigenically diversity and reassortment in these viruses. In particular pigs, as their cells can be infected by both avian and human influenza viruses, making them nice ‘mixing pots’.

In July this year Garten et al., published a paper in Science in which they characterised the 2009 A(H1N1) virus both antigenically and genetically. They start the paper by giving a small introduction on the influenza pandemics of the last century, and how we got from those to the current 2009 A(H1N1). Then it goes on to characterise the actual viruses. The closest ancestral gene for each of the eight segments seems to have a swine origin, although having originally come from avians and sometimes humans in different occasions. This is quite interesting, as swine influenza viruses had not, until now, caused much disease or been incredibly good at human-human transmission. As the authors point out, this virus probably had been circulating for a while in pigs, unnoticed due to lack of monitoring.

Analysis of the virus genome showed that none of the molecular signatures of increased transmissibility or virulence of A(H1N1) viruses can be found in this strain, and that functionally important receptor binding sites on HA do not differ from classic swine influenza viruses. No markers were also found that indicate adaptation to the human host or features of previous pandemic virus. The main important difference seems to be a genetic marker for resistance to adamantine antivirals, but the virus still seems to be sensitive to the other type of antivirals, the neuraminidase inhibitors. So, this study concludes, we must be worried about this virus firstly because we don’t really know what makes it good at replicating in humans, and secondly because it has a genetic composition not seen before, so we don’t really know what to expect.

I then went on to read a couple of papers regarding studies done in mammal models such as ferrets (apparently classic models for influenza studies) and mice.

The first study was published in Science also in July, by Maines et al. This post is becoming quite long already, so I’ll just summarise their results (based on 3 independently isolated 2009 A(H1N1) viruses as compared with a seasonal influenza strain). They basically inoculated 106 p.f.u in ferrets and monitored different indicators such as body weight, viral titres, direct and indirect transmissibility, etc. The main conclusion from the study was that 2009 A(H1N1) caused higher morbidity (weight loss, etc, depending on which virus isolate), showed, unlike seasonal flu, high viral titres in the lower respiratory tract or the intestine, but that it was less efficient at indirect transmission (putting healthy ferrets in cages near to inoculated animals).


The second animal study I looked at was published online by Nature, in what they call a ‘near final version’. They also used virus isolated from infected humans, though not all of which were the same as in the Science paper. They studied the effect of these viruses in mice, macaques, ferrets and pigs, though not all of the virus isolates seem to have been used in all of the experiments. They also looked at more indicators, such as pro-inflammatory cytokines, lung pathology, etc. In ferrets the results were similar to those of the Science paper, except that this time indirect transmission was successful. In mice and macaques, the 2009 A(H1N1) virus seems to be worse than the seasonal virus (at least one of the isolates that they seem to mostly use throughout, CA04) although according with which criteria varies with the model. The inoculated pigs were asymptomatic, explaining why the virus had not been noticed before in this animal.

So, what are the conclusions I could get, overall, from these three studies? Overall it seems that the 2009 A(H1N1) virus is worse than the seasonal influenza viruses in mammalian models. However, how much worse is probably hard to say. I am not familiar at all with viral studies, so it is hard for me to critically analyse these studies, but it seems to me that in most cases the n numbers were quite small (n=3 in some cases in the Nature study), but this is perhaps not surprising, as they must have been quite quick studies, considering the current need to understand this new virus. And, as it is probably the case in most animal studies in general, I reckon the doses used were probably much higher than what humans would be exposed to in the real world. In addition, there is always the question on how well do these animal models really reflect what happens in humans.

In any case, it seems that so far these studies indicate that 2009 A(H1N1) is, in these models, worse than seasonal flu. Whether it is as bad as some of the pandemics that have been affecting us in the last 100 years it is unknown. The other worry is of course that the virus might evolve into something much more dangerous. Though all the virus isolates obtained so far tend to be quite similar, 5 minor genome variants have already been detected. Restricting the spread of the virus, even if it is not so bad right now, might be a good way of preventing it from acquiring any more deadly features. Whether this data justifies the measures being taken by most government, that is really, as PHD comics puts it so well, beyong the scope of my area of study. I will leave that to those who study the spread of pandemics and know of population health. I think we have had enough speculation for one disease.

Garten, R., Davis, C., Russell, C., Shu, B., Lindstrom, S., Balish, A., Sessions, W., Xu, X., Skepner, E., Deyde, V., Okomo-Adhiambo, M., Gubareva, L., Barnes, J., Smith, C., Emery, S., Hillman, M., Rivailler, P., Smagala, J., de Graaf, M., Burke, D., Fouchier, R., Pappas, C., Alpuche-Aranda, C., Lopez-Gatell, H., Olivera, H., Lopez, I., Myers, C., Faix, D., Blair, P., Yu, C., Keene, K., Dotson, P., Boxrud, D., Sambol, A., Abid, S., St. George, K., Bannerman, T., Moore, A., Stringer, D., Blevins, P., Demmler-Harrison, G., Ginsberg, M., Kriner, P., Waterman, S., Smole, S., Guevara, H., Belongia, E., Clark, P., Beatrice, S., Donis, R., Katz, J., Finelli, L., Bridges, C., Shaw, M., Jernigan, D., Uyeki, T., Smith, D., Klimov, A., & Cox, N. (2009). Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans Science, 325 (5937), 197-201 DOI: 10.1126/science.1176225

Maines TR, Jayaraman A, Belser JA, Wadford DA, Pappas C, Zeng H, Gustin KM, Pearce MB, Viswanathan K, Shriver ZH, Raman R, Cox NJ, Sasisekharan R, Katz JM, & Tumpey TM (2009). Transmission and pathogenesis of swine-origin 2009 A(H1N1) influenza viruses in ferrets and mice. Science (New York, N.Y.), 325 (5939), 484-7 PMID: 19574347

Itoh, Y., Shinya, K., Kiso, M., Watanabe, T., Sakoda, Y., Hatta, M., Muramoto, Y., Tamura, D., Sakai-Tagawa, Y., Noda, T., Sakabe, S., Imai, M., Hatta, Y., Watanabe, S., Li, C., Yamada, S., Fujii, K., Murakami, S., Imai, H., Kakugawa, S., Ito, M., Takano, R., Iwatsuki-Horimoto, K., Shimojima, M., Horimoto, T., Goto, H., Takahashi, K., Makino, A., Ishigaki, H., Nakayama, M., Okamatsu, M., Takahashi, K., Warshauer, D., Shult, P., Saito, R., Suzuki, H., Furuta, Y., Yamashita, M., Mitamura, K., Nakano, K., Nakamura, M., Brockman-Schneider, R., Mitamura, H., Yamazaki, M., Sugaya, N., Suresh, M., Ozawa, M., Neumann, G., Gern, J., Kida, H., Ogasawara, K., & Kawaoka, Y. (2009). In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses Nature DOI: 10.1038/nature08260

Investigating the Smallest Bacterial Genome

During the first two terms of my final year at university I took on a dry project based on bacterial genetics. In retrospect this was quite a cheap move since it avoids so many of the problems involved in normal lab work, but in my defence it was the project that interested me most and I really wanted some computing experience before making PhD applications. My work was based on bacterial endosymbionts of insects, which have been of recent interest due to their extremely small genomes. Bacteria in these symbiotic relationships are given a protected, nutrient-rich environment and in return they allow insects to survive on unbalanced diets by synthesising scarce biomolecules.

Primary endosymbiotic bacteria live their entire lives inside insects and are vertically transmitted from generation to generation, a process that leads to coevolution between the bacteria and the insect. One of the results of this coevolution was major changes to the original bacterial genome, which contained many genes that are essential for free-living bacteria but are unnecessary for life within an insect. Consequently, common features of endosymbiotic genomes compared to those of free-living bacteria are severe gene loss, genome compaction and skewing of GC content.

Electron micrograph showing bacteriocytes taken from P. venusta

1 – Bacteriocyte; 2 – C. ruddii; 3 – Unidentified electron-dense mass

My project focused on Carsonella ruddii, the only bacterial endosymbiont of the psyllid, Pachypsylla venusta. It was hailed as the smallest bacterial genome chracterised when it was sequenced in 2006 and still holds that record. Its genome contains only 182 ORFs, less than 3% intergenic DNA and has a GC content of 16.5%. The bacteria appears to be provided with many nutrients by its host and its metabolism has been reduced to a few pathways: ATP synthesis, a section of the pentose phosphate pathway and biosynthesis of certain amino acids.

The early stages of my project involved a reannotation of the C. ruddii genome followed by a sequence-based functional analysis of its metabolic enzymes. Using the enzymes deemed functional in this analysis I built an updated model of the C. ruddii metabolism which could be divided into six pathways involved in amino acid biosynthesis, five of which were incomplete. The only fully intact pathway led to the production of isoleucine and valine. These are both essential amino acids for insects and are severely under-represented in the adult psyllid diet.

Four of the incomplete amino acid pathways were missing only one reaction and the conservation of the rest of each of the pathways suggested that they might still be functional in C. ruddii. The ‘missing’ reactions might occur spontaneously under some conditions or could be catalysed by unidentified enzymes. For three of these four missing reactions I found an example in the literature of a different bacterial endosymbiont which had lost that reaction but had retained the rest of the pathway. This seemed to suggest that the enzymes catalysing these reactions might be expendable and subject to loss during genome reduction in endosymbionts. Based on this and some other evidence from similar situations in endosymbionts I predicted that these pathways are probably functional in C. ruddii and that its main role symbiotic role is to provide the psyllid with essential amino acids.

The fourth of these incomplete pathways was the most interesting because I was unable to locate another endosymbiont which was missing the same reaction. The reaction was catalysed by the product of a gene, AS, which was present on the C. ruddii genome but which I had labelled as a pseudogene during functional analysis. Although it’s difficult to conclusively say that an enzyme is inactive solely by sequence analysis, multiple alignments showed that this copy of AS was extensively degraded and was missing both of its key catalytic residues as well as its substrate binding residues. However, later in the project when I was scanning an EST set taken from the insect host of C. ruddii I located another copy of AS which also had bacterial origin but which was not present on the C. ruddii genome. Sequence analysis showed that this version of AS seemed to be active and could potentially fill the gap in the pathway.

Where did this copy of AS originate from? It aligned well with the version of AS from P. aeruginosa and appeared to have a bacterial origin but was not found on the C. ruddii genome or the psyllid mitochondrial genome, both of which have been sequenced. Several lines of evidence ruled out the presence of a second bacterial endosymbiont in this symbiosis and since no plasmids had been reported during DNA sequencing of C. ruddii the source of this sequence appeared to be the nuclear genome of P. venusta itself. The presence of this bacterial sequence in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This would be one explanation for the fact that C. ruddii has only 182 ORFs, which is significantly lower than the predicted minimal bacterial genome. However, it is also possible that C. ruddii uses mitochondrial proteins to survive and so LGT is not the only explanation for the low ORF count.

This was my favourite line of investigation during my project but the symbiosis between C. ruddii and P. venusta had many more interesting features that I read about over the year. One of the questions I got in my viva was whether C. ruddii should be labelled as a bacterium or an organelle. I think this question is only really important when considering a minimal bacterial genome and if C. ruddii does turn out to be importing essential proteins from elsewhere then I think that the label organelle is definitely more appropriate. However, the definition of an organelle doesn't seem to be well-established and so whether or not C. ruddii really does have the smallest bacterial genome is a matter of opinion.


Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, & Hattori M (2006). The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science (New York, N.Y.), 314 (5797) PMID: 17038615

Gil, R., Silva, F., Pereto, J., & Moya, A. (2004). Determination of the Core of a Minimal Bacterial Gene Set Microbiology and Molecular Biology Reviews, 68 (3), 518-537 DOI: 10.1128/MMBR.68.3.518-537.2004

Glass, J. (2006). Essential genes of a minimal bacterium Proceedings of the National Academy of Sciences, 103 (2), 425-430 DOI: 10.1073/pnas.0510013103

Thao, M., Moran, N., Abbot, P., Brennan, E., Burckhardt, D., & Baumann, P. (2000). Cospeciation of Psyllids and Their Primary Prokaryotic Endosymbionts Applied and Environmental Microbiology, 66 (7), 2898-2905 DOI: 10.1128/AEM.66.7.2898-2905.2000

Non-B DNA structures and disease

People seem to have started contributing actively to the blog again so I thought it was my turn to try again. And this is an achievement, as facing any science, in particular anything written by me about it, would have been impossible a month ago.

I decided to keep things simple for this one and just give a short introduction on the theme of non-B DNA structures and how they influence disease, the topic of my open essay.

When we think about DNA, we think about its B-DNA structure, the one that Watson and Crick described in that famous Nature paper more than 50 years ago, i.e. a right-handed double helix, 20Å diameter, in which the base pairs are almost perpendicular to the axis of the helix, 10.5bps per turn. Although most DNA will be in this structure, it can also form other structures, the so called non-B DNA structures. Some of these are shown in the figure. These alternative structures have a few common characteristics: firstly, whether or not a structure is formed, and which specific structure, seems to be sequence dependent, as it often involves formation of new pairings of bases. Secondly, most of these structures are in higher energetic state than normal B-DNA, for example, because they require the separation and reformation of hydrogen bonds. Overall, therefore, DNA with a favourable sequence tends to remain in its B-DNA form, requiring events such as DNA replication, transcription or protein binding to be transiently converted to these unusual structures. Sequences with propensity to form unusual structures are quite common in the human genome, and it seems that in some cases they are necessary for the normal functioning of the cell. However, they have also been implicated in disease, and this is what I’ll be focusing till the end of this post.

There is a considerable list of diseases thought to involve, as part of their pathology, the formation of non-B DNA structures, but the mechanisms by which this is though to happen can vary. For example, certain sequences/structures have been thought to cause genomic instability, e.g. by causing chromosomal rearrangements due to the propensity of these structures to promote double strand breaks. Another interesting form of genomic instability associated with these unusual structures is repeat expansion, implicated in motor diseases such as Huntington’s disease. Non-B DNA structures, namely Z-DNA, have also been associated with viral infections.

Now, there isn’t really enough space here to talk about everything, so I’m going to give one examples of a situation in which a non-B DNA structure is though to be involved in disease. Friedreich ataxia (FRDA) is a disease caused by the expansion of GAA•TTC tracts in intron 1 of a gene encoding the protein frataxin, essential for mitochondrial function. In this disease, repeat expansion is associated with loss of protein expression. One of the current models by which frataxin production is thought to be reduced in expanded GAA•TTC repeats is based on their ability to form triplexes (an alternative model suggests that epigenetic changes may also be important). Duplex opening within the repeated region, due to the passage of RNA polymerase, is thought to allow one of the separated single strands to form Hoogsteen hydrogen bonds with the purine strand of a B-DNA duplex within the same repeated sequence. This leads to the formation of a 3-stranded helix. Its formation on the non-template GAA strand in frataxin probably interferes with RNA polymerase progression. The free template strand is then thought to base pair with the newly synthesised RNA transcript, forming stable RNA/DNA dimers and preventing further transcription.

Now, this is only a model, for a specific type of structure within the context of a specific disease. And although different sequences have been shown to form these unusual structures, and these structures to be somehow associated with specific diseases, to neatly demonstrate how exactly one influences the other seems to be quite hard. This is particularly difficult because different groups often use different model organisms or protocols, leading to sometimes contradictory results. Overall, although I liked writing about this topic, since I had never considered how the structure of DNA could have an impact on disease, I got the feeling that a lot of work still needs to be done before convincing evidence is given for how exactly these structures impact on our wellbeing, and what sort of therapeutics can be developed from this knowledge.

Red, GAA repeat strand; blue, GTT complementary strand; orange, RNA transcript; yellow, RNA polymerase. 1, Intramolecular triplex; 2, Stalled RNA polymerase; 3, DNA/RNA hybrid

Hebert, M. (2008). Targeting the gene in Friedreich ataxia Biochimie, 90 (8), 1131-1139 DOI: 10.1016/j.biochi.2007.12.005

Bacolla, A. (2004). Non-B DNA Conformations, Genomic Rearrangements, and Human Disease Journal of Biological Chemistry, 279 (46), 47411-47414 DOI: 10.1074/jbc.R400028200

WELLS, R. (2007). Non-B DNA conformations, mutagenesis and disease Trends in Biochemical Sciences, 32 (6), 271-278 DOI: 10.1016/j.tibs.2007.04.003

Wang, G., & Vasquez, K. (2009). Models for chromosomal replication-independent non-B DNA structure-induced genetic instability Molecular Carcinogenesis, 48 (4), 286-298 DOI: 10.1002/mc.20508