Why is the sequencing of the potato genome such big news?

The genome sequence of the humble potato was published in Nature last week (Nature 475, 189–195 (14 July 2011) and the story was taken up by the world’s media. As ever, hyperbole ruled, with claims that the new genome information would solve the problem of serious diseases of the crop and prevent starvation in the developing world. But given the fact that next generation sequencing technologies mean that whole genome sequencing is now both cheap and quick, why was this particular genome paper afforded the accolade of a place in Nature? Part of the answer is undoubtedly the ‘newsworthy’ nature of the work. Potato is the world’s fouth most important food crop and is especially important in the developing world. But there are two particular parts of the science presented in the paper that represent genuine breakthroughs.

The first is related to the difficulty of sequencing the genome. Like many of our crops potato is polyploid – meaning it has more than two copies of each chromosome – and is highly heterozygous with considerable variation between the same gene present on each of the 4 copies of each chromosome. This is a result of the fact that commercial tetraploid potato varieties are infertile and are propagated exclusively clonally through the tubers or stem cuttings. Without the homologous recombination that occurs between chromosomes during sexual reproduction, mutations in an individual copy of a gene are not redistributed to the other copies, permitting substantial differences between the four gene copies to accumulate. For technical reasons, this makes it much harder to reassemble the genome from the short fragment sequences that are obtained using current sequencing methods. The international consortium behind the potato genome sequencing solved this problem by creating an artificial ‘double monoploid’ clone (called ‘DM’) in which there were only two copies of each chromosome and more importantly, each copy was identical. This allowed them to completely sequence this simplified genome which then formed a framework for comparison and assembly of a more complex diploid genome (from a variety called ‘RH’ which closely resembles varieties that we consume).

The second breakthrough was the comparison of the DM and RH genomes revealed possible explanations for two major problems of potato: inbreeding depression and susceptibility to disease. Inbreeding depression in the phenomenon whereby a lack of genetic diversity in a population leads to reduced fitness of individuals. Although there is wide genetic diversity amongst the many thousands of species in South America, only a limited number of species were introduced from Europe and these formed the genetic base from which all modern farmed potatoes were derived.  Inbreeding depression is apparent in the two sequenced varieties: DM is much less vigourous than the RH variety. By examining the sequences, the consortium were able to show that there was a greater prevalence of genome mutations that disable gene function in the DM variety suggesting a possible reason for the reduced vigour. The sequencing also revealed a possible explanation for the susceptibility of modern potato to devastating pests such as  potato cyst nematode and diseases such as potato blight. More than 800 disease resistance genes were identified in the sequenced genome and importantly, many appeared to be broken due to mutation. While a second potato famine is unlikely to afflict the modern world, blight still is a cause of major losses of the crop every year and the genome sequencing now provides a possible route to a genetic fix.

Breeders create wheat ‘immune’ to a super-blight threatening world's crops

Scientists from the Mexico-based International Maize and Wheat Improvement Center (CIMMYT) will announce next week that they have developed new varieties of wheat that are resistant to UG99, a virulent new form of black stem rust that is spreading rapidly from East Africa and threatening the world’s wheat supply. The research will be presented at a ‘technical workshop’ of the Borlaug Global Rust Initiative, an international consortium to tackle the threat of new crop pathogens set up in 2005 by Norman Borlaug, the father of the green revolution. Borlaug had already taken on stem rust in the past, succeeding in breeding high-yielding, rust-resistant wheat in the 1950s and 1960s, after the pathogen had claimed 40 percent of the wheat crop in the US and Canada. It is estimated that 90% of the world’s wheat now uses the Sr31 gene introduced by Borlaug to confer resistance to stem rust and is now susceptible to UG99, the new race of Puccinia graminis tritici, the fungus responsible for black stem rust. First identified in Uganda, UG99 spores are rapidly dispersed in the wind and, according to David Hodson of the Global Cereal Rust Monitoring System at the Food and Agriculture Organization of the United Nations (FAO), “Future spread of these variants outside of Africa is inevitable". The new CIMMYT varieties are based on the introduction of several ‘minor’ resistance genes into CIMMYT’s wheat stocks, an outcome of a breeding experiment on a grand scale involving about 2 million wheat plants grown in field sites in Mexico and Kenya. The hard graft of the plant breeding done, Ravi Singh who led the CIMMYT research is now calling for political support for the introduction of the new varieties: “We need to see national governments making the investments in seed systems development, including seed production and distribution. In many areas there will need to be support and leadership from wealthy countries and international institutions to carry these innovations into farmers' fields."

BIOEFFECT EGF serum: a scientific revolution that only benefits its makers

I have steered away from poking at the cosmetics industry in this blog; it is simply too obvious, a sitting duck of marketing flim-flam atop nonsensical pseudoscience. But the latest skincare 'revolution' that has been sweeping the beauty world deserves a comment. It comes from Sif Cosmetics based in Iceland and is called BIOEFFECT EGF serum. The media is awash with the news of this miracle cream whose bioactive component is 'grown inside bio-engineered barley plants that thrive in bacteria-free ­volcanic ash' www.dailymail.co.uk. And there is plenty of chatter on the beauty blogs, not all of it as gushing as you might imagine (see www.juliegabriel.com)

The key ingredient in the magical cream is EGF or Epidermal Growth Factor. EGF is one of many proteins in our bodies that tells cells when to divide by binding to a receptor on their surface and triggering an internal signalling pathway. Human EGF has been used in a number of skin creams and it is claimed to improve your skin  / prevent ageing by speeding up the rate at which skin cells are replaced. As it is impossible to go around extracting EGF from 'donor' humans just so that other richer, vainer humans can spread it on their faces, EGF for face creams has to be produced in genetically modified organisms. Usually these are bacteria, yeast, or animal cell cultures engineered to express the human gene that encodes the EGF protein. The EGF protein is then extracted from these GM organisms or cells, purified and added to the usual concoction of glycerine and water to make a face cream.

The BIOEFFECT serum is different in that the EGF is produced in genetically modified barley plants. I can just about see why people might be more comfortable smearing a protein on their face that has been isolated from barley than bacteria, but is there really any benefit to making the protein in plants? Not to you there isn't. The protein is pretty much exactly the same whichever organism it is produced in and if it is properly isolated, then background contaminants are not an issue. In fact, almost all the benefits are in favour of the company making the product, Sif Cosmetics and their parent biotechnology company ORF genetics. The latter website helpfully lists all these benefits.

Most of them relate to the purity of the EGF. From the consumer point of view, pure ingredients are obviously best, but there is relatively little evidence that EGF from barley is any purer than that from bacteria or animal cells. However, it is almost certainly cheaper to produce pure EGF from barley than from bacteria. When any recombinant protein is produced, either for pharmaceutical or cosmetic purposes, it has to be separated from all the other proteins and molecules in the host organism. Usually this is done by altering the gene sequence slightly so that the recombinant protein is made with what is known as an 'affinity tag' at one end - a string of extra amino acids that has a high affinity for another molecule that in turn can be immobilised onto a solid chromatography matrix. This allows the recombinant protein to be purified by affinity chromatography. In the ORF genetics system, the recombinant EGF protein is expressed only in the seeds of the genetically modified barley plants. In comparison to bacteria or animal cells, the seed endosperm is a very simple system with only a few storage proteins present. This means that the protein profile (the number of different types of protein present) is very simple and cheaper, less sophisticated protein fractionation techniques can be used to isolate the EGF protein.

ORF genetics also claims that their EGF preparation from barley has lower endotoxin content (nonsense: endotoxins are small metabolites easily separated from proteins in all protein purification approaches), lists 'lower endoprotease activity' as an advantage (this just means that the recombinant protein is less likely to be degraded by host protein-digesting enzymes making it easier for ORF genetics to recover more intact recombinant protein) and says that there is no risk of transmission of 'infective agents' (ie disease causing bacteria or viruses). This last one is probably true, but rather overlooks other known dangers of plant materials such as allergenicity and the presence of bacteria such as Bacillus cereus that cause food poisoning (the latter is well known in connection with rice, but in fact is present in most cereals including barley!).

The other benefit that the ORF genetics website fails to mention is that it is substantially cheaper in general to produce recombinant proteins in plants than in bacteria or animal cell cultures. This is because the latter are grown in large vats known as chemostats which are expensive to run, requiring a constant supply of nutrient solution to support the growth of the bacteria or cells. Plants by contrast, can be grown relatively cheaply in a greenhouse (in the Icelandic case, the greenhouse is heated by geothermal energy). This, and the fact that production of recombinant proteins in plants can be massively scaled up (think fields of GM crops) has lead to an increasing uptake of plants as 'biofactories' for production of useful molecules. And not all of this sophisticated biotechnology is wasted on cosmetics. Sometimes, it is put to better use. For example, insulin is now being produced in a thistle-like plant called safflower (www.sembiosys.com).

Light bikes are faster, right?

You would think so. Otherwise Alberto Contador would have tackled the mountains of Le Tour on an old school steel boneshaker rather than on a delicate wafer of carbon fibre so light it was at risk of floating away on the breeze. Otherwise, I wouldn’t have several featherweights of my own (each for a different occasion, you understand). So it was with some consternation that I read an article in the British Medical Journal in which a doctor reported that, on his daily commute of 27 miles, his brand new carbon steed was no quicker than an old, second hand steel bike weighing nearly 50% more.

It is a strange article, part of BMJ's Christmas in which somewhat light hearted articles about a variety of medical issues are published. These light hearted themes are still dressed up in the language of science, so one is never quite sure whether they are to be taken seriously or not. In this particular piece, an English GP, Dr Groves, describes his experiment about his daily cycle to work as a “single centre, randomised non-blinded trial; n=1. What this means in plain English is that he tossed a coin every morning to see which of his two bikes he should ride, that he made no attempt to prevent himself from knowing which of his bikes he was riding and that he didn’t involve any other riders in the trial. Now there are all sorts of things wrong with this. Trials are blinded for a reason. For example, I know I ride faster on my carbon bike simply because I put more effort in, embarrassed to be seen pootling around on what is so obviously a high end machine. There are also problems with a noisy dataset in this trial: if you remove the four most extreme times (outliers) then the result is reversed – the carbon bike comes out marginally faster.

However, whatever the failings in the design of the trial, there is no doubting that in real world conditions it is difficult to demonstrate a substantial advantage in riding a light bike. This is because, even on a hilly route through the Derbyshire dales, bike weight is only one factor that determines the transformation of rider power into forward momentum. For a start, bike weight is usually a fraction of that of its rider, both of which have to be dragged up those hills. And while weight is important, overcoming drag is also a major sink of expended energy, a fact that any rider who has cycled into a headwind can attest to.

Dr Groves concludes his article by suggesting that perhaps we should all save our money and stick to cheap steel bikes because they are just as fast. Does the man have no soul? Since when do issues of mere efficiency come into the choice of bike? Has he never felt the thrill of hefting a bike in one hand to find that it barely weighs anything at all? Has he never lusted after a bike just for its sheer aesthetic perfection? Has he never been tempted by the prospect of owning the same machine that was ridden to victory on one of the Grand Tours? It may well owe nothing to logic, it may well be a triumph of the seduction of marketing, but many bike purchases, especially those made by the infamous MAMILS, are driven by the desires of the heart and not the reasoning of the head.

In any case, if Dr Groves really is that worried about cycling efficiency he should work on his flexibility. A helpful mathematician from Montreal, writing on the BMJ website in response to Dr Groves’ article, has calculated that a 20% decrease in ‘frontal area’ would save Dr Groves 6 minutes and 36 seconds on his daily commute. Time to stretch that lower back, old boy and ride in those drops. ‘Tis what the pros do, after all.

Cancer: an old disease, a new disease or something in between?

This is the title of an article published in Nature Reviews Cancer. It is an “opinion piece” – a review that puts forward a particular viewpoint, backed up by evidence from the scientific literature. The aim is to be provocative, to stimulate discussion among the relevant community of experts.  Sometimes an exchange of published letters to the journal might result. All very civilized and the sort of exchange of views that helps keep thinking sharp and prevent fields stagnating. All very academic.

This particular article stimulated far more discussion than the authors, Rosalie David (Professor and Director of the KNH Centre for Biomedical Egyptology at the University of Manchester, UK) and Michael Zimmerman (an anthropologist at the University of Pennsylvania, USA) could have ever imagined. I wonder what these two senior and well respected academics thought as their academic article turned into lurid headlines sent screaming across the world’s media. “Cancer is purely man-made, say scientists…”. And then the backlash: “Claims that cancer is only a ‘modern, man-made disease’ are false and misleading” huffed Cancer Research UK. “Cancer is not a disease of the modern world” puffed New Scientist. 

One almost feels sorry for David and Zimmerman. What their article actually says is that there is a paucity of evidence for the widespread occurrence of cancer in antiquity. This is based on a variety of sources from a lack of descriptions of cancer in ancient art and literature to a lack of evident tumours in mummified remains. At the end of their article they make the following cautious conclusion: “Despite the fact that other explanations, such as inadequate techniques of disease diagnosis, cannot be ruled out, the rarity of malignancies in antiquity is strongly suggested by the available palaeopathological and literary evidence. This might be related to the prevalence of carcinogens in modern societies”. It is this last sentence that has been seized upon and inflated to mean that modern life has caused cancer.

But David and Zimmerman are not entirely innocent. For a start, they contributed to a highly inflammatory press release published on the University of Manchester's website. “Scientists suggest that cancer is man-made” was the slightly less cautious headline. One can almost hear  news-hounds around the world sharpening their pencils. And then, perhaps carried away with their moment in the spotlight, they contributed statements to the press release that at best are downright wrong and at worst are plain misleading. “There is nothing in the natural environment that can cause cancer” trumpeted Professor David, “So it has to be a man-made disease, down to pollution and changes to our diet and lifestyle.” Er, UV radiation? Radon? Viruses and bacteria causing cervical cancer, stomach cancer etc.? Professor Zimmerman joined in the fun: “The virtual absence of malignancies in mummies must be interpreted as indicating their rarity in antiquity, indicating that cancer causing factors are limited to societies affected by modern industrialization”. This neatly overlooks the fact that human lifespan in antiquity was much less than today and that age is a major factor in terms of the prevalence of cancer. It is also at odds with the rather more balanced discussion of the age-factor in their paper. Naturally, the critics jumped on these errors and used them to discredit the article.

It is a shame, because they may well be on to something. Unfortunately, they have picked the wrong modern risk factors. Environmental carcinogens caused by industrialization are not the problem here. As Cancer Research UK says: “The evidence that pollution and industrialization have a widespread role in UK cancer rates is weak”. On the other hand, there is a wealth of evidence suggesting that lifestyle factors – smoking, booze, poor diet, lack of exercise – are major risk factors in a large number of cancers. The ‘Western’ lifestyle is just plain unhealthy.

So while it may be that age is also a factor, could it also be true that the rarity of cancer in ancient civilization could be put down to an avoidance of the worst of modern Western excesses? And what if, in the absence of those lifestyle excesses, cancer is no longer an inevitable consequence of age? Surprising as this may seem, it appears that neither ageing nor cancer are an inevitable consequence of long life. Take plants, for example. Despite being exposed to the full range of industrial carcinogens and pollutants, plants neither suffer from cancer (apart from the specific case of crown gall which is disease caused by a bacterial pathogen) nor age. Amazingly, even the most venerable of long-lived trees are as hale and hearty as they were as mere saplings (Penuelas & Munne-Bosch, 2010) still capable of producing new cells at an undiminished rate and apparently resistant to the accumulation of mistakes and errors that bring about our slow decline. It seems that it is not ageing that kills perennial plants, but changes in environment or physical damage. So, if ageing is not inevitable in biological organisms, then might it be possible that we humans could learn the trick? Is there hope for those who yearn for immortality after all? Well, it would take more than a change of lifestyle, but even that would be a start.

It’s not ADHD Sir, it’s in my genes….

Another headline (Daily Telegraph Friday 1^st October, 2010), another human genome versus disease study. And a very similar story to the genetics of myopia (see my previous post ill-communications.blogspot.com). Some serious science (published in The Lancet) looking at DNA variations in groups of individuals with a disease, in this case the psychological syndrome, attention deficit hyperactivity disorder. Some ill-advised press releases and comments: "Study is the first to find direct evidence that ADHD is a genetic disorder" (Lancet press release) and "Now we can say with confidence that ADHD is a genetic disease and that the brains of children with this condition develop differently to those of other children" (Prof Anita Thapar, the lead author of the Lancet paper). Lots of media hoo-haa. See the excellent blog by the BBC’s medical correspondent, Fergus Walsh,  for a summary of the main issues that got discussed.

Just like myopia, ADHD is a ‘complex’ condition caused by a whole variety of factors. These may include genetic risk factors but they also include environmental risk factors: smoking during pregnancy, pre-natal stress, and the usual social problems linked to child behavioural problems such as abuse, marital breakdown and poverty. And just like myopia, it appears that the environmental factors dwarf the genetic. In the Lancet paper, it is reported that 14% of children with ADHD had large variations in their DNA that were only present in 7% of children without ADHD. Or to put it another way, only 1 in every 7 children with ADHD had the genetic variant. Moreover, the particular type of genetic variation present, known as ‘copy number variations’ – deletions or duplications of large chunks of DNA  - do not resolve neatly down to this gene or that. In fact 57 different variations were found in the group of 366 children with ADHD. It is difficult to imagine, even in the science fiction world of routine genome tweaking, a treatment that will correct this.

So perhaps it is time the scientists got smart? As the debate about the amount of UK public money spent on scientific research reaches its zenith (see http://www.guardian.co.uk/science), is it really worth spending serious amounts of public money characterising the minute genetic risk factors of complex disorders like ADHD?

Found: the gene that causes short sight: now experts say condition could be halted by eye drops

The above was a headline (13^th September, 2010) from the UK tabloid The Daily Mail a well known arbiter of rationalism and restraint. To be fair to the Mail, the story was picked up by most of the UK media and tagged with similarly lurid headlines. E.g. “Short-sightedness gene discovery could consign glasses to history” from the Telegraph. And it was not just the UK press. The story had gone global: “Rogue gene causes short-sightedness” (Times of India), “Gene for nearsightedness found; treatment could eliminate need for eyeglasses, contact lenses” (New York Daily News). “Australian discovery of myopia gene link” (Sydney Morning Herald).

The headlines, I am afraid, are rather far from the truth as usual. Indeed, if one reads further into these articles you eventually get to the quotes from the poor scientists involved, caught between a desire to publicise their research while at the same time issuing a plaintive bleat for the facts.

The story originates with two papers published in Nature Genetics Hysi PG, Young TL, Mackey DA et al. A genome-wide association study for myopia and refractive error identifies a susceptibility locus at 15q25. Nature Genetics, 12 September 2010

Solouki AM, Verhoeven VJM, van Duijn CM et al. A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14. Nature Genetics, 12 September 2010

Both studies used DNA microarray technology to identify variations in DNA sequences amongst thousands of individuals. The idea is simple. Each cohort consists of individuals who are short sighted, those who are long sighted and those who have no sight defects. Thousands of positions of known DNA sequence variability known as single nucleotide polymorphisms – that is a change at a single letter of the DNA sequence - across the whole genome of each individual were analysed. Statistics was then used to identify DNA variants that are strongly associated with defective eyesight. The two studies identified different DNA variants, but in both cases the variations were close to genes that are known to be expressed strongly in eye tissues and in one case have been shown to be necessary for normal lens formation in mice eyes. Hence the headlines compelling us to believe that ‘the gene’ for short-sightedness has been discovered.

Even the most cursory reading of the above paragraph should reveal the fallacy of these headlines. The two studies identified different variants. So already, we know that there is more than one DNA variant involved in eyesight defects. In fact, variations near three different genes were identified. The second more fundamental issue is that variations in these genes do not cause sight defect in all individuals. In fact the effect is surprisingly small.  For example, individuals with the variant rs8027411 were only 1.16 times more likely to have myopia than no eye problems. So even if gene therapy was routine and it was possible to administer a magic eye drop that would fix the ‘bad’ DNA variant (conservative estimates reckon it will be at least ten years before such a treatment is possible) then the patients’ risk of developing eye problems would decrease by only 16%.

The problem is that the genetic component of vision defects seems to be swamped by environmental effects. In modern society short-sightedness is on the rise. In some parts of Asia, the incidence of myopia has reached extraordinary levels. Nowhere is this more so than in Singapore where 80% of 18-year old army recruits are now short sighted (up from 25% just 30 years ago). And before you Westerners get complacent, this is not some sort of genetic pre-disposition in the Asian population. For example, Ian Morgan and Kathryn Rose of the Australian National University show in their paper “How genetic is school myopia?” published in Progress in Retinal and Eye Research, 24 (2005) 1-38, that 70% of men of Indian origin living in Singapore are short sighted, even though the incidence of short sightedness in India itself is only 10%.

There is little doubt as to the cause. Too much time spent focused on close objects, the computer screen probably being the biggest evil. Light reaching the eye from a near source has to be bent more to bring it into focus on the retina. The eye compensates by growing longer so that the muscles of the lens have to work less hard. The problem then comes when you look up across the room and try to bring something from further away into focus. These more parallel waves of light fall into focus in front of the retina in the long eye. You are now short sighted. In countries like Singapore, a particularly reading-intensive school programme is thought to be behind the high incidence of short sightedness, the still developing eye the most likely to grow longer.

The solution appears to be simple. As Terri Young of Duke University Medical Center (a lead author of one of the Nature Genetics papers) said in a Duke University press release: “People need to go outside and look at the horizon”. Rather makes you wonder why they spent thousands of dollars doing all that genome analysis, doesn’t it?