David Bradley – Page 292

Genetic Research Hits Pay Dirt

DNA The budget for the Human Genome Project and all that post-genomic, proteomic, metabonomic, immunomic…research was almost on a par with defense spending; it was almost c-omical really. Well, maybe not quite, but it stretches out with a lot of zeros nevertheless. At the time the grants were written and the funding given, we, as a society, were promised all kinds of medical miracles from gene therapies and new treatments to cure all those nasties – cystic fibrosis, sickle cell, thalassemia, cancer, heart disease and more.

We were promised personal medicine courtesy of pharmacogenomics. This would allow your doctor to profile your genome and tailor your medication to the particular set of enzymes running in your liver and whether or not you were likely to respond positively, suffer adverse effects, or simply not respond at all. We have even seen, this last few days, the sequencing of James Watson’s genome; an effort that cost less than $1m and took under four months. But do any of these promises add up to very much beyond myriad PhD theses and thousands of biotech startups many of which have already crashed?

Hopefully, the answer is yes. In the next few years, gene science will hit pay dirt as genes finally give up their real secrets and the true meaning of so-called junk DNA will become clear. Our understanding and ability to treat a wide range of disease from breast cancer and obesity to hypertension and bipolar disorder will come of age and perhaps finally succumb to all this genetic scrutiny and manipulation.

Nature, Science and the Wellcome Trust provided a useful summary of the genetic state of the art for a recent Times report by Mark Henderson on our genetic future. In the summary Henderson highlighted the latest “in press” results, most of which are now online, so I am providing here the hyperlinked executive summary:

Breast cancer – Three papers published in Nature and Nature Genetics at the end of May reported four new genes and one genomic region associated with increased risk. 10.1038/nature05887, 10.1038/ng2075, 10.1038/ng2064

Obesity – An obesity gene, the FTO gene, was published in Science in April and reported in Sciencebase at the time.

Diabetes – Again in Science (and 10.1126/science.1142382 and 10.1126/science.1142358, three common genes for increased diabetes type 2 risk were reported, bringing the total known genes associated with diabetes to nine.

Alzheimer’s disease – New results also published this week in Neuron discuss an Alzheimer’s gene

Data that were still under press embargo at the time Henderson’s feature appeared in The Times, however, meaning he could only hint at the true potential of human genome results were revealed today.

The largest ever study of genetics of common diseases in which almost 10 billion pieces of genetic information were analysed were published just one minute ago, so I can now outline the findings in a little detail. The new study compared 2000 cases each of seven common diseases with 3000 shared control patients, and reveals new genetic associations with these disorders. A pair of related papers in Nature Genetics (a and b) offer further insights into two of the seven diseases investigated.

In the Nature article, scientists from the Wellcome Trust Case Control Consortium report genetic variants associated with the development of bipolar disorder, Crohn’s disease, coronary heart disease, type 1 and type 2 diabetes, rheumatoid arthritis and hypertension. This is the first study from this large scope and it, the scientists found one genetic region newly associated with bipolar disorder, and another with coronary artery disease. A separate group of three markers have been found to be associated with rheumatoid arthritis. The researchers also identify nine new genetic associations for Crohn’s disease and ten chromosome regions that contain genes related to diabetes.

These new results would suggest a medical revolution is at hand and that the Human Genome Project and its spinoff -omics really are about to hit pay dirt. But, are we really on the verge of a new era in medicine, or are the various genetic revelations simply more grant-baiting hyperbole?

Testing your rotten organics

Tobacco sky Will your molecules rot, is biodegradability an intrinsic property of those chemicals you handle on a daily basis? A study published today in the journal Molecular Systems Biology reveals whether or not thousands of chemicals will be biodegradable. The work could help in environmental risk assessment of production, transportation and disposal of organic compounds.

Biodegradability is determined primarily by whether or not there are microbes in the environment that can diget any given compound. Victor de Lorenzo and colleagues at the National Biotechnology Centre in Madrid, Spain, used a database of all known microbial metabolic reactions to train a computer algorithm to distinguish between the biodegradable from the recalcitrant compounds. With this in silico test kit they looked at almost 10000 chemicals.

This automatic predictive approach to assessing biodegradability could help researchers evaluate the potential of new compounds to pollute the environment and help in the implementation of international regulations on the use of new chemicals.

Perhaps not surprisingly, the press release associated with this work focused on those compounds, including herbicides, that are most resistant to biodegradation, but fails to mention the even larger group of compounds that are intrinsically biodegradable. The usual news write-ups about toxic chemicals and the environment 9999 times out of 10000 will inevitably highlight those that are the nastiest.

The huge benefits of the thousands of organic compounds used in the pharma, biotech, plastics, and other industries as well as medicine and agriculture will simply be ignored whether or not those compounds accumulate in the environment or not. Biodegradation is only one route by which thousands of compounds are destroyed naturally in the environment (heat, light and interaction with other non-living materials, are others). The predictive system will be useful, certainly, but its wider applicability should consider these other routes and the risk factors and toxicity associated with any particular chemical, rather than tarnishing all entries in the database simply on the basis of whether or not a microbial enzyme exists to digest it.

The original research paper can be read here.

Down to Earth Spectroscopy

Cheminformatics could help save forests from the damage caused by runaway widlfires. As long as there have been forests, there have been forest fires, from the bushfires of the Australian outback, across Africa, Asia, and Europe, to the Americas. Such fires often thought of has having a regenerative effect on old woodland, but predictions of an increasing frequency and intensity of wildfires because of climate change could lead to loss of forest and soil erosion rather than dendritic rebirth. Spanish researchers have now used near infrared spectroscopy, a simple calibration technique and cheminformatics analysis of their spectra to determine a key parameter of soil damage – the MTR, or maximum temperature reached. You can read the full story in the latest issue of SpectroscopyNOW.

Spiked innovations

Some time ago, the editors at Sp!ked-Online asked me to suggest what I thought was the greatest innovation of all time. I tried to be a bit esoteric and opted for the inorganic chemistry of ammonia and sulfuric acid, certainly not the most exciting sounding of entries in the sp!ked innovation survey, but I hope the chemists among their readership would appreciate it among all the more electrical technological suggestions and the tools of molecular biology.

It seems I was among some eminent participants, “key thinkers in science, technology and medicine” allegedly with some half a dozen Nobel laureates in their number. The survey aimed to identify the greatest innovations and a live discussion is scheduled to take place in London on June 6.

Surveying the responses, Mick Hume, sp!ked’s editor-at-large, says the survey “Provides some illuminating insight both into the important developments of the recent and more distant past, and into the way those involved at the cutting edge see the issue of innovation today.” My colleague Philip Ball, a fellow freelance science writer with a chemical bent, also stuck up for chemistry in his submission opting for innovations in analytical chemistry, including NMR spectroscopy and X-ray crystallography.

Among the other innovations suggested were The Internet, the alphabet, the discovery of nuclear fusion, X-rays, the brick, rockets, the eraser. I surely must posit that without sulfuric acid and ammonia not one of those innovations would ever have reached its full potential. Maybe I should also add an upside down exclamation mark, just to emphasize my point!

Among the other contributors to the event are Anjana Ahuja, science columnist, The Times, Ken Arnold Head of Public Programmes, Wellcome Trust, Peter Cochrane co-founder of ConceptLabs, and former chief technologist at BT, Marcus Du Sautoy professor of mathematics, Wadham College, Oxford, Sir Tim Hunt (FRS) principal scientist, Cancer Research UK, and David Roblin VP, Clinical R&D, Pfizer Global Research & Development.

Digg for Chemists

Berkeley chemist Mitch Garcia, who runs ChemicalForums.com has come up with a “novel” way to evaluate the chemical literature that will complement current ways of evaluating a particular paper. At the moment, the only way to determine whether a particular experiment is valid are to trust the quality of the peer review process for the particular journal in question, attempt to repeat the experiment yourself, check out how many other chemists are citing the paper, or somehow try to relate the quality of the paper to the author’s h-index, an altogether more ephemeral and perhaps elitist quality.

Garcia has now launched ChemRank, which will augment this unwieldy process by allowing individuals to post a reference and then see others vote on whether or not the paper in question is any good or not. Those papers with the most votes will rise to the top, while the less worthy will essentially sink. The system will rely on building a big enough userbase and somehow ensuring that chemists don’t simply spam their own papers or vote arbitrarily for their friends and Profs. How effective Garcia’s system will be remains to be seen as it has only just launched. The number of papers currently being voted on is small and the number of votes is low, so take a look and if you feel like digging chemistry, make your vote count.

Combined effort makes for glowing report

One of the most powerful techniques available to analytical scientists is Raman spectroscopy. Unfortunately, it is not easy to distinguish the low-intensity signals it produces when studying fluorescent species in cells because they are swamped by the much brighter glow from various cell components. Now, Dutch researchers have overcome this incompatibility to hybridize Raman with fluorescence microscopy by exploiting the optical properties of semiconductor fluorescent quantum dots (QDs). They have demonstrated hybrid Raman fluorescence spectral imaging in studies of single cells.

Biophysical engineers Henk-Jan van Manen and Cees Otto of the University of Twente, The Netherlands, have used fluorescent nanoparticles to broaden the scope of single-cell microscopy by combining it with intracellular chemical analysis based on Raman. The researchers explain that quantum dots allows weak Raman signals from DNA to shine through the ubiquitous glow from proteins and lipids.

You can read the full story in my SpectroscopyNOW column this week.

Udderly butterly

Cow Scientists in New Zealand hope to breed cows to produce low-fat, skimmed milk, not only that they are working on a new bovine breed that will produce milk that makes spreadable butter.

Apparently herd member Marge and her sisters and cousins, have the right genetic makeup required for producing skimmed milk straight from the udder and milk that makes and easily spreadable butter. The team hope to partner up with a friendly bull soon and have a commercial herd ready by 2011. Even more importantly from the human health perspective for those whole like the “white stuff” on their cereals in the morning, Marge’s milk is very low in saturated fats and so her offspring will hopefully produce high polyunsaturates and monounsaturated fat milk too.

Ed Komorowski, technical director at Dairy UK says that the New Zealand approach could be used to breed cows that still produce full-fat milk but with only the good fats, which could swing things back in favour of full-fat milk. In the UK, for example, only 25% of milk sold is full fat. “In future if whole milk can be made to contain unsaturated fats — which are good for you — then it might mean that people change back to whole milk products. The big thing about dairy products is taste, so this would be a way of giving the benefits of taste without the disadvantage of saturated fats,” he adds.

Milk from this new healthy breed of cattle could also overcome the problem of what to do with all the waste products of the dairy industry that are produced during the fat-reduction process. “If you can genetically produce milk without fat then that may turn out to be a very good solution to what might later be a big disposal issue,” says Komorowski.

The healthy cows were identified biotech company ViaLactia while screening milk compositions across the entire herd of 4 million New Zealand cattle. New Zealand dairy firm Fonterra has already made milk products from Marge’s milk and they maintain the positive taste.

The research is discussed in more detail in this week’s issue of Chemistry and Industry magazine from the UK’s Society of Chemical Industry.

Toxic hairdos, titanic smog, and paradoxical polymers

In my fortnightly Alchemist column over on ChemWeb, I take a fast and furious look at a few of the chemical happenings in the news. This week, geochemical biomarkers are rewarded for pioneering our historical understanding of climate change, while a seemingly paradoxical polymer emerges from mathematics to help compute future optical chips.

Also on the roster a Titanic effort has been undertaken to reveal the chemical nature of the smog that shrouds one of Saturn’s moons (Titan, in case you couldn’t guess) and we reveal the stickiest of sticky materials that can bond materials as disparate as copper and silica tighter than ever before.

At least one dyed in the wool media health scare story has been cut short this month with the discovery that chemical relaxers, used by African-American women to straighten their hair, do not cause breast cancer, after all.

And, finally, new forensic information can now be dabbed from fingerprints thanks to research carried out in the UK. Antibody assays carried out on fingerprints can now be used to tell if an unidentified suspect smokes, whether they use drugs, or even if they have an illness.

Chemrefer Chemspider Coupled

A mash up between Chemrefer, the search engine for open access chemistry papers, and molecular structure search engine Chemspider launched today. I have to confess to playing no small part in facilitating this collaboration having introduced the Chemspider team, virtually speaking, to the owner of Chemrefer, Will Griffiths, who was a Reactive Profilee in June 2006. You can access the chemical mash up here. Search for any term of interest and the new hybrid tool will return all the pertinent results that are available for instant free access from the journal publishers. There are something like 50000 papers accessible this way via a search of more than 14.5million+ chemical entities.

Ignore your internal critic and relax

Blogger in a hammock This item could have been called “How to out-psyche yourself”, it is not exactly rocket science, but then rocket science is not one of the common topics on Sciencebase, anyway. It’s a public holiday here, today. Yes, I know…again? Oh, and over there too? Anyway, I’ve pulled together some of the chillingest out posts from the last week or so and brought them together in an easy to catch, laid back post with few words, and a hammock on stand by in case the sun comes out. Incidentally, almost all these tips, or life-hacks as some people are wont to call them basically boil down to a simple phrase, that any analyst, physician, or psychiatrist could do well to hang on their surgery door, desk, and above their sphigmomanometer – Don’t Worry, Be Happy.

So, over on lifehack itself, they posted a top ten of simple ways to save yourself from messing up your life. Seems like heavy psychological stuff from the title, but it boils down to not worrying about your feelings, taking life in your stride, and avoiding dwelling on the ramblings of your internal critic. So far, so good.

Next, over on the American Lung Association site – heart I could understand, but lung? – they are touting, not ten, not twenty, not even fifty, but fifty-three (don’t ask), surefire ways to help you chill on any day of the week not just a public holiday. Among my favourites, is “Count to 1,000, not 10, before you say something that could make matters worse.” This goes for commenting on blog posts too: “Look, before you leap”, as my grandma used to say.

Some of the more “new-agey” stuff on the web often has a decent list of howtos for relaxation and such. I am not saying that WikiHow is new age, perish the thought, but they do have a how2relax section, with the classic: “Find a quiet place when you are feeling overwhelmed. Even the stall of a bathroom will work if you have no other place to go.” You can just picture all those overwhelmed office workers, “relaxing” in the bathroom, or maybe not, we do not want to revisit any kind of Ally McBeal moment on this site, thank you very much.

At this time of year, many poor unfortunates (PUs) will have to put aside worries about who is buying the next round, and concentrate on their exams. Thankfully, the venerable University of Cambridge offers those PUs, some useful advice on simple exam-time relaxation on their student counselling website. A classic tip offered there is: “don’t use your bed as a place to work during the day”. As if, have you ever heard anything so preposterous? Students using their beds to work on during the day? Of course not…

We now know how they do it in Cambridge, England, but what about across the Pond in that other townwise homonymous centre of excellence, Harvard University? Well, Harvard U, has a Relaxation Room, of course. “The body responds to stress with increased muscle tension,” so says the RR’s website and apparently in said room you can get a massage or give a massage. Now, I don’t know about you but I don’t recall any such offers while I was studying at university. How the times change.

Finally, an NYT article discusses how to deal with past bad experiences, not by ignoring them, but by retelling them in your internal narrative as if there happened to a third party rather than you.

Anyway, deciding the best way to relax is getting too stressful, I am going to fix that hammock and take that initial advice…the bit at the end of the first paragraph.