Category: Genetics

For Scousers, Londoners, fans of BBC’s Have I Got News for You satirical news quiz, and especially to everyone who watched this Beijing to London Olympic handover this week the name Boris Johnson likely drums up an image of some blonde, floppy haired, bedraggled and totally confused Tory toff, who just happens to be Mayor of London.

Well, it turns out that he has quite an interesting ancestry of which he was almost totally unaware until another BBC TV show (Who Do You Think You Are?, which is all about family history and genealogy of the rich and famous) helped him dig deep into the roots of his family tree. First off, not only was his great grandfather, Ali Kemal an outspoken journalist turned politician (like Johnson) who was apparently lynched by the state in the founding years of modern Turkey but his great-great-great-great-great-great-great-great grandfather was King George II of England (illegitimately due to a “wrong-side-of-the-sheets liaison between Johnson’s great grandmother and a descendant of George II. Such ancestry means Johnson is related to all the royal families of Europe.

How’s that for a bit of name dropping? Of course, there are probably tens of thousands of people who have illegitimate links to European royals, but it’s an interesting find nevertheless.

However, for those who think Johnson is nothing more than a blithering fop, it was his final words in this episode of “Who Do You Think You Are?” that were most poignant to lineage, heredity and most of all genetics, which is why I thought they warranted a holiday mention. I just hope they were spontaneous and unscripted.

We’re all just great, our genes just pulse down the lines. We’re not the ultimate expression of our genes. We’re the temporary custodians of these things. We don’t really know where they’ve come from, where they’re going, and the whole process is incredibly democratic.

You can view a segment from the show here, unfortunately, the closing quote is not included in this Youtube segment.

UPDATE: Following on from Mr Johnson’s genetic insights, I see there’s a paper in this week’s Nature from Cornell researchers that says: “One day soon, you may be able to pinpoint the geographic origins of your ancestors based on analysis of your DNA. The researchers describe the use of DNA to predict the geographic origins of individuals from a sample of Europeans, often within a few hundred kilometres of where they were born.”

Novembre, J et al (2008). Genes mirror geography within Europe Nature

Genetic disease is a complicated affair. Scientists have spent years trying to find genetic markers for diseases as diverse as asthma, arthritis and cardiovascular disease. The trouble with such complex diseases is that they are none of them simply a manifestation of a genetic issue. They involve multiple genes, various other factors within the body and, of course, environmental factors outside the body.

There are some genetic diseases, however, that are apparently caused by nothing more than a single mutation in the human genome. A single DNA base out of the many thousands on a person’s genetic material, if swapped for another the wrong base means the production of the protein associated with that gene goes awry.

For example, sickle cell disease is caused by a point mutation in the gene for beta-haemoglobin. The mutation causes the amino acid valine to be used in place of glutamic acid at one position in the haemoglobin. This faulty protein cannot fold into its perfect active form, which in turn leads to a cascade of effects, that result ultimately in faulty red blood cells and their associated health problems for sufferers. There are many other diseases associated with single point mutations, including achondroplasia, characterised by dwarfism, in one sense, cystic fibrosis, although different single mutations may be involved, and hereditary hemochromatosis, an iron overload disease.

“To be able to study and diagnose such diseases with limited material from patients, there is a need for methods to detect point mutations in situ,” explains Carolina Wählby of the Department of Genetics and Pat Centre for Image Analysis, at Uppsala University, Sweden, and her colleagues Patrick Karlsson, Sara Henriksson, Chatarina Larsson, Mats Nilsson, and Ewert Bengtsson. Writing in the inaugural issue of the International Journal of Signal and Imaging Systems Engineering (2008, 1, 11-17), they pointed out that this is a problem that can be couched in terms of “finding cells, finding molecules, and finding patterns”.

The researchers explain that the molecular labelling techniques used by biologists in research into genetic diseases often just produce bright spots of light on an image of the sample. Usually, these bright spots, or signals, are formed by selective reactions that tag specific molecules of interest with fluorescent markers. Fluorescence microscopy is then used to take a closer look.

However, signals representing different types of molecules may be randomly distributed in the cells of a sample or may show systematic patterns. Such patterns may hint at specific, non-random localisations and functions of those molecules within the cell. The team suggests that the key to interpreting any patterns of bright spots relies on slicing up the image quickly, applying signal detection, and finally, analysing for patterns. This is not a trivial matter.

One solution to this non-trivial problem could lie in employing data mining tools, but rather than extracting useful information from large databases, those tools would be used to extract information from digital images of cells captured using fluorescence microscopy. The spatial distribution patterns so retrieved would allow labelled molecular targets to analysed that builds on the latest probing and staining techniques.

Biological processes could thus be studied at the level of single molecules, and with sufficient precision to distinguish even closely similar variants of molecules, the researchers say, revealing the intercellular and sub-cellular context of molecules that would otherwise go undetected among myriad other chemicals.

The team has demonstrated proof of principle by developing an image-based data mining system that can look for variants in the genetic information found in mitochondria (i.e. mitochondrial DNA, mtDNA). They point out that MtDNA is present in multiple copies in the mitochondria of the cell, is inherited together with cytoplasm during cell replication and provides an excellent system for testing the detection of point mutations. They add that the same approach might also be used to detect infectious organisms or to study tumours.

Wahlby, C., Karlsson, P., Henriksson, S., Larsson, C., Nilsson, M., Bengtsson, E. (2008). Finding cells, finding molecules, finding patterns. International Journal of Signal and Imaging Systems Engineering, 1(1), 11. DOI: 10.1504/IJSISE.2008.017768

Are you happy to eat genetically modified foods? What about your friends and colleagues? Do the GM pros outweigh the cons?

I asked a few contacts for some answers by way of building up to a more formal response to those kinds of questions that will be published soon in the International Journal of Biotechnology (IJBT, 2008, 10, 240-259).

Plant geneticist Dennis Lee, Director of Research at mAbGen, in Houston, Texas, suggests that GM crops have several significant advantages. “Total cost per acre can actually be significantly less for GM crops,” he says. This is particularly true for crop species, such as maize, that have been modified to produce natural toxins that fend off insect pests or protect the crop from the herbicides need to keep weed growth at a minimum. However, he points out that, “In practice, this is often not the case – farmers tend to err on the side of caution and continue to use significant amounts of pesticides and herbicides.”

That said, crops can also be modified to grow in substandard conditions, such as strains of tubers grown in Kenya that are capable of surviving both drought conditions and high-salt soils. “Obviously, this is beneficial to yield – you can actually get some food out of places where you previously could not,” adds Lee. In addition, it could be possible to modify some crops to have greater nutritional content, such as the so-called “golden rice” project by Ingo Potrykus then at the Institute of Plant Sciences of the ETH Zurich.

One of the biggest perceived problems regarding GM crops is the possible contamination of other species. What if herbicide-resistant genes could jump into weed species, for instance? Lee points out that this putative problem can be overcome by using terminator technology to jumping genes. “However, in doing so, it creates a different problem,” Lee adds, namely that farmers must buy seed from the agbiotech company each year rather than save seed for planting.” One might say that this is an exploitative industry focused purely on maximizing profits, but at the same time it solves a serious technical problem that has been seen as one of the biggest stumbling blocks to the acceptance of GM crops.

Jeff Chatterton, a Risk and Crisis Communications Consultant at Checkmate Public Affairs, in Ottawa, points out that the pros are well documented: increased yield per acre, ease of use and perhaps, some day, increased ‘consumer level’ benefits such as higher nutritional values. But, echoes others’ comments on the hidden con of farmers the world over potentially being locked into the agbiotech company’s seed and having no recourse to produce their own from one year to the next.

“As traditional family farms are increasingly moving towards “Roundup Ready” corn or soybeans, you’re increasingly seeing a change in the business model of farming,” he says. “Rather than ‘family farms’ using traditional farming practices, agricultural operations are increasingly becoming factory farms.” It might be said that the emergence of factory farms is occurring outside the realm of GM crops, but with pressure being applied to produce more and more crops for non-food purposes, including, biofuels, unique polymers, and other products, the notion of a factory farm that doesn’t even feed us could become an increasing reality.

Lee also mentions an intriguing irony regarding the public perception of risk-benefits concerning GM crops and that is that the toxins produced by modified Bt maize is exactly the same toxin produced by the natural soil microbe Bacillus thuringiensis (Bt) itself and this is same Bt toxin that so-called “organic” farmers are usually allowed to use instead of “synthetic” pesticides.

Information Technology and Services Professional Bill Nigh of Bluenog, based in New York, provides perspective as a lay person. “We’ve been engaged in genetic manipulation for a long time now,” he says, “but it was limited by the technology at hand. With recombinant DNA it’s a remarkably more vast field of play and a whole new ball game.” He stresses that his main concern regarding GM crops is that, “We seem to be just smart enough to make drastic breakthroughs and inventions, and are driven by the dynamics of the marketplace and ego to produce a lot of new things quickly. However our systems of governance, oversight and coordination are not mature enough to work through the implications of those new things in a timely fashion, especially the unforeseen synergies the breakthroughs can unleash.”

All that said, an international team has now investigated the various issues and has assessed the public’s Willingness to Accept (WTA) GM foods based on experimental auctions carried out in France, UK, and USA. Lead author of the IJBT paper Wallace Yee now at the University of Liverpool, worked, while at Reading University, with colleagues in various disciplines, from agricultural and food to business and economics in Italy, New Zealand, UK and US to explore perceptions of risk and benefits, moral concerns and attitudes to the environment and technology.

“Trust in information provided by industry proved to be the most important determinant of risk/benefit perceptions,” the researchers conclude, “willingness to accept followed general attitudes to the environment and technology.” They also found that educational level and age could also enhance perceived benefits and lower perceived risks of GM foods. “Our research suggests that trust-building by industry would be the most effective approach to enhancing the acceptance of GM foods,” the team says.

“If the industry could educate people that GM technology does not pose any threat to the environment, but provides benefits to society as a whole and consumers as individuals, the attitudes of the public towards GM in food production would be favourable, and in turn increase their willingness to accept,” they conclude.

Computing professional Paul Boddie of Oslo, Norway, coming at the issue of GM crops from an indirect angle provides an allusion to computer programming that seems quite pertinent and was originally attributed to Brian Kernighan, which Boddie suggests readily transfers to other disciplines including genetic engineering: “Everyone knows that debugging is twice as hard as writing a program in the first place. So if you are as clever as you can be when you write it, how will you ever debug it?”

Yee, W.M., Traill, W.B., Lusk, J.L., Jaeger, S.R., House, L.O., Moore, M., Morrow, J.’., Valli, C. (2008). Determinants of consumers’ willingness to accept GM foods. International Journal of Biotechnology, 10(2/3), 240. DOI: 10.1504/IJBT.2008.018356

Sciencebase was recently invited to join the excellent DNA Network and as such our genetics news feed is now being pulled by the network’s feed system. If I had been a little slower off the mark, I could have been site number twenty in the list, but when I joined I think I jumped in at #18. There are, at the time of writing, nineteen members, no DNAying it.

So, here is a quick random selection of fellow network members. The links will take you to the individual RSS feed for each site whereby you can subscribe (for free) and get some great and timely information on DNA and the latest happenings and business news in genetics and DNA research.

VentureBeat Life Sciences

Discovering Biology in a Digital World

DNA Direct Talk

Epidemix

The Daily Transcript

henry: the human evolution news relay (genetics)

Mary Meets Dolly

Genetics News

Microarray and Bioinformatics

Gene Sherpas: Personalized Medicine and You

The Personal Genome

All excellent newsfeeds, all focused on one thing, DNA. You can find links to the others, including Eye on DNA, the owner of which led me to the DNA Network in the first place, via DNA Network. I’ll do another round-up of the remaining members later.