Sciencebase Science Blog » genetics

Rubbing Up the Gene Genie

David Bradley — Sun, 02 Mar 2008 11:00:07 +0000

Sciencebase is this week proud to play host to the Gene Genie Blog Carnival thanks to an offer from Bertalan “Berci” Meskó over on the excellent ScienceRoll. For those who don’t already know, a Blog Carnival doesn’t usually involve a lot of be-costumed revellers dancing through the streets to the sound of the samba band, but is a gathering of like-minded bloggers brought together through the power of the tubular Interwebs to share their latest posts on a given subject.

The Gene Genie carnival has an obvious theme. No, it’s not the songs of aging but outlandish popster David Bowie. No, it’s not the magical character of Arabian Nights entombed in a lamp, and no it’s nothing to do with quasi-sci-fi-retro-fit BBC cop show Ashes to Ashes. It’s about genes. See, I told you it was obvious.

Anyway, the carnival (from the Latin carnis, meaning meat, and levare, to put away) covers some of the hot topics in the world of genes, genetics, DNA and all things inherited.

So, here we go:

Gene Found for Ghosal Hematodiaphyseal Dysplasia Syndrome: A Rare Syndrome with Increased Bone Density (DNA And You)
Home DNA tests on the up, ’safer’ clinic DNA tests on the down (Genetics and Health)
Gene Plays a Role in Hair Loss Identified (The Biotech Weblog)
Extinction Fears of the Red-Headed Homo Sapien (GNIF Brain Blogger)
Where are brown people short? and Shadows of the Past in Genes (Gene Expression)
Genetics Cause of Smell Perception (ArticleBiz.com)
Why do we have common risk variants for metabolic diseases? (Genetic Future)
Researchers Discuss MEGF10 Gene Assocation To Schizophrenia (Scientificblogging)
Differences of gene expression between human populations (Anthropology)
Brain scan reveals cultural differences (Sciencebase)
Scientists Link Gene That Promotes Long Lifespan to Cholesterol (Biosingularity)

In the realm of personalized genetics:

NY Times: Insurance Fears and DNA Testing (DNA Direct Talk)
Ann Turner on Personal Genomics Companies 23andMe vs deCODEme and deCODE Launches PrCa Prostate Cancer DNA Test (Eye on DNA)
One Fifth of GDP! (Gene Sherpas)
Why should you get a free 23andme test? (bbgm)
23andMe Adds Paternal Ancestry and an Updated Gene Journal (Genetic Genealogist)
New York Times: Genetics and insurance (Tracing the Tribe)
SNPwatch: One SNP Makes Your Brown Eyes Blue (Spittoon)
Global Awakening in Genetic Counseling (Scienceroll)
Your Future IS Your Genes: Diagnosing Bipolar Disorder from a Blood Sample (Living the Scientific Life)
The next edition of Gene Genie will be hosted by DNA Direct Talk, watch out for it! For more information about the Carnival here.

a

Rubbing Up the Gene Genie

Intellectual genetics

David Bradley — Wed, 01 Aug 2007 15:00:08 +0000

Two worthy legal moratoria - the Agreement on the Trade-Related Aspects of Intellectual Property Rights (TRIPS)
and the Convention on Biological Diversity (CBD) - are potentially in direct conflict when it comes to plant genetic resources and intellectual property rights, at least that is the conclusion of legal expert Megan Bowman. However, potential conflicts could be reconciled in this context by applying the common sense notion of remaining true to the over-arching principle of global welfare-maximisation in TRIPS and by utilising patent exemptions in appropriate circumstances. This, Bowman claims, will allow TRIPS and CBD to operate in a way that achieves both their objectives equally well so that intellectual property rights can be appropriately recognised and biodiversity can be sustained.

Writing in the International Journal of Intellectual Property Management (2007, Vol. 1, pp 277-292), who is a trained barrister and a lecturer in the Law School and Centre of Strategic Economic Studies, at Victoria University, Melbourne, Australia, points out that international recognition of intellectual property rights has grown, particular in the biotech arena, as biodiversity levels have fallen across the globe. Bowman points out that these two trends have become related since the creation of TRIPS and CBD in 1993 whose spheres of operation overlap significantly, particularly in relation to plant genetic resources and intellectual property rights. Bowman states that this is because biological diversity, at both genetic and physical levels, is being exploited as the key ingredient for lucrative biotech and pharmaceutical industrial creation. Patent protection of that creation raises questions about biodiversity sustainability and also access to the resultant benefits and technologies derived from use of a raw product ‘owned’ by source countries or communities.

Currently we are experiencing global biodiversity degradation and decimation due to causes such as global warming that may result in the extinction of nearly half the current lifeforms by 2050. Bowman comments: “Apart from the intrinsic value of biological diversity, without healthy and diverse ecological systems on this planet there is no quality of life for humans – no fresh air or water, no arable land or edible food, and exposure to devastating storms, floods and droughts. But at the same time, humans are evolutionary creatures and we see that clearly with technological innovation. We are also wed to the dollar and we see that, in the context of this discussion, in the jealous guarding of rent for patents, specifically in the growing sector of biotechnology and pharmaceuticals based on plant genetic resources. So the question is how do we marry these components in a way that honours each of them? I look at this question from a purely legal standpoint. Undoubtedly any solution is complex, multi-faceted and multi-disciplined. Nonetheless, the legal principles embedded in the key international treaties on protection of biodiversity and protection of intellectual property rights in plant genetic resources share a commitment to global welfare enhancement. So it becomes clear that the legal foundations exist for cooperation between these two sectors. This knowledge paves the way for productive dialogue and action in boardrooms, patent offices and parliaments around the world.”

Related article from the Sciencebase archives on corporate academia: Will publicly funded research become mired in patent protection and intellectual property rights or remain purely altruistic?

(Updated: August 21, 2007)

Intellectual genetics

Ragworm Ragtime

David Bradley — Fri, 29 Jun 2007 15:00:19 +0000

When I was a youngster I used to do a spot of sea fishing on the freezing cold north east coast. It wasn’t so much a hobby as an obsession at one point. Key to success was a plentiful supply of lugworm which could be dug from the wet golden sand at lowtide and stored ready for the next angling venture, while ragworm, which have a nasty bite, came from the local fishing bait supplier. Never would it have occurred to my 11-year old self that these lowly creatures could harbour the secrets of our own evolution.

However, apparently it does. Detlev Arendt of the European Molecular Biology Laboratory has been studying the multifunctional neurones that sense the environment and release hormones in vertebrates (including ourselves), flies, and worms. The last common ancestor of all of these creatures must provide the evolutionary basis of our modern brains that endow us with the skills to varying degrees of success to dig up ragworm, take part in fishing trips, and ponder our origins.

Hormones control growth, metabolism, reproduction and other biological processes. In humans, as indeed in all vertebrates, the chemical signals are produced by the hypothalamus and other specialist brain centres and secreted into the blood for circulation around the body. This signalling system is not, it turns out, the preserve of those creatures with a backbone. Arendt and his colleagues now believe that the hypothalamus and its hormones have
their
evolutionary origins
in an ancient wormhormones have their evolutionary origins in an ancient worm-like creature that lived hundreds of millions of years ago and is the common ancestor of vertebrates, flies, and worms.

Hormones work slowly, on the whole, and have body-wide effects. Insects and nematode worms use hormones, but the specific molecules they use are very different from their vertebrate counterparts.

“This suggested that hormone-secreting brain centres arose after the evolution of vertebrates and invertebrates had split,” explains Arendt, “But then found vertebrate–type hormones in annelid worms and molluscs, indicating that these centres might be much older than expected.” Comparisons of two types of hormone-secreting nerve cells from zebrafish, a vertebrate, and the annelid worm Platynereis dumerilii, in Arendt’s lab have now revealed some stunning similarities that point to a shared and ancient ancestry for our hormonal systems.

“These findings revolutionise the way we see the brain,” says Kristin Tessmar-Raible who carried out the comparison, “So far we have always understood it as a processing unit, a bit like a computer that integrates and interprets incoming sensory information. Now we know that the brain is itself a sensory organ and has been so since very ancient times.” The research appears in detail in the journal Cell.

Bewildering to think that I used to skewer these little creatures on a barbed hook and cast them into the sea to catch scaly marine creatures. It almost makes no sense.

Ragworm Ragtime

DNA Network

David Bradley — Tue, 26 Jun 2007 15:00:39 +0000

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 DNAtimely 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.

DNA Network

Genetic Research Hits Pay Dirt

David Bradley — Wed, 06 Jun 2007 17:00:56 +0000

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 clearthe 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?

Genetic Research Hits Pay Dirt

Combined effort makes for glowing report

David Bradley — Thu, 31 May 2007 15:00:19 +0000

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.

Combined effort makes for glowing report

Hey good looking, what you got cooking, in those genes?

David Bradley — Tue, 27 Mar 2007 23:01:33 +0000

Here’s a puzzle. If evolution ensures that ‘good’ genes spread through a population, then why are individuals so different? Why don’t people get better and better looking through each generation to the detriment of ugliness and lead to a population of real lookers?

The problem with current evolutionary theory is that it would seem that if females select the most attractive mates, then the genes responsible for their attractive features would spread quickly, leading to all males becoming equally attractive (think peacock tails). Ultimately, further sexual selection would then no longer take place and evolution would stop in its tracks.

This is the so-called lek paradox and it has remained a foil in the weaponry of the intelligent design advocate’s arsenal for many years. Until now.

Thanks to research at Newcastle University, England, this apparent fundamental flaw in Darwin’s theory of evolution, latched on to by creationists can be explained quite effectively by evolution itself. The findings of Newcastle’s Marion Petrie and Gilbert Roberts research suggests that sexual selection leads to increased genetic diversity by a mechanism not previously understood.

Petrie reasoned that as genetic mutations occur naturally anywhere in the genome, some will actually affect those used to produce the DNA repair kit enzymes found in all cells. This would lead to those individuals with a malfunctioning or inefficient repair kit, having more mutations left unrepaired and so greater variation in their genome.

Usually, damaged DNA leads to an unviable organism that either dies quickly of the effects or is otherwise unable to reproduce. However, if those variations are present in sections of the genome responsible for disease defence, then variation can actually be beneficial as greater variation in the genome at these points means more chance of warding of bacteria and viruses.

Petrie modelled the spread of genes in a population and demonstrated that the tendency towards reduction in genetic diversity caused by sexual selection is outweighed by the maintenance in greater genetic diversity generated by mutations affecting genome repair.

The researchers began this research a decade ago and their model genes are now a great fit for the observations of variations. “We find that sexual selection can promote genetic diversity despite expectations to the contrary,” Petrie says. The team publishes details of their findings today in the journal Heredity.

Hey good looking, what you got cooking, in those genes?

Power up your genome with chemistry

David Bradley — Fri, 16 Mar 2007 12:00:12 +0000

Researchers have developed several tools to help them exploit the underlying chemistry of genomics, while novel chemistry has enabled faster, parallel sequencing methods that not only accelerate genomic research but also cut costs. The very same techniques allow sex chromosomes and complete genomes to be decoded faster and more cheaply than ever before.

Concomitantly, microfluidics technology is improving the way conventional fluorescence chemistry can be exploited in sequencing. Improved understanding of nanoscale channels - both synthetic and protein channels offers the possibility of studying individual biological macromolecules and microfabricated microarrays are opening up massively parallel opportunities. Novel chemical technologies are also opening up locked nucleic acids as well as non-DNA molecules such as microRNAs.

The so-called post-genomic era put the molecular smack in the middle of the biological quarter. Now, as cross-disciplinary communication matures, research at the intersection of chemistry and biology is working harder than ever to solve fundamental questions in science and medicine.

You can read the complete feature on the subject of chemistry in the post-genomic era from David Bradley in Science magazine today. It is the lead article on the Science Products page.

Power up your genome with chemistry

Being particular about DNA

David Bradley — Tue, 02 Jan 2007 23:00:07 +0000

Surface-enhanced Raman spectra (SERS) of DNA and RNA mononucleotides can be detected with high sensitivity, according to UK researchers. Using citrate-reduced silver colloidal nanoparticles aggregated with magnesium sulfate instead of the more common halide ions, reduces inappropriate enhancements and produces spectra that are sufficiently different to allow each to be distinguished.

“The main advantage of our SERS approach is that it allows direct label-free identification of mononucleotides in aqueous solution,” Steven Bell, Director of the Innovative Molecular Materials Group, at Queen’s University Belfast, explains, “There is no requirement for labels because the Raman signals of each of the mononucleotides are intrinsically different due to the differences in their chemical structures.” He adds that spectra can be obtained at ten nanograms per millilitre. “We were working with large samples but reducing the sampling volume to a few microlitres would move the sample down to tens of picograms,” he says.

More…

Being particular about DNA

Genetic Variation on a Theme

David Bradley — Thu, 23 Nov 2006 16:41:02 +0000

What does it mean to be human? We thought that the Human Genome Project had set the limites on the genetic make-up of our species. But, according to Steve Connor, writing in the Independent today, much of the genetic variation between individuals can best be explained by the presence of multiple copies of certain key genes rather than variations in the genome sequence.

The research suggests that whereas previously we thought all people shared 99.9% of their DNA, it could be that two individuals can differ by ten times that. The research has important implications for our understanding of inherited traits and genetic disease.

The findings appear in three simultaneous papers in three leading science journals, including Nature and were reported by teams from thirteen different research centres in the UK and the US.

Genetic Variation on a Theme