Science Helps Dig Up Your Genetic Family Tree

Genetic algorithm

My wife’s mother is very keen to trace her family tree and has dug up roots as far back as the early 18th century with possible hints at some ancestors dating back to the late 1600s. She has quite a rare and locally focused maiden name, so it has been a little easier for her than it would be for someone in England called Smith. Personally, I gave up any notion of trying to find my ancestors as my name, while not incredibly common is not rare, meaning as it does “broad field” and so is quite widespread in its various forms.

However, a group of computer scientists, mathematicians, and biologists from around the world have developed a new computer algorithm that could help anyone trace their genetic ancestry in minutes without any prior knowledge of their background. This will not, of course, help you find great, great, great grandfather Bartholemew or whoever, but it could provide important insights into your genetic heritage and the true origins of your germ line.

The new program is unique in that it searches for specific DNA markers, single nucleotide polymorphisms, or SNPs (pronounced snips), using nothing more than a DNA DNA sample collected by simple cheek swab. The researchers, led by Petros Drineas of Rensselaer Polytechnic Institute, New York, used genetic data from previous studies to perform and confirm their research, including the new HapMap database, which scientists are using to find variations in the human genome.

“The program will be a valuable tool for understanding our genetic ancestry and targeting drugs and other medical treatments because it might be possible that these can affect people of different ancestry in very different ways,” explains Drineas. The program will also help us understand our unique backgrounds and assist historians and anthropologists in studying the origins of different populations as well as how our global society evolved.

So, while it may not help mother-in-law find her great, great, great, great grandfather and add the final twigs to her individual family tree, the new program (details in Plos Genetics) could lead to a wider understanding our wider genetic heritage, which could lead to the keenly sought personalized medicine. If researchers can uncover the minute genetic details that set each of us apart, biomedical research and treatments can be better customized for each individual, Drineas adds.

Sciencebase archives and artefacts

Sharp-eyed readers may have spotted that, once established, Sciencebase moved on from a simplistic static site to a CMS-driven blog. As such, some of the pages (with a small p as opposed to a WordPress big P) don’t have the acoutrements of the CMS. This isn’t deliberate, it’s an artefact of the way I set up Sciencebase way-back when.

Here are a few that have already made the grade, hopping from an early edition of Elemental Discoveries (the proto-Sciencebase ezine) to the fully fledged CMS – Touch Wood – A Guide to Viagra Louts, the story of Viagra, The Real Butterfly Effect, how the physical structure of butterfly wings is helping technologists create new optically functional materials, and Scientific Stereotypes, in which I discussed children’s perception of scientists and whether or not that perception matters to science.

There are dozens more feature articles in the Sciencebase archives outside the blog system, which you can access using the Science Articles link in the menu above.

Healthy PubMed Searching

This post is more in the bio camp than the chemo field, but may be of interest both to chemists with a life sciences investment and/or hypochondriacs in your lab.

The Healia health portal has added a specially designed PubMed/Medline search to their site that helps consumers retrieve abstracts of scientific articles published in biomedical journals in a more user-friendly way than the standard PubMed search. The system still searches the National Library of Medicine’s (NLM) PubMed/Medline dataset, which includes more than 17 million abstracts and citations from approximately 5000 biomedical journals published since the 1950s. One of the unique capabilities of the additional Healia Clinical Trials Search is that you can restrict searches geographically and map locations of study sites.

It is possible to filter a search to Professionals, Females, Males, Kids, Teens, Seniors, African Heritage, Asian Heritage, Hispanic Heritage, Native Peoples and a few other categories.

What Will You Make with Your 3D Printer

3D Printer

Fancy a new vase or some unbreakable crockery for that camping trip, but haven’t got time to go shopping? What about a replacement for the broken spoke on your spectacles or an individually designed heads for your golf clubs? Or, how about a scale model of that new sports car your kids designed or a mini objet d’art created from photos of a Henry Moore sculpture? The possibilities for 3D printing are limited only by your imagination and what someone could come up with in a 3D drawing package or with CAD software.

3D printing, rapid prototyping, as it is often known, is not new. I first heard about 3D printing sometime in late 1980s while still a student. However, these devices, which have featured in TV shows such as CSI, could soon be coming to a workshop near you and may represent the biggest shift in commerce and manufacturing in decades. The Fab@Home wiki has more information on the technology, but 3D printing, essentially, turns a digitized representation of a solid object, which you might download, email, or create, into a real solid object. It using a vat of uncooked starting material (plastic, metal or alloy) and a laser, or other device, controlled by computer holding the digitized information to build up the object layer by layer.

There are numerous commercial 3D printers, known in some circles as fabbers, being used by the military for creating battle components in the field, in design studios for prototyping, and more recently for creating just about anything you care to name. However, once the killer app emerges, these machines will quickly enter the mainstream.

There are several videos of 3D printers in action on Youtube. But, I was brainstorming with my wife today, while walking the dog, to see if we could think of that killer app…clothes, disposable diapers or nappies, plastic paperclips, teacups, and buckets, were my first few suggestions. But, I blush to tell you what her first suggestion was…sex toys. Moreover, it’s our silicon wedding anniversary today, and all I could think was that she was trying to tell me something.

But, then it occurred to me, how 3D printing might rapidly move into the mainstream, and no, I’m not thinking of rubbery objects for the bedroom, but virtual gifts!

With the advent of social networking and web 2.0 communities there are often occasions when you might wish to reward or surprise someone you meet or interact with in such virtual spaces. Being sent a link to an interesting site, image, or music file as a gift is nice. But, what if you could send someone a solid object without actually having to buy it, package it up (discretely in some cases), and ship it out? A 3D printer suddenly becomes a way to spread the lurv in polymer resin. And, if you’re getting really close to that certain someone you met online, then you could always take on my wife’s original idea, and spread more than a little lurv, although I don’t a 3D printer exists yet that can produce 1.5 volt batteries.

What will you make with your 3D printer?

Diagnosing Disease With a CD Player

Chlorpyrifos structure

Years ago, I wrote about the lab-on-a-CD concept (actually it was in the September 2001 issue of Reactive Reports). Now, it seems the use of CD-ROMs and DVDs and the hardware used to play these popular audio and video compact discs (CDs) is coming of age in terms of home health monitoring and laboratory-based testing. Spanish scientists say CD technology could be adapted for tests ranging from the measurement of environmental toxins to at-home disease diagnosis.

Angel Maquieira and colleagues at Valencia Polytechnic University, Spain, have developed a CD with an immunoassay surface coating that can detect three pesticides, 2,4,5-TP, chlorpyrifos, and metolachlor, when samples are placed on the disc. By spinning the disc in a CD player the standard laser light can “read” the chemistry of the bound pesticides and a computer interpret the changes in laser intensity to identify them.

“The obtained results show the enormous prospective of compact discs in combination with CD players for multiresidue and drug discovery applications,” the researchers say. They are now improving sensitivity and versatility.

More information in the journal Analytical Chemistry

Microsoft and InChIKeys

Earlier this month, I hinted at how InChIKeys might be used in Googling for chemical information, well, I missed a trick. In 2006, at the BioIT World Life Sciences Conference and Expo, Microsoft announced the formation of the BioIT Alliance. The Alliance is a group of organizations working together to realize the potential of personalized medicine. Now, the Institute of Pure and Applied Chemistry (IUPAC) has joined the club. IUPAC’s contribution to the enterprise will lie primarily in being responsible for establishing standards in chemical information transmission. In this regard the InChI/InChIKey system will be critical to success.

IUPAC representative Stephen Heller says: The InChI/InChIKey is the first publicly available unique chemical identifier, which allows scientists to link and exchange information and data across the chemosphere and in the life sciences. The InChI/InChIKey is the molecular equivalent of a Digital Object Identifier (DOI), the journal article tracking code. “The InChI/InChIKey is an agent of change and an agent of the future for linking the chemical, biochemical, and biomedical information and data on the web,” says Heller. It will now provide the Microsoft BioIT Alliance with a much simpler, and free, way to work with chemical information.

Poison Darts and Poison Pens

Epibatidine

Many years ago, I reported on the earliest synthesis of the analgesic compound epibatidine from the poison frog Epipedobates tricolor. You’ll notice I was careful to say poison frog, not poison dart frog. In the prestigious pages of Science in 1993 I wasn’t quite so careful and describes this creature as a poison dart frog.

It was a simple mistake to make as there were dozens of references in the literature to this species as the toxic secretions of this and other frogs as being used in poison darts. However for E tricolor, this wasn’t and isn’t the case. It’s a toxic frog most certainly, but no one has ever tipped their darts with its secretions. The venom in the deluge of letters from readers wishing to highlight and correct my error while I was still a cub reporter writing freelance for the journal via its Cambridge office was enough to make my toes curl.

Anyway, the analgesic properties of epibatidine became famous. Several hundred times more potent than morphine, but with none of the addictive properties of its fellow opiates, it seemed that its career as a new painkiller was set. It has, as you can see from the picture, a quite stupendous chemical structure, which took several attempts to yield a total synthesis. Efforts are still ongoing I see from a quick scan of the current literature. A paper in JOC this month, has Armstrong, Bhonoah, and Shanahan wrestling with an aza-prins-pinacol approach to the 7-azabicyclo[2.2.1]heptanes of which epibatidine and its close cousin epiboxidine are examples.

It still surprises me that so little work seems to have been done to bring this compound and its analogs into the pharmaceutical fold. For instance, only a limited number of analogs have actually been synthesized and evaluated in vitro and negligible numbers have been tested in vivo. Given the enormous market a non-addictive painkiller with opiate-like power might share, I wonder why. Any pharma readers care to enlighten us?

Taking the P

Toilet

Sciencebase readers of a certain age will know exactly what I’m talking about if I were to ask, “Can I have a P, please, Bob?” The Bob in question being host of a TV game show for teens too long ago into my past for me to admit when. The Bob in question was almost marginally embarrassed by the question and mildly amused, although it referred only to the choice of letter.

Taking the P of course is a standard British pastime, although I’m not 100% certain about a couple of research papers published today in a special issue of the International Journal of Environmental Technology and Management on composting of solid waste and whether the P remains firmly in place or not.

One of the co-authors on the first paper (Post-composting techniques of digested household waste) is based at the WTO, and no, before you ask that’s not the World Trade Organization it is the World Toilet Organization in Singapore. Honestly. Apparently, the organization has a Toilet Entertainment link on its website (http://www.worldtoilet.org) and says that November 19th is World Toilet Day. Hmmm. Makes you wonder…that’s also the week of Thanksgiving in the US…

The second paper is entitled “Experience in improving fertilizer value of compost by enriching with urine” . The researchers say that “ecological sanitation concepts are closing the loop of nutrients contained in wastewater with agriculture.” Nice…

Personally, I’ve been taking the P to our compost heap for years. My wife, unfortunately, thinks it nothing more than an excuse to indulge in a little back garden naturism. It’s the phosphate and nitrogen content, I tell, her, they are good for the cucumbers! It is to no avail, of course, and the neighbours have told me they prefer theirs with dressing.

By the way, the Bob in question – Bob Holness – of BBC TV’s Blockbusters fame was the first radio broadcast actor to play James Bond.

Critical Acclaim

David Bradley Science Writer

A criticism levelled at the Sciencebase blog recently was that the subject matter is too diverse (check out the category list in the menu, to see what they mean) and that I, as blogger-in-chief on this humble site, simply alight on a subject of interest, almost at random (a random list under the heading Posts from the Past can be found in the menu), and fire off a short item about said subject (take you pick). Another reviewer tells me, rather positively I think, that the site is like a one-man New Scientist, and yet another suggests that although some of the posts are a bit long, there are plenty of subjects I don’t cover that I really ought to, and sometimes, perish the thought, I get things inadvertently not quite right…or even wrong!

Well, as they say, you cannot please all of the people all of the time. However, I’ve been blogging, in one sense or another, on subjects that interest me for almost two decades for dozens of different publications who more often than not come back for more and tell me that their readers are very happy with the words I produce. If the subjects I choose to write about on Sciencebase, my personal blog, are not to everyone’s taste 100% of the time, then, I’m afraid that’s just the nature of blogging.

I read dozens and dozens of blogs, sometimes it seems like thousands, usually via RSS, on a daily basis. I have to admit that not all of those I subscribe to are fascinating, in-depth, and unique 100% of the time. But, they do provide me with insights and inspiration into a wide range of subjects much of the time. Occasionally, they make me as angry as a least one recent commentator feels about Sciencebase.

But, like I say, a blog is personal. I write it for me first off and hope that it entertains or informs others across the blogosphere. Some of the posts are flippant, shallow, puerile even, some are more profound, and some of them reflect additional thoughts and comments from the various scientists I interview for the other publications I write for and link to.

I presume that a few of the more than 2500 regular RSS subscribers served each day, the average 8000-plus daily visitors who kindly turn up at my virtual door, and the many uncounted readers who see syndicated versions of this site on Techdispenser.com and elsewhere, actually quite like my seemingly random choice of subjects, appreciate my efforts at a unique and honest writing style, and find my alleged attempts at a one-man science portal to be, to some degree, informative, useful, and fun. If that sounds pretentious, then be thankful I didn’t use the words stakeholder, leverage, or incentivize.

Mighty Neat Diabetes Target

mitoneet protein

In this week’s SpectroscopyNOW column, I cover a wide range of subjects with the usual hint of spectroscopy, informatics, and crystallography. First up is a study on a unique protein, MitoNEET.

The protein was previously identified as a putative site for the activity of diabetes drugs known as thiazolidinediones, or which Actos is an example. The determination of the protein’s three-dimensional crystal structure coupled with bioinformatics information demonstrates that it is a clear target for small molecules. The mode of action was previously linked to an entirely different protein, according to biophysical chemist Patricia Jennings and physicist Mark Paddock, and their colleagues at the University of California at San Diego (UCSD) and Stanford Synchrotron Radiation Laboratory and the Hebrew University of Jerusalem, Israel.

“This is the first time that a protein like this has ever been found,” explains Paddock, “It is a brand new structure, a unique beast, which makes it an exciting target for structure-based drug design.” The structure shows two protomers intertwined to form a unique dimeric structure, explain the researchers, this constitutes a new fold not only among the 650 known Fe-S proteins structures but also among all known proteins.

Given that there is at least one clinically tested drug in this area it shouldn’t be too long before other novel compounds that can moderate insulin by interacting with MitoNEET are being investigated. However, it does highlight once again just how hit and miss the drug discovery process can be if the thiazolidinediones are not actually targeting the protein with which they were initially thought to interact.

Also in this week’s issue, more on the crab metabolite story from last week, copper blues and the toxic mouse, and Rod of Titania, the new superhero that could improve energy technologies and sunscreen simultaneously.