DNA Goes to the Tigers

by Dr. Hsien-Hsien Lei
Posted August 13, 2007 in DNA in General

From some of my recent posts, you might conclude that I’m an animal lover. And guess what? You’d be wrong! I own no pets – no dog, no cat, no hamster, no fish.

What I find fascinating about animals, however, is that they have DNA. Even more amazing, there’s an entire industry and field dedicated to testing animal DNA. DNA testing is the tool of the moment for nabbing doggy perpetrators to animal poachers.

While databases of DNA from criminals and assorted random people are the subject of contentious debate in New York State and Great Britain, a DNA database for tigers called the American Tiger Registry is also being proposed. Brian Werner of the Tiger Missing Link Foundation wants to use DNA testing to separate purebred tigers in captivity from those that are mixed. The plan is to develop breeding programs that “preserve the purity of the tiger subspecies.”

Another endangered species, the cougar, is under scrutiny in Michigan. Scientists are claiming that DNA “distilled” from cougar scat* proves that the wild cat can be found in Michigan. But objections soon arose that the DNA analysis was based on only 10 scat specimens.

Biologist Dave Hamilton:

It’s as if the scats fell out of the Michigan sky. Field collection methods are not described (by Brad Swanson and Patrick Rusz), they could not be replicated, and there is no reliable chain of custody described. Where is the rest of the evidence that supports the claim that free-ranging cougars exist in many areas of Michigan?

The last time I heard “chain of custody” was in relation to paternity tests. This stuff is serious! But not so serious that you can’t make your own edible wildlife scat.

* Part 2 of the Michigan Outdoor News report on using DNA evidence in cougar research.

Tags: cougars, tiger, dna, genetics, genes, wildlife, endangered species, animals, scat

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Eye on DNA Headlines for 12 August 2007

by Dr. Hsien-Hsien Lei
Posted August 12, 2007 in Eye on DNA Headlines

Request for Feedback: Do you like these headline round-ups in one post like this? Or would you prefer that each “headline” be an individual post on its own?

• Blaine at The Genetic Genealogist hosts Gene Genie #13: Into The Future.
• Dr. Paul Decelles pens a beautiful poem about the flower Datura and ties it into genetics.
• DNA tests have been used to identify cows that make A2 milk, which is supposedly healthier, safer, and easier to digest. An established product in Australia and New Zealand, about 100 stores in the American Midwest are selling the milk now. Has anyone tried A2 milk?
• New Scientist reports on simulations showing electrically charged dust that form DNA-like double helixes. They act like reproducing living organisms which can store information within the structure and copy itself. Scientists hypothesize that DNA dust helices could be a form of primitive life found in planetary rings containing fine ice grains. Reminds me of the extraterrestrial DNA stories that circulate once in a while.
• Last month, Katherine Bourzac of Technology Review wrote about mapping complex diseases. Researchers calculated the overlap between 161 different diseases and found that schizophrenia, bipolar disorder, and autism may be attributable to one set of common genes.
• Mark Henderson of The Times (UK) looks at the intersection between nature and nurture (curiously assigned to the women’s section of the website) as it relates to popular news item of the week – Friendship May Lie in the Genes.

  Matt Ridley writes in The Agile Gene:

  If personality is created by parents, peers, or society at large, then it is still determined; it is not free.

  In some ways the news that our genes are important contributors to our personality should be reassuring: the imperviousness of individual human nature to outside influences provides a bulwark against brainwashing. At least we are determined by our own intrinsic forces rather than somebody else’s.

Tags: genetics, genes, dna, nature, nurture, matt ridley, a2 milk

(8 comments)

DNA Video: Mutations

by Dr. Hsien-Hsien Lei
Posted August 11, 2007 in DNA Podcasts and Videos

A video on DNA point mutations from Nguyen Thnah Cong, a geneticist in Hanoi, Vietnam.

Tags: genetics, genes, dna, video

(3 comments)

Only One Gene for Exfoliative Glaucoma

by Dr. Hsien-Hsien Lei
Posted August 11, 2007 in DNA and Disease

Most common diseases like heart disease and diabetes are caused by more than one gene and are sometimes interchangeably called complex, polygenic diseases. But as this past week’s finding of the connection between exfoliative glaucoma and the lysyl oxidase-like 1 gene (LOXL1) shows, sometimes one gene is all it takes.

Exfoliative glaucoma is a common disease of aging. At least 10-20% of people after age 60 are affected to some degree by exfoliation syndrome. In Iceland and Finland (from where the researchers of this new study hail), exfoliative glaucoma rates are over 20% in persons over age 60. The build-up of extracellular material in the eye can lead to glaucoma and may also cause cataract, lens dislocation, and central retinal vein occlusion resulting in blindness. The causes of exfoliative glaucoma are not well understood.

Some of the major risk factors for glaucoma include:

• Age
• Family history
• Race – Blacks have a higher risk
• Diabetes
• Eye injury

In a recent genomewide association study of 16,000 Icelandic and Swedish participants, researchers from deCODE Genetics, the National University Hospital in Reykjavik and Uppsala University in Sweden found two single nucleotide polymorphisms (SNPs) on chromosome 15, single base differences in the sequence of the LOXL1 gene. Allele G of rs1048661 and allele G of rs3825942 accounted for 99% of all cases of exfoliative glaucoma. An estimated 25% of the general population is believed to have two copies of the high risk haplotype with a corresponding 100 times increased risk of developing the disease.

Kari Stefansson, CEO of deCODE:

This discovery is remarkable and important because the genetics has led us directly to what appears to be the sole cause of a devastating common disease. The risk conferred by these variants is such that it accounts for virtually all cases of exfoliation glaucoma, meaning that if we can neutralize the impact of these variants we might eliminate the disease [emphasis added]. The LOXL1 protein made by this gene appears to play a role in the accumulation of microfibullar deposits that causes XFG, providing a promising mechanism to target for developing therapy. We plan to conduct additional studies to examine how we can take advantage of this finding to begin drug discovery.

And, of course, diagnostic DNA tests to identify high risk patients carrying these gene variants may also help with treatment and prevention.

New York Times, August 10, 2007
Science, August 9, 2007

Tags: lysyl oxidase-like 1 gene, LOXL1, exfoliative glaucoma, glaucoma, eye, diseases, medicine, genome, genomics, genetics, genes, dna, decode, kari stefansson

(3 comments)

DNA Quote of the Day: Dr. Ruth Faden

by Dr. Hsien-Hsien Lei
Posted August 10, 2007 in DNA Quotes and Excerpts

Dr. Ruth Faden in the Johns Hopkins Public Health Magazine feature – The Genetic Journey:

We have to be thinking very broadly about how genetic information should be used—not only in a medical context, but also how that information could be used in employment settings and law enforcement settings and national security settings. Information can be useful for lots of different purposes, and the question is, which purposes are acceptable?

Tags: genetic privacy, genetics, genes, dna, genome, genomics, quotes, ruth faden

(3 comments)

DNA in Wildlife Investigations

by Dr. Hsien-Hsien Lei
Posted August 9, 2007 in DNA and the Law

There seems to be no end of possibilities for using DNA in everyday life. If you’re an animal lover, you may have heard of dog owners using DNA to figure out their pets’ breed. And then there’s the use of DNA to ID dogs that attack innocent bystanders.

In Idaho, wildlife DNA specialist Dr. Karen Rudolph uses tissue, hair, bone chip, or blood splatters to link poachers to the kill site. A suspect in one case cleaned and boiled his knife thinking that he’d destroyed all the evidence. But Dr. Rudolph still managed to retrieve a tiny speck of dried blood from the hinge of the folding knife. Enough to convict.

Another case involved attempted wolf poisoning. Tim Sundles made pesticide-laced meatballs that killed more than 20 pet dogs. DNA from the meatballs matched DNA from the blood found in his garage. DNA from human cells found in urine at the crime scene also matched Sundles’s DNA. He pled guilty.

NB: If you’re interested in hunting and fishing the legal way, visit my friend Steve Remington’s Skinny Moose Media network .

Tags: poaching, genetics, genes, dna, animals, dogs, wildlife, hunting

(3 comments)

Eye on DNA Headlines for 9 August 2007

by Dr. Hsien-Hsien Lei
Posted August 9, 2007 in DNA Fun, Eye on DNA Headlines

• Pat Washburn at The Health Wisdom Blog hosts the latest issue of Medicine 2.0.
• My post on medical tourism for preimplantation genetic diagnosis has been syndicated by MedTripInfo.
• Thanks to ifantabulous for adding Eye on DNA to her blogroll.
• Peggy at Biology in Science Fiction has a great review of creative biotechnology.
• John Hawks points to DNA rainbow which created graphics for all the human chromosomes by assigning a color to each of the A, C, G, T bases. They also present tons of other information on genetics, including a species comparison.

  Although scientists know already most of the sequence of the human DNA, the information the genetic code helds is not fully understood. Therefore we want to introduce a new idea to display and maybe better understand the code. Structures and repeating bases can be recognized faster and by resizing an image with an appropriate algorithm it is possible to get a quick overview of different sections in the chromosome.

• Jonathan Eisen sent me this story from The Onion – DNA Evidence Frees Man From Zoo. If they thought this guy was a giraffe, then I say it’s time we tested the DNA of supermodels!

Tags: genetics, genes, dna, dna rainbow, science

(6 comments)

Sara Ost of Healthbolt and I Will Blog for Health

by Dr. Hsien-Hsien Lei
Posted August 8, 2007 in DNA in General

Going slightly off topic today, I want to look at the ethics and practice of health blogging. I first wrote about this two years ago at ProBlogger where I mentioned an “honor roll” I used to maintain of blogs which answered a series of questions posed by the the National Center for Complementary and Alternative Medicine – 10 Things To Know About Evaluating Medical Resources on the Web.

As part of the pre-rounds interview for Grand Rounds, Dr. Nick Genes also touched upon ethics for medical bloggers asking:

If I recall, you were the first to propose an ethical code (honor roll) for medical bloggers. Did anything specific prompt that? Why do you think it hasn’t been widely adopted? How was your proposal
different from the HONcode, and the new initiative?

My response, which didn’t make the cut because of space limitations (so I talk a lot):

HONcode is great and I have always applied for my blogs but it really doesn’t require that bloggers reveal very much about themselves. When I started the Genetics and Health Honor Roll, I wasn’t intending to make it anything other than a full disclosure meme. I thought that if I could get some people to stop and think about what they were doing as well as making their motivations and qualifications public, it might up the credibility of healthcare blogging.

I was inspired to start the full disclosure meme when I came across blog after blog (healthcare and other) that didn’t fact check and were, in fact, spreading misinformation. In addition to that, I also don’t like bloggers who are hiding behind total anonymity. Why should I take the opinion of someone seriously if they’re using a pseudonym and won’t tell me anything about how they’ve gained their knowledge? Certainly, it’s within people’s rights to remain anonymous but at the very least, bloggers should show convincing evidence to their readers that they can trust the veracity of what they’re writing.

The new Healthcare Blogger Code of Ethics takes another stab at legitimizing healthcare blogging. It’s an honorable goal, and one to which I subscribe, but in the end, bloggers will still write what they want and must be responsible for it within the guidelines of their own situations. And that’s what blogging should be anyway – free expression with a pinch of thoughtful self-moderation.

~~~~~
And so, today I’d like to welcome guest blogger Sara Ost of Healthbolt. This prolific health blogger shares 7 Essential Steps for Non-Experts Blogging About Expert Things.

How can a blogger without the proper science or medical credentials provide a trustworthy (and worthy) resource for readers interested in health?

Hi, I’m Sara. I’m the editor of Mark’s Daily Apple, a quickly-growing alternative health blog with an irreverent tone, and Healthbolt, also decidedly irreverent and the top-ranked health ‘n body blog in the world. I’m not a doctor, I’m not a scientist, and in fact, the only science class I took in college was tropical biology in Costa Rica. Let’s just say I spent more time learning about the indigenous liquor (guaro) than anything scientific. Although I do remember that cashews are not related to other nuts and frogs are an indicator species. Still, that’s not very helpful.

I am trained as a writer, and for a year in graduate school, I paid the bills by researching and writing for a health show. It never took off from the pilot series, but the intensity of daily production was a good testing ground for the pace of blogging, and non-medical-expert me learned how to decipher even the most complicated medical studies. Within a few short weeks, I knew what murine trials were and I could rattle off the qualitative hierarchy of medical studies with the best of ‘em. Health bloggers needn’t be doctors, and they don’t even need to know their way around a medical study, but they do need to prove trustworthiness.

Though I’m obviously biased, I don’t think there is a problem with a non-expert blogging about expert matters, so long as we non-experts make that clear. You should do that with a visible disclaimer positioned in at least one place on your blog.

You should also write with passion, honesty and style – after all, that’s why your readers are reading you and not the medical studies (or another blog!). Spend two seconds at either of the blogs I write for and it’s apparent that I find value in humor and (on more caffeinated days) satire. That’s not for everyone, but the readers love it, and it immediately helps to establish that I’m not pretending to be an expert, while also offering them a unique experience.

I really cannot overstate the value of finding and establishing your own voice. Thousands of health blogs are really nothing more than tiresome retreads and summaries of the daily news (or worse, other blogs). You don’t read them, and neither do I. Most of these writers are not experts and many are poor writers. Be yourself – hone your writing craft and go no-holds-barred with your personality – and you’re guaranteed to stand out from the pack. Beyond that, it’s essential that you prove yourself to be trustworthy.

Here are my top tips for doing just that:

Continue reading…

(8 comments)

DNA Testing Too Expensive in Uganda

by Dr. Hsien-Hsien Lei
Posted August 8, 2007 in DNA Around the World, DNA Testing

Uganda may have gotten its first “DNA machine” but Josephine Nakato Matovu reminds us that costs are prohibitive for many people, including victims of sexual assault.

I know that the DNA machine could be utilised in solving crimes with the collection of DNA evidence to compare against suspects and/or offenders in sexual assault cases.

However, I am sure that few women and children are in a position to pay the large amounts of money for DNA testing that is required to prove their cases in court.

According to the UK Department for International Development , per capita income in Uganda is around $300 per year. With the average cost of paternity testing in Uganda set at $240*, it’s obvious that no average citizen could afford this. The question is, can the police?

DNA testing is not just too expensive for citizens of Uganda. The South Africa DNA Project was founded to address this issue and to support forensics DNA testing. Maybe charitable organizations, like the Bill & Melinda Gates Foundation, should consider tackling the availability of DNA tests not just for forensics, but for medical genetic testing as well. It’s certainly a more soluble problem than many other public health concerns.

*”At-home” paternity tests in the US where you collect your own DNA and send it in to the lab can be as little as $99.

Tags: uganda, south africa, dna testing, genetics, genes, dna, public health, forensics

(2 comments)

Grand Rounds at the Beach

by Dr. Hsien-Hsien Lei
Posted August 7, 2007 in DNA in General

Welcome to the Grand Rounds Beach House! Although the Grand Rounds party has been held for two years and 46 weeks, this is the first time it’s been at this beautiful beach house that I reserved especially for medicine and health bloggers and their guests. Thanks also to Dr. Nick Genes for his leadership and my pre-rounds interview at Medscape.

Please wander around the rooms at your leisure and strike up a conversation with the people there if you have time. They’d appreciate some attention and a drink if you have it!

PHENOM PARLOR

Kim at Emergiblog shares what it’s like to be a “baby” nurse raised by a village of other more experienced nurses and doctors.

Dean Moyer at Rebuild Your Back takes down alternative medicine and says that practitioners use endorphins as the “hook.”

Dr. Jonathan Eisen of The Tree of Life gives 10 reasons why medical professionals need to study evolution so you really have no excuse!

Tundra Medicine Dreams recounts an edge-of-the-seat story of a patient whose prostate was causing him pain. I hope he gets the treatment he needs way up there in Alaska!

Dr. Kristina Chew at AutismVox examines the concept of honesty in light of autism.

Colin Son at From Medskool wants to know why doctors act like car salesmen when it comes to discussing DNI/DNR (do no intubate/do not resuscitate) with their patients. I haven’t decided how I would make that choice for myself and loved ones. Have you?

ERnursey would avoid a pelvic exam in the emergency room at all costs but not everyone is so lucky. She’s seen and smelled some serious feminine maladies.

GruntDoc follows behind (ewww, terrible pun) and shares his experience removing a “rectal foreign body.”

Bertalan Mesko at ScienceRoll feels genetically naked at the thought of everyone having a peek at his genome. My advice? Get used to it, buddy. (Just kidding! More from Eye on DNA about whole genome sequencing for all.)

Continue reading…

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