Archive for the 'DNA' Category

One of my coworkers is expecting a child later this year and we got to talking about what color her child’s eyes would be. Nobody could remember the rules of eye color inheritance, so here’s the answer for my co-worker and others interested.

For starters, it’s quite complex. There are three genes called EYCL1, EYCL2, and EYCL3 that play a large role in determining the three main phenotypes brown, green, and blue. (Phenotype is a descriptive term used to define the manifestation of genetic and environmental factors.) These three phenotypes combine to make the six main eye colors: blue, grey, yellow, hazel, light brown, and dark brown.

There are also a number of SNPs (single nucleotide polymorphisms, pronounced “snips” that regulate the main genes. SNPs are changes in one single nucleotide letter of the DNA that affect gene expression.

These SNPs are located near genes for responsible for all sort of traits like eye and hair colors. For example, a recent study a few months ago talked about SNPs near the OCA2 gene that had effects on eye color. As the paper’s author Dr. Richard Strum told the BBC, “to use an analogy, one of the changes is like switching the light on and off, while the other is like changing the light bulb from brown to green.”

All these genes and SNPs come together to determine eye by regulating the amount of pigment produced. The main pigment in human eyes is called eumelanin. Brown eyes (the most dominate eye color in the world) contain high amounts of brown colored eumelanin. Another pigment that plays a role is the yellow colored lipofuscin.

Here’s a breakdown of eye colors and pigments:
Brown – high amounts of eumelanin
Amber or yellow – lipofuscin
Blue – a little yellow and little to none brown
Green – a lot of yellow and some brown
Hazel eyes – a combination of eye pigments that change with the amount of sunlight and clothing.
Gray – little to none of both yellow and brown
Albino eyes – gray is the color of eyes in people with complete albinism. The red eye feature that many people associate with albinos is due to the blood vessels that add a red tint. This tint can easily be augmented in the photographs because of the red eye effect.

As you can see, eye color genetics is far from straightforward. While eye color tends to run in families, it’s not unheard of two brown-eyed parents to have a blue-eyed child. To answer the original question that my expecting co-worker has: I found an interesting website that will take a shot at predicting the eye color of your future child. It’s called “What Color Eyes Would Your Children Have?”. I doubt they updated their formula for the recent discovery of the SNPs near the OCA2 gene (plus you would probably need to upload maternal and paternal DNA sequences for the SNPs), but it’s still an interesting little web application that will give you some decent odds.

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Posted by Tim Roth, author of the political blog Think Anew and Act Anew

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Sources:
1. Sturm R.A. and Frudakis T.N. “Eye color: portals into pigmentation genes and ancestry.” Trends Genet. 2004 Aug;20(8):327-32. PMID: 15262401. PDF Link
2. “Genetics of eye colour unlocked”, Paul Rincon, Science reporter, BBC News
3. “Eye color”, Wikipedia entry
4. “What Color Eyes Would Your Children Have”

For the first article of this science blog, I thought I would go back to beginning of my interest in science: Jurassic Park. Awesome book. Awesome movie. Awesome soundtrack. In fact, I’m currently listening to the soundtrack by John Williams as I write this. I can even faintly remember my 5th grade crush and I talking about it because she was also reading it for a book report.

Other than the foundation for my 5th grade love affair, Jurassic Park was and still is a fascinating science fiction book. Dinosaurs are very much part of our culture and they capture the imaginations of children and adults worldwide (like myself, in case if you haven’t figured that out).

So, is Jurassic Park possible? In theory, cloning an dinosaur is possible, but in practice it’s next to impossible with today’s technology and understanding of dinosaur embryology. When researching this article, I naturally hit up Wikipedia and sure enough, I found an article called “Biological issues in Jurassic Park” [2] A good portion of this article talks about idea of extracting dinosaur DNA (for more info DNA, see the Wikipedia entry) from mosquitoes fossilized in amber. The theory behind this concept of Jurassic Park was first discussed by George O. Poinar in the 1980s and involved the theory that a 65 to 230 million year old mosquito bit a dinosaur, ingested the blood cells, and ended up embedded in amber which is fossilized tree sap. [1 & 2] A very clever idea and it sounds good on paper and ancient DNA has been extracted this way. [3] However, no dinosaur DNA has been found using this method.

Even if an amber miner were to hit the jackpot, the quality of DNA yielded wouldn’t be sufficient to grow a dinosaur. The book acknowledged this fact and talked about how frog DNA was used to fill the gaps in the genetic code. Once again, this sounds good on paper but knowing how merge two species of DNA is next to impossible without knowing the original dinosaur DNA sequence. While dinosaur and frog DNA are relatively similar, slight differences in crucial genes like homeobox genes that regulate which parts of DNA are activated for a specific task (they essentially tell a developing dinosaur grow a leg here and here, etc.) would be gigantic hurdle to hatching a healthy infant dinosaur.

However, the bar was lowered a great deal with the publication of a March 2005 article in the journal Science. To the great astonishment of all, actual soft tissue of a Tyrannosaurus rex was found deep inside the thigh bone! This was a huge breakthrough because it was always assumed there was no way dinosaur soft tissue could escape the process of fossilization after 65 million years. Using a new technique to remove mineralized bone, researchers led by Mary H. Schweitzer of North Carolina State University discovered blood vessels, bones cells, and even blood cells with possible intact nuclei! (nuclei or nucleus are the portion of cells that holds DNA) While it highlly doubtful they will find the entire T.Rex genome (the term that describes the entire DNA sequence of an organism), the chances of finding valuable DNA fragments are “promising”. This process of DNA extraction will be long and difficult (story is almost 2 years old and I haven’t heard anything), but I will keep my ear to ground and do some more through searching for new developments. Even if this particular thigh bone doesn’t yield anything, this development means other bones will contain soft tissue. This particular T. Rex skeleton was well-preserved….that means they are other dinosaur skeletons that are even more preserved yet to be found, so and so forth. [4]

If finding the complete T. Rex genome wasn’t hard enough, the next step would present challenges that science can’t just handle at this moment. All embryos need extra hormones at precise levels and times to grow properly. It’s doubtful that the pregnancy hormones of currently living relatives like birds and crocodiles would be able to recognize the dinosaur DNA and act upon a dinosaur embryo, so the most likely route would be a synthetic egg. This technology currently exists, but the hormones would have to devised from the dinosaur genome. Without an real-life dinosaur mother and egg to study, this will be a daunting task and will require much experimenting with dinosaur DNA (once a complete genome is sequenced, of course).

In summary, from all the reading I did on this subject I think that one day in the very distant future something like Jurassic Park could be possible. When I say the very distant future, I’m talking like 500 years from now when we have hopefully figured out how to sustain food, water, energy, and first-rate medical care for all of humanity while sustaining a balance with the environment. After all, as little-kid-on-Christmas-morning exciting going to the real Jurassic Park would be, we have more important challenges to solve for now before the scientific community puts more weight behind this kind of research.

Stay tuned for more updates on this story and dinosaurs in general.

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Posted by Tim Roth, author of the political blog Think Anew and Act Anew

Sources:
1. “Biological issues in Jurassic Park”, Wikipedia entry
2. “Dinosaur DNA”
3. Cano RJ, Poinar H, Poinar Jr GO. 1992a. Isolation and partial characterisation of DNA from the bee Problebeia dominicana (Apidae:Hymenoptera) in 25-40 million year old amber. Med Sci Res 20:249-251
4. “Soft Tissues Recovered from Ancient Dinosaur” by Christopher Joyce, NPR broadcast