Genomics

How do you go about researching a genetic disease? This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio. A bit of background Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the conversation turns to Woody, and someone asks the question that no one wants to touch. Does Arlo's girlfriend know about Huntington's? ...dead silence... Now, I did see the movie ... Read more
If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner. According to GenomeWeb, the test identifies both the breed and origin of the animal.
The university and the company said meat traceability is necessary to ensure consumer safety, particularly in cases of infectious disease outbreaks or accidental feed contamination.
No more ... Read more
i-e3899186ef576991098fed4ff62eab0f-small_dice.gif'Tis the holiday season and, according to ancient lore, the time when miraculous events are most likely to take place. One of those well-known and miraculous events of ancient days was the birth of a son to a young girl, who, although she was married (Okay, I'm not sure about this part of the story) she was said to be a virgin and the birth to be a miracle. Hmmm. ... Read more
GenomeWeb reports that Rite Aid drug stores on the West coast are now selling kits for doing paternity tests. The kits are made by Sorenson Genomics in Utah. Sorenson Genomics calls it the "peace-mind-test." Really! Each kit contains a swab for collecting cheek cells from the inside of your mouth and a container for mailing the sample to the lab. As far as I can tell, you buy the kit for $29.99, take a sample, fill out the consent forms, and ... Read more
The genie is out of the bottle. Personal genomes are not just for Venter and Watson anymore. Three competing companies, 23andme, Decode, and Navigenics are betting that you want to do a little better than reading your horoscopes and playing with tea leaves. They think that you want to know something about your destiny and take control of your future. And when I look at the 23andme web site, I want it, too. I want it so badly, it makes me drool. ... Read more
Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread. Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used to look at ancestry. Genetic markers in the mitochondrial DNA are used to trace ancestry through the maternal line and markers on the Y chromosome can be used to learn about one ... Read more
Last year I wrote about an experiment where I compared a human mitochondrial DNA sequence to primate sequences in the GenBank. Since I wanted to know about the differences between humans, gorillas, and chimps, I used the Entrez query 'Great Apes' to limit my search to a set of sequences in the PopSet database that contained gorillas, bonobos, chimps, and human DNA. A week ago, I tried to repeat this experiment and...

It didn't work.

All I saw were human ... Read more

Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out who else shares our bodies, and lives in our skin, in our stomachs, and other places where the sun doesn't shine. Craig Venter used ... Read more
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles. The general process is this:
  • 1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is
  • ... Read more
Welcome Bio256 students! This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a subject that you can really grasp without getting your fingers dirty. So, this course will include a lot of hands-on work. My friend and collaborator at Johns Hopkins University has given me data sets from the past three years and ... Read more

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