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 backgroundAlice'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
'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
Sexual attraction is all in your brain. At least if you're a nematode.
Ricardipus has a great image if you want to see a nematode picture.
I always thought worms were hermaphrodites (both male and female) but the story, as usual, turns out to be a bit more complex. Researchers at the University of Utah have found that worms have definite preferences for one sex or the other. And, if they kill off certain kinds of cells, the preference for one sex or another can change.
From the University ... Read more
As many of you know, I'm a big fan of do-it-yourself biology. Digital biology, the field that I write about, is particularly well-suited to this kind of fun and exploration.
Last week, I wrote some instructions for making a phylogenetic tree from mitochondrial genomes. This week, we'll continue our analysis.
I wrote this activity, in part, because of this awful handout that my oldest daughter brought home last year. She presented me with an overly photocopied paper that showed ... 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...
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
A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much.
I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million.
That was an estimate, of course. But what did it really cost?
Genome Technology asked J. Craig himself. In the October 2007 issue of GT, JCV estimates that the cost from the first Celera human genome project ( ... Read more
October is a month of darkness, mystery, and dread. Only one holiday brings joy in October and even then, October joy is distilled through fear and apprehension. In the early evenings the sun hurries home and once familiar objects loom ominously in the dark. Giant spiders appear out the fog, lurking on webs that span our walkways and doors. Even Mendel's Garden is dark and malevolent when October greys our skies.
Horror stories for adults ... Read more