Genetics & Molecular Biology
sporte | December 19, 2007In which we're reminded that database searches are experiments, too.
One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes even a day later, is a different database. And, if you query a different database, you may get a different result.
The series that I'm currently posting is one that I started working on a couple of years ago. Originally, I was…
sporte | December 18, 2007How 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 quite a few years ago, so my memory…
sporte | December 3, 2007'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.
How do you think the news would be received if that sort of thing happened today?
Certainly, if the young girl were to produce a grilled cheese sandwich with a burn spot that vaguely resembled a woman in a robe, someone might be…
sporte | November 19, 2007Sexual 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 of Utah:
"They look like girls, but act and think like boys," says Jamie White, a postdoctoral…
sporte | November 16, 2007As 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 several protein sequences from cytochrome C in several creatures. She said she was supposed count the…
sporte | November 14, 2007Students 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's father.…
sporte | November 9, 2007Last 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 mitochondrial sequences. I know the other sequences match, but I didn't see them since there are so many human sequences that match…
sporte | October 21, 2007Welcome 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 we…
sporte | October 16, 2007A 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 (guess who?) was about $100 million and that the cost of his most recent genome project was at least $70 million.…
sporte | October 14, 2007October 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.
genetics, Mendel's garden, blog carnival.
Horror stories for adults
October looks bleaker than usual if you're out of work and not getting paid. If your income matches this…
sporte | September 19, 2007But I'm certain that you will find some interesting things.
Mendel's Garden will be ready for harvest, here on Sunday, October 7th, and I need your help.
You won't need to stay on the path, but I would like you to submit your best genetics & molecular biology articles by midnight, Friday October 5th.
Either send your articles to me: digitalbio at gmail dot com
or use the handy-dandy submission form.
With your help, Mendel's Garden is certain to bloom with earthly delights.
sporte | September 11, 2007Two protein structures from an avian influenza virus are shown below. One form of the protein makes influenza virus resistant to Oseltamivir (Tamiflu®)
Don't worry, these proteins aren't from H5N1, but they do come from a related influenza virus that also infects birds.
technorati tags: molecular models, protein structures, influenza, bioinformatics, Cn3D
One protein structure is from a strain that is sensitive to an anti-viral drug called "Tamiflu®". The other structure is from the same virus, except there's a slight difference. A single base change in the viral RNA changed the codon that…
sporte | September 7, 2007During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery.
If it's correct.
tags: DNA sequence analysis, antiobiotic resistance , microbiology, blastn
The way this sequence was identified as Β-lactamase was through a blastn search at the NCBI. And in fact, it was correct to…
sporte | September 6, 2007One of my readers asked: Why does genome sequencing cost so much?
My short answer is because it's big.
But I thought it would be fun to give a better answer to this question, especially since I'm sure many of you are wondering the same thing.
Okay, so let's do some math.
Don't worry, this math isn't very complicated and I'll explain where most of the numbers come from.
Estimating costs from salaries
First, we'll take the easy route. My experience with grant budgets has taught me that the greatest cost for any project comes from salaries. If we look at the PLoS paper with Craig Venter's…
sporte | September 5, 2007If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.)
You may be wondering, and rightly so: just what is a SNP?
Never fear, hopefully this post will answer some of those questions.
tags: DNA sequencing, DNA , SNPs, genetic testing
SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a…
sporte | September 4, 2007We were all thrilled last spring when the Genetic Information Nondiscrimination Act passed the House by a vote of 420 to 3. When GINA gets through the Senate, this act will protect individuals against discrimination based on their genetic information with health insurance and employment. The promise of genomic project won't ever be achieved until individuals (besides Watson and Venter) can use their own genetic information to benefit their own health, without fear of insurance repercussions.
Passing this act seems like a no-brainer.
But I glanced at Nature last night and noticed that…
sporte | September 4, 2007
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend."
The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value.
Holmes gazed thoughtfully at the map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your life and gave you a reason to do more than…
sporte | August 16, 2007Thanks to Steven Colbert you can hear about DNA directly from Dr. Spencer Wells from the National Genographic Project.
I read about this video in the GenomeWeb Daily Scan and had to check it out.
Who would have thought scientists could be so funny?
Watch it quick! There was a note at the Comedy Central site saying the video expires on Sept. 15th 2007.
or you can go here and find out whether DNA could happen to you, too!
sporte | July 30, 2007If you're in Seattle this week, and you're not going to the zoo concert on Wednesday night, you might enjoy this lecture series from the UW Genome Sciences department.
We missed the first two talks because of travel, but our college-age daughter and her friend persuaded us to go last Weds. and hear Debbie Nickerson talk about genetics and drugs.
Usually these sorts of talks are held during the school year and they're packed with high school students who're getting extra credit for attending and taking notes. This time it was different.
We looked around the room when we arrived, of course…
sporte | July 12, 2007By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes.
tags: blast, BLAST tutorial, science education
Because of these changes, and because I'm giving a workshop for teachers on BLAST at the Fralin Biotechnology Conference in Blacksburg, VA, next week, it seemed like a good time to update our animated BLAST tutorial at Geospiza Education and save myself some trouble.
I originally created the BLAST for beginners tutorial to…