Evolution:
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different...
Read on »
Posted on April 17, 2008 8:00 AM • 2 Comments •
Ribosomes are molecular machines that build new proteins. This process of synthesizing a protein is also known as translation. Many antibiotics prevent translation by binding to ribosomal RNA. In the class that I'm teaching, we're going to be looking at ribosome structures to see if the polymorphisms that we find in the sequences of 16S ribosomal RNA are related antibiotic...
Read on »
Posted on April 16, 2008 7:54 PM • 2 Comments •
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA)...
Read on »
Posted on March 27, 2008 9:11 AM • 24 Comments •
Two molecules are locked in a tight embrace. Who are they?
Read on »
Posted on December 28, 2007 10:12 AM • 0 Comments •
You can get a jump on the Darwin Day festivities. Once again the Alliance for Science is sponsoring an essay contest for Darwin Day. If you download their suggestions for good essay writing, you can get your essay done over winter break and have a good crack at winning on those cash prizes! The Alliance for Science is pleased to...
Posted on December 20, 2007 9:29 AM • 0 Comments •
This is a fun puzzle. The pink molecule is a protein and the other molecule is a nucleic acid....
Read on »
Posted on December 7, 2007 9:30 AM • 17 Comments •
You too, can compare chimp and human DNA.
Read on »
Posted on November 16, 2007 8:51 AM • 0 Comments •
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...
Read on »
Posted on November 14, 2007 4:04 PM • 9 Comments •
An evolution activity for the classroom.
Read on »
Posted on November 9, 2007 3:47 PM • 0 Comments •
Fun with molecular models!
Read on »
Posted on September 11, 2007 11:46 AM • 3 Comments •
One of the places that I've always wanted to visit in Portland, OR, is Powell's City of Books. Powell's is the kind of bookstore that people in Seattle discuss in the same reverent tones that they use when they're describing Cody's in Berkeley or City Light in San Francisco. It's not just a bookstore. It's a destination. I guess that's...
Read on »
Posted on September 10, 2007 8:30 AM • 6 Comments •
Thanks 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?...
Read on »
Posted on August 16, 2007 11:00 PM • 0 Comments •
Not content with his recent exploits in human experimentation and cavorting with Plosites in San Francisco, Professor Steve Steve jetted across the country once again, last week, hitting both both Blacksburg, VA and Seattle, WA, and creating pandemonium wherever he went. And raising the question - how does he get back and forth across the coast so quickly? Will you...
Read on »
Posted on July 25, 2007 8:32 AM • 0 Comments •
BLAST has gotten harder.
Read on »
Posted on July 12, 2007 1:39 PM • 4 Comments •
The best PCR animations on the web
Read on »
Posted on June 21, 2007 4:00 PM • 8 Comments •
Assigned readings on BLAST and phylogenetics.
Read on »
Posted on May 29, 2007 9:19 AM • 0 Comments •
An introduction to our Alaskan NSF Chautauqua course and a pre-course assignment. I don't know how well this will work, but I thought it might be interesting this year to experiment with blogging about our course and sharing some of our experiences with the rest of the world. Here's your chance readers, if you'd like to do some of the...
Read on »
Posted on May 27, 2007 10:34 AM • 13 Comments •
Why do high schoolers think doctors should understand evolution?
Posted on May 21, 2007 3:13 PM • 0 Comments •
Win cash or other prizes!
Read on »
Posted on February 17, 2007 11:37 AM • 2 Comments •
You can write about sex, but you can't write about
Read on »
Posted on February 13, 2007 5:18 PM • 4 Comments •
Who infected the children with HIV: Using the data to solve the puzzle.
Read on »
Posted on December 7, 2006 6:33 PM • 2 Comments •
Razib inspired me to share some of the story behind why white people are considered derivatives. Reposted from the Classic Digital Bio. No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1)....
Read on »
Posted on September 26, 2006 8:58 AM • 3 Comments •
If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3. We also learn something about the people who did the experiment....
Read on »
Posted on September 1, 2006 11:37 AM • 0 Comments •
Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest. If we agree that we have a common ancestor, then we can use that idea...
Read on »
Posted on August 25, 2006 8:10 AM • 2 Comments •
Did HIV become resistant to Atazanavir because of a genetic change? Was that genetic change inherited? Did HIV evolve? Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug? Let's find out....
Read on »
Posted on August 23, 2006 10:06 AM • 0 Comments •
In which we see the results and come to our own conclusions. If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share...
Read on »
Posted on August 21, 2006 10:00 AM • 0 Comments •
Let the experiment begin....
Read on »
Posted on August 19, 2006 11:35 AM • 0 Comments •
The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes. We started doing this here, where you can find directions for getting started. And, we've found some interesting things....
Read on »
Posted on August 18, 2006 3:43 PM • 2 Comments •
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide...
Read on »
Posted on August 17, 2006 11:59 AM • 2 Comments •
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra...
Read on »
Posted on August 11, 2006 1:14 PM • 5 Comments •
It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax. Eh, what's that you say? Yes, it's true. Back in March, when Nature Genetics published this paper from Yoshiura (and friends), this bit of fun just went...
Read on »
Posted on August 10, 2006 2:30 PM • 3 Comments •
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance shows that the ape with the most similar mitochondrial sequence...
Read on »
Posted on August 4, 2006 1:39 PM • 3 Comments •
We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong. We can do much, much more than identifying DNA sequences and obtaining crucial information, like who...
Read on »
Posted on July 28, 2006 8:00 AM • 0 Comments •
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
DigitalBio RSS feed
