classroom activities:
Dave Robinson and Joann Lau from Bellarmine College in Kentucky are going to be describing their student project in a free webinar next Friday, May 16th. Their students clone GAPDH (Glyceraldehyde 3-Phosphate Dehydrogenase) genes from new plants, assemble the DNA sequences, and submit them to the NCBI. Here's an example. Plus, since GAPDH is a highly conserved, it's a great...
Posted on May 8, 2008 7:36 PM • 3 Comments •
How to compare mutant and normal protein structures.
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Posted on April 26, 2008 1:21 PM • 2 Comments •
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...
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Posted on April 17, 2008 8:00 AM • 2 Comments •
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...
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Posted on March 13, 2008 6:42 PM • 0 Comments •
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...
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Posted on March 12, 2008 12:50 PM • 35 Comments •
Here's a fun puzzler for you to figure out. The blast graph is here:...
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Posted on March 7, 2008 12:28 PM • 2 Comments •
Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that...
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Posted on February 26, 2008 10:58 AM • 3 Comments •
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus....
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Posted on February 26, 2008 10:47 AM • 0 Comments •
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes....
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Posted on February 26, 2008 10:19 AM • 0 Comments •
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every...
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Posted on February 26, 2008 10:14 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....
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Posted on December 7, 2007 9:30 AM • 17 Comments •
You too, can compare chimp and human DNA.
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Posted on November 16, 2007 8:51 AM • 0 Comments •
Can you do it? This is what bioinformatics technicians or data analysts do in diagnostic labs.
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Posted on November 15, 2007 9:09 AM • 4 Comments •
An evolution activity for the classroom.
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Posted on November 9, 2007 3:47 PM • 0 Comments •
Fun ideas for your Halloween loot
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Posted on November 1, 2007 12:00 PM • 8 Comments •
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...
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Posted on October 28, 2007 2:24 PM • 0 Comments •
Sequencing the dirt: see how it's done
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Posted on October 27, 2007 7:00 PM • 0 Comments •
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....
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Posted on October 26, 2007 2:20 PM • 0 Comments •
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...
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Posted on October 24, 2007 4:05 PM • 0 Comments •
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...
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Posted on October 21, 2007 4:30 PM • 2 Comments •
Fun with molecular models!
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Posted on September 11, 2007 11:46 AM • 3 Comments •
I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper. I think the data themselves are awfully suspicious....
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Posted on August 24, 2007 6:44 PM • 4 Comments •
Charles Darwin was so fascinated by beetles he paid people to help him build his collection. The Coleopterists Society and the Smithsonian Institute want to help kids explore the wonders of beetles, too. They're providing grants for kids, in grades 7-12 to work on beetle biology. Applications are due by November 15, 2007....
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Posted on August 23, 2007 3:00 PM • 1 Comments •
Developing "biological intuition" through case studies
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Posted on August 17, 2007 1:53 PM • 0 Comments •
Amateur astronomers unite! The pros want your help! image from Astronomy Picture of the Day, Credit: NASA, ESA, A. Aloisi (STScI / ESA), Hubble Heritage (STScI / AURA) - ESA/Hubble Collaboration I learned about this from the Washington Science Teachers Assocation. Galaxy Zoo and the Sloan Digital Sky Survey are looking for your help in sorting out different galaxies. It's...
Posted on July 30, 2007 3:35 PM • 0 Comments •
I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it. So, here's one for you to chew on over the weekend. This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab book that I...
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Posted on July 27, 2007 4:17 PM • 3 Comments •
Some things I like, some were surprises.
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Posted on July 16, 2007 12:13 PM • 19 Comments •
BLAST has gotten harder.
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Posted on July 12, 2007 1:39 PM • 4 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...
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Posted on May 27, 2007 10:34 AM • 13 Comments •
Do you want to learn how to use some cool biotechnology and bioinformatics methods in your college or high school class? If you're on the East coast, the best place to go is the Fralin Biotechnology Conference at Virignia Tech, July 18-21st. (Yes, it's the same Virgina Tech, and that's why I waited to post this announcement). There's something for...
Posted on May 11, 2007 10:05 AM • 0 Comments •
Win cash or other prizes!
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Posted on February 17, 2007 11:37 AM • 2 Comments •
Start writing those essays! You could win cash and a chance to work in a lab!
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Posted on January 19, 2007 4:43 PM • 0 Comments •
The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses....
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Posted on January 12, 2007 1:37 PM • 10 Comments •
I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too...
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Posted on January 10, 2007 11:21 PM • 4 Comments •
Cute little tardigrades are great research subjects.
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Posted on November 13, 2006 11:46 AM • 2 Comments •
In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed....
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Posted on October 13, 2006 12:00 PM • 0 Comments •
Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)?...
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Posted on October 10, 2006 11:41 AM • 0 Comments •
Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at my college and web browsers, like Mosaic, had yet to...
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Posted on October 6, 2006 2:00 AM • 1 Comments •
Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure....
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Posted on September 15, 2006 2:18 PM • 0 Comments •
Why do I love Cn3D? Let me count the ways. What does Cn3D do? (Hint: say "Cn3D" out loud). Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and...
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Posted on September 8, 2006 11:38 AM • 0 Comments •
No biology course is complete these days without learning how to do a BLAST search. Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key. Development of the tutorial and the activity were supported by funding from the National Science Foundation. This is...
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Posted on September 7, 2006 9:59 AM • 0 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....
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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...
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Posted on August 21, 2006 10:00 AM • 0 Comments •
Let the experiment begin....
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Posted on August 19, 2006 11:35 AM • 0 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...
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Posted on August 17, 2006 11:59 AM • 2 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).
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