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 year, I collect the data from her students' experiments. Then, in the bioinformatics classes I teach, we work with the chromatograms and other data to see what we can find.
This is the first part of a four part video series ... 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
The simple fact is this: some DNA sequences are more believable than others.
The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad."
All they see are the base calls and sequences: ATAGATAGACGAGTAG, without any supporting information to help them evaluate if the sequence is correct. If DNA sequencing and personalized genetic testing are to become commonplace, the practice of ignoring data quality is (in my opinion) simply unacceptable.
So, for awhile anyway, I'm ... 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
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?
This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman. (See see "Sequencing the campus at the Johns Hopkins University" for more background.)
We are going to do a bit of metagenomics by using FinchTV and ... Read more
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.
Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things.
Step right up! Watch original research, as it happens, on the web!
I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants.
Are viral and fungal infections always a bad thing?
Maybe not if you're a plant.
In fact, if you're a plant trying to grow in the hot (65°; C) soils of Yellowstone National Park, you're going to need all the help you can get.
A new study by Márquez, et.al. (1) found that a type of grass (Dichanthelium lanuginosum) is able to grow in the hot soils of Yellowstone National Park because it gets help from some friends. A fungal friend. And that fungal friend is infected with a virus.
If you're not used to thinking in degrees centigrade, it's hard to grasp immediately ... Read more
The University of Nevada in Las Vegas is looking for a few good undergraduates to come do research this summer in environmental microbiology. Environmental microbiology goes way beyond hot springs bacteria and Yellowstone Park. At UNLV, you can do science in the desert.
It almost makes me wish I was an undergraduate again.
The Microbiology faculty at the UNLV and the Desert Research Institute are looking for inquisitive and eager undergraduates to participate in a 10 week summer research experience in the REU (Research Experience for Undergraduates) program.
Projects involve ... Read more
As they say, there's nothing like travel to learn new and unexpected things.
Especially from cab drivers.
One of my ScienceBlog Sibs, Shelly, spends time talking with cabbies about earwax, but I seem to invite other kinds of lectures.
Often times, my driver are ... Read more