Wednesday, July 27, 2005

BLASTing through the kingdom of life

This popular activity, designed to accompany the BLAST for beginners tutorial, has been updated to incorporate student comments and teacher requests. Originally developed for the BIO 99 teacher workshop, this activity has been one of the most popular items on Geospiza's web site. We have seen the activity used in several venues from high school courses to workshops for researchers at the Lawrence Livermore National Laboratory.

Students BLAST through the kingdom of life by using blastn to identify 16 "unknown" sequences. The 16 sequences were chosen to represent diverse organisms from RNA viruses that infect yeast, to humans. This set was compiled from a mixture of cDNA sequences and intronless sequences from bacteria or viruses to minimize confusion. Further, every sequence in this set codes for some kind of protein that might be recognizable to students, such as amylase (an enzyme found in spit that breaks down starch) or DNA polymerase (makes DNA). In this update, I added an new example sequence along with answers. Ideally, the strategies I used for answering questions with this sequence, will be a good example for students who are completing this activity.

The data set, worksheet, and answer key for this activity are all available on-line at:

Unlike "canned" activities, it should be noted that students use real sequences and real databases. Since new information is continually added to the databases, the answers to the questions may change, too. I once saw the contents of a database change between the beginning and the end of a three hour workshop. On one hand, this can be disconcerting when it's unexpected. On the other hand, knowing that these are living and changing resources is exciting. Students know when they use these resources and programs that they're not using old or simplified techniques that are only employed in a classroom setting.

An unfortunate consequence is that grading gets a bit more challenging. The continual addition of information to the NCBI databases, used in this activity, means that some information that's unknown today might be known tomorrow. The majority of the answers in our key will not change - but new information might be added. Our current plan is to update the answers on a yearly basis to incorporate new information.

The answer key is password-protected to limit access by students. If you wish to get the password, send an e-mail to with your name, position, and the name of your school.


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Friday, July 08, 2005

Trade publications in biology teaching

Trade publications; such as catalogs, technical bulletins, and web sites; are a valuable source of information for students in biotechnology-related courses. Not only do catalogs and technical publications provide current information, but they also contain a wealth of useful facts and physical constants that biologists need on-the-job. Further, using catalogs in the classroom mimics the way that science is carried out in the real world. In the research lab, scientists and technicians often rely on catalogs, technical bulletins, and web sites, for quick and useful information.

I'm not sure if this practice is common now, but in the earlier days of molecular biology many of the reagent vendors, like NEB, Stratagene, and BRL, were actively engaged in research and in spreading the news of new discoveries. I probably wouldn't know much about inteins – self-splicing proteins – for example if I hadn't seen the NEB newsletter sitting around in the coffee room.

Companies were also engaged in testing research protocols. In the late eighties, molecular biology students were very superstitious, possibly because we didn't really know what we were doing anyway and each protocol had so many steps. As a consequence, we tended to follow protocols somewhat blindly, with few deviations. The protocols were gold and we rarely went "off-book." Fortunately, BRL (a defunct reagent company) used to have a wonderful publication where they did experiments to test the pervasive myths of the molecular biology lab. If it weren't for the scientists at BRL, biologists would probably still be precipitating DNA in dry ice baths and using storing oligos in buffers with the wrong pH.

I frequently used catalogs or technical bulletins from reagent vendors as teaching resources in biotechnology courses at Seattle Central Community College. All my students had their own copies of the New England BioLabs catalog. They used this catalog to find information on restriction enzymes, buffers, absorbance constants, molecular weights, and other facts that they needed for doing molecular biology lab work.

The other catalog that I found essential was the Difco Manual. For microbiologists, the Difco Manual is the equivalent of Harold McGee's classic book for chefs ("On Food and Cooking"). For years, as a microbiologist, I used LB or BHI broth to grow bacteria and made media with all kinds of mysterious ingredients like tryptone and peptone. The Difco manual, with its wonderful descriptions of media ingredients, opened my eyes and provided enlightenment. Naturally, the Difco manual became required reading for students in our media and solution preparation course.

Fortunately, those two resources are available on line. You can get the NEB reference material at: and the Difco manual