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Archives for July, 2006

I’ve been fortunate, living in Seattle, to hear talks from many people that my colleagues and co-bloggers might consider to be rock stars – people like Mary-Claire King, Nancy Wexler, Francis Collins, Leroy Hood, Eugenie Scott, David Haussler, Harold Varmus, and Elaine Ostrander. But, if I think about who the public might see as a…

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…

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…

One of my favorite experiments, in our biotech program at Seattle Central Community College, was when my students sequenced promoters that they had cloned from E. coli . I liked this activity because it pulled lots of pieces together and allowed the students to connect the dots between the DNA sequences that regulate gene expression,…

A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different…

“Hey Rocky, watch me pull a rabbit out of my hat!” I realized that I should add just a bit more information to last answer on gene identification, so here it is. After the last installment, Diego commented: but still you do not know exactly what part of your DNA sequence is matching to the…

Welcome back! If you’ve just joined us, we’re in the middle of a quest to find the identity of an unknown nucleotide sequence. To summarize our results so far, we used this sequence to do a blastn search of GenBank, using all the default settings at the NCBI. You can see the beginning of the…

Last week, we embarked on an adventure with BLAST. BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you, dear readers, was…

Many regions in the United States, and the world for that matter, are seeking to entice biotech companies to relocate. As Lorraine Ruff and David Gabrilska describe in their Genetic Engineering News Article, “Metrics for Economic Development,” the exhibitors at meetings like BIO work hard to: “.. entice founders and CEOs with a wide spectrum…

Although, I certainly didn’t believe it. Truly in nature, it can be described as nonpareil. With all the years that I’ve heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure. Yet here is, on the screen, parallel DNA.