Genomics

I'm in Berkeley right now at the annual Bio-Link Summer Fellows forum. We're getting to hear talks from people in the biotech industry, listen to enthusiastic instructors describe their biotech programs and ideas, and try out new educational materials. Yesterday, two speakers (Damon Tighe and Jason Baumohl) from the Joint Genome Institute in Walnut Creek, CA, gave a fun talk about DNA sequencing and sequence assembly. They also showed some very nice Flash animations, made by Damon Tighe, at the JGI, that illustrate how DNA sequencing is done ... Read more
I got my copy of "A short guide to the human genome" by Stewart Scherer today from Cold Spring Harbor Laboratory Press (2008, ISBN 978-087969791-4). Usually, I would wait until after I've read a book to write a review, but this book doesn't require that kind of study. As soon I skimmed through it and read some of the questions and answers, I knew this would be the kind of quick reference that I would like to have sitting above my desk. Scherer has compiled a wonderful text that not only answers many of the kinds of questions that I can think to ask about the human ... Read more
RFLP is an acronym that stands for "Restriction Fragment Length Polymorphism." That's quite a mouthful and once you've said this phrase a few times, you realize why we use the initials instead. I know a Restriction Fragment Length Polymorphism sounds like something that must be impossibly complicated to understand, but if we take the name apart, it's really not so bad. ... Read more
After leading the Human Genome Project and the National Human Genome Research Institute at the NIH for many years, Francis Collins is retiring. No matter what you think of Francis Collins, he's been successful in getting the genome project done and he's done some amazing things during the 15 years that he's headed NHGRI. i-2262636f41f174ef9b3e184fd0bc4f13-collinswstudents2.jpgMy friend, Dr. Joan Messer, told me many times ... Read more
Good news! Good news! Last week the Senate passed the Genetic Nondiscrimination Act (GINA). This week it was passed by the House. It only needs one signature and GINA will become law. For years, those of us who teach genetics have had to caution students about genetic testing. The biggest reason was the fear that having a genetic test would cause them to lose their health insurance. There were just too many stories about people who had been denied insurance because they took a genetic test and discovered a predisposition to something like Huntington's disease or ... Read more
A potential link between lung cancer and human papilloma virus may make parents even more glad about vaccinating their children with Gardasil®. Not only are the children protected against viruses that commonly cause cervical cancer, they may be protected against some forms of lung cancer as well. The April 25th version of Nature News reports (1) that two viruses, HPV (Human papilloma virus) and measles virus, have been found in lung tumors. From Nature News:
Samuel Ariad of the Soroka Medical Center in Beer Sheva, Israel, and his colleagues began by analyzing ... Read more
Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions last night at a fascinating panel discussion on personal genomics at the University of Washington. We were fortunate to be in the audience. I'll share some of the questions and answers, in some cases shortened and paraphrased. The room in Kane Hall at the UW was already warm when we arrived last night (yes, I do go to evening seminars). A student handed us cards and cute little pencils for writing our questions and we sat down. We fought the impulse to write "What's the air ... Read more
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 ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes. Now, in one of our last projects we are determining where ... Read more
You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz.Read more
This morning I had a banana genome, an orange genome, two chicken genomes (haploid, of course), and some fried pig genome, on the side. Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably drank a bit of coffee DNA too, but didn't consume a complete coffee genome since my grinder isn't that powerful and much of the DNA would be trapped inside the ground up beans. Of course, microbes have genomes, too. But I do my best to cook those first. So, what is a genome? Is it a chromosome? Is it one of those DNA ... Read more

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