genomics
sporte | May 29, 2008I 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 genome, but the kinds of…
sporte | May 29, 2008RFLP 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.
Let's start with most familiar one of the four words and work from there. My guess is that for many of you, that word is "length." When we talk about length in this context, we are talking about the length of a piece of…
evolgen | May 28, 2008Francis Collins, head of the National Human Genome Research Institute (NHGRI), will be stepping down from that position in August. Collins has overseen the sequencing of the human genome, the HapMap project, the ENCODE project, and many other large advances in genomics. The NHGRI has had a major impact in the field of genetics while Collins was at its helm.
Collins also has a history of putting his foot in his mouth -- not that it's a bad thing to do so (lord knows my foot's spent more time lodged in my face than on the ground). He's been incorrect about morality and human evolution, to name…
sporte | May 28, 2008After 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.
My friend, Dr. Joan Messer, told me many times about the hours he spent talking with students at one of the AAAS meetings. I will always remember him from the NWABR fund-raising dinner where he pulled out his guitar and had the entire audience singing about DNA.
mikethemadbiologist | May 6, 2008Our Benevolent Seed Overlords have a poll about GINA. I posted about GINA earlier today; head on over and offer your opinion.
mikethemadbiologist | May 6, 2008While many of my fellow ScienceBloglings have discussed GINA (The Genetic Nondiscrimination Act), one other reason this is an important piece of legislation involves the Human Microbiome Project.
I've written about the Human Microbiome Project before, but, in a nutshell, it involves sequencing the microorganisms on us and in us. Basically, we take a biological sample--any collectable sample, preferably one that smells bad, and is icky and gross--will do, and sequence DNA from the sample. While some of the DNA will be microbial, much of it will be human (otherwise, DNA-based forensics wouldn…
sporte | May 1, 2008Good 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 breast cancer.
But…
edyong | April 28, 2008
They say that size doesn't matter, but try telling that to bacteria. Most are very small, for they rely heavily on passive diffusion to ferry important nutrients and molecules across their membranes. To ensure that this happens quickly enough, bacteria need to ensure that their surface area is large enough relative to their volume - become too big and they won't be able to import enough nutrients to support their extra size.
These constraints greatly limit the size of bacteria. The larger ones solve the problem by being extremely long and slender, or by using an internal compartment called…
sporte | April 27, 2008A 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 tumours taken from 65 lung…
sporte | April 24, 2008Bill 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 speed velocity of a coconut-…
evolgen | April 20, 2008Last year, Craig Venter became the first single person to have his genome sequence published (doi:10.1371/journal.pbio.0050254). That genome was sequenced using the old-school Sanger technique. It marked the second time the complete human genome had been published (which led to some discussion as to whether the publication deserved to be published in a high profile journal like PLoS Biology), and the first time all of the sequence came from a single individual.
This past week, Nature published the second complete genome sequence of a single individual (doi:10.1038/nature06884). Like Venter,…
sporte | April 17, 2008In 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…
sporte | April 9, 2008You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz.
evolgen | April 8, 2008Us dudes are always accused of thinking with our dicks. Perhaps it's because the genes expressed in our brains are similar to those expressed in our 'nads:
Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division.
The authors of the paper allege that their result has something to do with speciation. They even claim, "Brain is the most important tissue in…
sporte | April 4, 2008This 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 fragments or…
sporte | April 3, 2008Goodbye desktop, we're off to see the web.
Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have convincingly demonstrated that Open Office is a reasonable alternative.
But, now there's something new and cool on the web.
Okay, it's still in the beta stages, and apparently it can only be used by a limited number of people at a time, but it's certainly…
sporte | April 2, 2008A few months ago I posed some questions about the regulations that might oversee personal genomics companies (Who's your Daddy? and Step right up, get your very own DNA profile).
Why?
Because I am biased. At Geospiza, where I work, we make software products that help our customers, who do DNA testing, meet FDA and CLIA regulations. Since some of our customers do DNA testing for diagnostics and clinical studies, we are well aware of the regulatory issues that concern DNA sequencing and DNA sequence data. Most DNA diagnostics labs are regulated by CLIA, the Clinical Laboratory Improvement…
evolgen | March 31, 2008As I have mentioned before, de novo sequencing of whole eukaryotic genomes may be a thing of the past (or, at least, these whole genome projects won't be getting very much more common). Instead, I proposed that people would use the new high-throughput technologies to sequence parts of the genome they found interesting. What did I propose they'd sequence (based on discussion I'd had with various folks)? The transcriptome, or, essentially, a whole genome cDNA library. This allows for a much higher coverage of the genes in the genome, but sacrifices information regarding non-transcribed…
sporte | March 27, 2008I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to:
Build a data set
Align the sequences
Make a tree
In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we're interested in knowing how much they differ from each other. Later, we'll compare the 16S ribosomal RNA genes from multiple species of…
mikethemadbiologist | March 25, 2008If you missed my talk, then you missed this slide
I leave to give a talk for a few hours, and suddenly all hell breaks lose on ScienceBlogs over the whole PZ Myers getting expelled from the movie Expelled incident, you damn kids! So I thought I would peeplay too.
First, I'm not sure the charge that this helps the movie is true: since the Great Expulsion, there have been cancellations of some pre-release showings. But this incident, and various ScienceBloglings' reactions to it, to me, appears to be functioning as a Rorschach blot for a whole host of larger issues.
One of the things that…