This is a video that a friend made that shows, very clearly, how to pour an agarose gel, load the samples and run it. I especially like the way he used a bit of time lapse photography to show the dyes separating as the gel ran. ... Read more
Vaccines work by stimulating the immune system to respond to a specific thing. Most of the vaccines we use are designed to prime the immune system so that it's ready to fight off some kind of disease, like whooping cough, polio, or influenza. Some vaccines can have more specialized functions, like stimulating the body to attack cancer cells, kill rogue autoimmune cells, or prevent pregnancy. We'll look at what they do in later posts, for now, let's look at the kinds of things that can be used as vaccines.
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
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
I love the way you show me secret things. All I do is type: Select * from name_of_a_table And you share everything with me. Without you, my vision is obscured, and all I see is the display on the page. In fact, this was the push that finally made me decide to learn SQL. In our bacterial metagenomics experiment, I realized that my students could use FinchTV to enter their blast ... Read more

If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. You may be wondering, and rightly so: just what is a SNP?

Never fear, hopefully this post will answer some of those questions.

SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a sequence of bases, and other people will have a different base at that position. The two forms of SNP are called "alleles." (Usually there are two forms, but that's ... Read more

Science labs are not for all people. I've always enjoyed teaching lab courses, so some of you might find it strange that I agree with some of the comments from Steve Gimbel and fellow Sb'ers on the ... Read more
How do microbiologists determine which microbe caused a disease? As Tara has eloquently described (I, II), we are covered with bacteria and other microbes. A reasonable question then, is when we get sick, how do we which little devil deserves the blame?

In many cases, pathogens (disease-causing organisms) are identified by a common series of steps, known as Koch's postulates. Robert Koch described these steps in ... Read more

"Beware the Jabberwock, my son! The jaws that bite, the claws that catch! Beware the Jubjub bird, and shun The frumious Bandersnatch!" - from Jabberwocky, by Lewis Carroll

I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins.

Why? Because we always (well, almost always) get matches to hypothetical and putative proteins when we do a database search with a protein sequence.

Why? Because many of the protein sequences in GenBank (at the ... Read more

How to win the X PRIZE in genomics In October, 2006, the X PRIZE foundation announced that second X prize would focus on genomics. The first team to successfully sequence 100 human genomes in 10 days will win $10 million dollars. And I would venture to guess, that the winning team would also win in the IP (intellectual property) game and the genetic testing market since they will gain an unprecedented look at genetic variation. But when is done really done? The first ... Read more

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