Ask Dr. Science

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

A reader from the UK sent me these lovely photos that he took of a jellyfish and asked for my help in identifying it. Unfortunately, while I'm pretty good with bacteria, plants, and tropical fish, my taxonomy skills don't go much farther unless I have a sample of DNA. These photos were taken at La-Manga off the coast of southern Spain.

One of my readers asked: Why does genome sequencing cost so much? My short answer is because it's big. But I thought it would be fun to give a better answer to this question, especially since I'm sure many of you are wondering the same thing. Okay, so let's do some math. Don't worry, this math isn't very complicated and I'll explain where most of the numbers come from. Estimating costs from salaries First, we'll take the easy route. My experience with grant budgets has taught me that the greatest cost for any project comes from salaries. If ... 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

Vizzini: He didn't fall? Inconceivable! Inigio: You keep using that word. I do not think it means what you think it means. - William Goldman, The Princess Bride

Excuse me while I temporarily interrupt the genome sequencing series to define a word. Artifacts in the classroom It's disorienting. You learn a word in certain context. You're sure of it's meaning and then you end up in a situation where people use the word in ... Read more

To the ancient Greeks, a chimera was a kind of monster, with the body of a goat, the tail of a dragon, and a lion's head. To geneticists, a chimera can be an animal that's derived from two embryos, such as a transgenic mouse. Or if the organism is a plant, it can be a plant with a graft. We have a chimeric cherry tree in our back yard with branches from Rainier cherries, Bing cherries, and Van cherries. And you should see the chimeras that hang out at evolgen. Naturally, the DNA cloning and ... Read more

The general steps in genome sequencing were presented in the earlier installments ( there are links at the bottom of the page), but it's worth repeating them again since each of the earlier steps has a bearing on the outcome of those that come later. These are:

• Break the genome into lots of small pieces at random positions.
• Determine the sequence of each small piece of DNA.
• Use an assembly program to figure out which pieces fit together.

That first step, making a collection of DNA fragments (a library), with breakpoints at random positions is of ... Read more

"How much do I love you? I'll tell you no lie. How deep is the ocean? How high is the sky?" - Irving Berlin The other installments are here: Part I: Introduction Part II: Sequencing strategies Part III: Reads and chromats ... Read more