Ask Dr. Science
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 | September 13, 2007A 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.
My Sciblings have guessed: Rhizostoma, Stomolophus meleagris, or Mastigas
If you know, we'd all appreciate an answer in the comments.
And if you don't know about much jellyfish, RPM at evolgen would like your help answering a different reader's question…
sporte | September 6, 2007One 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 we look at the PLoS paper with Craig Venter's…
sporte | February 17, 2007How 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 1876 when he used them to prove that Bacillus anthracis was the cause of anthrax. During the past century, his steps have been used successfully many times.
Koch's steps are…
sporte | February 8, 2007"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 NCBI) are a result of conceptual translations.
What? !!
A conceptual translation…
sporte | February 5, 2007How 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 trick is defining what it means to be done. My husband says that "a sequencing project is done when the people who are…
sporte | February 2, 2007Vizzini: 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 a completely unexpected way and no one else seems bothered by this!
I had this happen once with the word "artifact." I had organized a conference and some workshop…
sporte | February 1, 2007To 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 sequencing world has it's chimeras, too. There are two main kinds that I know. Sometimes chimeras…
sporte | January 31, 2007The 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 critical importance to the success of later…
sporte | January 30, 2007"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: IntroductionPart II: Sequencing strategiesPart III: Reads and chromatsPart V: checking out the library
We all know that sequencing a genome must be a lot of work. But unlike love, it is something we can measure. In fact, an important part of genome sequencing is estimating just how much work needs to be done. This is especially important if you're the one paying for it or the one writing the grant proposal.
Coverage depth: or why do we…
sporte | January 28, 2007Shotgun sequencing. Sounds like fun.
Speculations on the origin of the phrase
I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage, transduce E. coli, and hope for the best. Consistent with the shotgun metaphor, we even used to store our microfuge tubes in plastic bullet boxes that my boss found at the sporting goods store. (Apparently this practice was unique to Minnesota, though. When I moved out west for graduate…
sporte | January 27, 2007Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes, 2145 viruses, and genome sequences from 407 phage.
Much of the methodology used for sequencing DNA is designed to confront one big technical hurdle.
That is, we can only determine the sequence of small pieces of DNA at a time. This means that you must break a larger…
sporte | January 22, 2007About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught.
I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question:
How do you sequence a genome?
Before we get into the technical details, there are some other genomic questions that you might like answered.
How much does it cost to sequence a genome?
I remember in 2002, when we were at the O'Reilly bioinformatics conference and we heard Lee Hood challenge the DNA sequencing community to lower the costs of genomic…
sporte | January 21, 2007In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted:
I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it would never get done.
Well, okay, technically speaking he didn't ask me for help. But, since I'm a biologist, as soon as I looked at the definition that he chose, from Modern Genetic Analysis (by Griffiths, Lewontin, Miller, and Gelbart), I couldn't help but find something wrong.
The definition from…
sporte | January 13, 2007Are there scientific terms or concepts that you'd like to know more about? Looking for a bit more of an explanation? Confused about the difference between DNA and RNA?
Some of my fellow SciBlings, Tara, Chad, John, Janet, and Bora; have proposed that we consider going back to basics. Others have pointed out that we ScienceBloggers might be a little clueless ourselves about which basics that you'd like us to define.
Here's my proposal:
You can ask me a question in the comments here - or via e-mail (digitalbio at gmail.com) and I will pick one every week or so and try to answer it. Or,…