bioinformatics
sporte | September 26, 2006Razib inspired me to share some of the story behind why white people are considered derivatives.
Reposted from the Classic Digital Bio.
No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1).
These zebra fish had an unusual golden color that turned out to be an important clue. Lamason and collaborators found that the golden zebra fish lost their normal color because of a mutation in the slc24a5 gene. When the zebra fish have the mutant form, they produce fewer melanosomes.
A short language lesson
Fewer…
mikethemadbiologist | September 25, 2006Do you want to know how to stop, or at least, lessen the next E. coli 0157:H7 outbreak? Improve our surveillance and public health infrastructure.
If we improve the infrastructure, we can speed the response time, making it easier to contain an outbreak.
Let's walk through each of the steps the CDC outlined in its response.
1. Incubation time: The time from eating the contaminated food to the beginning of symptoms. For E. coli O157, this is typically 3-4 days.
There's not much we can do to 'improve' this step. While random testing could be an option, when it comes to produce, I don't see…
sporte | September 22, 2006and what is the volume of the sea?
This sounds a bit like the beginning of a poem but it's really the answer to the question we posed last week on a Digital Biology Friday.
We can see, in the sequence window, that two strands are both labeled 5' on the left side and 3' on the right. We call this direction "five prime to three prime."
But, when we look in the structure window, we see that the two strands are oriented in the opposite direction relative to each other. The 5' end of one strand is located across from the 3' end of the other strand.
(Note: I added the arrow and labels, this…
sporte | September 19, 2006Modified from the original post.
Playing around with molecular structures is one of the more entertaining activities that you can do with digital biology. I've become totally entranced with molecular structures, both because they're a fascinating art form and because every structure has its own story.
I learned this because I ended up writing 69 different structure stories for the "Exploring DNA Structure" instructor guide. This was never in my original plan but my friend Charlotte Mulvihill wrote to ask me about the functions of different structures. I blithely replied that sometimes the…
sporte | September 15, 2006Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure.
First, we're going to get a structure for a double-stranded molecule of DNA and open it in Cn3D.
1K9L
If you want to do this at home and you haven't already downloaded a copy of Cn3D, you may want to read these instructions and get a copy. These directions also show how to download and open the structure. It's pretty simple once you've given it a try.
Hide a strand
Next, we're going to hide one of the strands. To do this, look in the menu bar for the Show/Hide menu and open…
sporte | September 8, 2006Why do I love Cn3D? Let me count the ways.
What does Cn3D do? (Hint: say "Cn3D" out loud).
Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and fun to use.
Have you ever used programs like MS Office? Using Cn3D is at least 10 times easier.
An added benefit is that you don't have to try and find old copies of Netscape or other bits of obsolete software…
sporte | September 7, 2006No biology course is complete these days without learning how to do a BLAST search.
Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key.
Development of the tutorial and the activity were supported by funding from the National Science Foundation.
This is reposted from the the original DigitalBio blog.
This popular activity, designed to accompany the BLAST for beginners tutorial, has been updated to incorporate student comments and teacher requests. Originally developed for…
sporte | September 1, 2006If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3.
We also learn something about the people who did the experiment.
At first it appears somewhat odd that there are many matching sequences that are all shorter than the genome and all the same length.
What's up with that?
It turns out that information doesn't have anything to do with the fraction of the genome that matches our query. These short segments are PCR products. They're the same size because the PCR…
sporte | August 25, 2006Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest.
If we agree that we have a common ancestor, then we can use that idea as a basis to ask some interesting questions about our genomes. For, example, we know that genomes change over time - we've looked at single nucleotide changes here and here, and we've seen that large chunks of DNA can move around here.
So, it's interesting to consider…
sporte | August 23, 2006Did HIV become resistant to Atazanavir because of a genetic change?
Was that genetic change inherited?
Did HIV evolve?
Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug?
Let's find out.
All of the sequences in the image below (except for the first) come from HIV strains that were isolated from patients who took Atazanavir and no other protease inhibitors. All of the strains of HIV from patients were resistant to the drug.
If an amino acid is different from other strains, the color at that position is changed. Since we see different…
sporte | August 22, 2006Have you ever wondered how people actually go about sequencing a genome?
If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed? What is the Golden Path?
Wonder no more!
You too, can take a virtual tour of the Washington University Genome Center.
I found this really excellent series of short videos that follows two genetics students, Libby and Bryce, as they meet on the bus to the Genome Center and learn about all the steps…
sporte | August 21, 2006In which we see the results and come to our own conclusions.
If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share the best on-line pharmacy and investment guide.
Ugh.
I prefer making my own decisions, thank you very much.
So, I want to give you a chance to look at the data and decide for yourself, if the data show HIV protease sequences changing over time.
Let's see the results.
We're…
sporte | August 19, 2006Let the experiment begin.
We're experimenting with HIV in this series. And yes, you can try this at home!
If you want to see where we've been and get an idea where we're going, here are the links.
Part I. Meet HIV and learn how we're going to use it look at evolution. An introduction to the experiment and a link to a short flash movie on HIV.
Part II. Instructions for doing the experiment.
Part III. Look at the sequence results.
Part IV. Look at protein structures and see if we can explain why the experiment worked the way it did.
Let's move onward.
1. I made a data set of amino acids…
sporte | August 18, 2006The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes.
We started doing this here, where you can find directions for getting started.
And, we've found some interesting things.
In this installment, we found that humans have practically an entire mitochondrial genome stuck in chromosome 17.
Last week, we found that human mitochondrial DNA is more similar to that of chimpanzees than to gorillas. We found that 90.6% of the bases in human mitochondrial DNA match bases in the Bonobo chimp and 90.7% match bases in the Chimpanzee.
This…
sporte | August 17, 2006When can a really bad virus be used to do something good?
When we can use it to learn.
The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide you through some experiments on HIV evolution that you can do yourself. You won't even have to put on any special clothing (unless you want to), wash glassware or find an autoclave. And, you don't need to any UNIX commands or borrow a…
sporte | August 11, 2006During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are.
Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra mitochondrial sequence probably complicates some genetic analyses. One of my readers also asked an interesting question about whether apes have a similar mitochondrial sequence in their equivalent of chromosome 17, and how it compares. We will…
sporte | August 10, 2006Bio::Blogs#2 is been out for a few days but it's certainly not out of interesting ideas and things to read.
There is some interesting stuff about Brisbane. Queensland looks like a lovely place and much different than my mental images of Australia. Sorry, but when I picture Australia, I get a strange image of a cross between Babe, old Mad Max movies, and Priscilla, Queen of the Desert. This is an image kind of like Eastern Washington, although I don't think Mel Gibson and the wild riders of Priscilla would be cavorting in the same sentence on that side of the mountains.
Back to Bio::…
sporte | August 9, 2006One of the commenters on a previous post, pointed out that proteases have pretty diverse structures, even though they also share a common function.
What else could I do? I had to take a look. I found structures for chymotrypsin (from a cow) and subtilisin (from a soil bacteria, Bacillus lentus) and used Cn3D to see how they compare (below the fold).
Both enzymes are proteases - that is they cut the peptide bonds in proteins that hold amino acids together. Many of you use proteases routinely, without knowing it or probably even thinking about it. Proteases, including subtilisin have…
sporte | August 4, 2006Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are.
The answer is: really, really, similar.
And you can see that, in the BLAST graph, below the fold.
A quick glance shows that the ape with the most similar mitochondrial sequence is Pan paniscus, the pigmy chimpanzee. Next, is Pan troglodytes, the chimp that we see in movies, and last we have Gorilla gorilla.
Then we have a really curious, and unexpected, matching sequence.
Click the picture to see a larger…
sporte | August 4, 2006It seems kind of funny to be thinking of anti-freeze at the moment, with heat waves blanketing the U.S., but all this hot weather makes me miss winter. And so I decided it was time to re-post this from the original DigitalBio.
Winter is coming soon, my bike ride to work was pretty chilly, and it seems like a good time to be thinking about antifreeze. Antifreeze proteins, that is. Antifreeze proteins help keep pudgy yellow meal worms from turning into frozen wormsicles and artic flounder from becoming frozen flat fish.
Funny, but I would have thought that one antifreeze protein would…