Sandra Porter
sporte
Posts by this author
September 1, 2006
If 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…
August 31, 2006
Have you ever wondered about Cheeze Whiz? why new cars have a distinctive smell? or what makes golf balls so springy?
Chemical and Engineering News, published by the American Chemical Society, has a wonderful section that you will certainly appreciate.
"What's that stuff?" is a collection of…
August 29, 2006
The fall soccer season is well underway and the Hummingbirds soccer team is kicking everything in sight. The hummingbirds in these two series of photos are much quicker, considerably smaller and certainly cute.
A friend sent me this link since I manage the Hummingbirds soccer team. Hopefully, the…
August 28, 2006
One of most wonderful things about the Internet has been the emergence of research projects that involve the general public. Universities like Cornell, Kansas University, and the University of Minnesota, to name a few, have established web sites and on-line databases that encourage both students…
August 25, 2006
Like 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,…
August 23, 2006
We heard quite a bit about rainforest destruction in the 80's and 90's. Even the Grateful Dead joined the efforts to raise awareness and gather support for rain forest preservation. In the past, the Dead stayed away from political activism because (quoting Jerry Garcia):
Power is a scary thing.…
August 23, 2006
Did 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…
August 22, 2006
Have 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?…
August 21, 2006
In 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…
August 20, 2006
August is the time when gardens look their best. Fruit becomes showy, flowers abound, and plants are large and plentiful. Mendel's Garden #4, currently blooming at The Inoculated Mind, is no exception. Evolgen pointed this out, so I had to go take a look.
I enjoyed this trip through the…
August 19, 2006
Let 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…
August 18, 2006
The 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…
August 17, 2006
Chad Orzel posted a cute bit about True Lab Stories: The Party Game. I like these things because, yes, they make it clear that those of us who do science put coffee cups on top of our cars and drive off, just like everyone else. For those of who are thinking about careers in science, you don't…
August 17, 2006
When 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…
August 15, 2006
Folks have been enthusiastically commenting around the clock on the possiblity of using prisoners in clinical trials.
Meanwhile, Thomas Hargrove has analyzed obesity and death rates in the National Football League. He suggests that those pharmaceutical companies with anti-obesity drugs might be…
August 14, 2006
But that hasn't always been true.
When I was in college, I had part-time jobs drawing blood from patients in the university hospital and as a phlebotomist at local plasma center. Plus, I was a volunteer EMT on an ambulance crew. Needless to say, I saw plenty of blood.
And those were the days…
August 11, 2006
During 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…
August 10, 2006
Bio::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…
August 10, 2006
It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax.
Eh, what's that you say?
Yes, it's true. Back in March, when Nature Genetics published this paper from…
August 9, 2006
One 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)…
August 4, 2006
Last 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…
August 4, 2006
It 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…
July 31, 2006
I've been fortunate, living in Seattle, to hear talks from many people that my colleagues and co-bloggers might consider to be rock stars - people like Mary-Claire King, Nancy Wexler, Francis Collins, Leroy Hood, Eugenie Scott, David Haussler, Harold Varmus, and Elaine Ostrander. But, if I think…
July 28, 2006
We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong.
We can do much, much more than identifying DNA…
July 26, 2006
Trade publications; such as catalogs, technical bulletins, and web sites; are a valuable source of information for students in biotechnology-related courses. Not only do catalogs and technical publications provide current information, but they also contain a wealth of useful facts and physical…
July 24, 2006
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the…
July 21, 2006
"Hey Rocky, watch me pull a rabbit out of my hat!"
I realized that I should add just a bit more information to last answer on gene identification, so here it is.
After the last installment, Diego commented:
but still you do not know exactly what part of your DNA sequence is matching to the…
July 21, 2006
Welcome back!
If you've just joined us, we're in the middle of a quest to find the identity of an unknown nucleotide sequence. To summarize our results so far, we used this sequence to do a blastn search of GenBank, using all the default settings at the NCBI. You can see the beginning of the…
July 14, 2006
Last week, we embarked on an adventure with BLAST.
BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you,…
July 12, 2006
Many regions in the United States, and the world for that matter, are seeking to entice biotech companies to relocate. As Lorraine Ruff and David Gabrilska describe in their Genetic Engineering News Article, "Metrics for Economic Development," the exhibitors at meetings like BIO work hard to:
"..…