sporte | August 14, 2006But 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 when no one wore gloves. We used to be tested every few months for hepatitis, since it was pretty common for the hospital lab techs to get that, so I did worry about hepatitis.
When I went to graduate school, and realized that the hospital where I had worked, had been treating some of the first…
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 10, 2006It'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 Yoshiura (and friends), this bit of fun just went in one ear and out the other. But then I read this really funny blog about a person, some ear wax, and an NMR machine, and well, you guessed it, I couldn't resist.
To me, it's been a jelly bean flavor that I studiously try to avoid. To several…
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…
sporte | July 31, 2006I'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 about who the public might see as a rock star, the list gets much shorter.
To the kids, I know, there are two people who qualify as rock star scientists.
One, of course is Jane Goodall. I am seriously disappointed in Afrensis for not mentioning her. I nominate Jane for the Aretha Franklin of…
sporte | July 28, 2006We'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 sequences and obtaining crucial information, like who left their DNA behind on that little blue dress.
Today, we're going to a deeper question about who we are and who are our relatives.
Drumroll, okay, here it comes:
How similar are DNA sequences between humans and apes?
Your assignment is to find…
sporte | July 26, 2006Trade 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 constants that biologists need on-the-job. Further, using catalogs in the classroom mimics the way that science is carried out in the real world. In the research lab, scientists and technicians often rely on catalogs, technical bulletins, and web sites, for quick and useful information.
I probably…
sporte | July 24, 2006A 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 campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify 16s ribosomal DNA by PCR, and check their PCR results by gel electrophoresis.
DNA samples are next sent to the university's Genetic Resources Core Facility , where scientific staff, in…
sporte | 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 annotated protein.
Ahh, but we do.
And I was negligent in not showing you.
There are multiple ways to view the GenBank record that we arrived at while following links from our matching sequence.
A very handy way, especially if you're looking at where sequences align to a larger subject sequence, like…
sporte | July 21, 2006Welcome 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 project here.
And we had some rather curious results.
It appeared that our sequence matched sequences from very diverse organisms, like Dengue virus, E. coli, and Simian Immunodeficiency virus. Very strange!
There was another curious word, too, that appeared in the descriptions for each of the results…
sporte | July 14, 2006Last 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, dear readers, was to a pick a sequence, any sequence, from a set of 16 unknown sequences and use BLAST to identify that sequence.
This week, we'll examine the results.
I did the experiment, too, with a completely different unknown sequence that's pasted below. This sequence is not part of the data…
sporte | July 12, 2006Many 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:
".. entice founders and CEOs with a wide spectrum of inducements: institutional and technological excellence, free land, preferential tax rates, and low electricity and/or water rates. They punctuate the sale with regional culinary novelties: home of the famous crawfish (with plush toy), tasty sour mash…
sporte | July 10, 2006Although, I certainly didn't believe it. Truly in nature, it can be described as nonpareil.
With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure.
Yet here is, on the screen, parallel DNA.
The image that I posted a couple of days ago came from this same structure. In that image, I hid the rest of the bases, to make it easier to see why this structure is so strange.
Here are some images that show the landmarks a bit better. I hid the hydrogens and used different rendering styles to portray the backbone and the…
sporte | July 10, 2006How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes?
In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more background, see the post on qualitative measures of DNA quality.
Later on, when the genome sequencing turned into a race, and the pace of DNA sequencing began to increase, some genome centers realized that it was too expensive and time consuming to have Ph.D. scientists, or even technicians, review all…
sporte | July 8, 2006I mean phone call. Because, if I thought he remembered me, I would call and say "thank you."
Because of the time I spent in his lab, I know that cloning started long before Dolly. The first vertebrate animal was cloned over 50 years ago.
And it wasn't a sheep.
Raising Rana pipiens
Several years ago, I had the good fortune to work as a student intern for one of the kings of cloning, Robert McKinnell, now an emeritus professor in the Cell Biology and Genetics Department at the University of Minnesota. Reminiscing on history a bit, reminds me how grateful I am that he gave me the chance to…
sporte | July 5, 2006What do genetic testing and genealogy have in common?
The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one.
Another answer is that both tests can involve DNA sequence data.
And that leads us to another question. If the sequence of my mitochondrial DNA is only two bases different from Cleopatra's, am I really a distant relative? And how do I really even know that my mitochondrial DNA is only two bases different in the first place? What does having a DNA sequence really mean?
Students sequencing mitochondrial DNA
I wrote earlier…
sporte | June 28, 2006Some of us walk by the bus stop and nervously glance at the scruffy-looking man carrying the ragged sign. I try not to breathe through my nose while I read the sign, carefully pretending all the while that I'm not really interested. Ah, it says "Repent! The world will end tomorrow!"
I smile since I always love a testable hypothesis. Tomorrow morning, I will wake up and I will know the scruffy street preacher got it all wrong.
It is "An Inconvenient Truth" that global warming presents us with another testable hypothesis.
But this one doesn't make me smile.
Al Gore has described some…