biotechnology
sporte | January 9, 2007It's true. Chimeras are out and walking among us. These aren't quite the chimeras that RPM is obsessed with, but they're certainly bothersome to some.
From Genome Technology Online, we have a report that James Derr, at Texas A&M College of Veterinary Medicine, wants to sequence the genome from a real buffalo, but those buffalo are hard to find.
To quote Genome Technology:
Problem is, that legacy has been mingled with domestic cattle in efforts to "make a better beef animal." Meatier, more docile hybrids are known as cattelo, if you were wondering.
Where do real buffalo roam?
Maybe not…
sporte | November 29, 2006What's the difference between a synthetic drug and an antibiotic?
Sometimes there's no difference at all.
Let's take a look at chloramphenicol and couple of pencillins.
Chloramphenicol kills many different kinds of bacteria by interfering with their ability to make new proteins. Here's a point where language gets tricky. Originally, chloramphenicol was isolated and purified from Streptomyces (a kind of bacteria). But, chloramphenicol is small and chemists are able to synthesize it. So even though we consider antibiotics to be natural products, they don't have to be made in a "natural…
sporte | November 8, 2006I touched a nerve in another post by mentioning molecular biology kits.
Let's face it. Cloning kits, sequencing kits, and their relatives are the laboratory equivalent of frozen cookie dough.
With frozen cookie dough, anyone can bake hot, steamy, chocolate chip cookies that taste great. You don't have to read a recipe, do any math, or figure out how to "cream" butter and sugar together. Just spoon the dough on the pan, put the pan in the oven, and 10 short minutes later: ummm, cookies.
Lab work and cooking have much in common. At one time, only a few people were good cooks. Now,…
sporte | November 6, 2006I wrote earlier about videos of lab protocols and the benefit these could bring to people who are trying to learn new techniques or perhaps troubleshoot their own. Unfortunately, I suspect that the people who would benefit the most from movies of others doing lab procedures correctly are those who are already pretty observant.
Nevertheless, I have some ideas for improvements to these kinds of movies, ala acting and editing, that could benefit the truly-technically-impaired.
We need lab movies of people doing things wrong.
Last night we watched the episode of Monty Python's Flying Circus,…
sporte | November 4, 2006You've probably heard about enterprising researchers attaching cameras to dolphins, dogs, and other animals, in order to learn how things look from the critter-point of view. Now, some enterprising lab rats have added a new twist to this technique.
It's lab cam!
From Attila Csordas , we have a report about researchers documenting their work through film in an unusual way. They put on a funky-looking hat with a digital camera attached and film their hands doing the experiments. There's even a short movie made by John Cumbers from OpenWetWare, on preparing Drosophila embryo chromatin for…
sporte | November 1, 2006These are the real things that give nightmares to post-docs and graduate students.
One thing that you don't learn, until you either do a research project in a lab or you start graduate school, is that science isn't really the straightforward cut and dry: we do this step, then we do this step; sort of field that you might imagine. You come to graduate school all bright-eyed and amazed, with the scientific method burned into your brain, only to find out that it's usually the little things that no one told you about that make the difference between productive experiments and a waste of time.…
sporte | October 18, 2006Reposted from the original Digitalbio.
About a decade ago, I took a fascinating summer course at the UW on bioethics. We read about the Nuremburg trials and the Geneva conventions. We learned about horizon problems and eugenics. And we discussed lots of challenging scenarios with genetic testing, autonomy, family relationships, and the problems faced by people seeking to have children, trying to get insurance, or looking for a job.
So naturally, when I started a biotechnology course for non-science majors (Biotechnology and Society) at our community college, I used many of those examples…
sporte | October 11, 2006When does a little artistic license go a little too far?
We don't always expect the truth in science journalism imagery. We've all seen the newspaper pictures of the famous scientist wearing a lab coat and gazing intently at a gel, looking through a microscope, or contemplating an agar plate streaked with lovely colonies of bacteria. Some of us find these pictures pretty funny, especially if we know that the subject of the photo hasn't run a gel in the past twenty years and never wears a lab coat unless they have to give a lecture to medical students.
Okay, perhaps the glossified,…
sporte | October 11, 2006No one in a life science-related industry or research lab, in Western Washington, is safe at this time of year.
Surely, you're joking!
No, seriously, there are teachers and science enthusiasts everywhere looking to sign you up! And don't call me "Shirley."
Sign me up?
That's right, it's time to prepare for the
BIOTECH EXPO
This is the Western Washington version of the science Olympics! Those science enthusiasts are out scouting for anyone who does something related to science or a life-science industry to act as an advisor (sort a mentor with a lower committment level) to high school…
sporte | October 9, 2006In the Big Rock Candy Mountains, there's a land that's fair and bright,
The handouts grow on bushes and you sleep out every night
Where the boxcars all are empty and the sun shines every day
On the birds and the bees and the cigarete trees,
The lemonade springs where the bluebird sings
In the Big Rock Candy Mountains
Big Rock Candy Mountain by Harry "Haywire Mac" McClintock (Warning: this site plays the music)
To some inhabitants of the ivory tower, industry looks like paradise.
When I was a graduate student and my husband first started working in a biotech company downtown, sometimes I'…
sporte | September 12, 2006The Ask a Science Blogger question of the week asks if organic foods are really worth the hype. I'm afraid my answer can't fit into one blog post.
Let me start by telling you about my garden.
This year my garden has been a home to local wildlife, but during the years that I do garden, I have a semi-organic garden.
I don't use any pesticides but I do occasionally break down and use Miracle Grow and, sometimes Epsom salts (magnesium sulfate). Overall, though I don't see any justification for using chemicals that might be harmful to fish or other animals in my garden, so I don't.
Even in the…
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 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…