biotechnology
sporte | August 3, 2007Last Friday, we had another in the series of weird DNA structures. (You can see the first here).
I asked the audience to identify the unusual feature in this molecule. Here's the first picture:
tags: DNA structure, DNA , molecular structure, biochemistry
Here's the answer:
Steve L. guessed it correctly. This is not just DNA, it's a DNA:RNA hybrid. I circled a 2' hydroxyl group here to make it easier to see the difference. (Remember - the "D" in DNA stands for "deoxy.") The oxygens are red and it's easiest to tell the difference between the strands if you count them.
For extra credit -…
sporte | August 2, 2007What do malaria, sleeping sickness, yellow fever, and dengue virus have in common? Sure, they're all tropical diseases, but there's something else.
All of these diseases have some kind of insect vector.
image from the Public Health Library
tags: tropical disease, yellow fever, sleeping sickness, insect control,
malaria
At one time, I thought it was merely a matter of an insect biting one organism and then transmitting the parasite to another organism because the parasite was stuck on the insect proboscis, or something like that, kind of like the way cold viruses might get transmitted…
sporte | July 31, 2007I don't usually blog about work for wide variety of reasons. But, last week, since I wanted to write about bioinformatics software companies, I broke with tradition and wrote about Geospiza as an example.
Naturally, I got some feedback about this. Some people liked it, but one of the most opinionated people said that I had given the software engineering and IT side short shrift and that I should write about that side a bit more.
Today, is my attempt at a remedy.
tags: biotechnology careers, biotechnology, career+descriptions,
bioinformatics
The tip of the iceberg
This diagram was…
sporte | July 17, 2007I had an enlightening experience recently, after I wrote some bioinformatics activities, under contract, for a community college. At the end of the project, the person at the college asked me if the activities were anything like the things that a "bioinformatics technician" would do on the job.
tags: biotechnology careers, biotechnology, career+descriptions,
bioinformatics
Well no, I said, and added that I'd never heard of a bioinformatics technician before and I really didn't know what they would do. I thought that the people most likely to use our activities on-the-job would be…
sporte | July 11, 2007What do people in biotechnology do on the job?
What can students do with a science degree once they've finished college? Some answers can be found at the "Life Sciences Central web site. Created by the Workforce Development Council of Seattle-King County, this is a wonderful resource for anyone who's considering biotechnology for a potential career.
My favorite part of the site is the series of short video interviews from people in the biotech industry, describing what they do on the job and how they got there.
tags: biotechnology careers, biotechnology, career+descriptions
Ten interviews…
sporte | June 20, 2007Quoth Dr. Stemwedel, from Adventures in Science and Ethics.
In the case of Universities and four-yr colleges, I completely agree. If you're looking for job training, go to a community college.
This post is in response to one of the comments from the other day. This commenter expressed frustration at having a completed a bioinformatics training program that left him/her with a certificate but without the right skills to find a job.
tags: bioinformatics, education
He/she suggested that "the government must select candidates for teaching from industry"
This post is my answer.
In the U.S.,…
zooillogix | May 29, 2007In 2001, scientists at New Zealand biotechnology firm ViaLactia (that translates to Milk Road, right?), identified a cow with a genetic mutation that resulted in its producing skim milk. Since then, Milk Road has successfully bread a strain of cows from the original- Marge - that only produce skim milk. Marge and her offspring produce milk that is very low in saturated fats but high in healthier polyunsaturates and monounsaturated fats. This type of milk is apparently ideal for technological marvels like more-spreadable butter. Currently, dairy company's specializing in skim milk must…
sporte | May 11, 2007Do you want to learn how to use some cool biotechnology and bioinformatics methods in your college or high school class?
If you're on the East coast, the best place to go is the Fralin Biotechnology Conference at Virignia Tech, July 18-21st.
(Yes, it's the same Virgina Tech, and that's why I waited to post this announcement).
There's something for everyone at this conference. For beginners, there's a pre-conference Biotech Boot camp where you can learn to run gels and clone genes. For instructors with more experience, there are great talks, new techniques to test, and plenty of…
sporte | March 12, 2007It looked like just any other rainy Saturday morning in the Pacific Northwest, but no, this Saturday was a day for microbiology. Reluctantly, I crawled out of my warm bed and headed over to the University of Washington to attend a meeting of the Pacific NW branch of the American Society for Microbiology (ASM).
My goals for this venture were diverse. Of course, I wanted to go hear some good science and see some old friends. But I also wanted to learn more about what microbiologists are actually doing these days, out there in the wild.
In my world, since all we hear about are nucleic acid…
sporte | March 10, 2007It must be spring. Summer course announcements are popping up everywhere and this site is no exception.
Last Friday, I posted an announcement about our summer bioinformatics course in Alaska, June 27-29th.
This week, I have a couple more conferences to announce. Naturally, I'll be at both of them, leading hands-on workshops for college and high school teachers in using the technology.
Today, I want to tell you about the Bio-Link Summer Fellows Workshop, June 4th-8th Berkeley, CA
I became involved with Bio-Link ten years ago when I was running the biotechnology program at Seattle…
sporte | February 21, 2007Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things.
Step right up! Watch original research, as it happens, on the web!
I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants.
Previous parts:
Part I. The research
Part II. An introduction
Today: Part III: An inordinate fondness for hypothetical proteins
After today, we will have:
Part IV: Did we get lost in translation?
(I will add the link after it's posted)
Let's begin
Sigh.
It always happens when I have homework to…
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 | 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: Introduction
Part II: Sequencing strategies
Part III: Reads and chromats
Part 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 24, 2007Tired of waiting for congress and you don't want to move to California or out of the US? Attila Csordas shows us in a few photographs how to isolate placental stem cells at home.
His series brings back memories. My very first paid technician job in college involved visiting the maternity ward, collecting placentas, and starting primary cell cultures from umbilical epithelial cells. I would tie one end of umbilical cord, squirt a bit of media with some trypsin, and incubate the thing for a while so that the trypsin could digest some of the proteins that held the cells together. After a…
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 12, 2007The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses.
Why not use the Web?
Before going on, I should probably explain, why we use desktop programs, we have so many things available on the web. We do use the web whenever we can. Web services are nice because you can shift the computation burden to someone else's computer. (I think this…