sporte | February 13, 2007I received a mysterious file last week, via e-mail from one of my students. According the e-mail, the file contained the answers to an assignment.
I downloaded the file and double-clicked it. Nada.
I did notice that the file had an unusual extension. Most Word documents have ".doc" at the end. This one had ".docx"
I thought that must be a mistake, so I tried other options for opening it with Microsoft WORD, even editing the extension to change it to ".doc"
No. That didn't work.
Then, I tried TextEdit, all I saw were strange characters.
I did a few other things, but all I could see was…
sporte | February 13, 2007Evolution!
Wow! A jolt of electricity went down my spine. I feel like Harry Potter saying "Voldemort."
Apparently, in biomedical journals, drug resistance and other phenomena can "emerge," "arise," or "spread." It can "appear", "develop", "become common", or "be acquired."
As long as you don't say it "evolves."
A group of researchers, at the University of Virginia, discovered that authors who were studying evolution and publishing in biomedical journals were reluctant to use the word (1). They found that:
In research reports in journals with primarily evolutionary or genetic content, the…
sporte | February 9, 2007I found it in the MeSH database.
Really!
Looking for a quick answer? Don't ask a scientist
It doesn't take long to realize that scientists can spend countless hours debating the meaning of words. Our very own ScienceBlogs is a great example, just look at the many ways we can define (and debate) the meaning of a small, four-letter word like "gene". We also like to qualify our answers with a thousand conditions "usually, it's like this, but...."
This habit can be very frustrating if all you want is a quick concise answer.
On your marks, define that term!
So, many people turn to Google and…
sporte | February 8, 2007"Beware the Jabberwock, my son!
The jaws that bite, the claws that catch!
Beware the Jubjub bird, and shun
The frumious Bandersnatch!"
- from Jabberwocky, by Lewis Carroll
I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins.
Why?
Because we always (well, almost always) get matches to hypothetical and putative proteins when we do a database search with a protein sequence.
Why?
Because many of the protein sequences in GenBank (at the NCBI) are a result of conceptual translations.
What? !!
A conceptual translation…
sporte | February 7, 2007Yesterday, both Joshua and I wrote about grasses that grow in the unusually hot soil at Yellowstone National Park.
Now, I knew that hot springs bacteria can tolerate high temperatures, but I was really surprised to learn that plants could.
It was even more surprising to learn that this amazing ability was conferred on the plants by an infected fungus. I presented the data yesterday. If the fungus wasn't infected, the plants couldn't tolerate high temperatures. And, not only was the fungus-virus combination important for the grass, it had the unusual ability to confer temperature…
sporte | February 6, 2007Are viral and fungal infections always a bad thing?
Maybe not if you're a plant.
In fact, if you're a plant trying to grow in the hot (65°; C) soils of Yellowstone National Park, you're going to need all the help you can get.
A new study by Márquez, et.al. (1) found that a type of grass (Dichanthelium lanuginosum) is able to grow in the hot soils of Yellowstone National Park because it gets help from some friends. A fungal friend. And that fungal friend is infected with a virus.
If you're not used to thinking in degrees centigrade, it's hard to grasp immediately, just how hot 65°; C is…
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 3, 2007`When I make a word do a lot of work like that,' said Humpty Dumpty, `I always pay it extra.'
-Through the Looking Glass by Lewis Carroll
In biology, we often ask our words do a lot of work.
In what other field would we write direction like this
"Transfer 10 lambda of lambda phage DNA into a cuvette and determine the lambda max."
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 | February 2, 2007BioHacking is not listing in Wikipedia but it can still be found in the blogosphere. In Bio::Blogs 7, Paraschopra muses about biomathematics, synthetic biology, conferences, and bioinformatics entrepeneurship in in India. He must have seen the news about Accelrys shutting down their R&D shop in Bangalore, India.
sporte | February 1, 2007To the ancient Greeks, a chimera was a kind of monster, with the body of a goat, the tail of a dragon, and a lion's head. To geneticists, a chimera can be an animal that's derived from two embryos, such as a transgenic mouse. Or if the organism is a plant, it can be a plant with a graft. We have a chimeric cherry tree in our back yard with branches from Rainier cherries, Bing cherries, and Van cherries. And you should see the chimeras that hang out at evolgen.
Naturally, the DNA cloning and sequencing world has it's chimeras, too. There are two main kinds that I know. Sometimes chimeras…
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: IntroductionPart II: Sequencing strategiesPart III: Reads and chromatsPart 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 29, 2007The University of Nevada in Las Vegas is looking for a few good undergraduates to come do research this summer in environmental microbiology. Environmental microbiology goes way beyond hot springs bacteria and Yellowstone Park. At UNLV, you can do science in the desert.
It almost makes me wish I was an undergraduate again.
The Microbiology faculty at the UNLV and the Desert Research Institute are looking for inquisitive and eager undergraduates to participate in a 10 week summer research experience in the REU (Research Experience for Undergraduates) program.
Projects involve studying…
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 25, 2007Note to self: doing live BLAST searches during a lecture is not a good idea.
Would Julia Child make her viewers watch the food bake?
Standing in front of a class and waiting for results to appear, makes me realize how much instructors can learn a lot from watching Julia Child demonstrate cooking. I think if Julia Child taught bioinformatics this is how she would discuss BLAST results with her class:
Afer a BLAST search has been submitted to the NCBI, your results are stored there for 24 hours, and you can get them with the request ID. If you do searches ahead of time and save the…
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 21, 2007In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted:
I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it would never get done.
Well, okay, technically speaking he didn't ask me for help. But, since I'm a biologist, as soon as I looked at the definition that he chose, from Modern Genetic Analysis (by Griffiths, Lewontin, Miller, and Gelbart), I couldn't help but find something wrong.
The definition from…