sequence analysis

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Quick synopsis: A type of grass grows in Yellowstone National Park in hot (65° C), unfriendly soil. How the plant manages this feat is a mystery. What we do know, is that the grass can only tolerate high temperatures if it's been infected by a fungus, and the fungus has to be infected by an RNA virus. In the paper describing this discovery, the researchers provided the GenBank accession numbers for the viral sequences. I decided to see if I could find out more about the proteins and what they do. Read ... Read more
Grasses 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:
"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 ... Read more

Yesterday, 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 ... Read more
Vizzini: 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 ... Read more
To 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 ... Read more
I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too happy about it, though. By this time of the school year, they've caught on that every snowday has a price. And, they will pay ... Read more
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants? Two reports in Nature (1, 2) suggest that bacterial populations differ between people who are obese and people who not, and that the bacterial inhabitants of their guts, may be partly to blame. In one study, the authors studied the bacterial populations of their volunteers' intestines by compiling a data set of 18,348 DNA sequences for bacterial 16S ribosomal RNA by sampling feces. Wow! That's a lot of ... well, I won't say it, but you know what ... Read more
Five Bulgarian nurses and a Palestinian doctor (dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children, it's the Libyan government that will be killing innocent people. The clock is ticking. Some of you might be wondering (I know I was): How exactly is molecular sequence data being used to solve the crime? Why are scientists and science bloggers claiming that the ... Read more
Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)? Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools. If ... Read more

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