sporte | September 13, 2007A reader from the UK sent me these lovely photos that he took of a jellyfish and asked for my help in identifying it. Unfortunately, while I'm pretty good with bacteria, plants, and tropical fish, my taxonomy skills don't go much farther unless I have a sample of DNA.
These photos were taken at La-Manga off the coast of southern Spain.
My Sciblings have guessed: Rhizostoma, Stomolophus meleagris, or Mastigas
If you know, we'd all appreciate an answer in the comments.
And if you don't know about much jellyfish, RPM at evolgen would like your help answering a different reader's question…
sporte | September 11, 2007Two protein structures from an avian influenza virus are shown below. One form of the protein makes influenza virus resistant to Oseltamivir (Tamiflu®)
Don't worry, these proteins aren't from H5N1, but they do come from a related influenza virus that also infects birds.
technorati tags: molecular models, protein structures, influenza, bioinformatics, Cn3D
One protein structure is from a strain that is sensitive to an anti-viral drug called "Tamiflu®". The other structure is from the same virus, except there's a slight difference. A single base change in the viral RNA changed the codon that…
sporte | September 10, 2007One of the places that I've always wanted to visit in Portland, OR, is Powell's City of Books. Powell's is the kind of bookstore that people in Seattle discuss in the same reverent tones that they use when they're describing Cody's in Berkeley or City Light in San Francisco.
It's not just a bookstore. It's a destination.
I guess that's why I was soooo disappointed.
From the outside Powell's looks pretty low key and you're really relieved to have escaped the overpowering smell of patchouli and the feeling that maybe Jerry didn't die, he just moved to Portland and hangs out at the…
sporte | September 9, 2007If you haven't, then hustle over to Mendel's Garden for a wonderful story about the monk and his life as a scientist, check out Gene Genie for best drawing of Craig Venter that I've ever seen; and if you're into computers, take a good long look at the lightning edition of Bio::blogs. I've visited them all out myself and I assure you, they're all a good time and chock full of fun links.
sporte | September 8, 2007Bertalan Meskó shares his strategies for keeping up and gives instructions so you can do the same.
He shows how you can save your favorite PubMed searches and have NCBI send you e-mails about new papers. He describes some third party PubMed tools that make pretty graphs. Last, he discusses RSS readers, Connotea, and BioWizard. It's all very helpful and nicely described.
sporte | September 7, 2007During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery.
If it's correct.
tags: DNA sequence analysis, antiobiotic resistance , microbiology, blastn
The way this sequence was identified as Β-lactamase was through a blastn search at the NCBI. And in fact, it was correct to…
sporte | September 6, 2007Yes, indeed. I got the Red Hot blog of the Day award from RedOrbit.
Not for science, though; it's for showing why genome sequencing is expensive.
Sigh.
sporte | September 6, 2007One of my readers asked: Why does genome sequencing cost so much?
My short answer is because it's big.
But I thought it would be fun to give a better answer to this question, especially since I'm sure many of you are wondering the same thing.
Okay, so let's do some math.
Don't worry, this math isn't very complicated and I'll explain where most of the numbers come from.
Estimating costs from salaries
First, we'll take the easy route. My experience with grant budgets has taught me that the greatest cost for any project comes from salaries. If we look at the PLoS paper with Craig Venter's…
sporte | September 5, 2007If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.)
You may be wondering, and rightly so: just what is a SNP?
Never fear, hopefully this post will answer some of those questions.
tags: DNA sequencing, DNA , SNPs, genetic testing
SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a…
sporte | September 4, 2007We were all thrilled last spring when the Genetic Information Nondiscrimination Act passed the House by a vote of 420 to 3. When GINA gets through the Senate, this act will protect individuals against discrimination based on their genetic information with health insurance and employment. The promise of genomic project won't ever be achieved until individuals (besides Watson and Venter) can use their own genetic information to benefit their own health, without fear of insurance repercussions.
Passing this act seems like a no-brainer.
But I glanced at Nature last night and noticed that…
sporte | September 4, 2007
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend."
The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value.
Holmes gazed thoughtfully at the map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your life and gave you a reason to do more than…
sporte | September 3, 2007The Capitol Hill Seattle blog has a great set of lunar eclipse photos on flickr.
sporte | August 27, 2007Some of them work for Bayer.
technorati tags: biotechnology, education, biotechnology education, high school biotechnology
The San Francisco Chronicle has a nice article on a 15 year old education program in Berkeley that serves students from Berkeley High and Life Academy. Over 1500 students have participated in this program, with 862 placed in internships.
I really liked reading about some of the kids who started in the Bayer Biotech partners program and finding out what they're doing now. One of those interviewed started the program in 1992, as a 15 year old. He liked it so much, his…
sporte | August 25, 2007Why the ABRF of course!
I spend a fair amount time every summer giving workshops for college and high-school teachers on genomics and bioinformatics. One of the things that always surprises them, is the amount of lab work that's carried out by people working in shared, or core lab facilities. For example, if I was working at a research university and I wanted to sequence some DNA, maybe several patient samples, or a bacterial genome, I would send the DNA to a core lab and they would send me the sequences. I would analyze the data and write the paper.
I've simplified that process a bit in…
sporte | August 24, 2007I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper.
I think the data themselves are awfully suspicious.
So, last week I suggested that you, dear readers, go and find out why. I gave you a link to the abstract and a place to get started.
Perhaps that was too hard.
Sigh.
Okay, here's a little more help and another clue.
I highlighted the accession numbers. Post your guesses in the comments.
sporte | August 24, 2007What's the connection?(image from Newton TAB blog)
I have to admit, I don't know.
But, I do know where you can find out.
Dr. Gerard Cangelosi, from the Seattle Biomedical Research Institute, will be speaking about tuberculosis, godzilla, and XDR-TB, Monday night, 7 pm at the Pub at Ravenna Third Place as part of Science on Tap.
tags: tuberculosis, informal science education, Science on Tap, Science in Seattle
sporte | August 23, 2007Charles Darwin was so fascinated by beetles he paid people to help him build his collection. The Coleopterists Society and the Smithsonian Institute want to help kids explore the wonders of beetles, too.
They're providing grants for kids, in grades 7-12 to work on beetle biology.
Applications are due by November 15, 2007.
The Coleopterists Society, an international organization of professionals and hobbyists interested in the study of beetles, has established a program to recognize young people studying beetles.
The Society has pledged to provide up to $300 each year for the Youth…
sporte | August 22, 2007I get asked this question often enough and now that's it's come up again, it seems that I might as well answer it once and for all and get it over with.
First, I want to change the question. Of course they don't need to learn programming.
A better question is would it benefit biologists to learn programming?
My flip half-way serious answer is yes, if they want to change careers.
You see, programming is really seductive when you've been a wet-bench biologist. It's like heroin. (At least I suspect it is, I know about programming, I don't have any experience with the other beyond reading…
sporte | August 21, 2007or maybe seminars on parade?
They're calling them PubCasts, but I don't think I'll be watching them in a pub.
Seriously, SciVee is kind of cute, and has lots of potential down the road, and even has a few unintentional moments of humor right now, but....
It's a bit distracting. I can't watch these without imagining that the speakers are standing on tiptoe, desperately trying to peak their heads above the large bits of text that appear mysteriously on the screen and can't be removed.
Considering the technical glitch, it's just a bit ironic that many of the movies are from the PLoS journal…
sporte | August 21, 2007
If you've read the previous posts on this topic, here and here, you're probably aware by now that I have this weird (okay, maybe fanatical) obsession with data. Or at least, with knowing if my data are right so I can get on with life, do the analysis and figure out the results.
My results from last week suggested that re-processing chromatogram data (from the ABI 3730) with phred was probably a bad idea, but still, I only had one data point and I really wanted to know if anyone had done a more thorough study and compared larger numbers of chromatograms.
Naturally, someone had.
tags: DNA…