sporte | September 25, 2008Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank
This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things.
In this last part, I discuss a general method for finding novel things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III.…
sporte | September 24, 2008Would you like to win a cash prize and maybe an expense paid trip to New York City?
If you're in grades 7-12 and like research, you might be interested in the 2009 Young Naturalist contest from the American Museum of Natural History.
Winners (2 from each grade) will receive cash awards, from $500 to $2,500, and an all-expense paid trip to New York City to attend the awards ceremony at the Museum.
The contest involves investigating questions in ecology, biology, Earth science and astronomy and writing an essay. More information can be found here.
sporte | September 24, 2008If you like cool and unusual photos be sure to take a look at the 2008 Nikon Small World competition site. You can view lots of lovely pictures of things found under a microscope and vote for your favorite ones. You don't even have to focus the microscope!
One of my favorites is the tubeworm larva. It looks something from outer space.
There's even a contest to identify some of the more unconventional images. I only got three out of five. ;-(
You can find them at www.nikonsmallworld.com
sporte | September 24, 2008Part IV. Assembling the details and making the case for a novel paramyxovirus
This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.
image from the Public Health Library
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a novel mosquito paramyxovirus
V. A…
sporte | September 23, 2008Every fall, we had to confront it. People would let their dogs run around on the field in the morning and by the time soccer practice started, the field would be full of deadly doo.
There's nothing that hurts soccer practice more than a soccer ball or shoes that went through a pile of dog poo.
That's why I'm so exciting to see this new application for DNA testing. That's right. Kids will be able to play soccer without worry and dog owners will be held responsible for cleaning up after their pets.
The forward thinking city that's going to implement this plan is Petah Tikva, in Isreal.…
sporte | September 23, 2008Part III. Serendipity strikes when we Blink
In which we find an unexpected result when we Blink while looking at the mumps polymerase.
This is the third in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes. And yes, this is where the discovery happens.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
To paraphrase Louis Pasteur,…
sporte | September 23, 2008The National Girls Collaborative Project, as you might guess from the title, focuses on helping girls and engaging girls in science, technology, engineering, and math (aka "STEM").photos used with permission from NGCP
Quoting from the NGCP website, (the emphasis is mine):
Numerous programs and initiatives seek to create gender equity in the areas of science, technology, engineering, and mathematics (STEM) have been implemented only to lose effectiveness or fade away. Had these programs had the benefit of collaboration with other girl-serving projects, organizations and institutions, and…
sporte | September 22, 2008Part II. What do mumps proteins do? And how do we find out?
This is the second in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes, and a general method for finding interesting things.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
In Part I, we looked at the NCBI SeqViewer, and found a new way to check out a genome map, and learn more…
sporte | September 22, 2008Wow! One of my commenters, Ms. Baker, suggested an entirely new way that scientists can help with science education. The only requirement is that a science class have their own blog.
So, if your science class has a blog, let me know, so I can share the URL and maybe recruit some scientists or at least graduate students, to take a look.
I think this idea is so great! It doesn't involve any kind of traveling and many, many different scientists can participate, thus minimizing volunteer burn out. It also gives students a way to practice writing about what they do and interacting with the…
sporte | September 21, 2008Part I. The back story from the genome record
Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
I began this series on mumps intending to write about immunology and how vaccines work to stimulate the immune…
sporte | September 21, 2008What do you do if you're a scientist and want to volunteer in a classroom?
How do you find the right place to go and right kind of activity that suites your talents?
One of my commenters asked about this a few weeks ago. With the new school year up and running, it seems like a good time to tackle this question.
What kinds of volunteer activities do scientists do?
Your effort can be big or small. Small efforts can involve speaking in a classroom, mentoring students via ea-mail, judging science fair projects, or assisting with homework questions. Larger efforts can entail doing or…
sporte | September 20, 2008Hey high school teachers! Are your students interested in the brain?
Who isn't?
Three winners will win all-expense-paid trips to present their work in a poster session in Seattle at the 2009 Annual Meeting of the American Academy of Neurology. Their teachers get to come too! I can tell you, Seattle is a fun place to visit.
Low tide at Golden Gardens, July 2008
Plus, three student winners will get $1000 in cash in addition to the trip.
Find out more at www.aan.com/achieve.
sporte | September 19, 2008Every now and then, people hire me to travel places and give workshops for college instructors and teachers on using bioinformatics. In a couple of weeks, I'll go to Long Branch, NJ. This week, I went to Corpus Christi, Texas and gave two workshops at Del Mar College; one on using Cn3D to understand protein DNA structure, and another on using BLAST to identify the source of unknown DNA sequences.
Del Mar College has a beautiful science facility, with an amazing assortment of fancy high tech equipment. The workshops were fun and I enjoyed seeing the student posters showcasing work on the…
sporte | September 17, 2008Okay, occasional readers, friends, and former students, the date is official. I walked over to Ozzie's, chatted with one of the waitresses (a Garfield grad, no less!), talked with a manager on the phone, and we're on for the party.
You can find us on Saturday, Sept. 27th at 4 pm in the upstairs mezzanine at Ozzie's.
Address: 105 W. Mercer St., Seattle, WA 98119
Dave Bacon will be there (I don't think he's related to Kevin, but here's your chance to ask, and we could start a new game! Six degrees of David Bacon!). Grrl Scientist will be signing autographs. And, we'll get a chance to…
sporte | September 3, 2008PubMed is an on-line database at the National Center for Biotechnology Information (NCBI) that contains information from scientific literature. Most of the information is related to medical research.
To search PubMed, you use a program called Entrez. You go to the NCBI, select PubMed from the menu, type words into the text box, and start the search. Sometimes that's all you need to do. Sometimes you get several million results and need to use more specific words to limit the results the ones that you really want.
Many scientists use PubMed on a daily basis. But the NCBI has noticed that…
sporte | September 2, 2008David Ng from The World's Fair has made this wonderful video on public speaking. Or shall we say the funnier side of public speaking? I really enjoyed it!
I'd say Dave's video ranks right up there with one of my other favories, the classic: "Chicken chicken chicken"
sporte | August 28, 2008Mumps was a common childhood disease when I was a child. We grew up learning that it was better to get mumps as a child because getting it as an adult would make you sterile. No doubt that idea arose from symptoms like swollen glands, swollen testicles, etc. When I looked in PubMed though, I couldn't find much data on sterility (at least not easily).
I did find data on hearing loss.
Death is not a common outcome of mumps. Between 1953 and 1962, there were 162,344 cases of mumps in the U.S. every year and only 39 deaths per year. People, mostly children, did die from mumps, but other…
sporte | August 27, 2008It's déjà vu all over again.
The first chapter in Arthur Allen's book "Vaccine" describes the history of smallpox vaccination in the United States. In 1721, in Boston, the prevailing belief was that to get vaccinated was to intervene with "divine providence." If you tried to protect yourself, it meant that you lacked faith in God.
Today, I read that a mumps outbreak is happening in Vancouver, Canada. So far 116 cases have been confirmed.
Why is mumps, a preventable and serious disease, causing problems in Canada?
photo of a child with mumps by by Barbara Rice, from the Public…
sporte | August 26, 2008Last night we went to a pub to hear about some new technology for diagnostic testing. A wonderful speaker, Karen Hedine from Micronics came and told us about the work that her company is doing. She brought along a demonstration machine and passed the machine and several plastic test chambers around the pub so we could all take a look.
The technology, microfluidics, is fascinating stuff. I've written about it a little before( "From Louis Pasteur to "Lab on a chip"").
A biological sample (blood, poop, urine, saliva, a vaginal smear) is drawn into the card. Molecules move into the card via…
sporte | August 25, 2008A few days ago, I wrote about a cool project that some high school students did where they used DNA sequencing to identify seafood.
One question that came up from one of my commenters was how a school would start a project like this. I'm totally biased, but I think DNA sequencing (well, actually the data analysis) is one of the most interesting things that a class can do as part of a research project. These days, getting started with this kind of project, wouldn't be so hard.
Here's are some ways that I would get started:
Find an existing project where my students could collaborate and get…