July 2007
So one thermocycler is O.O.C., bands in negative controls like to appear in our gels, the pipet fairy is taking the P10s, and now pens are nowhere to be had! Needless to say, the lab is still functioning and Lindsay and I are working hard. I PCRed the genomic DNA from abalone that she purified last week with the tollip and chemotrypsin like protease primers. No good results, but still cut out the...
"PRIM2" input interface →
A tool aligning 2 homolog sequences to design primers on the consensus sequence
UPS: Tracking Information: Temp logger →
plate070716_top5 - here at last... (but was it... →
Want to learn more about C_gigas? →
note: Tushara, these links should provide plenty of info
More free online storage...
If you’re a Firefox and Gmail user (Gmail accounts are available to anyone now, so you might want to get one or two or five for this) you can add a plug-in to Firefox that will allow you to store your files on your Gmail storage space! That’s up to 2GB per Gmail account. Here’s the link: Getspace.com I haven’t tried it, but it sounds pretty sweet! Sam
Nice BLAST Tutorial with new interface →
[via Geospiza] BLAST for beginners
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Episode IV: A New (Sequencing) Hope
A long time ago, in a galaxy far, far away… The Empire has increased its security measures for guarding the plans for its newest space station, the Death Star. They have sent a group of Imperial Troops to the Dagobah System in an attempt to hide the plans from Rebel forces…
Well, not really. All that stuff up above is really just a euphemism for some stuff related to the sequencing...
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-80 freezer
Did a little cleaning out and organization in the -80. Found some great sample sets and some stuff to trash. Plenty of room for the abalone samples which we should start playing with this week. Specifically, (and cryptically) we have 07-12: 1-20: 5 each from both sites/ exposed vs non/ 11-20 exposed?. Also there is at least 4 more clinicals, 07-19—SR
lets go ahead and add a Map too...
While maybe not productive use of time, I have started a lab map (via Google ofcourse). The intent it to map field sites and other areas of interest. I am heading over to Big Beef Creek (its on the map!) in the next couple of weeks to check out research options. —SR
Guidelines for keeping a proper lab notebook →
Courtesy of Professor Carolyn Friedman
Abalone Galore!
You know, after starting this work on abalone, I realized I’ve never ate any before… I’ll have to try some now! But really, this past week has been almost entirely devoted to the abalone project. I PCRed and ran gels for 3 different primers; one of which was actually targeted to pathogen. Nothing came of that one, which probably means that the abalone which we got our RNA to make...
What I've been up to for the last week
Hey again, time for another post! This past week+ I’ve been doing lots of PCR and DNA purification from gels. The practice is definitely good, and I’m still learning a lot, such as if you overwhelm your PCR reaction with too much bacteria you won’t get any bands from your 24 samples. Or, if I don’t drink coffee before lab, my natural clumsiness comes out and I knock boxes...
http://www.wehi.edu.au/education/wehi-tv/dna/dogma2... →
And a cool look at transcription. I think it’s suppose to be in real time… -Cullen
http://www.wehi.edu.au/education/wehi-tv/dna/dogma3... →
A pretty cool look at translation. - Cullen
Sequencing!
There are not many people in this world who, one, even know what the heck that means and, two, might even be remotely excited about this. But, I guess that’s their loss! To help out those newbs, I’ve put together a quick and dirty tutorial on what goes on behind the scenes in molecular biology lab in order to prepare DNA samples for sequencing. So, most of the week’s work has...
PubMed C.gigas and pollution findings
The majority of information about Crassostrea gigas and pollution I have found so far deal with how humans can be affected by eating C. gigas harvested from polluted waters (for example, paralytic shellfish poisoning). I have only found a few items dealing with how pollution actually affects the oysters themselves. Below is a listing of journal abstracts I found from PubMed: Exposure and response...
SHELL GAMES: With old ways and new ideas, Willapa...
Here is an interesting article I found discussing the future of oyster growers in Washington State. http://seattletimes.nwsource.com/pacificnw/2005/0515/cover.html — tushara
Shellfish farms
I have found several oyster (Crassostrea gigas) hatcheries / farms in Washington State: Coast Seafoods — World’s largest oyster hatchery Taylor Shellfish Company Penn Cove Shellfish — Located on Whidbey Island. Little Skookum Shellfish Growers — Located in Shelton. JJ Brenner Oyster Company Seattle Shellfish Bay Center Farms — Willapa Bay. No website: Wiegardt and...
FedEx | Track: Oyster Samples →
keep your fingers crossed, 5th times the charm
Literature Search
I thought I would give some suggestions on where to go to look for what your looking for, if you are looking for something. Primarily I use Pubmed. Most genomic / molecular journals will be covered here. For more traditional fisheries articles, head over to ASFA: Aquatic Sciences and Fisheries Abstracts. For this one you need to be on the UW network. And what list would be complete without a...
Mashups: Google launches Mapplets →
just talking to Tushara yesterday on how something simple like this sure would be nice
fun in lab
So it’s been fun in the lab lately. I’ve been learning the techniques for the past few weeks by doing some plating, PCRs, gels, and extracting the DNA from the gels. Now I think I need to do some research to better understand the genes we’re looking for when running these gels. Lindsay and I researched today for information on genetics work already done on abalone. I’ll...
C. gigas genes
Here are some of the genes that could possibly be involved in C. gigas stress response: GO:0001302 1 replicative cell aging GO:0001558 2 regulation of cell growth GO:0006281 4 DNA repair GO:0006950 3 response to stress GO:0006952 3 defense response GO:0006954 3 inflammatory response GO:0006955 2 immune response GO:0006968 1 cellular defense response GO:0006974 1 response to DNA damage...
Washington State Food and Agriculture Suppliers →
The Pacific Coast Shellfish Growers Association -... →
Second post!
So, it’s been awhile since I last posted. I spent a very nice week in Hawaii, but now I’m back and working hard to get enough DNA samples to send out for sequencing by this Friday. In the past week I redid the PCR for the abalone genes DQ821491 and DQ821497 with the correct set of primers. For 491 I got a strong band on the gel, which I cut out, purified and determined its...
what is needed in notebooks
If you have not noticed, we do a lot of PCR, a lot has to be re-done for various reasons (ie I asked Sam to order dog primers; or was that just a test to see if anyone was paying attention??) Anyway when recording your PCR recipe etc. indicate primer names and more importantly PCR conditions (ie temps, times) if you need refreshing of why temp changes see previous post. —-SR
PCR Animation →
refresher on what is happening in your tubes
Sequence in 5 days
Should be an interesting week. Looks like everyone’s re streaks grew. Now I imagine there will be PCR screens then sequencing of those products. Note: it would be more interesting if we could read first-hand accounts on the blog. Everyone must be too busy PCRing:) If anything comes back as interesting it will be off to co-IP columns. Lindsay is pretty confident she has two new abalone...
FedEx | Track: Dungan isolates, qpx, and... →
DNA from Dungan isolates (marked 1-29). I still have cell pellets from the original cultures that are not extracted. I also included DNA from Roxanna’s QPX cultures (marked 31-35), including her yellow isolate (just because they were in the box, and I thought it might be interesting - your choice with what you do with those).
Decorin Gene Transfer Promotes Muscle Cell... →
Mozy Online Backup: Free. Automatic. Secure. →
nice offsite backup option, can never be too safe —SR
C. gigas EST GO analysis →
Tushara, let me know if you see any term describing a gene that could be involved in stress response…
haliotis_go_count →
Function of Haliotis sp. sequences (Biological, Cellular, Molecular)
Washington state shellfish growers
One of my objectives for today is to find a list of major shellfish farms in Washington State. The Washington State Department of Health Division of Environmental Health Office of Shellfish and Water Protection (whew!) has a pdf file that lists all of the state’s licensed shellfish farms. You can find this file at the link below:...
Hi it's Tushara!
Everyone else has introduced themselves on the blog so I’d better follow suit. I’m Tushara, a capstone student here in the Roberts Lab. I’m a senior here in the University of Washington’s Aquatic and Fisheries science program. In my spare time you can find me belly dancing, eating fire, cracking a whip and other various things with local fire and performing arts uber-circus...
Tushara's adventures in beachcombing
2007 / 2008 Public Beach List — Special Rules http://wdfw.wa.gov/fish/shelfish/beachreg/07clamoysterseasons.pdf — This pdf has a list of beaches and when their oyster and clam seasons are open. Click on the beach name link and an individualized report for the beach pops up. WDFW Shellfish Regulations: WA Public Beaches for Clam and Oyster Harvest...
Google Docs and Spreadsheets: The most useful... →
