February 2008
31 Jan
Big month. The Martha’s Vineyard Oyster project wrapped up, reports in the mail. Sounds like lots of potentially cool genes will be sent off for sequences tomorrow. Maybe Tollip introns, 5’s, numerous novel RLP genes, and a couple of copepods. PCRs must have really been cranking this month. I did notice the TAE tap was dry. Speaking of gels I imagine we will be getting some helpful...
January 2008
Candidatus Xenohaliotis californiensis →
bands!
To recap last week and some of this week I extracted RNA from my November samples and reverse transcribed them. This was a rather interesting ordeal as I discovered then the tiniest thing such as no homogenizers (the blue stiring sticks) can prevent work from being done. It turned out that Steven was hiding them from me, which was okay as the time was was spent studying for Fish 311 midterm! My...
“I started putting my digests into the microwave oven now for 10 seconds at...”
– Fast restriction digests? | Bitesize Bio
WatchScience Videos [60 Second Science]
SYTO13 qPCR
[via Lisa Crosson] …the paper which compares different dyes for real-time. They suggest the optimum concentration of SYTO13 in your recipe to be 2-5uM. I worked out a recipe for a 2uM concentration that seems to be outperforming the brilliant SYBR green kit: Recipe per 25/ul rxn 12.5 ul of 2X immomix (~$75/100rxns-Bioline) 0.8 ul fwd primer 0.8 ul rev primer 1.5 ul BSA (may exclude this and...
Warning: Dihydrogen Monoxide is Worse Than... →
Google Docs Bar - Companion for Firefox →
rna extractions and new primers
Well, the title pretty much sums up my week of work. Dr. Roberts and I spent at least six hours extracting RNA from 12 abalone samples. I’ll start looking at expression next week. I spec’d each and only one had really low concentrations, all others look fine. Also, ran PCRs on a new primer I ordered last week. Hopefully I’ll get longer TOLLIP bands, but still not the complete...
Sandwalk: Ribosomal RNA Genes in Eukaryotes →
A BAND!
Well last Friday, my OmpA primer amplified something. First time I’ve actually had something show-up! Sam says it will be sequenced next week and I can’t wait. Today I’m extracting DNA from abalone fecal material and running a PCR on some bacterial growth from the above mentioned fecal matter to see if any of it is RLP. Time to take the samples out of their bath… Steph
WRAC
WRAC is seeking pre-proposals for the following six research areas: 1. Alternative Species 2. Microalgae Culture in the West 3. Effect and Interaction of Alternative Ingredients in Fish Diets 4. Tilapia Nutrition for Modern Intensive Production 5. Salmonid Gamete Quality 6. Alternative and Dependable Sterilization Techniques
HEMA - online winkelen →
now thats web design (wait a bit after it loads)
undergrad
So let’s see…. Last week I purified my total RNA from someone elses oyster tissues, ran a PCR, ran it again as it was contaminated, and ordered some primers. Seems kinda sad that all that work can be summed up in one sentence. So to add to that I decided to start working on the methods portion of my paper and begin plowing through some more research which began by discarding papers...
Predictor and Splicing Features Analyser →
Preps in the Zyppy: | Bitesize Bio →
tollip progress
So as I said, I ran some samples from other tissues with the two forward degenerate primers. I got a whole lot of nothing!! But as I started to think about it, I’m not sure the samples of tissue I used were from infected abalone, so it would make sense that the gene isn’t being expressed. Wednesday I spent most of my time submitting black abalone tollip and Mn superoxide dismutase...
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The Annual UW Undergraduate Research Symposium →
'Candidatus Xenohaliotis californiensis' →
Ribosomal Database Project II →
Macworld | Expo Keynote - Live Update →
153 days left as an undergrad!
After a restful month long break the first week of winter quater felt like a bucket of cold water being emptied over my head. After a rather unpleasent wake up call, I opened up planner with its no longer empty white lines and told myselt that there were only 153 more days til graduation. Which then remided me that there are only 9 weeks left until my capstone is due… I took my last...
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How exciting - our own BLAST server →
more from an undergrad
Steph is correct, we’re back in force! I officially started my capstone this quarter and will continue working with abalone and TOLLIP. I started the week by analyzing the sequences from the degenerate forward primer that were sent off last month. Unfortunately, I didn’t get anything new. Today I repeated some PCRs with those degenerate primers and included other tissue samples like...
What Next Generation DNA Sequencing Means For You →
via Adaptive Complexity:
The undergrads are back
Hello- I admit, I was horrid at this last quarter, so my NewYears Resolution is to keep up on posting. I’ll never be as witty as Steven or Sam, but I’ll try. This week I worked on primers to find some gene, ANY GENE, involved with virulence in RLP. Sam is going to send away for 4 of them for me. A couple of outer membrane protiens, one involved with actin polmerization, and finally...
Bio-Rad - Scientists for Better PCR →
Dear Undergrads If you’re doing research with a faculty member for at least Winter and Spring 2008 (even if you started the project already), you should consider applying for a Mary Gates Research Grant (below). If you’re awarded one, it’s a minimum of $4000!!! And we regularly have at least a couple of students in AFS get one each year. It works particularly well if...
TimeBridge →
Get Your Clone 90% Of The Time with Ligation... →
Week One
Things have been rather slow over the past few weeks for me, however Sam has been trucking right along as evident be those nice protein gels below. As obvious from the posts below I finally re-figured out to post slide shows and kwout has caught my attention, though I am not thrilled with the quote marks. Most of this week has been spent on reviews but I am relieved that finally a test has been...
Early Student Recruitment Day →
VOA News - Aquaculture: Key to Sustainable... →
FTR Social Trip →
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Opticon_data_to_Miner.mov →
Tutorial on how to take raw data through PCR Miner
