PGS in Oysters (click for hi-res)
Mac’s Nov Goals
I can’t believe it’s November and I still haven’t published that article on C.gigas DMNT1 yet! Ok, maybe that’s a little unrealistic – and maybe I should just rejoice in the fact that I had a band in my 5’RACE PCR. I’m excited to get the bands sent out for sequencing this week and with any luck (fingers crossed), have 900bp of new DNMT1 sequence to look at. This would make completing some of October’s goals (i.e. gene expression and phylogenetic analysis) a bunch easier.
I don’t want to jinx myself, but I think I can safely say that I have completed the EPA-STAR fellowship application (although I won’t submit until Friday so I’ll continue to obsess about it til then). It will be nice to move on from this and get into the lab to work on making methylation-enriched fractions of fragmented C.gigas DNA using the MethylMiner kit. This ‘4 hour procedure’ has the largest manual I’ve ever seen – but bring it on, anything to get me away from this desk. Once the ‘highly methylated’, ‘less methylated’, and ‘unmethylated’ pools are made they’ll be ready for SOLiD library prep.
Progress was made this month with the Nanostring project to detect site-specific methylation in oysters using the nCounter platform. Codesets have been designed for 56 potentially methylated (CCGG) sites, so in Nov. I’ll be working on getting oyster samples digested with the methylation sensitive restriction enzyme MspI. It will be important to have these digests run all the way to completion, so I’d like to try a few protocols (e.g. serial addition of enzyme, 2 sequential digests, extended single digest) to make sure I’m using the best one.
And, towards the end of the month, I would really like to focus on eating as many carbohydrates (sorry Steven) and as much turkey (and Emma) as humanly possible.
Mac’s Goals for October:
1. be the first person to post October goals (check that one off)
2. then gloat about it (oh, check that one off too!)
3. write proposal for EPA-STAR Fellowship: Effects of endocrine disrupting compounds in the Pacific oyster: a systems biology approach (working title)
4. characterize DNMT1 gene in C.gigas:
a. gene expression across tissue types
b. full-length cDNA cloning
c. phylogenetic analysis
5. continue work on DNA libraries for methylation analysis (MeDIP-seq)
6. just for fun: create a quick reference guide for analytical methods to determine DNA methylation – to be included in analysis: cost, time, chance for success in non-models
Grand Bay National Estuarine Research Reserve
Today I went to sample ‘impacted oysters’ at the Grand Bay National Estuarine Research Reserve in Mississippi. The plan was to go with the whole Auburn crew who were going to be scoping out field sites, but the weather was not great, and in the end it just ended up being a quick trip out with Courtney and I to get oyster samples. It’s really unfortunate to be in this estuary because I’m looking for oysters that have been exposed to oil, it is a breathtaking landscape. Jay McIlwain, who works at the reserve, took us by boat to the first site which was a Native American shell midden. Very cool. We didn’t have any luck finding live oysters here, only four or five tiny juveniles, but we did see tar balls - my first up close and personal with the oil. The tar balls have the consistency of melted Tootsie Rolls and are mushed around some of the oyster shells. We moved on to another site and Jay used the paddle to find submerged oysters, then I hung over the side of the boat to collect them from the bottom. Awkward, yes, but it worked great. A few of the oysters had a really funny orange color to them (I didn’t get a picture), which makes you wonder about oil and/or dispersants, but there was definitely no oil smell. The whole thing just makes you pretty paranoid, maybe for good reason, I don’t know. When we got back to the Shellfish Lab on Dauphin, I had another batch of oysters to sample. Glen Chaplin, a research associate, had collected intertidal oysters near the lab where oil washed up. I should mention they were five feet underwater at the time of sampling! Everyone here has been so welcoming and helpful and informative and pretty awesome in general, so it was reluctantly that I left Dauphin Island and set out on the five hour drive to Apalachicola, FL.
-Mac
August 11th, Dauphin Island and Bayou La Batre, Alabama
We are meeting Bill Walton, Assistant Professor, Auburn University Dept. of Fisheries & Allied Aquacultures at Auburn’s Shellfish Laboratory on Dauphin Island. We’ll be joining them on a trip to their field site in Bayou La Batre, AL (yup, like Forrest Gump) where I’ll be able to take samples of ‘non-impacted’ oysters (meaning no one has visibly seen oil here, and water samples came back oil free (although I’m not exactly sure when these tests were done)). Before we go, we get a tour of the hatchery and help Courtney, a grad student, finish up some oyster measurements. This is nerdy, but their calipers are so rad I have to mention them. They are electronic, waterproof, and today plugged into the computer so each measurement automatically gets put into a cell in a spreadsheet – amazing :). Anyway, the field site is gorgeous. There’s a lot of cool stuff going on here. They are looking at growth (various characteristics) and survivorship in oysters grown in four different gear types and Courtney is looking at the effects of ‘tumbling’ on these characteristics as well (see their facebook page for more information). Bill sends me into the water under the dock just along the marsh grass boundary to grab wild oysters for sampling. I’m the first in the water while the others are unloading the bags and I have to admit I’m a bit nervous about the stingrays we were just warned about. “Just shuffle your feet and you’ll be ok”. great. These oysters are intertidal, but with the tide today, I’m in water over my knees. After I lose 15 minutes digging around in the muck for the oyster knife I dropped, sampling goes really quickly (I think they may be easier to shuck than Pacifics). Then I walk down the dock and see my father (who can’t swim) up to his chest in water helping move the boat with the oyster bags to get them back on the lines. I’m proud :). We are shown oyster drills (not like ours, huge!), juvenile blue crabs (they have the cutest red armpits!) and some plastic debris that they are finding left over from the pom-pom booms used in the spill response efforts. It leads to a bit of a discussion regarding potential impacts of the clean-up efforts themselves. What will be the effect of the plastic debris left over from booms, increased foot traffic in sensitive ecosystems, use of dispersants, low salinity from dam releases? It’s an interesting point. We finish the afternoon helping Courtney fix floats on some of the bags. Then we eat some oysters. Very tasty and pretty for that matter. Amazing day. I heart Alabama.
-Mac
Grand Isle, Louisiana
August 8th and 9th in Grand Isle, LA. All of the beaches here were closed due to the spill as they had gotten another dose of oil just last week. The scene here felt very militaristic. Lots of orange fences, ‘keep out’ type signs, even security in the state park observation tower. We were allowed to walk out on the fishing pier in the park and see crabs, shore birds and even a dolphin. Folks who lived there all seemed optimistic about the efforts. [photos]
Big Beef Creek 2009 Pics! This year with blood!
