Bringing Ocean Acidification System online

Posted by & filed under Miscellaneous.

I was out at Manchester yesterday to help Laura out with getting things going. tldr- Water is flowing, rising temperature seems to be an issue. This could be attributed to air temp and/or pumps. When we arrived water temperature was up to 19C after about a week. We decided to drain down system refill, calibrate… Read more »

No code required

Posted by & filed under Ostrea lurida.

Today Sam and I took care of the daily maintenance of F2 Olympia oysters grown at the Ken Chew Shellfish Hatchery at Manchester, WA. In short, larvae are being described from Fidalgo (North: NF), Oyster Bay (South: SS), and Hood Canal (HC) broodstock. Though I had done most aspects before, never without Katherine, thus she… Read more »

There is something about TEs

Posted by & filed under Cgigas DNA Methylation.

For purposes of proposaling and reports, I have gone back to look at a small project done in collaboration with scientist at IFREMER looking at pesticide exposure on oyster larvae methylation. The control library had limited yield so the number of loci with data from the treated and the control library was restricted. However using… Read more »

Differentially methylated loci – repeats or TEs

Posted by & filed under Cgigas DNA Methylation.

In our original effort (bioRxiv doi:¬†http://dx.doi.org/10.1101/012831) we characterized DMLs in relationship to genomic regions, including putative transposable elements. In this case TEs were defined as tandem repeats and targets that had sequence similarity to protein sequences in other species. Transposable elements were identified using RepeatMasker, a program that screens and annotates interspersed repeats (Smit et… Read more »