DNA methylation plays a complex role in regulating genome activity
Mackenzie Gavery’s new paper on DNA methylation and gene expression in oysters is out in PeerJ. Abstract: Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA...
Read MoreDiscoveries of FHL EIMD Course Published
This week the manuscript “Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression” was published. Photo: Students in FHL EIMD course hard at work on bioinformatic analysis of transcriptome and genomic data from the hard clam pathogen quahog parasite unknown (QPX). Abstract: Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic...
Read MoreChanges in brain tissue of senescent sockeye
Caroline Storer’s master thesis research was recently published in the journal Biogerontology. She examined gene expression patterns in sockeye salmon on their return to their natal stream. From the Abstract: Senescence varies considerably among fishes, and understanding the evolutionary basis for this diversity has become an important area of study. For rapidly senescing species such as Pacific salmon, senescence is a complex process as these fish are initiating anorexia while migrating to natal spawning grounds, and die within days of reproduction. To better understand senescence in...
Read MoreOlympia Oyster Outplanting
This week oysters from 3 sites across Puget Sound will be outplanted. This very large reciprocal transplant experiment will test for a home field advantage in survival, maturation and growth in Olympia oysters. The overall goals of this project are to increase our knowledge of local adaptation in Olympia oysters to address concerns that interbreeding between potentially maladapted cultured and wild stocks could negatively impact wild populations. Check back soon for details.
Read MoreEver hear of Nostrasamus?
[This is reposted from our Tumblr where Sam reflects on his time in the lab, since the beginning... back in 2007] That’s not a typo. Of course everyone’s heard of that old fool Nostradamus, who was supposed to be able to predict the fate of the world (including the OJ Simpson trial!). However, I think he’s a miserable failure. NostraSAMus (that refers to me, by the way), on the other hand, seems to actually have a good grasp on reality and the future. As reference, notice what I wrote in this 2007 Genefish post (my first post to the lab blog, in fact!): “Soon, I’m sure...
Read MoreShotgun proteomics and the Pacific oyster
Emma’s paper on shotgun proteomics was recently published where she describes the value of shotgun proteomics in physiological studies. Timmins-Schiffman EB* Nunn BL, Goodlett DR and Roberts SB. (2013) Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. Conservation Physiology. doi:10.1093/conphys/cot009 Abstract: Shotgun proteomics offers an efficient means to characterize proteins in a complex mixture, particularly when sufficient genomic resources are available. In order to assess the practical application of shotgun proteomics in the...
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