gene|fish

A comparison: Growth and Genes in two species

A Capstone Research paper from years past.

Fulkerson capstone paper

Are they opening?

via Tidal Cycles - oystergen.es http://bit.ly/YfMB3F

Oyster Hisotology

​Day 7 Histology from Estrogen Exposure Trial

Oyster Sampling - the sciencey kind.

Abstract - The influence of food supply on the response of Olympia oyster larvae to ocean acidification

 Abstract. Increases in atmospheric carbon dioxide drive accompanying changes in the marine carbonate system as carbon dioxide (CO2) enters seawater and alters its pH (termed “ocean acidification”). However, such changes do not occur in isolation, and other environmental factors have the potential to modulate the consequences of altered ocean chemistry. Given that physiological mechanisms used by organisms to confront acidification can be energetically costly, we explored the potential for food supply to influence the response of Olympia oyster (Ostrea lurida) larvae to ocean acidification. In laboratory experiments, we reared oyster larvae under a factorial combination of pCO2 and food level. High food availability offset the negative consequences of elevated pCO2 on larval shell growth and total dry weight. Low food availability, in contrast, exacerbated these impacts. In both cases, effects of food and pCO2 interacted additively rather than synergistically, indicating that they operated independently. Despite the potential for abundant resources to counteract the consequences of ocean acidification, impacts were never completely negated, suggesting that even under conditions of enhanced primary production and elevated food availability, impacts of ocean acidification may still accrue in some consumers.

Oyster data (and more) published by FISH546 students

Check out the final projects from students in FISH546: Bioinformatics for Environmental Sciences at http://bit.ly/ZWUhrG

Filesets include data and analysis from a variety of aquatic themes including microbe abundance, shellfish gene and protein expression, and partial genomic characterization of a fish pathogen.

Filetypes range from presentations, code, figures, genome feature tracks, fasta files, and data tables.

All students published their filesets on Figshare and altmetrics provided courtesy of ImpactStory.

Monster oysters

Prepping to be RAD

A new fileset was just published that provides new insights into Olympia oyster genomics.​

Facilitating analysis of genomic variation in Olympia oysters
Mackenzie Gavery. figshare
http://bit.ly/ZWUhrE

This along with other filesets from FISH546 are featured at oystergen.es/fish546

This dataset includes genomic intervals (BED format) to facilitate RADSeq design and functional annotation of SNPs in Olympia oysters (Ostrea lurida). 

The files include a transcriptome (FASTA format) and the following 8 genomic interval files (BED format):

Oly_snps_bed: location of SNPs with variant annotated in the name column
Oly_geneID_bed: these intervals cover the entire length of the transcript and are annoated with the SwissProt ID in the name column
Oly_regionofblasthits_bed: these intervals cover only the region of homology between the subject and query for the blastx output
Oly_inducible_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: cell-cell signaling, signal transduction, cell adhesion, development, stress response
Oly_housekeeping_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: DNA metabolism, RNA metabolism, protein metabolism
Oly_EcoRIsites_bed: location of EcoRI restriction sites
Oly_NotIsites_bed: location of NotI restriction sites
Oly_SbfI_bed: location of SbfI restriction sites

This dataset was generated as part of the requirements for FISH 546: Bioinformatics for Environmental Science.  The slides for the final presentation are included (FISH546.pdf)

​