Project description:This study compares gene expression in the testis of three offshore (Pelican Shoal) and three near-shore (Tingler Island) adult male queen conchs (Strombus gigas) collected from the wild on February 15, 2007.
Project description:Single cell RNA-seq is a powerful methodology, but with important limitations. In particular, the process of enzymatic separation of cells at 37O C can be expected to result in artifact changes in gene expression patterns. We here describe a dissociation method that uses protease from a psychrophilic microorganism with high activity in the cold. The entire procedure is carried out at 6O C or colder, where mammalian transcriptional machinery is largely inactive. To test this method we carry out single cell RNA-seq on about 9,000 cells, comparing the results of the cold method with a method using 37O C incubations for multiple times. We show that the cold active protease method results in a great reduction in gene expression artifacts.
Project description:Whole blood was collected as part of annual health assessments of beluga whales from the healthy Bristol Bay, Alaska stock during 2012-2014. Gene expression from 24 animals (8 from each year) was analyzed to establish baseline information on the content and variation of the beluga whale blood transcriptome.
Project description:We subjected three inshore and four offshore genotypes of the coral Orbicella faveolata to 30, 31, 32, or 33ºC for 31 days and measured photochemical efficiency (Fv/Fm), the types and relative abundance of dinoflagellate endosymbionts, and gene expression of the host and symbiont. All inshore coral genotypes, regardless of symbiont type, were significantly more thermotolerant than offshore genotypes based on declines in Fv/Fm. The most heat-tolerant inshore genotype (In1) was dominated by Durusdinium trenchii; all other genotypes were Breviolum-dominated, suggesting local adaptation or acclimatization contributes to the heat tolerance of inshore genotypes. After 31 days of heat stress, all coral genotypes (except In2) had lost most of their Breviolum and became dominated by D. trenchii. Host genotype In1 presented unique expression patterns of genes involved in heat shock response, immunity, and protein degradation. There were few changes in the symbiont transcriptomes of inshore corals under heat stress, but significant changes in symbiont gene expression from the offshore colonies, including increases in ribosomal and photosynthetic proteins. These data show that the differential thermotolerance between inshore and offshore O. faveolata in the Florida Keys is associated with statistically significant differences in both host and symbiont gene expression that provide insights into the mechanisms underlying holobiont heat tolerance.
Project description:Reproduction of queen conchs at nearshore sites in the Florida Keys is known to be impaired (Delgado et al. 2004). A recent microarray study of male queen conchs collected from the Florida Keys during the early part of the reproductive season (February, 2007) indicated that NS conchs show differences in expression of spermatogenesis-related and small GTPase signaling transcripts (Spade et al. 2010). The current study investigates gene expression in the ovary of female queen conchs from the same sampling effort in February, 2007. One-color (Cy3) oligonucleotide array experiment. Each array sample is an individual biological replicate. The study includes four biological replicates offshore and three biological replicate nearshore. Offshore conchs exhibit normal reproduction, and so were considered the reference group in the analysis.