Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard Two color array (cy3 and cy5): the universal standard 20 bp oligo (fluoresced with cy5) is printed to the slide with a 70-mer. Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer will bind to it. Signal is the cy3/cy5. Up to four arrays per sample, with two biological replicates made into two targets, each run on duplicate arrays.
Project description:Variation in transciptomic patterns between shallow and mesophotic corals was assessed using tag-based RNA-Seq (Tag-Seq) through analysis of natural populations across four regions in the Gulf of Mexico. Additionally, colonies were fate-tracked and repeatedly sampled to assess changes in gene expression through time in a transplant experiment between shallow and mesophotic depth zones at West and East Flower Garden Banks. This repository contains the raw .fastq.gz files for all sequenced samples.
Project description:Archived blood samples collected during common bottlenose dolphin health assessments in the northern Gulf of Mexico from 2013 to 2018 were analyzed by RNA-seq to support and enhance the assessment of animal health. The transcriptomic data were analyzed in conjunction with the substantial pool of health and environmental data collected during health assessments to investigate the utility of transcriptomic data in overall assessment of dolphin health and/or as markers of specific health concerns.
Project description:Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification. Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure. To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Gene expression was analyzed using principal component analysis, differential expression testing, and gene co-expression networks, and the results correlated to season, location, and contaminant burden. Season had a significant impact, with over 30% of genes differentially expressed between spring/summer and winter months. Geographic location exhibited lesser effects on the transcriptome, with 15% of genes differentially expressed between the northern Gulf of Mexico and the southeastern U.S. Atlantic locations. Despite a large overlap between the seasonal and geographical gene sets, the pathways altered in the observed gene expression profiles were somewhat distinct. Co-regulated gene modules and differential expression analysis both identified epidermal development and cellular architecture pathways to be expressed at lower levels in animals from the northern Gulf of Mexico. Although contaminant burdens measured were not significantly different between regions, some correlation with contaminant loads in individuals was observed among co-expressed gene modules, but these did not include classical detoxification pathways. Instead, this study identified other, possibly downstream pathways, including those involved in cellular architecture, immune response, and oxidative stress, that may prove to be contaminant responsive markers in bottlenose dolphin skin.
Project description:Bathymodiolin mussels are a group of bivalves associated with deep-sea reducing habitats, such as hydrothermal vents and cold seeps. These mussels usually engage in an obligatory symbiosis with sulfur and/or methane oxidizing Gammaproteobacteria. In addition to these bacteria, Bathymodiolus heckerae that inhabit gas and oil seeps in Campeche Bay, the southern Gulf of Mexico, host bacteria phylogenetically with the Cycloclasticus genus. We recently discovered the capability for short-chain alkane degradation in draft genomes of symbiotic Cycloclasticus. With proteomics, we investigated whether the genes required for this process are expressed by the symbionts.
