Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish
Ontology highlight
ABSTRACT:
ORGANISM(S): Hypomesus transpacificus
PROVIDER: GSE67190 | GEO | 2015/08/25
SECONDARY ACCESSION(S): PRJNA279207
REPOSITORIES: GEO
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Project description:Thermal history plays a role in the response of corals to subsequent heat stress. Prior heat stress can have a profound impact on later thermal tolerance, but the mechanism for this plasticity is not clear. The understanding of gene expression changes behind physiological acclimatization is critical in forecasts of coral health in impending climate change scenarios. Acropora millepora fragments were preconditioned to sublethal bleaching threshold stress for a period of 10 days; this prestress conferred bleaching resistance in subsequent thermal challenge, in which non-preconditioned coral bleached. Using microarrays, we analyze the transcriptomes of the coral host, comparing the bleaching-resistant preconditioned treatment to non-preconditioned and control treatments. This experiment compared host gene expression of Acropora millepora across control, non-preconditioned, and preconditioned treatments. Fragments were sampled prior to preconditioning (Day 4), following 10 days of thermal preconditioning (Day 20), and after two (Day 23), four (Day 25), and eight days (Day 29) of 31M-BM-0C thermal challenge. The analysis implements 45 arrays, representing 5 sampling points of three treatments (n=3).
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Project description:Research on the effects of contaminants on fishes is often conducted on well-studied model test species, whose responses may be different than those of species of conservation concern. We used an oligonucleotide microarray to examine the effects of permethrin, a widely used pyrethroid pesticide, on a critically endangered fish species endemic to Northern California, the delta smelt (Hypomesus transpacificus). These results demonstrate the effects of a widely used pesticide on a sensitive fish species at concentrations below those that affect model test species.
2015-09-01 | GSE67521 | GEO
Project description:The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary, California, and considered an indicator of ecosystem health. The experimental combination of molecular biomarkers with higher level condition indicators may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by contaminant exposure. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. We have developed and applied a delta smelt microarray in order to screen for probable candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses are presented along with quantitative Polymerase Chain Reaction (qPCR) assessments measuring effects upon neuromuscular, digestive and immune responses in delta smelt exposed to copper. Differences in sensitivity were measured between juvenile and larval delta smelt (LC¬5096h= 25.2 and 80.4 ?g/L Cu2+ respectively). Swimming velocity declined with higher exposure concentrations in a dose-dependent manner, though were not statistically significant to controls. Genes encoding for aspartoacylase (ASPA), hemopexin, alpha-actin and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whilst downregulation of tumor necrosis factor indicated a probable compromised immune system.
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Project description:Background: Geographic variation in the thermal environment impacts a broad range of biochemical and physiological processes and can be a major selective force leading to local population adaptation. In the intertidal copepod Tigriopus californicus, populations along the coast of California show differences in thermal tolerance that are consistent with adaptation, i.e., southern populations withstand thermal stresses that are lethal to northern populations. To understand the genetic basis of these physiological differences, we use an RNA-seq approach to compare genome-wide patterns of gene expression in two populations known to differ in thermal tolerance. Results: Observed differences in gene expression between the southern (San Diego) and the northern (Santa Cruz) populations included both the number of affected loci as well as the identity of these loci. However, the most pronounced differences concerned the amplitude of up-regulation of genes producing heat shock proteins (Hsps) and genes involved in ubiquitination and proteolysis. Cuticle genes were up-regulated in SD but down-regulated in SC, and mitochondrial genes were downregulated in both populations. Among the hsp genes, orthologous pairs show markedly different thermal responses as the amplitude of hsp response was greatly elevated in the San Diego population, most notably in members of the hsp70 gene family. There was no evidence of accelerated evolution at the sequence level for hsp genes. Conclusions: Marked changes in gene expression were observed in response to acute sublethal thermal stress in the copepod T. californicus. Although some qualitative differences were observed between populations (e.g., cuticle gene regulation), the most pronounced differences involved the magnitude of induction of numerous hsp and ubiquitin genes. These differences in gene expression suggest that evolutionary divergence in the regulatory pathway(s) involved in acute temperature stress may offer at least a partial explanation of latitudinal trends in thermal tolerance observed in Tigriopus.
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Project description:The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary, California, and considered an indicator of ecosystem health. The experimental combination of molecular biomarkers with higher level condition indicators may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by contaminant exposure. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. We have developed and applied a delta smelt microarray in order to screen for probable candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses are presented along with quantitative Polymerase Chain Reaction (qPCR) assessments measuring effects upon neuromuscular, digestive and immune responses in delta smelt exposed to copper. Differences in sensitivity were measured between juvenile and larval delta smelt (LC¬5096h= 25.2 and 80.4 ?g/L Cu2+ respectively). Swimming velocity declined with higher exposure concentrations in a dose-dependent manner, though were not statistically significant to controls. Genes encoding for aspartoacylase (ASPA), hemopexin, alpha-actin and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whilst downregulation of tumor necrosis factor indicated a probable compromised immune system. We utilized 3 replicates for exposed samples and 3 replicates for controls, both of which were hybridized to a reference pool. Each replicate contained 4 pooled larval delta smelt. The Reference pool consisted of delta smelt samples from this experiment and a number of prior tests. No dye swaps were performed due to limited material. Supplementary file linked below reports candidate differentially expressed cDNAs. Data represented as filtered, normalized, Log-2 Alexa (547/555) ratios.
2010-08-18 | E-GEOD-23238 | biostudies-arrayexpress
Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 57-day old larvae after a 4-day exposure to ammonia; one of multiple contaminants arising from wastewater treatment plants and agricultural runoff. Genomic assessments were carried out between larvae exposed to 10 mg/L total ammonium; the lowest observed effect concentration (LOEC), and controls.
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