Single-Larva RNA Sequencing Identifies Markers of Copper Toxicity and Exposure in Early Larvae.

One of the challenges facing efforts to generate molecular biomarkers for toxins is distinguishing between markers that are indicative of exposure and markers that provide evidence of the effects of toxicity. Phenotypic anchoring provides an approach to help segregate markers into these categories based on some phenotypic index of toxicity. Here we leveraged the mussel embryo-larval toxicity assay in which toxicity is estimated by the fraction of larvae that exhibit an abnormal morphology, to isolate subsets of larvae that were abnormal and thus showed evidence of copper-toxicity, versus others that while exposed to copper exhibited normal morphology.

Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpins.

Background: The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influenced by an interplay of factors such as genetic architecture, phylogenetic history and population demography. To determine if there is convergence or divergence in mechanisms underlying phenotypic similarity, we assessed whether gene transcription patterns differed among species with similar levels of hypoxia tolerance.

Transcriptional and metabolomic characterization of spontaneous metabolic cycles in Mytilus californianus under subtidal conditions.

Intertidal mussels are often used to understand how life is orchestrated under tidal regimes of submergence and aerial emersion. The California ribbed mussel, Mytilus californianus, occurs predominantly in the rocky intertidal and is generally studied in the context of intertidal adaptation. We monitored M.

Modulation of digestive physiology and biochemistry in Mytilus californianus in response to feeding level acclimation and microhabitat.

The intertidal mussel Mytilus californianus is a critical foundation species that is exposed to fluctuations in the environment along tidal- and wave-exposure gradients. We investigated feeding and digestion in mussels under laboratory conditions and across environmental gradients in the field. We assessed whether mussels adopt a rate-maximization (higher ingestion and lower assimilation) or a yield-maximization acquisition (lower ingestion and higher assimilation) strategy under laboratory conditions by measuring feeding physiology and digestive enzyme activities.

Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds.

The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA makers. Here, higher density, second-generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes).

The environmentally tuned transcriptomes of Mytilus mussels.

Transcriptomics is a powerful tool for elucidating the molecular mechanisms that underlie the ability of organisms to survive and thrive in dynamic and changing environments. Here, we review the major contributions in this field, and we focus on studies of mussels in the genus Mytilus, which are well-established models for the study of ecological physiology in fluctuating environments. Our review is organized into four main sections.

Analysis of the basal chordate Botryllus schlosseri reveals a set of genes associated with fertility.

Background: Gonad differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. The colonial ascidian, Botryllus schlosseri is a chordate model organism which offers two unique traits that can be utilized to characterize the genes underlying germline development: a colonial life history and variable fertility. These properties allow individual genotypes to be isolated at different stages of fertility and gene expression can be characterized comprehensively.

Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins.

Transcriptionally mediated phenotypic plasticity as a mechanism of modifying traits in response to an environmental challenge remains an important area of study. We compared the transcriptional responses to low oxygen (hypoxia) of the hypoxia-tolerant intertidal fish, the tidepool sculpin (Oligocottus maculosus) with the closely related hypoxia-intolerant subtidal fish, the silverspotted sculpin (Blepsias cirrhosus) to determine whether these species use different mechanisms to cope with hypoxia. Individuals from each species were exposed to environmental O(2) tensions chosen to yield a similar level of tissue hypoxia, and gene transcription was assessed in the liver over time.

The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution.

The caspases, a family of cysteine proteases, play multiple roles in apoptosis, inflammation, and cellular differentiation. Caspase-8 (Casp8), which was first identified in humans, functions as an initiator caspase in the apoptotic signaling mediated by cell-surface death receptors. To understand the evolution of function in the Casp8 protein family, casp8 orthologs were identified from a comprehensive range of vertebrates and invertebrates, including sponges and cnidarians, and characterized at both the gene and protein levels.

The candidate histocompatibility locus of a Basal chordate encodes two highly polymorphic proteins.

The basal chordate Botryllus schlosseri undergoes a natural transplantation reaction governed by a single, highly polymorphic locus called the fuhc. Our initial characterization of this locus suggested it encoded a single gene alternatively spliced into two transcripts: a 555 amino acid-secreted form containing the first half of the gene, and a full-length, 1008 amino acid transmembrane form, with polymorphisms throughout the ectodomain determining outcome. We have now found that the locus encodes two highly polymorphic genes which are separated by a 227 bp intergenic region: first, the secreted form as previously described, and a second gene encoding a 531 amino acid membrane-bound gene containing three extracellular immunoglobulin domains.

High-resolution analysis of metabolic cycles in the intertidal mussel Mytilus californianus.

Inhabitants of the marine rocky intertidal live in an environment that alternates between aquatic and terrestrial due to the rise and fall of the tide. The tide creates a cyclical availability of oxygen with animals having access to oxygenated water during episodes of submergence, while access to oxygen is restricted during aerial emergence. Here we performed liquid chromatography and gas chromatography-mass spectrometry enabled metabolomic profiling of gill samples isolated from the California ribbed mussel, Mytilus californianus, to investigate how metabolism is orchestrated in this variable environment.

Circadian cycles are the dominant transcriptional rhythm in the intertidal mussel Mytilus californianus.

Residents in the marine intertidal, the zone where terrestrial and marine habitats converge, inhabit an environment that is subject to both the 24-h day and night daily rhythm of the terrestrial earth and also the 12.4-h ebb and flow of the tidal cycle. Here, we investigate the relative contribution of the daily and tidal cycle on the physiology of intertidal mussels, Mytilus californianus, by monitoring rhythms of gene expression in both simulated and natural tidal environments.

Hypoxia-induced mobilization of stored triglycerides in the euryoxic goby Gillichthys mirabilis.

Environmental hypoxia is a common challenge that many aquatic organisms experience in their habitat. Responding to hypoxia requires metabolic reprogramming so that energy-demanding processes are regulated to match available energy reserves. In this study we explored the transcriptional control of metabolic reorganization in the liver of a hypoxia-tolerant burrow-dwelling goby, Gillichthys mirabilis.

Mass mortality in Pacific oysters is associated with a specific gene expression signature.

Mass mortality events occur in natural and cultured communities of bivalve molluscs. The Pacific oyster, Crassostrea gigas, is a dominant species in many intertidal locations as well as an important aquacultured bivalve species, and for the last 50 years, adult oysters have suffered frequent and extreme mass mortality events during summer months. To investigate the molecular changes that precede these mortality events, we employed a novel nonlethal sampling approach to collect haemolymph samples from individual oysters during the period that preceded a mortality event.

Application of ESTs in microarray analysis.

Microarray analyses provide information on the relative expression levels of large numbers of gene products (transcripts). As such they have been widely used to examine differences in gene expression across a variety of samples such as tissues and life-cycle stages. Due to a previous lack of sequence data, microarray analyses have typically centred on the study of well-characterised model organisms.

Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus).

We conducted a large-scale gene expression screen using the 3,200 cDNA probe microarray developed specifically for Ursus americanus to detect expression differences in liver and skeletal muscle that occur during winter hibernation compared with animals sampled during summer. The expression of 12 genes, including RNA binding protein motif 3 (Rbm3), that are mostly involved in protein biosynthesis, was induced during hibernation in both liver and muscle. The Gene Ontology and Gene Set Enrichment analysis consistently showed a highly significant enrichment of the protein biosynthesis category by overexpressed genes in both liver and skeletal muscle during hibernation.

Rhythms of gene expression in a fluctuating intertidal environment.

The physiological strategies that enable organisms to thrive in habitats where environmental factors vary dramatically on a daily basis are poorly understood. One of the most variable and unpredictable habitats on earth is the marine rocky intertidal zone located at the boundary between the terrestrial and marine environments. Mussels dominate rocky intertidal habitats throughout the world and, being sessile, endure wide variations in temperature, salinity, oxygen, and food availability due to diurnal, tidal, and climatic cycles.

Ancient and modern duplication events and the evolution of stearoyl-CoA desaturases in teleost fishes.

Stearoyl-CoA desaturases (SCDs) are key enzymes of fatty acid biosynthesis whose regulation underpins responses to dietary, thermal, and hormonal treatment. Although two isoforms are known to exist in the common carp and human and four in mouse, there is no coherent view on how this gene family evolved to generate functionally diverse members. Here we identify numerous new SCD homologs in teleost fishes, using sequence data from expressed sequence tag (EST) and cDNA collections and genomic model species.

Global cooling: cold acclimation and the expression of soluble proteins in carp skeletal muscle.

The common carp (Cyprinus carpio) has a well-developed capacity to modify muscle properties in response to changes in temperature. Understanding the mechanisms underpinning this phenotypic response at the protein level may provide fundamental insights into the molecular basis of adaptive processes in skeletal muscle. In this study, common carp were subjected to a cooling regimen and soluble extracts of muscle homogenates were separated by 1-D SDS-PAGE and 2-DE.

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data.

Background: In practice many biological time series measurements, including gene microarrays, are conducted at time points that seem to be interesting in the biologist's opinion and not necessarily at fixed time intervals. In many circumstances we are interested in finding targets that are expressed periodically. To tackle the problems of uneven sampling and unknown type of noise in periodicity detection, we propose to use robust regression.

Interpreting physiological responses to environmental change through gene expression profiling.

Identification of differentially expressed genes in response to environmental change offers insights into the roles of the transcriptome in the regulation of physiological responses. A variety of methods are now available to implement large-scale gene expression screens, and each method has specific advantages and disadvantages. Construction of custom cDNA microarrays remains the most popular route to implement expression screens in the non-model organisms favored by comparative physiologists, and we highlight some factors that should be considered when embarking along this path.

An explicit test of the phospholipid saturation hypothesis of acquired cold tolerance in Caenorhabditis elegans.

Protection of poikilothermic animals from seasonal cold is widely regarded as being causally linked to changes in the unsaturation of membrane phospholipids, yet in animals this proposition remains formally untested. We have now achieved this by the genetic manipulation of lipid biosynthesis of Caenorhabditis elegans independent of temperature. Worms transferred from 25 degrees C to 10 degrees C develop over several days a much-increased tolerance of lethal cold (0 degrees C) and also an increased phospholipid unsaturation, as in higher animal models.

Beyond the lipid hypothesis: mechanisms underlying phenotypic plasticity in inducible cold tolerance.

The physiological adjustment of organisms in response to temperature variation is a crucial part of coping with environmental stress. An important component of the cold response is the increase in membrane lipid unsaturation, and this has been linked to an enhanced resistance to the debilitating or lethal effects of cold. Underpinning the lipid response is the upregulation of fatty acid desaturases (des), particularly those introducing double bonds at the 9-10 position of saturated fatty acids.

The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis.

The cellular response to stress relies on the rapid induction of genes encoding proteins involved in preventing and repairing macromolecular damage incurred as a consequence of environmental insult. To increase our understanding of the scope of this response, a cDNA microarray, consisting of 9207 cDNA clones, was used to monitor gene expression changes in the gill and white muscle tissues of a eurythermic fish, Gillichthys mirabilis (Gobiidae) exposed to ecologically relevant heat stress. In each tissue, the induction or repression of over 200 genes was observed.