Joseph R. Shaw

The ecoresponsive genome of Daphnia pulex

The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions. We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

Identification of putative peptide paracrines/hormones in the water flea Daphnia pulex (Crustacea; Branchiopoda; Cladocera) using transcriptomics and immunohistochemistry

The cladoceran crustacean Daphnia pulex has emerged as a model species for many biological fields, in particular environmental toxicology and toxicogenomics. Recently, this species has been the subject of an extensive transcriptome project, resulting in the generation and public deposition of over 150,000 expressed sequence tags (ESTs). This resource makes D. pulex an excellent model for protein discovery using bioinformatics. Here, in silico searches of the D. pulex EST database were conducted to identify transcripts encoding putative peptide precursors. Moreover, the mature peptides contained within the deduced prepro-hormones were predicted using online peptide processing programs and homology to known arthropod isoforms. In total, 63 putative peptide-encoding ESTs were identified encompassing 14 distinct peptide families/subfamilies: A-type allatostatin, B-type allatostatin, C-type allatostatin, bursicon (both alpha and beta subunit peptides), crustacean cardioactive peptide (CCAP), crustacean hyperglycemic hormone (CHH)/ion transport peptide (both CHH- and moult-inhibiting hormone-like subfamilies), diuretic hormone (calcitonin-like), ecdysis-triggering hormone (ETH), FMRFamide (both neuropeptide F and short neuropeptide F subfamilies), orcokinin and pigment dispersing hormone. From these transcripts, the structures of 76 full-length/partial peptides were predicted, which included the first C-type allatostatin-like peptide identified from a crustacean, the first crustacean calcitonin-like diuretic hormone, an undescribed CCAP isoform, two hitherto unknown ETH variants, and two new orcokinins. Neuronal localization of several of the identified peptide families was confirmed using immunohistochemitry (i.e. A-type allatostatin, CCAP, FMRFamide and PDH). In addition, immunohistochemical analyses identified other putative neuropeptides for which no ESTs had been found (i.e. corazonin, insect kinin, proctolin, red pigment concentrating hormone, SIFamide, sulfakinin and tachykinin-related peptide). Collectively, the data presented here not only catalog an extensive array of putative D. pulex peptide paracrines/hormones, but also provide a strong foundation for future investigations of the effects of environmental/anthropogenic stressors on peptidergic control in this model organism.

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

Mapping genetic adaptations to pollution Many organisms have evolved tolerance to natural and human-generated toxins. Reid et al. performed a genomic analysis of killifish, geographically separate and independent populations of which have adapted recently to severe pollution (see the Perspective by Tobler and Culumber). Sequencing multiple sensitive and resistant populations revealed signals of selective sweeps for variants that may confer tolerance to toxins, some of which were shared between resistant populations. Thus, high genetic diversity in killifish seems to allow selection to act on existing variation, driving rapid adaptation to selective forces such as pollution. Science, this issue p. 1305; see also p. 1232 Genetic diversity in Atlantic killifish has allowed for convergent evolution of pollution tolerance. Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.

Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins

BackgroundGenomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.ResultsOur microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the Daphnia genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT)-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT). The gene structures and predicted translated sequences of D. pulex MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs.ConclusionThe genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in Daphnia genomics will enable the further development of this species as a model organism for the environmental sciences.

Comparative toxicity of cadmium, zinc, and mixtures of cadmium and zinc to daphnids

Investigations were conducted to determine acute (48-h) effects of cadmium and zinc presented individually and in combination on Ceriodaphnia dubia, Daphnia magna, Daphnia ambigua, and Daphnia pulex. Toxicity tests were conducted with single metals to determine lethal effects concentrations (lethal concentrations predicted for a given percent [x] of a population, LCx value). These were used to derive metal combinations that spanned a range of effects and included mixtures of LC15, LC50, and LC85 values calculated for each metal and species. In single-metal tests, 48-h LC50 values ranged from 0.09 to 0.9 micromol/L and 4 to 12.54 micromol/L for cadmium and zinc, respectively. For each metal, D. magna was most tolerant and showed a different pattern of response from all others as determined by slope of concentration-response curves. In the combined metal treatments, all daphnids showed a similar pattern of response when LC15 concentrations were combined. This trend continued with few exceptions when LC15 concentrations of cadmium were combined with LC50 or LC85 values for zinc. However, when this treatment was reversed (LC15, zinc + LC50 or LC85, cadmium), responses of all species except D. magna indicated less-than-additive effects. For C. dubia, a near complete reduction in toxicity was observed when the LC15 for zinc was combined with LC85 for cadmium. Multimetal tests with D. magna did not differ from additive. Collectively, these studies suggest that D. magna may not be representative of other cladocerans.

Daphnia as an emerging model for toxicological genomics

Daphnia are already an established model species in toxicology. This freshwater crustacean is used commonly for environmental monitoring of pollutants around the globe and plays an important role in establishing regulatory criteria by government agencies (e.g., US EPA, Environment Canada organization for Economic Cooperation and Development, Environment Agency of Japan). Consequently, daphniids represent 8% of all experimental data for aquatic animals within the toxicological databases (Denslow et al., 2007). As such, their incorporation within the new field of toxicological genomics is limited only by the advancement of genomic resources. Because the development of these technologies requires the input and feedback of a large research community that extends far beyond the boundaries of any one discipline, the Daphnia Genomics Consortium (DGC) was formed in 2001 to: (i) provide the organizational framework to coordinate efforts at developing the Daphnia genomic toolbox; (ii) facilitate collaborative research and (iii) develop bioinformatics strategies for organizing the rapidly growing database. This chapter reviews the progress in establishing Daphnia as model species for genomic studies, with emphasis on toxicological applications. As the goals of the DGC are defined largely by extending the boundaries of current biological research in light of genomic information, this chapter first reviews Daphnias unique biological attributes that make it ideal for such an expansion of research efforts. These attributes include a long tradition of ecological, evolutionary and toxicological study, culminating in the benefits provided by emerging genomic tools.

The Role of SGK and CFTR in Acute Adaptation to Seawater in Fundulus Heteroclitus

Killifish are euryhaline teleosts that adapt to increased salinity by up regulating CFTR mediated Cl- secretion in the gill and opercular membrane. Although many studies have examined the mechanisms responsible for long term (days) adaptation to increased salinity, little is known about the mechanisms responsible for acute (hours) adaptation. Thus, studies were conducted to test the hypotheses that the acute homeostatic regulation of NaCl balance in killifish involves a translocation of CFTR to the plasma membrane and that this effect is mediated by serum-and glucocorticoid-inducible kinase (SGK1). Cell surface biotinyation and Ussing chamber studies revealed that freshwater to seawater transfer rapidly (1 hour) increased CFTR Cl- secretion and the abundance of CFTR in the plasma membrane of opercular membranes. Q-RT-PCR and Western blot studies demonstrated that the increase in plasma membrane CFTR was preceded by an increase in SGK1 mRNA and protein levels. Seawater rapidly (1 hr) increases cortisol and plasma tonicity, potent stimuli of SGK1 expression, yet RU486, a glucocorticoid receptor antagonist, did not block the increase in SGK1 expression. Thus, in killifish SGK1 does not appear to be regulated by the glucocorticoid receptor. Since SGK1 has been shown to increase the plasma membrane abundance of CFTR in Xenopus oocytes, these observations suggest that acute adaptation (hours) to increased salinity in killifish involves translocation of CFTR from an intracellular pool to the plasma membrane, and that this effect may be mediated by SGK1.

Derivation of a toxicity-based model to predict how water chemistry influences silver toxicity to invertebrates ☆

The effect of altering water chemistry on acute silver toxicity to three invertebrate species, two Daphnids, Daphnia magna and Daphnia pulex, as well as an amphipod Gammarus pulex was assessed. In addition, the physiological basis of Ag(I) toxicity to G. pulex was examined. Daphnia magna and D. pulex were more sensitive than G. pulex and 48 h LC(50) values in synthetic ion poor water were 0.47, 0.65 and 2.1 microg Ag(I) l(-1), respectively. Increasing water [Cl(-)] reduced Ag(I) toxicity in all species, and increasing water [Ca(2+)] from 50 to 1,500 microM reduced Ag(I) toxicity in G. pulex. Whole body Na(+) content, but not K(+) or Ca(2+) was significantly reduced in G. pulex exposed to 6 microg Ag(I) l(-1) for 24 h, but there was no inhibition of whole body Na(+)/K(+)-ATPase activity. Both increasing water [Cl(-)] and [Ca(2+)] reduced this Ag(I)-induced Na(+) loss. For D. magna, the presence of 10 mg l(-1) humic acid or 0.5 microM 3-mercaptoproprionic acid (3-MPA) increased the 48 h LC(50) values by 5.9 and 58.5-fold, respectively, and for D. pulex the presence of 1 microM thiosulfate increased the 48 h LC(50) value by four-fold. The D. magna toxicity data generated from this study were used to derive a Daphnia biotic ligand model (BLM). Analysis of the measured LC(50) values vs. the predicted LC(50) values for toxicity data from the present and published results where water Cl(-), Ca(2+), Na(+) or humic acid were varied showed that 91% of the measured toxicity data fell within a factor of two of the predicted LC(50) values. However, the daphnid BLM could not accurately predict G. pulex toxicity. Additionally, the Daphnia BLM was under-protective in the presence of the organic thiols 3-MPA or thiosulphate and predicted an increase in the LC(50) value of 114- and 74-fold, respectively. The Daphnia toxicity based BLM derived from the present data set is successful in predicting Daphnia toxicity in laboratory data sets in the absence of sulfur containing compounds, but shows its limitations when applied to waters containing organic thiols or thiosulphate.

Methyl farnesoate synthesis is necessary for the environmental sex determination in the water flea Daphnia pulex.

Sex-determination systems can be divided into two groups: genotypic sex determination (GSD) and environmental sex determination (ESD). ESD is an adaptive life-history strategy that allows control of sex in response to environmental cues in order to optimize fitness. However, the molecular basis of ESD remains largely unknown. The micro crustacean Daphnia pulex exhibits ESD in response to various external stimuli. Although methyl farnesoate (MF: putative juvenile hormone, JH, in daphnids) has been reported to induce male production in daphnids, the role of MF as a sex-determining factor remains elusive due to the lack of a suitable model system for its study. Here, we establish such a system for ESD studies in D. pulex. The WTN6 strain switches from producing females to producing males in response to the shortened day condition, while the MFP strain only produces females, irrespective of day-length. To clarify whether MF has a novel physiological role as a sex-determining factor in D. pulex, we demonstrate that a MF/JH biosynthesis inhibitor suppressed male production in WTN6 strain reared under the male-inducible condition, shortened day-length. Moreover, we show that juvenile hormone acid O-methyltransferase (JHAMT), a critical enzyme of MF/JH biosynthesis, displays MF-generating activity by catalyzing farnesoic acid. Expression of the JHAMT gene increased significantly just before the MF-sensitive period for male production in the WTN6 strain, but not in the MFP strain, when maintained under male-inducible conditions. These results suggest that MF synthesis regulated by JHAMT is necessary for male offspring production in D. pulex. Our findings provide novel insights into the genetic underpinnings of ESD and they begin to shed light on the physiological function of MF as a male-fate determiner in D. pulex.

Metal trophic transfer from algae to cladocerans and the relative importance of dietary metal exposure

We initially investigated effects and uptake of cadmium and copper on Pseudokirchneriella subcapitata (primary producer; formerly known as Selenastrum capricornutum). Our major efforts focused on the effects of metal-laden (i.e., Cd, Cu) P. subcapitata when used to provide dietary metal exposure to Ceriodaphnia dubia (primary consumer). Major test endpoints included feeding rate, survival, and reproduction. Metal body burden in C. dubia increased dose dependently at dietary exposure concentrations of 0.6 microg/g algal dry weight or less for cadmium and 74.7 microg/g algal dry weight or less for copper. However, it decreased sharply when dietary concentrations exceeded 0.6 microg/g algal dry weight for cadmium and 74.7 microg/g algal dry weight copper. Both dietary cadmium and copper affected all the major test endpoints. Whereas reproduction was observed to be the most sensitive endpoint, survival was observed to be the least sensitive endpoint. These results demonstrated the potential importance of dietary exposure for consideration in metal regulations or risk assessment.