A vitellogenin chain containing a superoxide dismutase-like domain is the major component of yolk proteins in cladoceran crustacean Daphnia magna

Daphnia stress response to environmental concentrations of chloramphenicol-multi-omics approach

Commonly used medicines, when discarded or improperly disposed of, are known to contaminate freshwater ecosystems. Pharmaceuticals can be toxic and mutagenic, and can modify freshwater organisms, even at environmentally relevant concentrations. Chloramphenicol (CAP) is an antibiotic banned in Europe. However, it is still found in surface waters around the world. The aim of this study was to evaluate the impact of chloramphenicol contamination in freshwater on the model organism Daphnia magna. Specific life history parameters, proteome, and host-associated microbiome of four D. magna clones were analyzed during a three-generation exposure to CAP at environmental concentrations (32 ng L-1). In the first generation, no statistically significant CAP effect at the individual level was detected. After three generations, exposed animals were smaller at first reproduction and on average produced fewer offspring. The differences in D. magna's life history after CAP treatment were in accordance with proteome changes. D. magna's response to CAP presence indicates the high stress that the tested organisms are under, e.g., male production, upregulation of ubiquitin-conjugating enzyme E2 and calcium-binding protein, and downregulation of glutathione transferase. The CAP-exposed D. magna proteome profile confirms that CAP, being reactive oxygen species (ROS)-inducing compounds, contributes to structural changes in mitochondria. Microbiome analysis showed a significant difference in the Shannon index between control and CAP-exposed animals, the latter having a more diverse microbiome. Multilevel analyses, together with long exposure in the laboratory imitating conditions in a polluted environment, allow us to obtain a more complete picture of the impact of CAP on D. magna.

Daphnia magna model for the study of mycotoxins present in food: Gliotoxin, ochratoxin A and its combination

Mycotoxins are low molecular weight compounds present in food and feed. Although their effects on human health have been widely described, their mechanisms of action are still undefined. Gliotoxin (GTX) and ochratoxin A (OTA) are among the most dangerous mycotoxins produced by Aspergillus spp. Therefore, their toxicity was studied in the Daphnia magna model, which has high capacity to predict cytotoxicity and assess ecotoxicity, comparable to mammalian models. The study consisted of a series of tests to evaluate the effects of mycotoxins GTX, OTA and their combinations at different dilutions on Daphnia magna that were conducted according to standardized OECD 202 and 211 guidelines. The following assays were carried out: acute toxicity test, heartbeat, delayed toxicity test, reproduction, growth rate test. Reproducibility was determined by observing the offspring after 21 days of GTX exposure. In acute and delayed toxicity transcript levels of genes involved in xenobiotic metabolism (mox, gst, abcb1, and abcc5), and oxidative stress (vtg-SOD) were analyzed by qPCR. GTX showed acute toxicity and decreased heart rate in D. magna compared to OTA. On the other hand, OTA showed a delayed effect as evidenced by the immobility test. Both mycotoxins showed to increase genes involved in xenobiotic metabolism, while only the mycotoxin mixture increased oxidative stress. These results suggest that the mycotoxins tested could have negative impact on the environment and human health.

Unveiling the multilevel impact of four water-soluble polymers on Daphnia magna: From proteome to behaviour (a case study)

The ubiquitous presence of water-soluble polymers (WSPs) in freshwater environments raises concerns regarding potential threats to aquatic organisms. This study investigated, for the first time, the effects of widely used WSPs -polyvinyl alcohol (PVA), polyvinylpyrrolidone (PVP), polyacrylic acid (PAA), and polyethylene glycol (PEG)- using a multi-level approach in the freshwater biological model Daphnia magna. This integrated assessment employed a suite of biomarkers, evaluation of swimming behaviour, and proteomic analysis to investigate the effects of three environmentally relevant concentrations (0.001, 0.5, and 1 mg/L) of the tested WSPs from molecular to organismal levels, assessing both acute and chronic effects. Our findings reveal that exposure to different WSPs induces specific responses at each biological level, with PEG being the only WSP inducing lethal effects at 0.5 mg/L. At the physiological level, although all WSPs impacted both swimming performance and heart rate of D. magna specimens, PAA exhibited the greatest effects on the measured behavioural parameters. Furthermore, proteomic analyses demonstrated altered protein profiles following exposure to all WSPs, with PVA emerging as the most effective.

Sex-Biased Transcription Expression of Vitellogenins Reveals Fusion Gene and MicroRNA Regulation in the Sea Louse Caligus rogercresseyi

The caligid ectoparasite, Caligus rogercresseyi, is one of the main concerns in the Chilean salmon industry. The molecular mechanisms displayed by the parasite during the reproductive process represent an opportunity for developing novel control strategies. Vitellogenin is a multifunctional protein recognized as a critical player in several crustaceans' biological processes, including reproduction, embryonic development, and immune response. This study aimed to characterize the C. rogercresseyi vitellogenins, including discovering novel transcripts and regulatory mechanisms associated with microRNAs. Herein, vitellogenin genes were identified by homology analysis using the reference sea louse genome, transcriptome database, and arthropods vitellogenin-protein database. The validation of expression transcripts was conducted by RNA nanopore sequencing technology. Moreover, fusion gene profiling, miRNA target analysis, and functional validation were performed using luciferase assay. Six putative vitellogenin genes were identified in the C. rogercresseyi genome with high homology with other copepods vitellogenins. Furthermore, miR-996 showed a putative role in regulating the Cr_Vitellogenin1 gene, which is highly expressed in females. Moreover, vitellogenin-fusion genes were identified in adult stages and highly regulated in males, demonstrating sex-related expression patterns. In females, the identified fusion genes merged with several non-vitellogenin genes involved in biological processes of ribosome assembly, BMP signaling pathway, and biosynthetic processes. This study reports the genome array of vitellogenins in C. rogercresseyi for the first time, revealing the putative role of fusion genes and miRNA regulation in sea lice biology.

Trans- and Multigenerational Effects of Isothiazolinone Biocide CMIT/MIT on Genotoxicity and Epigenotoxicity in Daphnia magna

The mixture of 5-chloro-2-methylisothiazol-3(2H)-one and 2-methylisothiazol-3(2H)-one, CMIT/MIT, is an isothiazolinone biocide that is consistently detected in aquatic environments because of its broad-spectrum usage in industrial fields. Despite concerns about ecotoxicological risks and possible multigenerational exposure, toxicological information on CMIT/MIT is very limited to human health and within-generational toxicity. Furthermore, epigenetic markers altered by chemical exposure can be transmitted over generations, but the role of these changes in phenotypic responses and toxicity with respect to trans- and multigenerational effects is poorly understood. In this study, the toxicity of CMIT/MIT on Daphnia magna was evaluated by measuring various endpoints (mortality, reproduction, body size, swimming behavior, and proteomic expression), and its trans- and multigenerational effects were investigated over four consecutive generations. The genotoxicity and epigenotoxicity of CMIT/MIT were examined using a comet assay and global DNA methylation measurements. The results show deleterious effects on various endpoints and differences in response patterns according to different exposure histories. Parental effects were transgenerational or recovered after exposure termination, while multigenerational exposure led to acclimatory/defensive responses. Changes in DNA damage were closely associated with altered reproduction in daphnids, but their possible relationship with global DNA methylation was not found. Overall, this study provides ecotoxicological information on CMIT/MIT relative to multifaceted endpoints and aids in understanding multigenerational phenomena under CMIT/MIT exposure. It also emphasizes the consideration of exposure duration and multigenerational observations in evaluating ecotoxicity and the risk management of isothiazolinone biocides.

High-quality genome of Diaphanosoma dubium provides insights into molecular basis of its broad ecological adaptation

Diaphanosoma dubium Manuilova, 1964, is a widespread planktonic water flea in Asian freshwater. Although sharing similar ecological roles with species of Daphnia, studies on D. dubium and its congeners are still few and lacking a genome for the further studies. Here, we assembled a high quality and chromosome level genome of D. dubium by combining long reads sequencing and Hi-C technologies. The total length of assembled genome was 101.8 Mb, with 98.92 Mb (97.2%) anchored into 22 chromosomes. Through comparative genomic analysis, we found the genes, involved in anti-ROS, detoxification, protein digestion, germ cells regulation and protection, underwent expansion in D. dubium. These genes and their expansion helpfully explain its widespread geographical distribution and dominance in eutrophic waters. This study provides insight into the adaptive evolution of D. dubium at genomic perspectives, and the present high quality genomic resource will be a footstone for future omics studies of the species and its congeners.

Alterations in Daphnia magna exposed to enniatin B and beauvericin provide additional value as environmental indicators

Mycotoxins beauvericin (BEA) and enniatin B (ENN B) affect negatively several systems and demand more studies as the mechanisms are still unclear. The simultaneous presence of contaminants in the environment manifests consequences of exposure for both animals and flora. Daphnia magna is considered an ideal invertebrate to detect effects of toxic compounds and environmental alterations. In this study, the potential toxicity and the basic mechanism of BEA and ENN B individually and combined were studied in D. magna. Acute and delayed toxicity were evaluated, and transcript levels of genes involved in xenobiotic metabolism (mox, gst, abcb1, and abcc5), reproduction, and oxidative stress (vtg-SOD) were analyzed by qPCR. Though no acute toxicity was found, results revealed a spinning around and circular profile of swimming, a strong decrease of survival after 72 h for BEA and ENN B at 16 µM and 6.25 µM, respectively, while for BEA + ENN B [8 + 1.6] µM after 96 h. The amount of mycotoxin remaining in the media revealed that the higher the concentration assayed the higher the amount remaining in the media. Differential regulation of genes suggests that xenobiotic metabolism is affected denoting different effects on transcription for tested mycotoxins. The results provide new insights into the underlying risk assessment of BEA and ENN B not only through food for consumers but also for the environment.

The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia

Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia, and short-term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress-tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia; to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 h of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis, showing upregulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia-by-habitat of origin or chronic-by-acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through upregulation of cuticular proteins and neurotrophins, respectively.

Juvenile hormone synthesis and signaling disruption triggering male offspring induction and population decline in cladocerans (water flea): Review and adverse outcome pathway development

Juvenile hormone (JH) are a family of multifunctional hormones regulating larval development, molting, metamorphosis, reproduction, and phenotypic plasticity in arthropods. Based on its importance in arthropod life histories, many insect growth regulators (IGRs) mimicking JH have been designed to control harmful insects in agriculture and aquaculture. These JH analogs (JHAs) may also pose hazards to nontarget species by causing unexpected endocrine-disrupting (ED) effects such as molting and metamorphosis defects, larval lethality, and disruption of the sexual identity. This critical review summarizes the current knowledge of the JH-mediated effects in the freshwater cladoceran crustaceans such as Daphnia species on JHA-triggered endocrine disruptive outputs to establish a systematic understanding of JHA effects. Based on the current knowledge, adverse outcome pathways (AOPs) addressing the JHA-mediated ED effects in cladoceran leading to male offspring production and subsequent population decline were developed. The weight of evidence (WoE) of AOPs was assessed according to established guidelines. The review and AOP development aim to present the current scientific understanding of the JH pathway and provide a robust reference for the development of tiered testing strategies and new risk assessment approaches for JHAs in future ecotoxicological research and regulatory processes.

DNMT3.1 controls trade-offs between growth, reproduction, and life span under starved conditions in Daphnia magna

The cladoceran crustacean Daphnia has long been a model of energy allocation studies due to its important position in the trophic cascade of freshwater ecosystems. However, the loci for controlling energy allocation between life history traits still remain unknown. Here, we report CRISPR/Cas-mediated target mutagenesis of DNA methyltransferase 3.1 (DNMT3.1) that is upregulated in response to caloric restriction in Daphnia magna. The resulting biallelic mutant is viable and did not show any change in growth rate, reproduction, and longevity under nutrient rich conditions. In contrast, under starved conditions, the growth rate of this DNMT3.1 mutant was increased but its reproduction was reciprocally reduced compared to the wild type when the growth and reproduction activities competed during a period from instar 4 to 8. The life span of this mutant was significantly shorter than that of the wild type. We also compared transcriptomes between DNMT3.1 mutant and wild type under nutrient-rich and starved conditions. Consistent with the DNMT3.1 mutant phenotypes, the starved condition led to changes in the transcriptomes of the mutant including differential expression of vitellogenin genes. In addition, we found upregulation of the I am not dead yet (INDY) ortholog, which has been known to shorten the life span in Drosophila, explaining the shorter life span of the DNMT3.1 mutant. These results establish DNMT3.1 as a key regulator for life span and energy allocation between growth and reproduction during caloric restriction. Our findings reveal how energy allocation is implemented by selective expression of a DNMT3 ortholog that is widely distributed among animals. We also infer a previously unidentified adaptation of Daphnia that invests more energy for reproduction than growth under starved conditions.

Metabolic adjustments during starvation in Daphnia pulex

Zooplankton organisms face a variable food supply in their habitat. Metabolic adjustments during periods of starvation were analysed from changes in metabolite level to gene expression in the microcrustacean Daphnia pulex during starvation. The animals exploited their carbohydrate stores first, but their lipid and protein reserves were also degraded, albeit more slowly. Glycogenolysis and probably gluconeogenesis led to hyperglycaemia after 16 h of starvation. The concentration of α-ketoglutarate and the rate of oxygen consumption also reached maxima during this period. Nuclear HIF-1α levels and α-ketoglutarate concentration showed inverse correlation. Effects of this 2-oxoacid on prolyl hydroxylase activity, HIF-1α stability and the role of this transcription factor in the changes of the expression level of several putatively HIF-1-mediated metabolic genes are discussed. Transcriptome profiling via RNA-Seq revealed a downregulation of genes for protein biosynthesis and an upregulation of genes for carbohydrate metabolism during starvation. Thus, the adjustments of energy metabolism in response to food deprivation were quantified from the level of metabolites, signal transduction and gene expression, and possible connections of the respective dynamics of observed changes were analysed.

Changes in lipid profiles in Daphnia magna individuals exposed to low environmental levels of neuroactive pharmaceuticals

Disruptive effects of chemicals on lipids in aquatic species are mostly limited to obesogens and vertebrates. Recent studies reported that antidepressants, anxiolytic, antiepileptic and β-adrenergic pharmaceuticals, with putative distinct mechanisms of action at low environmental relevant concentrations, up-regulated common neurological and lipid metabolic pathways and enhanced similarly reproduction in the crustacean Daphnia magna. Conversely CRISPR mutants for the tryptophan hydrolase enzyme gene (TRH) that lack serotonin had the opposed phenotype: the lipid metabolism down-regulated and impaired reproduction. Lipid metabolism is strongly linked to reproduction in D. magna. The aim of this study is to test if the above mentioned neuro-active chemicals disrupted common lipid groups and showed also the opposed lipidomic effects as those individuals lacking serotonin. This study used ultra-high performance liquid chromatography/time-of-flight mass spectrometry (UHPLC/TOFMS) to study how neuro-active chemicals (carbamazepine, diazepam, fluoxetine and propranolol) at low (0.1 μg/L) and higher concentrations (1 μg/L) and three CRISPR TRH mutant clones disrupt the dynamics of glycerophospholipids and glycerolipids in Daphnia adults. Lipidomic analysis identified 267 individual lipids corresponding to three classes of glycerolipids, eleven of glycerophospholipids, one of sterols and one of sphingolipids, of which 132 and 125 changed according to the chemical treatments or across clones, respectively. Most pharmaceutical treatments enhanced reproduction whereas mutated clones lacking serotonin reproduced to a lesser extent. Except for carbamazepine, most of the tested pharmaceuticals increased some triacylglycerol species and decreased monoacylglycerols, lysophospholipids, sphingomyelins and cholesterol esters in exposed females. Opposed lipidomic pattern was observed in mutated clones lacking serotonin. Lipidomic data, thus, indicate a close link between reported transcriptomic and lipidomic changes, which are likely related to serotonin and other neurological signalling pathways.

Linking multiple biomarker responses in Daphnia magna under thermal stress

Temperature is an important abiotic variable that greatly influences the performance of aquatic ectotherms, especially under current anthropogenic global warming and thermal discharges. The aim of the present study was to evaluate thermal stress (20 °C vs 28 °C) in Daphnia magna over 21 d, focusing on the linkage among molecular and biochemical biomarker responses. Thermal stress significantly increased the levels of reactive oxygen species (ROS) and lipid peroxidation, especially in the 3-d short-term exposure treatment. This change in the ROS level was also correlated with mitochondrial membrane damage. These findings suggest that oxidative stress is the major pathway for thermally-induced toxicity of D. magna. Additionally, the expression levels of genes related to hypoxia (Hb), development (Vtg1), and sex determination (Dsx1-α, Dsx1-β, and Dsx2) were greatly increased by elevated temperature in a time-dependent manner. The cellular energy allocation was markedly decreased at the elevated temperature in the 3-d exposure treatment, mainly due to carbohydrates consumption for survival (oxidative stress defense). The present study showed that linking multiples biomarker responses are crucial for understanding the underlying mechanism of thermal stress on D. magna.

Vitellogenin offsets oxidative costs of reproduction in female painted dragon lizards

Vitellogenesis ('yolking' of follicles) is a bioenergetically costly stage of reproduction requiring enlargement of the liver to produce vitellogenin (VTG) yolk precursor proteins, which are transported and deposited at the ovary. VTG may, however, serve non-nutritive anti-oxidant functions, a hypothesis supported by empirical work on aging and other life-history transitions in several taxa. We test this hypothesis in female painted dragon lizards (Ctenophorus pictus) by examining covariation in VTG with the ovarian cycle, and relative to reactive oxygen species (ROS) including baseline superoxide (bSO). Plasma VTG decreased prior to ovulation, when VTG is deposited into follicles. VTG, however, remained elevated post-ovulation when no longer necessary for yolk provisioning and was unrelated to reproductive investment. Instead, VTG was strongly and positively predicted by prior bSO. ROS, in turn, was negatively predicted by prior VTG, while simultaneously sampled VTG was a positive predictor. These findings are consistent with the hypothesis that VTG functions as an anti-oxidant to counteract oxidative stress associated with vitellogenesis. The relationship between bSO and VTG was strongest in post-ovulatory females, indicating that its function may be largely anti-oxidant at this time. In conclusion, VTG may be under selection to offset oxidative costs of reproduction in egg-producing species.

Cloning and molecular characterization of estrogen-related receptor (ERR) and vitellogenin genes in the brackish water flea Diaphanosoma celebensis exposed to bisphenol A and its structural analogues

Although it has previously been shown that bisphenol (BP) analogues may interfere with the normal hormonal regulation by acting as endocrine disrupting chemicals (EDCs), little information is available on effects of BP analogues in invertebrates, particularly on cladocerans. In the present study, we identified estrogen-related receptors (EER), vitellogenin (VTG), and VTG receptor (VtgR) from the brackish water flea Diaphanosoma celebensis, and examined the effects of BPA and the substitutes, BPF and BPS, in different sublethal concentrations. Gene expression varied with time well matched with brooding, suggesting that DcEER, DcVTG, and DcVtgR play a role in reproduction in D. celebensis. qRT-PCR analysis showed that BPA and its substitutes differently modulated mRNA expressions of DcEER, DcVTG, and DcVtgR, indicating that these compounds adversely affect the normal reproduction-related pathway. This study facilitates better understanding of the molecular mode of action of BP analogues on the reproductive system of D. celebensis.

Reproductive workers insufficiently signal their reproductive ability in a paper wasp

Why workers forfeit direct reproduction is a crucial question in eusocial evolution. Worker reproduction provides an excellent opportunity to understand the mechanism of kin conflict resolution between the queen and workers. We evaluated behavioral and physiological differences among females in the paper wasp Polistes chinensis antennalis to examine why some workers reproduce under queenright conditions. Reproductive workers were old and foraged less early in the season; their cuticular hydrocarbon (CHC) profiles overlapped with those of queens but were significantly different. The distinct CHC profile of the eggs of the queen likely represented a cue for policing against those by workers. Juvenile hormone (JH) and dopamine seemed to be associated with gonadotropic function, and the JH level of reproductive workers was similar to that of the queen. The high JH level of reproductive workers likely facilitated their reproduction even under queenright conditions. Gene expression levels of the queen and reproductive workers differed only in vitellogenin. These results suggest that worker reproduction is facilitated by an increase in JH level; however, CHC is not a fertility-linked signal, but a queen-linked signal; consequently, reproductive workers without a queen-linked signal might be allowed to stay within the colony.

Quantitative Proteomics Reveals Remodeling of Protein Repertoire Across Life Phases of Daphnia pulex

Although the microcrustacean Daphnia is becoming an organism of choice for proteomic studies, protein expression across its life cycle have not been fully characterized. Proteomes of adult females, juveniles, asexually produced embryos, and the ephippia-resting stages containing sexually produced diapausing freezing- and desiccation-resistant embryos are analyzed. Overall, proteins with known molecular functions are more likely to be detected than proteins with no detectable orthology. Similarly, proteins with stronger gene model support in two independent genome assemblies can be detected, than those without such support. This suggests that the proteomics pipeline can be applied to verify hypothesized proteins, even given questionable reference gene models. In particular, upregulation of vitellogenins and downregulation of actins and myosins in embryos of both types, relative to juveniles and adults, and overrepresentation of cell-cycle related proteins in the developing embryos, relative to diapausing embryos and adults, are observed. Upregulation of small heat-shock proteins and peroxidases, as well as overrepresentation of stress-response proteins in the ephippium relative to the asexually produced non-diapausing embryos, is found. The ephippium also shows upregulation of three trehalose-synthesis proteins and downregulation of a trehalose hydrolase, consistent with the role of trehalose in protection against freezing and desiccation.

Different as night and day: Behavioural and life history responses to varied photoperiods in Daphnia magna

Nearly all animal species have utilized photoperiod to cue seasonal behaviours and life history traits. We investigated photoperiod responses in keystone species, Daphnia magna, to identify molecular processes underlying ecologically important behaviours and traits using functional transcriptomic analyses. Daphnia magna were photoperiod‐entrained immediately posthatch to a standard control photoperiod of 16 light/ 8 dark hours (16L:8D) relative to shorter (4L:20D, 8L:16D, 12L:12L) and longer (20L:4D) day length photoperiods. Short‐day photoperiods induced significantly increased light‐avoidance behaviours relative to controls. Correspondingly, significant differential transcript expression for genes involved in glutamate signalling was observed, a critical signalling pathway in arthropod light‐avoidance behaviour. Additionally, period circadian protein and proteins coding F‐box/LRR‐repeat domains were differentially expressed which are recognized to establish circadian rhythms in arthropods. Indicators of metabolic rate increased in short‐day photoperiods which corresponded with broadscale changes in transcriptional expression across system‐level energy metabolism pathways. The most striking observations included significantly decreased neonate production at the shortest day length photoperiod (4L:20D) and significantly increased male production across short‐day and equinox photoperiods (4L:20D, 8L:16D and 12L:12D). Transcriptional expression consistent with putative mechanisms of male production was observed including photoperiod‐dependent expression of transformer‐2 sex‐determining protein and small nuclear ribonucleoprotein particles (snRNPs) which control splice variant expression for genes like transformer. Finally, increased transcriptional expression of glutamate has also been shown to induce male production in Daphnia pulex via photoperiod‐sensitive mechanisms. Overall, photoperiod entrainment affected molecular pathways that underpin critical behavioural and life history traits in D. magna providing fundamental insights into biological responses to this primary environmental cue.

Toxicity of biomining effluents to Daphnia magna: Acute toxicity and transcriptomic biomarkers

Increasing metal consumption is driving the introduction of new techniques such as biomining to exploit low grade ores. The biomining impacts notably aquatic ecosystems, yet, the applicability of ecotoxicological tests to study the complex mixture effects of mining waters is insufficiently understood. The aim of the present work was to test if transcriptomic biomarkers are suitable and sensitive for the ecotoxicity assessment of biomining affected waters. The study site had been affected by a multimetal biomine, and the studied water samples formed a concentration gradient of contamination downstream from the biomining site. Cadmium and nickel were used as positive controls in the toxicity tests. Selected transcriptomic biomarkers, previously shown to be differentially regulated by metals, were used to evaluate the ecotoxicity of the water samples. Parallel samples were used to compare the transcriptomic biomarkers with the conventional acute D. magna toxicity test. In the acute test, one sample was acutely toxic to D. magna, when pH was adjusted according to the standard, whereas, in the native pH, three samples caused total immobility. Monooxygenase was up-regulated by the highest concentration of Cd in control samples and three of the water samples. Vtg-SOD was up-regulated by one of the water samples, and catalase by the second highest concentration of Cd. The results show that transcriptomic biomarkers in D. magna can be used as sensitive bioindicators for metal mixture toxicity assessment in complex environmental water samples.

Transcriptional and Translational Relationship in Environmental Stress: RNAseq and ITRAQ Proteomic Analysis Between Sexually Reproducing and Parthenogenetic Females in Moina micrura

Moina micrura is a kind of small-bodied water flea within the family Moinidae. Similar to Daphnia, M. micrura could also switch its reproduction mode from parthenogenetic female (PF) to sexual female (SF) to adapt to the external environment. To uncover the mechanisms of reproductive switching in M. micrura, we used both RNA-Seq and iTRAQ analyses to investigate the differentially expressed genes (DEGs) and their protein products between SF and PF in M. micrura. A total of 1665 DEGs (702 up-regulated, 963 down-regulated) and 600 differentially expressed proteins (DEPs) (102 up-regulated, 498 down-regulated) were detected in SF. Correlation analyses indicated that 31 genes were expressed significantly differentially at both transcriptomic and proteomic levels, including 15 up-regulated genes and 16 down-regulated genes in SF. Meanwhile, our data also showed that 528 DEPs have discordant expression at transcript level, implying post-transcriptional (including translational) regulation. These top up-regulated genes and their protein products in SF were mainly grouped into the globin-related family, vitellogenin-related family, cuticle-related family, Hsp-related family and methyltransferases-related family, which were all involved in the reproductive switching in Daphnia. In contrast, a cluster of orthologous groups revealed that up-regulated genes and their protein products in PF were strongly associated with the metabolic process, which may be responsible for rapid population proliferation in M. micrura.

The transcriptomic and proteomic responses of Daphnia pulex to changes in temperature and food supply comprise environment-specific and clone-specific elements

Background

Regulatory adjustments to acute and chronic temperature changes are highly important for aquatic ectotherms because temperature affects their metabolic rate as well as the already low oxygen concentration in water, which can upset their energy balance. This also applies to severe changes in food supply. Thus, we studied on a molecular level (transcriptomics and/or proteomics) the immediate responses to heat stress and starvation and the acclimation to different temperatures in two clonal isolates of the model microcrustacean Daphnia pulex from more or less stressful environments, which showed a higher (clone M) or lower (clone G) tolerance to heat and starvation.

Results

The transcriptomic responses of clone G to acute heat stress (from 20 °C to 30 °C) and temperature acclimation (10 °C, 20 °C, and 24 °C) and the proteomic responses of both clones to acute heat, starvation, and heat-and-starvation stress comprised environment-specific and clone-specific elements. Acute stress (in particular heat stress) led to an early upregulation of stress genes and proteins (e.g., molecular chaperones) and a downregulation of metabolic genes and proteins (e.g., hydrolases). The transcriptomic responses to temperature acclimation differed clearly. They also varied depending on the temperature level. Acclimation to higher temperatures comprised an upregulation of metabolic genes and, in case of 24 °C acclimation, a downregulation of genes for translational processes and collagens. The proteomic responses of the clones M and G differed at any type of stress. Clone M showed markedly stronger and less stress-specific proteomic responses than clone G, which included the consistent expression of a specific heat shock protein (HSP60) and vitellogenin (VTG-SOD).

Conclusions

The expression changes under acute stress can be interpreted as a switch from standard products of gene expression to stress-specific products. The expression changes under temperature acclimation probably served for an increase in energy intake (via digestion) and, if necessary, a decrease in energy expenditures (e.g, for translational processes). The stronger and less stress-specific proteomic responses of clone M indicate a lower degree of cell damage and an active preservation of the energy balance, which allowed adequate proteomic responses under stress, including the initiation of resting egg production (VTG-SOD expression) as an emergency reaction.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4742-6) contains supplementary material, which is available to authorized users.

Protein profiling as early detection biomarkers for TiO2 nanoparticle toxicity in Daphnia magna

The mode of action for nanoparticle (NP) toxicity in aquatic organisms is not yet fully understood. In this work, a strategy other than toxicity testing was applied to Daphnia magna exposed to TiO₂-NPs: the use of nuclear microscopy and the assessment of protein profile. D. magna is a keystone species broadly used as a model system in ecotoxicology. Titanium (Ti) was found in the D. magna digestive tract, mainly in the gut. The penetration of Ti into the epithelial region was greater at higher exposure levels and also observed in eggs in the brood pouch. The protein profile of individuals exposed to different concentrations showed that 2.8 and 5.6 mg/L TiO₂-NP concentrations induced an over-expression of the majority of proteins, in particular proteins with molecular weight of ∼120, 85 and 15 kDa, while 11.2 mg/L TiO₂-NP had an inhibitory effect on protein expression. The Matrix-assisted laser desorption ionization with tandem time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis of these proteins consistently identified them as vitellogenin (Vtg)-like proteins, associated with enzymes involved in redox balance. These results indicate that Vtg-like proteins are up-regulated in D. magna exposed to TiO₂-NPs. Vitellogenesis is associated with the reproduction system, suggesting that TiO₂-NP exposure can impair reproduction by affecting this process. The precise mode of action of TiO₂-NPs is still unclear and the results from this study are a first attempt to identify specific proteins as potential markers of TiO₂-NP toxicity in D. magna, providing useful information for future research.

How cyclophosphamide at environmentally relevant concentration influences Daphnia magna life history and its proteome

The waste of commonly used medicines is known to contaminate freshwater ecosystems. Pharmaceuticals can be toxic, mutagenic, or modifying to freshwater organisms even at low concentrations if consider their permanent presence in the environment. Chemotherapeutics used to treat cancer, and in particular alkylating agents, contribute significantly to this form of pollution, the latter introducing cytotoxic and/or mutagenic lesions to the DNA and RNA of organisms which can be disruptive to their cells. The aim of the present study was to investigate the influence of the alkylating anticancer agent cyclophosphamide (CP) on Daphnia magna clones. We evaluated the life history parameters and protein profiles of this crustacean following exposure to environmentally relevant CP concentration of 10 ng L^-1. Even at this low concentration, the alkylating agent caused modification of the life history parameters and proteome profile of the Daphnia. These changes were clone-specific and involved growth rate, age at first reproduction, neonate number, and proteins related to cell cycle and redox state regulation. The disturbance caused by pharmaceuticals contaminating freshwater ecosystem is probably weaker and unlikely to be cytotoxic in character due to the high dilution of these substances in the water. However, our results indicate that prolonged exposure of organisms to these toxins may lead to modifications on the organismal and molecular levels with unpredictable significance for the entire ecosystem.

Neonicotinoid insecticides imidacloprid, guadipyr, and cycloxaprid induce acute oxidative stress in Daphnia magna

Cycloxaprid (CYC) and guadipyr (GUA) are two new and promising neonicotinoid insecticides whose effects on Daphnia magna are as yet unknown. In this study, the acute toxicities of CYC and GUA to D. magna, including immobilization and embryo-hatching inhibition, and their effects on antioxidant enzymes and related gene expression were determined after a 48-h exposure. Imidacloprid (IMI) was evaluated at the same time as a reference agent. The 48-h EC₅₀ values of IMI, GUA, and CYC for neonate immobilization were 13.0-16.5mg/L and for embryo hatching were 11.3-16.2mg/L. The specific activity of the enzymes superoxide dismutase (SOD) and catalase (CAT) were interfered by IMI, but not by GUA and CYC, while the activity of acetylcholinesterase (AChE) was significantly increased by IMI, but inhibited by GUA and CYC. The relative expressions of the Sod-Cu/Zn, Sod-Mn, Cat, and Ache genes were usually inhibited by IMI, GUA, and CYC, except for Cat by CYC, Ache by GUA, and Sods by IMI. For vitellogenin genes with a SOD-like domain (Vtg1/2-sod), relative expression was increased by IMI and inhibited by GUA and CYC, indicating that IMI, GUA, and CYC have potential toxicity toward reproduction. CYC and GUA are highly active against IMI-resistant pests, and considering the similar toxicity of IMI to D. magna, CYC and GUA are suitable for use in future integrated pest management systems.

Endocrine-disruption potential of perfluoroethylcyclohexane sulfonate (PFECHS) in chronically exposed Daphnia magna

Perfluoroethylcyclohexane sulfonate (PFECHS), mainly used in hydraulic fluids in aircrafts, is a member of the perfluoroalkyl sulfonate family which includes the regulated perfluorooctane sulfonate (PFOS). PFECHS has been reported in environmental samples but its toxicity to aquatic organisms is unknown. The objectives of this study were to identify biological pathways altered by sublethal exposure (12 d) of D. magna to PFECHS (0.06, 0.6, and 6 mg/L) using microarray and quantitative real-time PCR and to identify potential biomarkers to link transcriptomic to phenotypic responses. PFECHS was also quantified in surface water samples (1.04-1.38 ng/L) collected from the St. Lawrence River, Canada. Transcriptomic analyses indicated the under-regulation of vitellogenin-related genes (VTG1) in PFECHS-exposed groups. PFECHS exposure also led to the up-regulation of genes related to cuticle. VTG was selected as a potential cellular marker and identified in D. magna using an immuno-specific assay and quantified using Western blot and LC/MS/MS. Results indicated a decrease of VTG content in exposed D. magna which was in concordance with the transcription of VTG-related genes. No effects were observed on survival, molting, or reproduction at the individual/population levels. Overall, results suggest endocrine disruption potential for PFECHS in D. magna at concentrations higher than levels reported in the aquatic environment.

Reproductive switching analysis of Daphnia similoides between sexual female and parthenogenetic female by transcriptome comparison

The water flea Daphnia are planktonic crustaceans commonly found in freshwater environment that can switch their reproduction mode from parthenogenesis to sexual reproduction to adapt to the external environment. As such, Daphnia are great model organisms to study the mechanism of reproductive switching, the underlying mechanism of reproduction and development in cladocerans and other animals. However, little is known about the Daphnia's reproductive behaviour at a molecular level. We constructed a genetic database of the genes expressed in a sexual female (SF) and a parthenogenetic female (PF) of D. similoides using Illumina HiSeq 2500. A total of 1,763 differentially expressed genes (865 up- and 898 down-regulated) were detected in SF. Of the top 30 up-regulated SF unigenes, the top 4 unigenes belonged to the Chitin_bind_4 family. In contrast, of the top down-regulated SF unigenes, the top 3 unigenes belonged to the Vitellogenin_N family. This is the first study to indicate genes that may have a crucial role in reproductive switching of D. similoides, which could be used as candidate genes for further functional studies. Thus, this study provides a rich resource for investigation and elucidation of reproductive switching in D. similoides.

iTRAQ technology-based identification of human peripheral serum proteins associated with depression

Clinical depression is one of the most common and debilitating psychiatric disorders and contributes to increased risks of disability and suicide. Differentially expressed serum proteins may serve as biomarkers for diagnosing depression. In this study, samples from depressed patients are aggregated into a pool (22×100μL serum was used) and samples from healthy volunteers are aggregated into the other pool (20×100μL serum was used). Isobaric tag for relative and absolute quantitation (iTRAQ) technology and tandem mass spectrometry were employed to screen for differentially expressed serum protein in two separate pools. We identified 472 proteins in the serum samples, and 154 of these presented differences in abundance between the depression and control groups. Ingenuity pathway analysis (IPA) was employed to identify the highest scoring proteins in signaling pathway networks. Finally, four differentially expressed proteins were validated by enzyme-linked immuno sorbent assay (ELISA). Proteomic studies revealed that levels of c-reaction protein (CRP), inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), serum amyloid A1 (SAA1) and angiopoietin-like 3 (ANGPTL3) were substantially increased in depressed patients compared with the healthy control group. Therefore, these differentially expressed proteins may represent potential markers for the clinical diagnosis of depression.

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex

Background

Predator-induced defences are a prominent example of phenotypic plasticity found from single-celled organisms to vertebrates. The water flea Daphnia pulex is a very convenient ecological genomic model for studying predator-induced defences as it exhibits substantial morphological changes under predation risk. Most importantly, however, genetically identical clones can be transcriptionally profiled under both control and predation risk conditions and be compared due to the availability of the sequenced reference genome. Earlier gene expression analyses of candidate genes as well as a tiled genomic microarray expression experiment have provided insights into some genes involved in predator-induced phenotypic plasticity. Here we performed the first RNA-Seq analysis to identify genes that were differentially expressed in defended vs. undefended D. pulex specimens in order to explore the genetic mechanisms underlying predator-induced defences at a qualitatively novel level.

Results

We report 230 differentially expressed genes (158 up- and 72 down-regulated) identified in at least two of three different assembly approaches. Several of the differentially regulated genes belong to families of paralogous genes. The most prominent classes amongst the up-regulated genes include cuticle genes, zinc-metalloproteinases and vitellogenin genes. Furthermore, several genes from this group code for proteins recruited in chromatin-reorganization or regulation of the cell cycle (cyclins). Down-regulated gene classes include C-type lectins, proteins involved in lipogenesis, and other families, some of which encode proteins with no known molecular function.

Conclusions

The RNA-Seq transcriptome data presented in this study provide important insights into gene regulatory patterns underlying predator-induced defences. In particular, we characterized different effector genes and gene families found to be regulated in Daphnia in response to the presence of an invertebrate predator. These effector genes are mostly in agreement with expectations based on observed phenotypic changes including morphological alterations, i.e., expression of proteins involved in formation of protective structures and in cuticle strengthening, as well as proteins required for resource re-allocation. Our findings identify key genetic pathways associated with anti-predator defences.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-015-0109-x) contains supplementary material, which is available to authorized users.

Ecotoxicogenomic approaches for understanding molecular mechanisms of environmental chemical toxicity using aquatic invertebrate, Daphnia model organism

Due to the rapid advent in genomics technologies and attention to ecological risk assessment, the term “ecotoxicogenomics” has recently emerged to describe integration of omics studies (i.e., transcriptomics, proteomics, metabolomics, and epigenomics) into ecotoxicological fields. Ecotoxicogenomics is defined as study of an entire set of genes or proteins expression in ecological organisms to provide insight on environmental toxicity, offering benefit in ecological risk assessment. Indeed, Daphnia is a model species to study aquatic environmental toxicity designated in the Organization for Economic Co-operation and Development’s toxicity test guideline and to investigate expression patterns using ecotoxicology-oriented genomics tools. Our main purpose is to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and relevant modes of toxicity in Daphnia magna. These approaches enable us to address adverse phenotypic outcomes linked to particular gene function(s) and mechanistic understanding of aquatic ecotoxicology as well as exploration of useful biomarkers. Furthermore, key challenges that currently face aquatic ecotoxicology (e.g., predicting toxicant responses among a broad spectrum of phytogenetic groups, predicting impact of temporal exposure on toxicant responses) necessitate the parallel use of other model organisms, both aquatic and terrestrial. By investigating gene expression profiling in an environmentally important organism, this provides viable support for the utility of ecotoxicogenomics.

Transcriptional changes during Daphnia pulex development indicate that the maturation decision resembles a rate more than a threshold

Maturation is a critical developmental process, and the age and size at which it occurs have important fitness consequences. Although maturation is remarkably variable, certain mechanisms, including a minimum size or state threshold, are proposed to underlie the process across a broad diversity of taxa. Recent evidence suggests that thresholds may themselves be developmentally plastic, and in the crustacean Daphnia pulex it is unclear whether maturation follows a threshold or is a gradual process more akin to a rate. Changes in gene expression across four instars before and during maturation were compared in a cDNA microarray experiment. Developmental stage was treated statistically both as a discontinuous and as a continuous variable, to determine whether genes showed gradual or discrete changes in expression. The continuous analysis identified a greater number of genes with significant differential expression (45) than the discontinuous analysis (11). The majority of genes, including those coding for histones, factors relating to transcription and cell cycle processes, and a putative developmental hormone showed continuous increases or decreases in expression from the first to the fourth instars that were studied, suggestive of a prolonged and gradual maturation process. Three genes coding for a fused vitellogenin/superoxide dismutase showed increases in expression following the second instar and coincided with the posited maturation threshold, but even their expression increased in a continuous fashion.

Application of a redox-proteomics toolbox to Daphnia magna challenged with model pro-oxidants copper and paraquat

The redox status of cells is involved in the regulation of several cellular stress-response pathways. It is frequently altered by xenobiotics, as well as by environmental stressors. As such, there is an increasing interest in understanding the redox status of proteins in different scenarios. Recent advances in proteomics enable researchers to measure oxidative lesions in a wide range of proteins. This opens the door to the sensitive detection of toxicity targets and helps decipher the molecular impact of pollutants and environmental stressors. The present study applies the measurement of protein carbonyls, the most common oxidative lesion of proteins, to gel-based proteomics in Daphnia magna. Daphnids were exposed to copper and paraquat, 2 well-known pro-oxidants. Catalase activity was decreased by paraquat, whereas global measurement of protein carbonyls and thiols indicated no change with treatment. Despite the absence of observed oxidative stress, 2-dimensional electrophoresis of the daphnid proteins and measurement of their carbonylation status revealed that 32 features were significantly affected by the treatments, showing higher sensitivity than single measurements. Identified proteins affected by copper indicated a decrease in the heat-shock response, whereas paraquat affected glycolysis. The present study demonstrates the applicability of redox-proteomics in daphnids, and indicates that the heat-shock response plays a counterintuitive role in metal resistance in daphnids.

Proteomic evaluation of citrate-coated silver nanoparticles toxicity in Daphnia magna

Recent decades have seen a strong increase in the promise and uses of nanotechnology. This is correlated with their growing release in the environment and there is concern that nanomaterials may endanger ecosystems. Silver nanoparticles (AgNPs) have some of the most varied applications, making their release into the environment unavoidable. In order to assess their potential toxicity in aquatic environments, the acute toxicity of citrate-coated AgNPs to Daphnia magna was measured and compared to that of AgNO3. AgNPs were found to be ten times less toxic by mass than silver ions, and most of this toxicity was removed by ultracentrifuging. At the protein level, the two forms of silver had different impacts. Both increased protein thiol content, while only AgNP increased carbonyl levels. In 2DE of samples labelled for carbonyls, no feature was significantly affected by both compounds, indicating different modes of toxicity. Identified proteins showed functional overlap between the two compounds: vitellogenins (vtg) were present in most features identified, indicating their role as a general stress sensor. In addition to vtg, hemoglobin levels were increased by the AgNP exposure while 14-3-3 protein (a regulatory protein) carbonylation levels were reduced by AgNO3. Overall, this study confirms the previously observed lower acute toxicity of AgNPs, while demonstrating that the toxicity of both forms of silver follow somewhat different biologic pathways, potentially leading to different interactions with natural compounds or pollutants in the aquatic environment.

Evolution of yolk protein genes in the Echinodermata

Vitellogenin genes (vtg) encode large lipid transfer proteins (LLTPs) that are typically female-specific, functioning as precursors to major yolk proteins (MYPs). Within the phylum Echinodermata, however, the MYP of the Echinozoa (Echinoidea + Holothuroidea) is expressed by an unrelated transferrin-like gene that has a reproductive function in both sexes. We investigated egg proteins in the Asterozoa (Asteroidea + Ophiuroidea), a sister clade to the Echinozoa, showing that eggs of the asteroid Parvulastra exigua contain a vitellogenin protein (Vtg). vtg is expressed by P. exigua, a species with large eggs and nonfeeding larvae, and by the related asterinid Patiriella regularis which has small eggs and feeding larvae. In the Asteroidea, therefore, the reproductive function of vtg is conserved despite significant life history evolution. Like the echinozoan MYP gene, asteroid vtg is expressed in both sexes and may play a role in the development of both ovaries and testes. Phylogenetic analysis indicated that a putative Vtg from the sea urchin genome, a likely pseudogene, does not clade with asteroid Vtg. We propose the following sequence as a potential pathway for the evolution of YP genes in the Echinodermata: (1) the ancestral echinoderm produced YPs derived from Vtg, (2) bisexual vtg expression subsequently evolved in the echinoderm lineage, (3) the reproductive function of vtg was assumed by a transferrin-like gene in the ancestral echinozoan, and (4) redundant echinozoan vtg was released from stabilizing selection.

Vitellogenin-like protein measurement in caged Gammarus fossarum males as a biomarker of endocrine disruptor exposure: inconclusive experience

A vitellogenin (Vg) mass spectrometry-based assay was recently developed to actively biomonitor and assess the exposure of the amphipod Gammarus fossarum to endocrine-disrupting chemicals in freshwater hydrosystems. This paper focuses on the appropriate use of this biomarker, which requires good knowledge of its basal level in males and its natural variability related to intrinsic biotic and environmental abiotic factors. To obtain the lowest biomarker variability, we first studied some of these confounding factors. We observed that the spermatogenesis stage did not have an impact on the Vg level, allowing flexibility in the choice of transplanted gammarids. In the second part of the study, males were transplanted in two clean stations for 21 days, with results indicating a spatial and temporal variability of Vg levels. These Vg changes could not be correlated to environmental factors (e.g., temperature, pH and hardness of waters). Vg induction was then assessed in 21 stations having various levels of contamination. Inductions were observed for only two of the impacted stations studied. Under reference and contaminated conditions, a high interindividual variability of Vg levels was observed in caged organisms, severely limiting the sensitivity of the biomarker and its ability to detect a significant endocrine-disruptor effect. This may be explained by unidentified environmental factors that should later be determined to improved the use of Vg as a biomarker in male G. fossarum. Moreover, as discussed in this paper, recent advancements regarding the pleiotropic functions of the Vg gene in some species may complicate the application of this biomarker in males of invertebrate species.

Vitellogenin-like proteins among invertebrate species diversity: potential of proteomic mass spectrometry for biomarker development

Cost-effective methodologies along with cross-species applicability constitute key points for biomarker development in ecotoxicology. With the advent of cheaper affordable genomic techniques and high throughput sequencing, omics tools could facilitate the assessment of effects of environmental contaminants for all taxa biodiversity. We assessed the potential of absolute quantification of proteins using mass spectrometry to develop vitellogenin (Vg)-like protein assays for invertebrates. We used available sequences in public databases to rapidly identify Vg-proteotypic peptides in seven species from different main taxa of protostome invertebrates (mollusk bivalves, crustacean amphipods, branchiopods, copepods and isopods, and insect diptera). Functional validation was performed by comparing proteomic signals from reproductive female tissue samples and negative controls (male or juvenile tissues). In a second part, we demonstrate in gammarids, daphnids, drosophilids, and gastropods that the assay validated in Vg-sequenced species can be applied to Vg-unsequenced species thanks to the evolutionary conservation of Vg-proteotypic peptide motifs. Finally, we discuss the relevance of mass spectrometry for biomarker development (specific measurement, rapid development, transferability across species). Our study supplies an illustration of the promising strategy to address the challenge of biodiversity in ecotoxicology, which consists in employing omics tools from comparative and evolutionary perspectives.

Toxicity evaluation of verapamil and tramadol based on toxicity assay and expression patterns of Dhb, Vtg, Arnt, CYP4, and CYP314 in Daphnia magna

In this study, the toxicities of two pharmaceuticals, verapamil and tramadol were evaluated in Daphnia magna using the conventional toxicity tests (acute and chronic test) and the expression patterns of five stress responsive genes. In the chronic toxicity test, several parameters, such as the survival percentage, the body length of D. magna, the time of first reproduction, and the number of offspring per female, were adversely affected during the exposure to 4.2 mg L(-1) verapamil and 34 mg L(-1) tramadol. During the 24-h short-term exposure, verapamil particularly caused a downregulated expression of the CYP4 and CYP314 genes, whereas tramadol upregulated the expression of the CYP314 gene. Neither pharmaceutical affected the expression of Dhb, Arnt, and Vtg. However, during the 21-day long-term exposure, both verapamil and tramadol significantly reduced the expression level of the Vtg gene, a biomarker of the reproduction ability in an oviparous animal, whereas neither affected the other genes.

Transcriptional responses in neonate and adult Daphnia magna in relation to relative susceptibility to genotoxicants

Little information is available on the responses of lower animals to genotoxic chemicals or on their sensitivity for detecting genotoxic chemicals, especially at different life-stages, despite the established use of the water flea Daphnia magna in ecotoxicity testing. Comet assay methodology was developed and applied to daphnid cells but only limited, non-statistically significant responses to the genotoxicants sodium dichromate (0.2-1 μM), chrysoidine (0.1-2 μM), and mixtures of benzo-a-pyrene (BaP) and sodium dichromate were found (from 0.01 μM BaP & 0.1 μM sodium dichromate to 0.25 μM BaP & 0.75 μM sodium dichromate). Transcriptomic analyses using Agilent D. magna oligonucleotide microarrays were undertaken to assess the effect of a mixture of sodium dichromate and BaP (designed to produce both adducted and oxidised DNA) on gene transcription. Neonates (<24h) and adults (day 7) were exposed for 6h and 24h at two combination concentration levels (0.02 μM BaP & 0.15 μM sodium dichromate and 0.1 μM BaP & 0.75 μM sodium dichromate). The greatest differences in transcriptional profile occurred between adults and neonates. Subsets of the transcriptional profiles distinguished genotoxicant-exposed animals from controls, both for neonates and adults. Higher transcript levels of DNA repair genes were found in adults and adults also displayed significant induction of DNA repair gene transcripts in response to exposure whereas neonates did not. Transcriptional changes in response to genotoxicant exposure proved more sensitive than measurement of DNA strand breaks by the Comet assay and the extensive differences in transcription between adults and neonates emphasized the importance of life stage in toxicant testing with Daphnia.

Gene transcription and higher-level effects of multigenerational Zn exposure in Daphnia magna

Zn exposure of Daphnia magna during one generation has been shown to modulate gene transcription differently in Zn exposed organisms compared to their non-exposed offspring. Here we studied the transcriptional gene regulation with a cDNA microarray in D.magna exposed to Zn for three generations (F0-F2). For the first time molecular effects of multigeneration toxicant exposure in D. magna are described. Out of 73 differentially transcribed genes in the F1Zn exposed generation (compared to the F1 control), only seven genes were also differentially transcribed in the same direction in the F0Zn exposed daphnids (up or down, compared to the F0 control). The majority of the differentially transcribed unigenes in F1Zn exposed daphnids (78%) were not differentially transcribed in the F0Zn exposed organisms. This indicates that Zn exposure affected other molecular pathways in the second exposed generation, although a reduced reproduction and a reduction in juvenile growth were observed in both Zn exposed generations, compared to the respective controls. In the third Zn exposed generation (F2), no reduction in growth or reproduction compared to the control was observed. This acclimation was reflected in a significantly lower number of differentially transcribed genes, compared to the Zn exposed F0 and F1 generations.

Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms

BACKGROUND

Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered.

PRINCIPAL FINDINGS

Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions.

CONCLUSIONS

The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades.

Effects of glyphosate and methidathion on the expression of the Dhb, Vtg, Arnt, CYP4 and CYP314 in Daphnia magna

In this study, the expression of five stress responsive genes was quantified and analyzed using a semi-quantitative RT-PCR to study the changes in their expression in Daphnia magna after exposure to known pesticides, glyphosate and methidathion. Hemoglobin (Dhb), which was used to show the effect of the oxygen level in the aquatic system, was significantly expressed in D. magna after exposure to glyphosate and methidathion. Additionally, aryl hydrocarbon receptor nuclear translocator (Arnt), a gene related to the metabolism of aryl hydrocarbons, had lower expression levels in D. magna than within the control. CYP4, which was used among cytochrome P450s (CYPs) to show the effects on the fatty acid and steroids metabolisms, was down-regulated in D. magna exposed to glyphosate. However, methidathion affected the expression of CYP314, which was used to show effects of ecdysis, not CYP4 in D. magna. Therefore, glyphosate and methidathion probably caused physiological effects with different patterns in D. magna, especially metabolisms related to CYPs. On the other hand, only vitellogenin (Vtg), which was responsive to the estrogenic potency, did not show any differences in D. magna after exposure to glyphosate or methidathion.

Acclimatory responses of the Daphnia pulex proteome to environmental changes. II. Chronic exposure to different temperatures (10 and 20 degrees C) mainly affects protein metabolism

BACKGROUND

Temperature affects essentially every aspect of the biology of poikilothermic animals including the energy and mass budgets, activity, growth, and reproduction. While thermal effects in ecologically important groups such as daphnids have been intensively studied at the ecosystem level and at least partly at the organismic level, much less is known about the molecular mechanisms underlying the acclimation to different temperatures. By using 2D gel electrophoresis and mass spectrometry, the present study identified the major elements of the temperature-induced subset of the proteome from differently acclimated Daphnia pulex.

RESULTS

Specific sets of proteins were found to be differentially expressed in 10 degrees C or 20 degrees C acclimated D. pulex. Most cold-repressed proteins comprised secretory enzymes which are involved in protein digestion (trypsins, chymotrypsins, astacin, carboxypeptidases). The cold-induced sets of proteins included several vitellogenin and actin isoforms (cytoplasmic and muscle-specific), and an AAA+ ATPase. Carbohydrate-modifying enzymes were constitutively expressed or down-regulated in the cold.

CONCLUSION

Specific sets of cold-repressed and cold-induced proteins in D. pulex can be related to changes in the cellular demand for amino acids or to the compensatory control of physiological processes. The increase of proteolytic enzyme concentration and the decrease of vitellogenin, actin and total protein concentration between 10 degrees C and 20 degrees C acclimated animals reflect the increased amino-acids demand and the reduced protein reserves in the animal's body. Conversely, the increase of actin concentration in cold-acclimated animals may contribute to a compensatory mechanism which ensures the relative constancy of muscular performance. The sheer number of peptidase genes (serine-peptidase-like: > 200, astacin-like: 36, carboxypeptidase-like: 30) in the D. pulex genome suggests large-scaled gene family expansions that might reflect specific adaptations to the lifestyle of a planktonic filter feeder in a highly variable aquatic environment.