LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia

Proteomic Applications in Aquatic Environment Studies

Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.

Long-term exposure of Daphnia magna to polystyrene microplastic (PS-MP) leads to alterations of the proteome, morphology and life-history

In the past years, the research focus on the effects of MP on aquatic organisms extended from marine systems towards freshwater systems. An important freshwater model organism in the MP field is the cladoceran Daphnia, which plays a central role in lacustrine ecosystems and has been established as a test organism in ecotoxicology. To investigate the effects of MP on Daphnia magna, we performed a chronic exposure experiment with polystyrene MP under strictly standardized conditions. Chronic exposure of D. magna to PS microparticles led to a significant reduction in body length and number of offspring. To shed light on underlying molecular mechanisms induced by microplastic ingestion in D. magna, we assessed the effects of PS-MP at the proteomic level, as proteins, e.g., enzymes, are especially relevant for an organism's physiology. Using a state-of-the-art mass spectrometry based approach, we were able to identify 28,696 different peptides, which could be assigned to 3784 different proteins. Using a customized bioinformatic workflow, we identified 41 proteins significantly altered in abundance (q-value <0.05) in the PS exposed D. magna. Among the proteins increased in the PS treated group were several sulfotransferases, involved in basic biochemical pathways, as well as GABA transaminase catalyzing the degradation of the neurotransmitter GABA. In the abundance decreased group, we found essential proteins such as the DNA-directed RNA polymerase subunit and other proteins connected to biotic and inorganic stress and reproduction. Strikingly, we further identified several digestive enzymes that are significantly downregulated in the PS treated animals, which could have interfered with the affected animal's nutrient supply. This may explain the altered morphological and life history traits of the PS exposed daphnids. Our results indicate that long-term exposure to PS microplastics, which are frequently detected in environmental samples, may affect the fitness of daphnids.

Nanomaterials in the Environment Acquire an "Eco-Corona" Impacting their Toxicity to Daphnia Magna-a Call for Updating Toxicity Testing Policies

Nanomaterials (NMs) are particles with at least one dimension between 1 and 100 nm and a large surface area to volume ratio, providing them with exceptional qualities that are exploited in a variety of industrial fields. Deposition of NMs into environmental waters during or after use leads to the adsorption of an ecological (eco-) corona, whereby a layer of natural biomolecules coats the NM changing its stability, identity and ultimately toxicity. The eco-corona is not currently incorporated into ecotoxicity tests, although it has been shown to alter the interactions of NMs with organisms such as Daphnia magna (D. magna). Here, the literature on environmental biomolecule interactions with NMs is synthesized and a framework for understanding the eco-corona composition and its role in modulating NMs ecotoxicity is presented, utilizing D. magna as a model. The importance of including biomolecules as part of the current international efforts to update the standard testing protocols for NMs, is highlighted. Facilitating the formation of an eco-corona prior to NMs ecotoxicity testing will ensure that signaling pathways perturbed by the NMs are real rather than being associated with the damage arising from reactive NM surfaces "acquiring" a corona by pulling biomolecules from the organism's surface.

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.

Quantitative proteomics using SILAC-MS identifies N-acetylcysteine-solution-triggered reversal response of renal cell carcinoma cell lines

N-acetylcysteine (NAC), a precursor for glutathione (GSH), causes permeable antioxidation protecting normal cells and disrupting cancer cells. In the present study, we found that a NAC-based medium can trigger a reversal response of human clear cell renal cell carcinoma (ccRCC). To further investigate the action of a NAC-based solution in ccRCC cell lines, 786-O and SN12C were incubated in a serum-free acid medium (low pH) in the presence of 2 mM NAC for 24 hours or in a serum-free medium (normal pH) as the control, and then a phenotypic and proteomic analyses were performed. To determine the reversal occurrence, we tested the phenotypic features associated with cancer cells. Under this premise, a systematic and in-depth analysis of NAC-solution-triggered protein alterations was carried out by quantitative proteomics in both cell lines. Among the paramount protein signature, we identified a large number of proteins associated with cancer features were downregulated, but other proteins in the KEGG pathways associated with recovery of the missing tumorigenicity, such as the p53 pathway and repair pathway, were significantly upregulated. Quantification of notable proteins was validated by messenger RNA (mRNA) and protein levels in the ccRCC cell line. Collectively, our data indicate that the NAC-based solution inhibits human ccRCC cell growth by decreasing cell proliferation and inducing apoptosis, limiting their migration by limiting cell motility and completely changing their metabolic mode. Thus, NAC-based solutions could be used for the prevention or treatment of ccRCC.

Proteome Analysis Reveals the Conidial Surface Protein CcpA Essential for Virulence of the Pathogenic Fungus Aspergillus fumigatus

The mammalian immune system relies on recognition of pathogen surface antigens for targeting and clearance. In the absence of immune evasion strategies, pathogen clearance is rapid. In the case of Aspergillus fumigatus, the successful fungus must avoid phagocytosis in the lung to establish invasive infection. In healthy individuals, fungal spores are cleared by immune cells; however, in immunocompromised patients, clearance mechanisms are impaired. Here, using proteome analyses, we identified CcpA as an important fungal spore protein involved in pathogenesis. A. fumigatus lacking CcpA was more susceptible to immune recognition and prompt eradication and, consequently, exhibited drastically attenuated virulence. In infection studies, CcpA was required for virulence in infected immunocompromised mice, suggesting that it could be used as a possible immunotherapeutic or diagnostic target in the future. In summary, our report adds a protein to the list of those known to be critical to the complex fungal spore surface environment and, more importantly, identifies a protein important for conidial immunogenicity during infection.

Aspergillus fumigatus is a common airborne fungal pathogen of humans and a significant source of mortality in immunocompromised individuals. Here, we provide the most extensive cell wall proteome profiling to date of A. fumigatus resting conidia, the fungal morphotype pertinent to first contact with the host. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified proteins within the conidial cell wall by hydrogen-fluoride (HF)–pyridine extraction and proteins exposed on the surface using a trypsin-shaving approach. One protein, designated conidial cell wall protein A (CcpA), was identified by both methods and was found to be nearly as abundant as hydrophobic rodlet layer-forming protein RodA. CcpA, an amphiphilic protein, like RodA, peaks in expression during sporulation on resting conidia. Despite high cell wall abundance, the cell surface structure of ΔccpA resting conidia appeared normal. However, trypsin shaving of ΔccpA conidia revealed novel surface-exposed proteins not detected on conidia of the wild-type strain. Interestingly, the presence of swollen ΔccpA conidia led to higher activation of neutrophils and dendritic cells than was seen with wild-type conidia and caused significantly less damage to epithelial cells in vitro. In addition, virulence was highly attenuated when cortisone-treated, immunosuppressed mice were infected with ΔccpA conidia. CcpA-specific memory T cell responses were detectable in healthy human donors naturally exposed to A. fumigatus conidia, suggesting a role for CcpA as a structural protein impacting conidial immunogenicity rather than possessing a protein-intrinsic immunosuppressive effect. Together, these data suggest that CcpA serves as a conidial stealth protein by altering the conidial surface structure to minimize innate immune recognition.

Proteomic Profile of Daphnia pulex using Data-Independent Acquisition Mass Spectrometry and Ion Mobility Separation

Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on genomic analysis. In this study, various sample preparation and mass spectrometry acquisition methods are performed for the purpose of improving D. pulex proteome exploration. Benefits for employing both in-gel and in-solution methods of trypsin digestion are observed. Furthermore, acquisition methods employing ion mobility separation greatly increase peptide identification and more than doubled the proteome coverage. Bioinformatic analysis suggests that mitochondrial and hydrolytic activities are enriched in D. pulex compared to closely related invertebrates or Homo sapiens. Also, novel D. pulex proteins possessing putative genome modifying functional domains are identified. Data are available via ProteomeXchange with identifier PXD008455.

Accumulation of Polychlorinated Biphenyls in Mussels: A Proteomic Study

Polychlorinated biphenyls (PCBs) are environmental pollutants of industrial origin that can contaminate food, mainly food of animal origin. Although production of PCBs has been banned in many countries since the 1980s, they are still present in the environment and are considered dangerous pollutants for human health. In fact, they can bioaccumulate in living organisms such as marine organisms because of their chemical and physical properties. New analytical approaches are useful to monitor the presence of such contaminants in seafood products and in the environment. In this work, we evaluate changes in protein expression of Mytilus galloprovincialis (Lam.) experimentally exposed to a PCB mixture and identify chemically specific protein expression signatures by using a proteomic approach. In particular, we identify 21 proteins whose levels of expression are sensibly modified after 3 weeks of exposure. The present work shows that a proteomic approach can be a useful tool to study alterations of protein expression in mussels exposed to PCBs and represents a first step toward the development of screening protocols to be used for biomonitoring surveys of fishery products.

Changes in iTRAQ-Based Proteomic Profiling of the Cladoceran Daphnia magna Exposed to Microcystin-Producing and Microcystin-Free Microcystis aeruginosa

Global warming and increased nutrient fluxes cause cyanobacterial blooms in freshwater ecosystems. These phenomena have increased the concern for human health and ecosystem services. The mass occurrences of toxic cyanobacteria strongly affect freshwater zooplankton communities, especially the unselective filter feeder Daphnia. However, the molecular mechanisms of cyanobacterial toxicity remain poorly understood. This study is the first to combine the established body growth rate (BGR), which is an indicator of life-history fitness, with differential peptide labeling (iTRAQ)-based proteomics in Daphnia magna influenced by microcystin-producing (MP) and microcystin-free (MF) Microcystis aeruginosa. A significant decrease in BGR was detected when D. magna was exposed to MP or MF M. aeruginosa. Conducting iTRAQ proteomic analyses, we successfully identified and quantified 211 proteins with significant changes in expression. A cluster of orthologous groups revealed that M. aeruginosa-affected differential proteins were strongly associated with lipid, carbohydrate, amino acid, and energy metabolism. These parameters could potentially explain the reduced fitness based on the cost of the substance metabolism.

The influence of simulated microgravity on the proteome of Daphnia magna

Background:

The waterflea Daphnia is an interesting candidate for bioregenerative life support systems (BLSS). These animals are particularly promising because of their central role in the limnic food web and its mode of reproduction. However, the response of Daphnia to altered gravity conditions has to be investigated, especially on the molecular level, to evaluate the suitability of Daphnia for BLSS in space.

Methods:

In this study, we applied a proteomic approach to identify key proteins and pathways involved in the response of Daphnia to simulated microgravity generated by a two-dimensional (2D) clinostat. We analyzed five biological replicates using 2D-difference gel electrophoresis proteomic analysis.

Results:

We identified 109 protein spots differing in intensity (P<0.05). Substantial fractions of these proteins are involved in actin microfilament organization, indicating the disruption of cytoskeletal structures during clinorotation. Furthermore, proteins involved in protein folding were identified, suggesting altered gravity induced breakdown of protein structures in general. In addition, simulated microgravity increased the abundance of energy metabolism-related proteins, indicating an enhanced energy demand of Daphnia.

Conclusions:

The affected biological processes were also described in other studies using different organisms and systems either aiming to simulate microgravity conditions or providing real microgravity conditions. Moreover, most of the Daphnia protein sequences are well-conserved throughout taxa, indicating that the response to altered gravity conditions in Daphnia follows a general concept. Data are available via ProteomeXchange with identifier PXD002096.

Proteogenomic insights into the core-proteome of female reproductive tissues from crustacean amphipods

As a result of the poor genome sequence coverage of crustacean amphipods, characterization of their evolutionary biology relies mostly on phenotypic traits. Here, we analyzed the proteome of ovaries from five amphipods, all from the Senticaudata suborder, with the objective to obtain insights into the core-proteome of female reproductive systems. These amphipods were from either the Gammarida infraorder: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, or the Talitrida infraorder: Parhyale hawaiensis and Hyalella azteca. Ovaries from animals sampled at the end of their reproductive cycle were dissected. Their whole protein contents were extracted and their proteomes were recorded by high-throughput nanoLC-MS/MS with a high-resolution mass spectrometer. We interpreted tandem mass spectrometry data with the protein sequence resource from G. fossarum and P. hawaiensis, both recently established by RNA sequencing. The large molecular biodiversity within amphipods was assessed by the ratio of MS/MS spectra assigned for each sample, which tends to diverge rapidly along the taxonomic level considered. The core-proteome was defined as the proteins conserved along all samples, thus detectable by the homology-based proteomic assignment procedure. This specific subproteome may be further enriched in the future with the analysis of new species and update of the protein sequence resource.

Next-generation proteomics: toward customized biomarkers for environmental biomonitoring

Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.

Alteration in endometrial proteins during early- and mid-secretory phases of the cycle in women with unexplained infertility

BACKGROUND

Compromised receptivity of the endometrium is a major cause of unexplained infertility, implantation failure and subclinical pregnancy loss. In order to investigate the changes in endometrial protein profile as a cause of unexplained infertility, the current study was undertaken to analyze the differentially expressed proteins of endometrium from early-secretory (LH+2) to mid-secretory phase (LH+7), in women with unexplained infertility.

METHODS

2-D gel electrophoresis was performed to analyze the proteomic changes between early- (n = 8) and mid-secretory (n = 8) phase endometrium of women with unexplained infertility. The differentially expressed protein spots were identified by LC-MS analysis and validated by immunoblotting and immuno-histochemical analysis in early- (n = 4) and mid-secretory (n = 4) phase endometrium of infertile women. Validated proteins were also analyzed in early- (n = 4) and mid-secretory (n = 4) phase endometrium of fertile women.

RESULTS

Nine proteins were found to be differentially expressed between early- and mid- secretory phases of endometrium of infertile women. The expression of Ras-related protein Rap-1b, Protein disulfide isomerase A3, Apolipoprotein-A1 (Apo-A1), Cofilin-1 and RAN GTP-binding nuclear protein (Ran) were found to be significantly increased, whereas, Tubulin polymerization promoting protein family member 3, Superoxide dismutase [Cu-Zn], Sorcin, and Proteasome subunit alpha type-5 were significantly decreased in mid- secretory phase endometrium of infertile women as compared to early-secretory phase endometrium of infertile women. Validation of 4 proteins viz. Sorcin, Cofilin-1, Apo-A1 and Ran were performed in separate endometrial biopsy samples from infertile women. The up-regulated expression of Sorcin and down-regulated expression of Cofilin-1 and Apolipoprotein-A1, were observed in mid-secretory phase as compared to early-secretory phase in case of fertile women.

CONCLUSIONS

De-regulation of the expression of Sorcin, Cofilin-1, Apo-A1 and Ran, during early- to mid-secretory phase may have physiological significance and it may be one of the causes for altered differentiation and/or maturation of endometrium, in women with unexplained infertility.

Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods

Because of their ecological importance, amphipod crustacea are employed worldwide as test species in environmental risk assessment. Although proteomics allows new insights into the molecular mechanisms related to the stress response, such investigations are rare for these organisms because of the lack of comprehensive protein sequence databases. Here, we propose a proteogenomic approach for identifying specific proteins of the freshwater amphipod Gammarus fossarum, a keystone species in European freshwater ecosystems. After deep RNA sequencing, we created a comprehensive ORF database. We identified and annotated the most relevant proteins detected through a shotgun tandem mass spectrometry analysis carried out on the proteomes from three major tissues involved in the organism's reproductive function: the male and female reproductive systems, and the cephalon, where different neuroendocrine glands are present. The 1,873 mass-spectrometry-certified proteins represent the largest crustacean proteomic resource to date, with 218 proteins being lineage specific. Comparative proteomics between the male and female reproductive systems indicated key proteins with strong sexual dimorphism. Protein expression profiles during spermatogenesis at seven different stages highlighted the major gammarid proteins involved in the different facets of reproduction.

Effect of deltamethrin (pyrethroid insecticide) on two clones of Daphnia magna (Crustacea, Cladocera): a proteomic investigation

Deltamethrin is a class II pyrethroid insecticide commonly used in agriculture. It is hazardous to freshwater ecosystems, especially for the cladoceran Daphnia magna (Straus 1820). The results of our previous studies based on acute and chronic ecotoxicity experiments revealed differences in the sensitivity between two different clones. In this work, to investigate deltamethrin toxicity mechanisms in two clones of D. magna, we used a proteomic approach in order to analyze changes in protein expression profiles after 48 h of exposure. We detected 1339 spots; then applying statistical criteria (ANOVA p<0.001 and minimum fold change 1.5), only 128 spots were significantly different in the normalized volume. Among the preselected proteins there were 88 up-regulated and 40 down-regulated proteins. Results showed differences in sensitivities after deltamethrin exposure between the clones. Moreover, using the 2-DIGE method, proteomic investigation for deltamethrin exposure proved to be a reliable and powerful approach to investigate effects of deltamethrin as part of research for new metabolic and cellular biomarkers. After identification by mass spectrometry, there were 39 proteins recognized and identified, in which 21 and 18 were up- and down-regulated, respectively, in deltamethrin-exposed clone A compared to three other conditions (controls of each clone and deltamethrin-exposed clone 2). Up- and down-regulated proteins belonged to 12 biological processes (i.e. metabolic processes, apoptosis and stimulus response) and 5 molecular functions (i.e. catalytic activity, binding, structural molecular activity, antioxidant and receptor activities). Identification of these deregulated proteins opens a new way in discovering new molecular targets and putative biomarkers in daphnids exposed to deltamethrin.

Non-model organisms, a species endangered by proteogenomics

Previously, large-scale proteomics was possible only for organisms whose genomes were sequenced, meaning the most common model organisms. The use of next-generation sequencers is now changing the deal. With "proteogenomics", the use of experimental proteomics data to refine genome annotations, a higher integration of omics data is gaining ground. By extension, combining genomic and proteomic data is becoming routine in many research projects. "Proteogenomic"-flavored approaches are currently expanding, enabling the molecular studies of non-model organisms at an unprecedented depth. Today draft genomes can be obtained using next-generation sequencers in a rather straightforward way and at a reasonable cost for any organism. Unfinished genome sequences can be used to interpret tandem mass spectrometry proteomics data without the need for time-consuming genome annotation, and the use of RNA-seq to establish nucleotide sequences that are directly translated into protein sequences appears promising. There are, however, certain drawbacks that deserve further attention for RNA-seq to become more efficient. Here, we discuss the opportunities of working with non-model organisms, the proteomic methods that have been used until now, and the dramatic improvements proffered by proteogenomics. These put the distinction between model and non-model organisms in great danger, at least in terms of proteomics!

BIOLOGICAL SIGNIFICANCE

Model organisms have been crucial for in-depth analysis of cellular and molecular processes of life. Focusing the efforts of thousands of researchers on the Escherichia coli bacterium, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plant, Danio rerio fish and other models for which genetic manipulation was possible was certainly worthwhile in terms of fundamental and invaluable biological insights. Until recently, proteomics of non-model organisms was limited to tedious, homology-based techniques, but today draft genomes or RNA-seq data can be straightforwardly obtained using next-generation sequencers, allowing the establishment of a draft protein database for any organism. Thus, proteogenomics opens new perspectives for molecular studies of non-model organisms, although they are still difficult experimental organisms. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Quantification of proteins by label-free LC-MS(E.)

Quantitative proteomics by LC-MS/MS is a widely used approach for quantifying a significant portion of any complex proteome. Among the different techniques used for this purpose, one is by use of Data Independent Acquisition (DIA). We present a descriptive protocol for label-free quantitation of proteins by one DIA method termed LC-MS(E), which facilitates large-scale quantification of proteins without the need for isotopic labelling and with no theoretical limit to the number of samples included in an experiment.

Charting the cellular and extracellular proteome analysis of Brevibacterium linens DSM 20158 with unsequenced genome by mass spectrometry-driven sequence similarity searches

Brevibacterium linens DSM 20158 is an industrially important actinobacterium which is well-known for the production of amino acids and enzymes. However, as this strain has an unsequenced genome, there is no detailed information regarding its proteome although another strain of this microbe, BL2, has a shotgun genome sequence. However, this still does not cover the entire scope of its proteome. The present study is carried out by first identifying proteins by homology matches using the Mascot search algorithm followed by an advanced approach using de novo sequencing and MS BLAST to expand the B. linens proteome. The proteins identified in the secretome and cellular portion appear to be involved in various metabolic and physiological processes of this unsequenced organism. This study will help to enhance the usability of this strain of B. linens in different areas of research in the future rather than mainly in the food industries.

BIOLOGICAL SIGNIFICANCE

The present study describes the construction of the first detailed proteomic reference map of B. linens DSM 20158 with unsequenced genome by comparative proteome research analysis. This opens new horizons in proteomics to understand the role of proteins involved in the metabolism and physiology of other organisms with unsequenced genomes.

Controlling proteome degradation in Daphnia pulex

An attempted proteomic study of Daphnia pulex response to sodium chloride exposure revealed an unexpected result: very strong proteome degradation previously observed in D. pulex is halted when animals have been exposed to elevated salinity prior to protein extraction. Further characterization of conditions controlling proteome degradation shows that the proteolytic factor(s) is/are present in an active form under chemically denaturing conditions in extract from control "normal/healthy" animals, and can be negatively regulated by prior in vivo salinity exposure of animals or inhibited by post-homogenization heating of samples. We interpret these data as evidence for salinity-induced inhibition of proteolysis in Daphnia.

Marine proteomics: a critical assessment of an emerging technology

The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.

Needle core biopsies provide ample material for genomic and proteomic studies of kidney cancer: observations on DNA, RNA, protein extractions and VHL mutation detection

The use of needle biopsies in basic research is increasing, and our study provides a comprehensive analysis of their adequacy in genomic and proteomic studies of kidney cancer. Frozen clear cell renal cell carcinoma (ccRCC) needle core biopsies and sections from core biopsies embedded in optimal cutting temperature (OCT) compound were used to extract DNA, RNA and protein. Their integrity was determined using genomic and proteomic analyses. VHL mutation testing was performed on ccRCC biopsies and corresponding tumors using bulk and laser capture microdissection (LCM) extractions for comparison. Adequate amounts of good quality DNA (5.8-13.3 μg/whole core, 0.6-2.7 μg/20 sections), RNA (2.9-11.9 μg/whole core, 0.5-1.3 μg/20 sections) and protein (137.4-444 μg/whole core, 39.9-74.1 μg/20 sections) were obtained from whole core and frozen sections of ccRCC needle biopsies, respectively. We observed VHL sequence mutations in 75% of ccRCC tumors and, in most cases, the same mutations were detected in both tumors and corresponding biopsies. Mutations observed by bulk extractions from tumors and biopsies were also detected by LCM without significant differences between both methodologies. ccRCC needle biopsies provide ample material for genomic and proteomic studies of kidney cancer. They are good representatives of their corresponding tumors for VHL mutation detection using both bulk and LCM extractions. LCM does not increase sensitivity of VHL mutation detection.

Progress and promises in toxicogenomics in aquatic toxicology: is technical innovation driving scientific innovation?

In the last decade, new technologies have been invented to analyze large amounts of information such as gene transcripts (transcriptomics), proteins (proteomics) and small cellular molecules (metabolomics). Many studies have been performed in the last few years applying these technologies to aquatic toxicology, mainly in fish. In this article, we summarize the current state of knowledge and question whether the application of modern technology for descriptive purposes truly represents scientific advancement in aquatic toxicology. We critically discuss the advantages and disadvantages of these technologies and emphasize the importance of these critical aspects. To date, these techniques have been used mainly as a proof of principle, demonstrating effects of model compounds. The potential to use these techniques to better analyze the mode-of-action of a toxicant or the effects of a compound within organisms has rarely been met. This is partly due to a lack of baseline data and the fact that the expression of mRNA and protein profiles is rarely linked to physiology or toxicologically meaningful outcomes. It seems premature to analyze mixtures or environmental samples until more is known about the expression profiles of individual toxicants. Gene transcription, protein, or metabolic data give only a partial view of these effects. Thus, we emphasize that data obtained by these technologies must be linked to physiological changes to fully understand their significance. The use of these techniques in aquatic toxicology is still in its infancy, data cannot yet be applied to environmental risk assessment or regulation until more emphasis is placed on interpreting the data within their physiological and toxicological contexts.

Candidate innate immune system gene expression in the ecological model Daphnia

The last ten years have witnessed increasing interest in host-pathogen interactions involving invertebrate hosts. The invertebrate innate immune system is now relatively well characterised, but in a limited range of genetic model organisms and under a limited number of conditions. Immune systems have been little studied under real-world scenarios of environmental variation and parasitism. Thus, we have investigated expression of candidate innate immune system genes in the water flea Daphnia, a model organism for ecological genetics, and whose capacity for clonal reproduction facilitates an exceptionally rigorous control of exposure dose or the study of responses at many time points. A unique characteristic of the particular Daphnia clones and pathogen strain combinations used presently is that they have been shown to be involved in specific host-pathogen coevolutionary interactions in the wild. We choose five genes, which are strong candidates to be involved in Daphnia-pathogen interactions, given that they have been shown to code for immune effectors in related organisms. Differential expression of these genes was quantified by qRT-PCR following exposure to the bacterial pathogen Pasteuria ramosa. Constitutive expression levels differed between host genotypes, and some genes appeared to show correlated expression. However, none of the genes appeared to show a major modification of expression level in response to Pasteuria exposure. By applying knowledge from related genetic model organisms (e.g. Drosophila) to models for the study of evolutionary ecology and coevolution (i.e. Daphnia), the candidate gene approach is temptingly efficient. However, our results show that detection of only weak patterns is likely if one chooses target genes for study based on previously identified genome sequences by comparison to homologues from other related organisms. Future work on the Daphnia-Pasteuria system will need to balance a candidate gene approach with more comprehensive approaches to de novo identify immune system genes specific to the Daphnia-Pasteuria interaction.

Review of recent proteomic applications in aquatic toxicology

Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic invertebrates. A brief discussion on proteomic methods is also presented. We conclude with some ideas for future proteomic studies with fish and aquatic invertebrates.

Proteins in ecotoxicology - how, why and why not?

The growing interest in the application of proteomic technologies to solve toxicology issues and its relevance in ecotoxicology research has resulted in the emergence of "ecotoxicoproteomics". There is a general consensus that ecotoxicoproteomics is a powerful tool to spot early molecular events involved in toxicant responses, which are responsible for the adverse effects observed at higher levels of biological organization, thus contributing to elucidate the mode of action of stressors and to identify specific biomarkers. Ultimately, early-warning indicators can then be developed and deployed in "in situ" bioassays and in environmental risk assessment. The number of field experiments or laboratory trials using ecologically relevant test-species and involving proteomics has been, until recently, insufficient to allow a critical analysis of the real benefits of the application of this approach to ecotoxicology. This article intends to present an overview on the applications of proteomics in the context of ecotoxicology, focusing mainly on the prospective research to be done in invertebrates. Although these represent around 95% of all animal species and in spite of the key structural and functional roles they play in ecosystems, proteomic research in invertebrates is still in an incipient stage. We will review applications of ecotoxicoproteomics by evaluating the technical methods employed, the organisms and the contexts studied, the advances achieved until now and lastly the limitations yet to overcome will be discussed.