DNA damage as a bivalve biomarker

Bivalves have been used in numerous environmental assessment studies, chiefly because they are sessile deposit or suspension feeding organisms found in or near sites of environmental concern, and they can be easily collected, sorted and deployed at sites of interest. Monitoring studies utilizing bivalves currently rely on the comparison of growth, survival, and contaminant bioaccumulation. Data gathered from 'reference' sites are compared with those of populations at assessment sites. These studies require extended periods of exposure, lasting weeks to months, and the use of a well defined population of test organisms of similar size, age, and condition. In many cases time and resources require researchers to restrict their sampling to the organisms on-hand at a particular site without the benefit of any reference data. Therefore more versatile and sensitive assessment methods are needed. Because effects at higher levels of organization such as growth, development, and survival are initiated at the molecular and cellular levels attempts have been made to identify useful biomarkers at these levels. The proposed advantages of molecular/cellular biomarkers are that they will respond to stress predictably and more rapidly, and will be indicative of the mechanisms of toxicity thereby yielding a rudimentary characterization of the contaminant(s) influencing them. In the following communication we will report on past and current developments in the monitoring of DNAdamage as an environmental biomarker.     

Effects of contaminants on genetic patterns in aquatic organisms: a review.

There is increasing awareness of the need to evaluate the effects of contaminants at the population level. Genetic techniques offer a powerful approach to assess contaminant-induced changes in populations. Yet studies to date are relatively few and not always carefully designed to maximize the utility inherent in this approach. We present a summary of contemporary genetic assessment methods and a review of published studies of genetic effects in field-exposed aquatic organisms. We discuss evaluations of genetic patterns that use genetic adaptation, allozyme variation, and molecular genetic (DNA) variation. Direct tests of genetic adaptation are very effective in establishing a concrete, and potentially deleterious population-level effect of contaminant exposure, but they are difficult to accomplish with most field-exposed organisms. Allozyme surveys are relatively simple and common, and may provide data that are suggestive of contaminant effects. However, these are rarely conclusive, primarily because few allozyme loci are variable and these few loci represent extremely small portions of the genome. Molecular genetic techniques have the potential to be very effective. But, there is a tendency to emphasize the power of the techniques, rather than the underlying causes of the molecular genetic patterns observed. The strength of the conclusions of each study varies widely, partially derived from variation in the strength of the techniques. We caution that all these approaches are greatly improved by careful experimental design that includes adequate numbers of reference and contaminated sites and sample size. In addition, careful exposure assessment is required, including site and tissue chemistry, biomarker responses, and measures of potentially deleterious effects, such as DNA damage, or reduced reproductive output or survival.     

The use of biomarkers in biomonitoring: a 2-tier approach assessing the level of pollutant-induced stress syndrome in sentinel organisms

The paper outlines a 2-tier approach for wide-scale biomonitoring programmes. To obtain a high level of standardization, we suggest the use of caged organisms (mussels or fish). An "early warning", highly sensitive, low-cost biomarker is employed in tier 1 (i.e. lysosomal membrane stability (LMS) and survival rate, a marker for highly polluted sites). Tier 2 is used only for animals sampled at sites in which LMS changes are evident and there is no mortality, with a complete battery of biomarkers assessing the levels of pollutant-induced stress syndrome. Possible approaches for integrating biomarker data in a synthetic index are discussed, along with our proposal to use a recently developed Expert System. The latter system allows a correct selection of biomarkers at different levels of biological organisation (molecular/cellular/tissue/organism) taking into account trends in pollutant-induced biomarker changes (increasing, decreasing, bell-shape). A selection of biomarkers of stress, genotoxicity and exposure usually employed in biomonitoring programmes is presented, together with a brief overview of new biomolecular approaches.     

环境污染物对水生生物产生氧化压力的分子生物标志物

为了能够建立一种简单、快速、准确的环境污染监测预警体系,人们进行了广泛的研究,其中有关环境污染物对分子生物标志物的影响已成为研究热点。生物体内的氧自由基和其它活性氧分子（ROS）对组织和细胞成分造成的伤害,称之为氧化压力,环境中的有毒物质能够对生物体产生不同程度的氧化压力。生物体内的强氧化剂或体外因素（如环境污染物）引起的强氧化物与抗氧化防御系统之间的平衡能够用于评估环境压力对生物体产生影响的程度,尤其适合于评估不同种化学物质引起氧化损伤的程度。这些抗氧化防御系统及其对氧化压力的敏感性在环境毒物学研究中占有非常重要的地位,大量研究结果表明：过渡金属、多环芳烃、有机氯和有机磷农药、多氯联苯、二氧芑和其它异型物质都能够对生物体产生氧化压力。这些有毒物质能够引起各种有害影响,如对膜脂、DNA和蛋白产生损伤;改变抗氧化酶的活性等。总结了这种氧化压力的研究进展情况,并讨论了这些分子生物标志物在水生生物中的应用。     

Changes in antioxidant defense system in gills of Capoeta umbla caught from Uzuncayir Dam Lake,Turkey

The aim of this work was to determine the seasonal changes in the activities of selected biomarkers in Capoeta umbla (Heckel, 1843) caught from Uzuncayir Dam Lake (Tunceli, Turkey) and to evaluate the effects of environmental factors on these activities. Fish were sampled on seasonal basis, and superoxide dismutase, catalase, glutathione peroxidase activities and levels of glutathione and malondialdehyde in gills were determined. Significant variations of oxidative stress biomarkers were observed between seasons and sites. The results of this study show that seasonal variations of oxidative stress responses and lipid peroxidation in gills of C. umbla are sensitive to the contaminants present in water of Uzuncayir Dam Lake and selected parameters are in valuable biomarkers for monitoring of water systems, since they give an early warning signal of effects of xenobiotics on aquatic organisms at molecular levels which help to prevent their effects at organismal level.     

Historical Case Analysis of Uranium Plume Attenuation

Groundwater plumes containing dissolved uranium at levels above natural background exist adjacent to uranium ore bodies, at uranium mines, milling locations, and at a number of explosive test facilities. Public health concerns require that some assessment of the potential for further plume movement in the future be made. Reaction-transport models, which might conceivably be used to predict plume movement, require extensive data inputs that are often uncertain. Many of the site-specific inputs are physical parameters that can vary spatially and with time. Limitations in data availability and accuracy means that reaction-transport predictions can rarely provide more than order-of-magnitude bounding estimates of contaminant movement in the subsurface. A more direct means for establishing the limits of contaminant transport is to examine actual plumes to determine if, collectively, they spread and attenuate in a reasonably consistent and characteristic fashion. Here a number of U plumes from ore bodies and contaminated sites were critically examined to identify characteristics of U plume movement. The magnitude of the original contaminant source, the geologic setting, and the hydrologic regime were rarely similar from site to site. Plumes also spanned a vast range of ages, and no complete set of time-series plume analyses based on the spatial extent of U contamination exist for a particular site. Despite the accumulated uncertainties and variabilities, the plume data set gave a clear and reasonably consistent picture of U plume behavior. Specifically, uranium plumes: ??Appear to reach steady-state, that is, they quit spreading, rapidly (within a few years). ??Exceed roughly 2 km in length only in special cases (e.g., where in situ leaching has been carried out). The majority are much smaller. ??Exhibit very similar U chemistry between sites. This implies analogous contaminant attenuation mechanisms despite their location.     

Effects of pulp and paper mill effluents on estuarine and marine ecosystems in Canada: a review

This review examines the impact of pulp and paper mill effluents by comparing effects from Canada's east and west coasts at a time when revisions to the federal Fisheries Act (Pulp and Paper Effluent Regulations) are being finalized. Pulp and paper mill effluents from Canadian coastal mills were usually acutely toxic at source, and in many cases had marked deleterious effects on receiving waters due to toxicity, high biochemical oxygen demand (BOD), and total suspended solids (TSS) loadings. Extreme reductions in ambient dissolved oxygen, impacts on benthic and intertidal organisms, changes in water colour and primary productivity, have been demonstrated over the years and continue to cause environmental damage. Contamination of biota by a wide range of chlorinated organic compounds has been more recently the focus of investigations.While sublethal effects of lowered dissolved oxygen levels and suspended solids on the water column and bottom communities are well known, the potential effects of major organochlorine contamination of water (measured as Adsorbable Organic Halogens=AOX), sediments, and biota are not fully understood, especially under natural and perturbated conditions. The findings of recent North American and Scandinavian studies which describe liver enzyme activation, histological damage, reproductive and population level changes in fish, are a major concern as they are a sign of ecosystem stress and pathology.The environmental effects described herein are long-term impacts which will not respond quickly to changes in pollutant loading. Integrated site-specific assessments need to be undertaken to document ecosystem response to process and treatment improvements at mill sites. Current biomonitoring techniques including measures of population structure and ecosystem function are needed in addition to sensitive biochemical indicators of contaminant exposure.     

Prospects for incorporation of epigenetic biomarkers in human health and environmental risk assessment of chemicals

Epigenetic mechanisms have gained relevance in human health and environmental studies, due to their pivotal role in disease, gene × environment interactions and adaptation to environmental change and/or contamination. Epigenetic mechanisms are highly responsive to external stimuli and a wide range of chemicals has been shown to determine specific epigenetic patterns in several organisms. Furthermore, the mitotic/meiotic inheritance of such epigenetic marks as well as the resulting changes in gene expression and cell/organismal phenotypes has now been demonstrated. Therefore, epigenetic signatures are interesting candidates for linking environmental exposures to disease as well as informing on past exposures to stressors. Accordingly, epigenetic biomarkers could be useful tools in both prospective and retrospective risk assessment but epigenetic endpoints are currently not yet incorporated into risk assessments. Achieving a better understanding on this apparent impasse, as well as identifying routes to promote the application of epigenetic biomarkers within environmental risk assessment frameworks are the objectives of this review. We first compile evidence from human health studies supporting the use of epigenetic exposure‐associated changes as reliable biomarkers of exposure. Then, specifically focusing on environmental science, we examine the potential and challenges of developing epigenetic biomarkers for environmental fields, and discuss useful organisms and appropriate sequencing techniques to foster their development in this context. Finally, we discuss the practical incorporation of epigenetic biomarkers in the environmental risk assessment of chemicals, highlighting critical data gaps and making key recommendations for future research within a regulatory context.     

Transcriptomics and proteomics. Applications to ecotoxicology

Researchers from Europe and the USA met at the Joint Research Center (JRC) of the European Commission to discuss how to integrate gene and protein expression analyses with bioinformatic tools in the field of ecotoxicology and how this new approach could be translated in improved risk assessment procedures. The measurements of gene and/or protein expression levels, upon exposure to a chemical or a stressor, can be used to develop robust molecular biomarkers that will allow the early detection of environmental stress, study long-term exposure and infer the mechanism of action. These molecular biomarkers should be linked to phenotypic end points of exposure such as adverse effects in growth and reproduction in single organisms and populations. At environmentally realistic exposure levels there could be “non-linear” dose-response curves, which should be accounted for in the experimental design and in the analyses of microarray and proteomic data. The application of gene and protein expression profiling in ecotoxicology will have a significant impact on the ecotoxicology field in the near future and international collaborations will play an important role in accelerating the application of those techniques.     

The influence of fundamental traits on mechanisms controlling appendage regeneration

One of the most compelling questions in evolutionary biology is why some animals can regenerate injured structures while others cannot. Appendage regeneration appears to be common when viewed across the metazoan phylogeny, yet this ability has been lost in many taxa to varying degrees. Within species, the capacity for regeneration also can vary ontogenetically among individuals. Here we argue that appendage regeneration along the secondary body axis may be constrained by fundamental traits such as body size, aging, life stage, and growth pattern. Studies of the molecular mechanisms affecting regeneration have been conducted primarily with small organisms at early life stages. Such investigations disregard the dramatic shifts in morphology and physiology that organisms undergo as they age, grow, and mature. To help explain interspecific and intraspecific constraints on regeneration, we link particular fundamental traits to specific molecular mechanisms that control regeneration. We present a new synthesis for how these fundamental traits may affect the molecular mechanisms of regeneration at the tissue, cellular, and genomic levels of biological organization. Future studies that explore regeneration in organisms across a broad phylogenetic scale, and within an ontogenetic framework, will help elucidate the proximate mechanisms that modulate regeneration and may reveal new biomedical applications for use in regenerative medicine.     

Activities of biomarkers in multiple life stages of the model crustacean, Palaemonetes pugio

Increased urbanization of coastal areas has led to increased contaminant levels in adjacent sediments and waters. Consequently, many studies have been conducted to determine the potential impacts on estuarine organisms, including the grass shrimp, Palaemonetes pugio. This study investigated baseline levels of four cellular biomarkers (glutathione (GSH), lipid peroxidation (LPx), acetylcholinesterase (AChE), and cholesterol (CHL)) in multiple life stages (stage IV, V, VI, and VII embryos, newly-hatched larvae, 18-day-old larvae, juveniles, and adults) of P. pugio to determine which biomarkers may potentially be useful as indicators of contaminant exposure. There was a similar pattern in both LPx and AChE levels, with a clear increase occurring from the embryonic to the adult stages. Detectable levels of AChE did not occur until embryo stage V. Glutathione shared a similar pattern to LPx and AChE from the newly-hatched larvae through the adult stage, however, it did not exhibit any distinguishable pattern overall with highly variable levels among all life stages. Likewise, CHL did not exhibit any distinguishable pattern, but in contrast, CHL levels were similar throughout all life stages. This research provides valuable background information that may be used in future assessments of grass shrimp population health.     

Molecules are more than markers: new directions in molecular microbial ecology

Macromolecules such as DNA, RNA, and proteins are widely used to quantify diversity in natural communities, to monitor the dispersal of organisms and their genes, and to trace phylogenetic relationships among organisms. With such widespread use of molecules as markers, it is easy to forget that they perform functions that are integral to the survival of organisms. The structural and functional properties of macromolecules have been intensively studied in genetics, biochemistry, and physiology. These fields, however, have not generally focused on the ecological significance of molecular variation, but instead have used defective variants as tools for identifying structure and function. Understanding the significance of molecular variation for organismal success or failure is a central problem in ecology, one whose solution will require the integration of diverse approaches and perspectives from ecology, molecular biology, genetics, physiology, and evolutionary biology. I review several studies of bacterial populations evolving in simple environments that have begun to integrate these approaches and perspectives in order to examine the consequences of molecular variation for ecological performance.     

Use of Biomarkers in Oil Spill Risk Assessment in the Marine Environment

Numerous molecular, cellular, and physiological biomarkers have been used to assess the responses of marine animals to petroleum compounds. To be used in ecological risk assessment after an oil spill, a biomarker response needs to be linked to petroleum exposure and not strongly influenced by internal and external confounding factors. Biomarker responses to petroleum PAH, dominated by alklated two-and three-ringed aromatics, can be quite different than responses to pyrogenic PAH, dominated by four-and five-ringed aromatics. In many field sites there is a mixture of petrogenic and pyrogenic PAH, along with other contaminants, making it difficult to relate biomarker responses to a particular contaminant class. Biomarkers used to assess marine animal responses in the field include the cytochrome P450 system, heat stress protein, histopathology, and bile fluorescent compounds (FAC). Other biomarkers, including DNA/chromosomal damage and phase 2 enzymes, have been shown to respond after laboratory exposure, but more work needs to be done to demonstrate their usefulness in the field. One of the most useful biomarkers of petroleum exposure are the FAC responses in fish, which can be used to distinguish between petrogenic and pyrogenic PAH exposure. Few of the presently used biomarkers are linked to higher order biological effects, e.g. toxicity, reproductive failure.     

生物标志物（Biomarkers）在海洋环境监测中的研究与进展

污染物的存在给海洋环境和生态健康带来了巨大的压力,如何监测这些污染物并对其毒性进行科学的评价,成为当今环境科学关心的热点问题。生物标志物（Biomarkers）是毒理学研究的重要工具,它能对污染事件进行早期预警,并能在一定程度上评估生态风险。对近十多年来生物标志物的研究与应用进行了回顾,总结了不同水平（分子、细胞、个体、系统）生物标志物的种类、特征、检测方法和应用特点,并对现存挑战和未来发展趋向进行了展望,旨在系统的认识生物标志物,并为其在海洋环境监测中的合理应用提供理论借鉴。     

Environmental proteomics and metallomics

Monitoring environmental pollution using biomarkers requires detailed knowledge about the markers, and many only allow a partial assessment of pollution. New proteomic methods (environmental proteomics) can identify proteins that, after validation, might be useful as alternative biomarkers, although this approach also has its limitations, derived mainly from their application to non-model organisms. Initial studies using environmental proteomics were carried out in animals exposed to model pollutants, and led to the concept of protein expression signatures. Experiments have been carried out in model organisms (yeast, Arabidopsis, rat cells, or mice) exposed to model contaminants. Over the last few years, proteomics has been applied to organisms from ecosystems with different pollution levels, forming the basis of an environmental branch in proteomics. Another focus is connected with the presence of metals bound to biomolecules, which adds an additional dimension to metal-biomolecule and metalloprotein characterization - the field of metallomics. The metallomic approach considers the metallome: a whole individual metal or metalloid species within a cell or tissue. A metallomic analytical approach (MAA) is proposed as a new tool to study and identify metalloproteins.     

Ancestry-Tracking of Stress Response GPCR Clades: A Conceptual Path to Treating Depression

The environmental complexity in which living organisms found themselves throughout evolution, most likely resulted in various encounters that would continuously challenge the organisms' ability to survive. Coping with this stress can prove energetically demanding and might require the proper coupling between mechanisms aimed at sensing external stimuli and cellular strategies geared at producing energy. In this issue of BioEssays, Lovejoy and Hogg hypothesize that preservation of this bifaceted coupling can be detected by the maintenance and evolution of stress response mechanisms at the genomic, molecular and cellular levels. Through ancestry-tracking, they identify a group of related G protein-coupled receptor systems with intersecting stress-modulating properties which might represent an essential part of a complex organism's coping mechanisms to stress, an attribute that they suspect may be affected in individuals suffering from mood disorders such as depression.     

环状RNA及其在生态毒理学研究中的应用进展

环状RNA（circular RNAs,circRNAs）是一类共价闭合环状非编码RNA,具有进化上保守、结构上稳定、组织特异性表达等特点。CircRNAs可作为miRNAs海绵影响其对基因的调控,还可与RNA结合蛋白（RNA binding proteins,RBPs）相互作用,也有研究表明某些circRNAs还具有被翻译成蛋白质的潜能。CircRNAs已被证实对某些疾病具有特异性、稳定性和调节功能,如癌症、糖尿病、心血管疾病、神经退行性疾病等,其可作为潜在的诊断、预后生物标志物和治疗靶点。最近,有研究发现circRNAs参与了环境化学污染物诱导的毒性效应发生及发展的过程。目前,生态毒理学研究中评价环境化学污染物和毒效应之间关系的毒性终点通常会受遗传多态性和表观遗传学影响,考虑到经环境化学污染物暴露后生物体内circRNAs差异性表达的现象,或许在生态毒理学研究中circRNAs也有作为生物标志物的可能性。基于此,对circRNAs的生物合成与降解、生物学功能、分析方法及其目前在生态毒理学研究中的应用展开综述,并对其作为分子生物标志物在环境污染物暴露早期诊断和生态风险评价中的应用进行了展望,以期为生态毒理学研究和环境风险评价提供参考。     

Biomarkers of Dissolved Oxygen Stress in Oysters: A Tool for Restoration and Management Efforts

The frequency and intensity of anoxic and hypoxic events are increasing worldwide, creating stress on the organisms that inhabit affected waters. To understand the effects of low dissolved oxygen stress on oysters, hatchery-reared oysters were placed in cages and deployed along with continuously recording environmental data sondes at a reef site in Mobile Bay, AL that typically experiences low oxygen conditions. To detect and measure sublethal stress, we measured growth and survival of oysters as well as expression of three biomarkers, heat shock protein 70 (HSP70), hypoxia inducible factor (HIF) and phospho-p38 MAP kinase, in tissues from juvenile and adult oysters. Survival rates were high for both juvenile and adult oysters. Expression levels of each of the 3 isoforms of HSP 70 were negatively correlated to dissolved oxygen (DO) concentrations, suggesting that HSP 70 is useful to quantify sublethal effects of DO stress. Results for HIF and phospho-p38 MAP kinase were inconclusive. Test deployments of oysters to assess expression of HSP 70 relative to environmental conditions will be useful, in addition to measuring abiotic factors, to identify appropriate sites for restoration, particularly to capture negative effects of habitat quality on biota before lethal impacts are incurred.