Finding biomarkers is getting easier

Towards Sustainable Environmental Quality: Priority Research Questions for the Australasian Region of Oceania

Environmental challenges persist across the world, including the Australasian region of Oceania, where biodiversity hotspots and unique ecosystems such as the Great Barrier Reef are common. These systems are routinely affected by multiple stressors from anthropogenic activities, and increasingly influenced by global megatrends (e.g., the food-energy-water nexus, demographic transitions to cities) and climate change. Here we report priority research questions from the Global Horizon Scanning Project, which aimed to identify, prioritize, and advance environmental quality research needs from an Australasian perspective, within a global context. We employed a transparent and inclusive process of soliciting key questions from Australasian members of the Society of Environmental Toxicology and Chemistry. Following submission of 78 questions, 20 priority research questions were identified during an expert workshop in Nelson, New Zealand. These research questions covered a range of issues of global relevance, including research needed to more closely integrate ecotoxicology and ecology for the protection of ecosystems, increase flexibility for prioritizing chemical substances currently in commerce, understand the impacts of complex mixtures and multiple stressors, and define environmental quality and ecosystem integrity of temporary waters. Some questions have specific relevance to Australasia, particularly the uncertainties associated with using toxicity data from exotic species to protect unique indigenous species. Several related priority questions deal with the theme of how widely international ecotoxicological data and databases can be applied to regional ecosystems. Other timely questions, which focus on improving predictive chemistry and toxicology tools and techniques, will be important to answer several of the priority questions identified here. Another important question raised was how to protect local cultural and social values and maintain indigenous engagement during problem formulation and identification of ecosystem protection goals. Addressing these questions will be challenging, but doing so promises to advance environmental sustainability in Oceania and globally.

Carbonic anhydrase activity as a potential biomarker for acute exposure to copper in corals

Coral reefs are subjected to climate change and are severely impacted by human activities, with copper (Cu) being a relevant physiological stressor for corals at local scale. The ecological relevance of parameters measured at biochemical or cellular level is now considered an extremely important feature in environmental studies, and can be used as early warning signs of environmental degradation. In this context, the effects of acute exposure (96 h) to Cu were assessed on the maximum photochemical efficiency of zooxanthellae (Fv/Fm) and on the activity of key enzymes [carbonic anhydrase (CA) and Ca-ATPase] involved in coral physiology using the scleractinian coral Mussismilia harttii as a biological model. Corals were exposed to different concentrations of dissolved Cu (4.6-19.4 μg/L) using two different experimental approaches: a laboratory closed system and a marine mesocosm system. Fv/Fm values and Ca - ATPase activity were not affect by exposure to Cu in any of the exposure systems. However, a significant reduction in CA activity was observed in corals exposed to 11.9 and 19.4 μg Cu/L in the laboratory and at all concentrations of Cu tested in the mesocosm system (4.6, 6.0 and 8.5 μg/L). Based on the sensitivity of this enzyme to the short period of exposure to sublethal concentrations of Cu in both experimental approaches, the present study suggests the use of CA activity as a potential biomarker to be used in biomarker-based environmental monitoring programs in coral reefs.

An evaluation of coral lophelia pertusa mucus as an analytical matrix for environmental monitoring: A preliminary proteomic study

For the environmental monitoring of coral, mucus appears to be an appropriate biological matrix due to its array of functions in coral biology and the non-intrusive manner in which it can be collected. The aim of the present study was to evaluate the feasibility of using mucus of the stony coral Lophelia pertusa (L. pertusa) as an analytical matrix for discovery of biomarkers used for environmental monitoring. More specifically, to assess whether a mass-spectrometry-based proteomic approach can be applied to characterize the protein composition of coral mucus and changes related to petroleum discharges at the seafloor. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) screening analyses of orange and white L. pertusa showed that the mucosal protein composition varies significantly with color phenotype, a pattern not reported prior to this study. Hence, to reduce variability from phenotype difference, L. pertusa white individuals only were selected to characterize in more detail the basal protein composition in mucus using liquid chromatography, mass spectrometry, mass spectrometry (LC-MS/MS). In total, 297 proteins were identified in L. pertusa mucus of unexposed coral individuals. Individuals exposed to drill cuttings in the range 2 to 12 mg/L showed modifications in coral mucus protein composition compared to unexposed corals. Although the results were somewhat inconsistent between individuals and require further validation in both the lab and the field, this study demonstrated preliminary encouraging results for discovery of protein markers in coral mucus that might provide more comprehensive insight into potential consequences attributed to anthropogenic stressors and may be used in future monitoring of coral health.

Comparative Proteomics for the Evaluation of Protein Expression and Modifications in Neurodegenerative Diseases

Together with hypothesis-driven approaches, high-throughput differential proteomic analysis performed primarily not only in human cerebrospinal fluid and serum but also on protein content of other tissues (blood cells, muscles, peripheral nerves, etc.) has been used in the last years to investigate neurodegenerative diseases. Even if the goal for these analyses was mainly the discovery of neurodegenerative disorders biomarkers, the characterization of specific posttranslational modifications (PTMs) and the differential protein expression resulted in being very informative to better define the pathological mechanisms. In this chapter are presented and discussed the positive aspects and challenges of the outcomes of some of our investigations on neurological and neurodegenerative disease, in order to highlight the important role of protein PTMs studies in proteomics-based approaches.

Biomarkers in autism spectrum disorder: the old and the new

RATIONALE

Autism spectrum disorder (ASD) is a complex heterogeneous neurodevelopmental disorder with onset during early childhood and typically a life-long course. The majority of ASD cases stems from complex, 'multiple-hit', oligogenic/polygenic underpinnings involving several loci and possibly gene-environment interactions. These multiple layers of complexity spur interest into the identification of biomarkers able to define biologically homogeneous subgroups, predict autism risk prior to the onset of behavioural abnormalities, aid early diagnoses, predict the developmental trajectory of ASD children, predict response to treatment and identify children at risk for severe adverse reactions to psychoactive drugs.

OBJECTIVES

The present paper reviews (a) similarities and differences between the concepts of 'biomarker' and 'endophenotype', (b) established biomarkers and endophenotypes in autism research (biochemical, morphological, hormonal, immunological, neurophysiological and neuroanatomical, neuropsychological, behavioural), (c) -omics approaches towards the discovery of novel biomarker panels for ASD, (d) bioresource infrastructures and (e) data management for biomarker research in autism.

RESULTS

Known biomarkers, such as abnormal blood levels of serotonin, oxytocin, melatonin, immune cytokines and lymphocyte subtypes, multiple neuropsychological, electrophysiological and brain imaging parameters, will eventually merge with novel biomarkers identified using unbiased genomic, epigenomic, transcriptomic, proteomic and metabolomic methods, to generate multimarker panels. Bioresource infrastructures, data management and data analysis using artificial intelligence networks will be instrumental in supporting efforts to identify these biomarker panels.

CONCLUSIONS

Biomarker research has great heuristic potential in targeting autism diagnosis and treatment.

A semiautomated framework for integrating expert knowledge into disease marker identification

BACKGROUND

The availability of large complex data sets generated by high throughput technologies has enabled the recent proliferation of disease biomarker studies. However, a recurring problem in deriving biological information from large data sets is how to best incorporate expert knowledge into the biomarker selection process.

OBJECTIVE

To develop a generalizable framework that can incorporate expert knowledge into data-driven processes in a semiautomated way while providing a metric for optimization in a biomarker selection scheme.

METHODS

The framework was implemented as a pipeline consisting of five components for the identification of signatures from integrated clustering (ISIC). Expert knowledge was integrated into the biomarker identification process using the combination of two distinct approaches; a distance-based clustering approach and an expert knowledge-driven functional selection.

RESULTS

The utility of the developed framework ISIC was demonstrated on proteomics data from a study of chronic obstructive pulmonary disease (COPD). Biomarker candidates were identified in a mouse model using ISIC and validated in a study of a human cohort.

CONCLUSIONS

Expert knowledge can be introduced into a biomarker discovery process in different ways to enhance the robustness of selected marker candidates. Developing strategies for extracting orthogonal and robust features from large data sets increases the chances of success in biomarker identification.

Assessing and managing sediment contamination in transitional waters

Sediment contamination remains a global problem, particularly in transitional waters such as estuaries and coastal lagoons, which are the recipients of chemicals from multiple near- and far-field sources. Although transitional waters are highly productive ecosystems, approaches for assessing and managing their sediment contamination are not as well developed as in marine and fresh waters. Further, although transitional waters remain defined by their variable and unique natural water quality characteristics, particularly salinity, the biota inhabiting such ecosystems, once thought to be defined by Remane's "paradox of brackish water", are being redefined. The purpose of the present paper is to build on an earlier but now dated (>12years old) review of methods to assess sediment contamination in estuaries, extending this to all transitional waters, including information on integrative assessments and on management decision-making. The following are specifically discussed: chemical assessments; bioindicators; biomarkers; and, biological surveys. Assessment and management of sediment contamination in transitional waters need to be focused on ecosystem services and, where appropriate and possible, be proactive rather than reactive when uncertainty has been suitably reduced.