Systems biology: Leading the revolution in ecotoxicology

Abstract

Abstract-The rapid development of new technologies such as transcriptomics, proteomics, and metabolomics (Omics) are changing the way ecotoxicology is practiced. The data deluge has begun with genomes of over 65 different aquatic species that are currently being sequenced, and many times that number with at least some level of transcriptome sequencing. Integrating these top-down methodologies is an essential task in the field of systems biology. Systems biology is a biology-based interdisciplinary field that focuses on complex interactions in biological systems, with the intent to model and discover emergent properties of the system. Recent studies demonstrate that Omics technologies provide valuable insight into ecotoxicity, both in laboratory exposures with model organisms and with animals exposed in the field. However, these approaches require a context of the whole animal and population to be relevant. Powerful approaches using reverse engineering to determine interacting networks of genes, proteins, or biochemical reactions are uncovering unique responses to toxicants. Modeling efforts in aquatic animals are evolving to interrelate the interacting networks of a system and the flow of information linking these elements. Just as is happening in medicine, systems biology approaches that allow the integration of many different scales of interaction and information are already driving a revolution in understanding the impacts of pollutants on aquatic systems. Environ. Toxicol. Chem. 2011;30:265-273. # 2010 SETAC

A review of reproductive toxicity of microcystins

“…Classic/conventional ecotoxicology has focused upon a bottomup approach to understand stressor effects in which a few genes, proteins or biochemical reactions are studied at a time [165]. However, due to the complexity of organisms and the possible interactions and interrelationships of MCs with various environmental factors, classic techniques cannot meet the development of toxicology and therefore high-throughput analytical techniques are required.…”

“…genomics, proteomics, and metabolomics (or metabonomics). Genomics refers to the study of the genome of an organism, either at the DNA or at the mRNA (transcriptomics) level [165]. Proteomics is the global profiling of the proteins of an organism, their structure, function and expression.…”

“…Proteomics is the global profiling of the proteins of an organism, their structure, function and expression. Metabolomics, on the other hand, is often known as systematic investigation of low molecular weight (<1000 Da) metabolites that are the end products in various biological systems including cells, organs, tissues, biofluids, or even whole organisms [165].…”

“…Bioinformatics tools, such as a pathway analysis, will be important in providing functional insight into "omics" and physiological outcomes, and the integration of the above analysis (a tandem "topdown and bottom-up" approach) is termed "Systems toxicology". Systems analysis can be applied to many different levels, such as molecules, cells, organs, individuals, populations, and even ecosystems [165]. Systems biology uses a similar holistic approach first described by Aristotle in his work, Metaphysics: "The whole is more than the sum of its parts.…”

In Silicoanalysis of perturbed steroidogenesis and gonad growth in fathead minnows (P. promelas) exposed to 17α-ethynylestradiol

“…In an era of 'Systems Toxicology' there is increasing requirement to integrate knowledge of perturbed molecular initiating events with adverse phenotypic and population-level outcomes [Ankley et al 2010;Garcia-Reyero and Perkins 2011;Hartung 2009;Kavlock et al 2008;Miracle and Ankley 2005;Sturla et al 2014]. With such high expectations, the traditional use of apical endpoints in toxicological studies such as growth (or morphometric indices), survival, and reproduction are expected to provide limited insights into mechanisms of toxicity [Volz et al 2011].…”