Implications of informatics approaches in ecological research

Metzger, Kelsey J.; Klaper, Rebecca; Thomas, Michael A.

doi:10.1016/j.ecoinf.2010.11.003

Cited by 15 publications

(6 citation statements)

References 97 publications

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“…We used a microarray platform for fathead minnow (Klaper et al, 2010) that was enhanced by the annotation of human gene homologs for array elements (Thomas et al, 2011), allowing gene-class analysis, which tests for enrichment of specific human neuronal systems and processes (Subramanian et al, 2005; Metzger et al, 2011). We hypothesized that FLX, VNX and CBZ would induce altered gene expression enrichment and that a mixture of these three compounds (MIX) would cause a different gene expression profile than the effects of the pharmaceuticals when tested individually.…”

Section: Introductionmentioning

confidence: 99%

Gene-class analysis of expression patterns induced by psychoactive pharmaceutical exposure in fathead minnow (Pimephales promelas) indicates induction of neuronal systems

Thomas

Joshi

Klaper

2012

Comparative Biochemistry and Physiology Part C: Toxicology &

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Psychoactive pharmaceuticals are among the most frequently prescribed drugs, contributing to persistent measurable concentrations in aquatic systems. Typically, it is assumed that such contaminants have no human health implications because they exist in extremely low concentrations. We exposed juvenile fathead minnows (Pimephales promelas) to three pharmaceuticals, fluoxetine, venlafaxine and carbamazepine, individually and in a mixture, and measured their effect on the induction of gene expression in fish brains using microarray analysis. Gene expression changes were accompanied by behavioral changes and validated by qPCR analysis. Gene Set Enrichment Analysis was used to perform gene-class analysis of gene expression, testing for enrichment of gene sets known to be involved in human neuronal development, regulation and growth. We found significant enrichment of gene sets for each of the treatments, with the largest induction of expression by the mixture treatment. These results suggest that the psychoactive pharmaceuticals are able to alter expression of fish genes associated with development, regulation and differentiation of synapses, neurons and neurotransmitters. The results provide a new perspective for the consideration of potential consequence for human health due to environmental exposure to unmetabolized psychoactive pharmaceuticals.

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Section: Introductionmentioning

confidence: 99%

Gene-class analysis of expression patterns induced by psychoactive pharmaceutical exposure in fathead minnow (Pimephales promelas) indicates induction of neuronal systems

Thomas

Joshi

Klaper

2012

Comparative Biochemistry and Physiology Part C: Toxicology &

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“…As new ecological and environmental observational systems are moving ecology into the realm of big science, transdisciplinary collaboration will be needed to accumulate and analyze massive amounts of data in order to answer grand challenge questions in biological and environmental sciences. With regard to ecoinformatics, there are a series of review papers in the journal Ecological Informatics, which cover a wide range of topics: current trends and future challenges [11], information management [12], spatiotemporal ecological models [13], and hybrid modelling [14].…”

Section: B Key Review Papers In the Bioenvironmental Sciencesmentioning

confidence: 99%

A short review on the application of computational intelligence and machine learning in the bioenvironmental sciences

Fukuda

Baets

2012

The 6th International Conference on Soft Computing and Intelligent Systems, and the 13th International Symposium on Advanced In

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This paper aims to provide a short review on the application of computational intelligence (CI) and machine learning (ML) in the bioenvironmental sciences. To clearly illustrate the current status, we limit our focus to some key approaches, namely fuzzy systems (FSs), artificial neural networks (ANNs) and genetic algorithms (GAs) as well as some ML methods. The trends in the application studies are categorized based on the targets of the model such as animal, fish, plant, soil and water. We give an overview of specific topics in the bioenvironmental sciences on the basis of the review papers on model comparisons in the field. The summary of the modelling approaches with respect to their aim and potential application fields can promote the use of CI and ML in the bioenvironmental sciences.

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“…Until very recently, ecological investigations at the molecular level relied heavily on methods and instruments developed for medical research, and the transfer of technology across disciplines was greatly impeded by lack of awareness and ability to adapt procedures used on cell cultures to samples collected from natural populations of microorganisms, algae, plants, invertebrates and vertebrates. New technologies, especially in the “‐omics” fields are meeting past challenges and providing opportunities for new insights into ecological issues, particularly for those taxa that can be observed in situ , but not cultured for detailed laboratory evaluation . A tremendous benefit in this regard is the ability to sample natural communities of mixed populations and be able to discriminate species‐specific responses ( e.g .…”

Section: Dna Damage and Repairmentioning

confidence: 99%

Beyond Xeroderma Pigmentosum: DNA Damage and Repair in an Ecological Context. A Tribute to James E. Cleaver

Karentz

2014

Photochem & Photobiology

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The ability to repair DNA is a ubiquitous characteristic of life on Earth and all organisms possess similar mechanisms for dealing with DNA damage, an indication of a very early evolutionary origin for repair processes. James E. Cleaver's career (initiated in the early 1960s) has been devoted to the study of mammalian ultraviolet radiation (UVR) photobiology, specifically the molecular genetics of xeroderma pigmentosum and other human diseases caused by defects in DNA damage recognition and repair. This work by Jim and others has influenced the study of DNA damage and repair in a variety of taxa. Today, the field of DNA repair is enhancing our understanding of not only how to treat and prevent human disease, but is providing insights on the evolutionary history of life on Earth and how natural populations are coping with UVR-induced DNA damage from anthropogenic changes in the environment such as ozone depletion.

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Implications of informatics approaches in ecological research

Cited by 15 publications

References 97 publications

Gene-class analysis of expression patterns induced by psychoactive pharmaceutical exposure in fathead minnow (Pimephales promelas) indicates induction of neuronal systems

Gene-class analysis of expression patterns induced by psychoactive pharmaceutical exposure in fathead minnow (Pimephales promelas) indicates induction of neuronal systems

A short review on the application of computational intelligence and machine learning in the bioenvironmental sciences

Beyond Xeroderma Pigmentosum: DNA Damage and Repair in an Ecological Context. A Tribute to James E. Cleaver

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