Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach

CORC > 烟台海岸带研究所 > 中国科学院烟台海岸带研究所 > 中科院海岸带环境过程与生态修复重点实验室 > 污染过程与控制实验室

	Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
	Williams, Tim D.1; Turan, Nil 1; Diab, Amer M.2; Wu, Huifeng1,3 ; Mackenzie, Carolynn 2; Bartie, Katie L.2; Hrydziuszko, Olga 1; Lyons, Brett P.4; Stentiford, Grant D.4; Herbert, John M.1
刊名	PLOS COMPUTATIONAL BIOLOGY
	2011-08-01
卷号	7 期号:8 页码:e1002126
关键词	Flounder Platichthys-flesus Histopathological Biomarkers Pleuronectes-platessa Endocrine Disruption Gene-expression Liver Fibrosis Marine Fish Receptor Microarray Proteasome
ISSN号	1553-734X
通讯作者	Williams, TD, Univ Birmingham, Sch Biosci, Birmingham, W Midlands, England. f.falciani@bham.ac.uk
产权排序	[Williams, TD; Turan, N; Wu, HF; Hrydziuszko, O; Herbert, JM; Viant, MR; Chipman, KJ; Falciani, F] Univ Birmingham, Sch Biosci, Birmingham, W Midlands, England; [Diab, AM; Mackenzie, C; Bartie, KL; Leaver, MJ; Taggart, JB; George, SG] Univ Stirling, Inst Aquaculture, Stirling FK9 4LA, Scotland; [Wu, HF] Acad Sci, Yantai Inst Coastal Zone Res, Yantai, Peoples R China; [Lyons, BP; Stentiford, GD; Katsiadaki, I] Weymouth Lab, Weymouth, Dorset, England; [Abraham, JK] Case Western Reserve Univ, Dept Epidemiol & Biostat, Cleveland, OH 44106 USA; [Abraham, JK] Iowa State Univ, Dept Anim Sci, Ames, IA USA
文献子类	Article
英文摘要	The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations.; The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations.
学科主题	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS关键词	FLOUNDER PLATICHTHYS-FLESUS ; HISTOPATHOLOGICAL BIOMARKERS ; PLEURONECTES-PLATESSA ; ENDOCRINE DISRUPTION ; GENE-EXPRESSION ; LIVER FIBROSIS ; MARINE FISH ; RECEPTOR ; MICROARRAY ; PROTEASOME
WOS研究方向	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
语种	英语
WOS记录号	WOS:000294299700010
资助机构	UK NERC[NE/C507661/1]; UK BBSRC; EU[EKV-2001-0057]; BBSRC[6/JIF 13209]; Department for Environment, Food and Rural Affairs (Defra); [G.4500017]
公开日期	2011-11-11
内容类型	期刊论文
源URL	[http://ir.yic.ac.cn/handle/133337/5126]
专题	烟台海岸带研究所_污染过程与控制实验室
作者单位	1.Univ Birmingham, Sch Biosci, Birmingham, W Midlands, England 2.Univ Stirling, Inst Aquaculture, Stirling FK9 4LA, Scotland 3.Acad Sci, Yantai Inst Coastal Zone Res, Yantai, Peoples R China 4.Weymouth Lab, Weymouth, Dorset, England 5.Case Western Reserve Univ, Dept Epidemiol & Biostat, Cleveland, OH 44106 USA 6.Iowa State Univ, Dept Anim Sci, Ames, IA USA
推荐引用方式 GB/T 7714	Williams, Tim D.,Turan, Nil,Diab, Amer M.,et al. Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach[J]. PLOS COMPUTATIONAL BIOLOGY,2011,7(8):e1002126.
APA	Williams, Tim D..,Turan, Nil.,Diab, Amer M..,Wu, Huifeng.,Mackenzie, Carolynn.,...&Falciani, Francesco.(2011).Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach.PLOS COMPUTATIONAL BIOLOGY,7(8),e1002126.
MLA	Williams, Tim D.,et al."Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach".PLOS COMPUTATIONAL BIOLOGY 7.8(2011):e1002126.