A transcriptomic analysis of land-use impacts on the oyster, Crassostrea virginica, in the South Atlantic bight

Molecular Ecology

Volumn 18, Issue 11, 2009, Pages 2415-2425

  Chapman, Robert W ^a,b,c,d,e   Mancia, Annalaura ^b,d,g   Beal, Marion ^a,d   Veloso, Artur ^c,d   Rathburn, Charles ^c,d   Blair, Anne ^d   Sanger, Denise ^d,f   Holland, A F ^d   Warr, Gregory W ^b,c,d,e   Didonato, Guy ^d  

^a SOUTH CAROLINA DEPARTMENT OF NATURAL RESOURCES   (United States)

^b MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

^c Department of Teacher Education and Department of Sociology and Anthropology   (United States)

^d Hollings Marine Laboratory   (United States)

^e CLEMSON UNIVERSITY   (United States)

^f South Carolina Sea Grant Consortium   (United States)

^g UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

American oyster; Artificial neural networks; Land use; Microarrays; Transcript profiling

Indexed keywords

BIOLOGICAL MARKER;

ALGORITHM; ANIMAL; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOLOGICAL MODEL; DNA MICROARRAY; ECOSYSTEM; ENVIRONMENTAL MONITORING; GENE EXPRESSION PROFILING; GENETICS; GILL; HEPATOPANCREAS; METABOLISM; OYSTER; POLLUTANT; POPULATION DYNAMICS; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; ANIMALS; BIOLOGICAL MARKERS; CRASSOSTREA; ECOSYSTEM; ENVIRONMENTAL MONITORING; ENVIRONMENTAL POLLUTANTS; GENE EXPRESSION PROFILING; GILLS; HEPATOPANCREAS; MODELS, BIOLOGICAL; NEURAL NETWORKS (COMPUTER); OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POPULATION DYNAMICS; SENSITIVITY AND SPECIFICITY;

CRASSOSTREA VIRGINICA; OSTREIDAE;

EID: 65949092011     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04194.x     Document Type: Article

References (48)

1. Adams SM (2005) Assessing cause and effect of multiple stressors on marine systems. Marine Pollution Bulletin, 51, 649 657.
2. Bayne BL, Anderson J, Engel D, Gilfillan E, Hoss D, Lloyd R (1980) Physiological Techniques for Measuring the Biological Effects of Pollution in the Sea. Journal du Conseil International pour l'Exploration de la Mer, 179, 88 99.
3. Beach D (2002) Coastal Sprawl: The Effects of Urban Design on Aquatic Ecosystems in the United States. Pew Oceans Commission, Arlington, Virginia.
4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B, 57, 289 300.
5. Bishop CM (2006) Pattern Recognition and Machine Learning. Springer, New York.
6. Bradley AP (1997) The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recognition, 30, 1145 1159.
7. Braga AC, Oliveira P (2003) Diagnostic analysis based on ROC curves: theory and applications in medicine. International Journal for Quality in Health Care, 16, 191 198.
8. Chapman RW (2001) EcoGenomics: a consilence for comparative immunology. Developmental and Comparative Immunology, 25, 549 551.
9. Chapman RW, Robalino J, Trent HF III (2006) EcoGenomics: analysis of complex systems using fractal geometry. Integrative and Comparative Biology, 46, 902 911.
10. Chapman RW, Sedberry GR, Koenig CC et al 1999) Stock identification of gag, Mycteroperca microlepis, along the southeast coast of the United States. Marine Biotechnology, 1, 137 146.
11. Cho SB, Won HH (2003) Machine learning in DNA microarray analysis for cancer classification. First Asia-Pacific Bioinformatics Conference (APBC 2003), Adelaide, Australia, February 2003, 189 198.
12. Cui Y, McBride SJ, Boyd WA et al 2007) Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity. Genome Biology, 8, R122.
13. Culliton TJ (1998) Population, distribution, density and growth. NOAA's State of the Coast Report. 18 December 2001. Available from http://www.state-of- coast.noaa.gov/bulletins/html/pop-01/pop.htmli. National Oceanic and Atmospheric Administration, Silver Spring, Maryland.
14. Dankbar DM, Dawson ED, Mehlmann M et al 2007) Diagnostic microarray for influenza B viruses. Analytical Chemistry, 79, 2084 2090.
15. Engel DW (1999) Accumulation and cytosolic partitioning of metals in the American oyster Crassotrea virginica. Marine Environmental Research, 47, 89 102.
16. Fisher WS, Oliver LM, Winstead JT, Long ER (2000) A survey of oysters Crassostrea virginica from Tampa Bay, Florida: associations of internal defense measurements with contaminant burdens. Aquatic Toxicology, 51, 115 138.
17. Funes V, Alhama J, Navas JI, Lopez-Barea J, Peinado J (2006) Ecotoxicological effects of metal pollution in two mollusc species from the Spanish South Atlantic littoral. Environmental Pollution, 139, 214 223.
18. Geffard O, Budzinski H, His E (2002) The effects of elutriates from PAH and heavy metal polluted sediments on Crassostrea gigas (Thunberg) embryogenesis, larval growth and bio-accumulation by the larvae of pollutants from sedimentary origin. Ecotoxicology, 11, 403 416.
19. Gentleman RC, Carey VJ, Bates DM et al 2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biology, 5, R80.
20. Hanley JA, McNeil BJ (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology, 143, 29 36.
21. Holland AF, Sanger DM, Gawle CP et al 2004) Linkages between tidal creek ecosystems and the landscape and demographic attributes of their watersheds. Journal of Experimental Marine Biology and Ecology, 298, 151 178.
22. Huber W, Von Heydebreck A, Sültmann H et al 2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18, S96 S104.
23. Jenny MJ, Chapman RW, Mancia A et al 2007) A cDNA microarray for Crassostrea virginica and C. gigas. Marine Biotechnology, 9, 577 591.
24. Khan J, Wei JS, Ringnér M et al 2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nature Medicine, 7, 673 679.
25. Kirby MX, Miller HM (2005) Response of a benthic suspension feeder (Crassostrea virginica Gmelin) to three centuries of anthropogenic eutrophication in Chesapeake Bay. Estuarine, Coastal and Shelf Science, 62, 679 689.
26. Linder R, Dew D, Sudhoff H et al 2004) The 'subsequent artificial neural network' (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses. Bioinformatics, 20, 3544 3552.
27. Mallin MA, Parsons DC, Johnson VL et al 2004) Nutrient limitation and algal blooms in urbanizing tidal creeks. Journal of Experimental Marine Biology and Ecology, 298, 211 231.
28. Mancia A, Warr GW, Chapman RW (2008) A transcriptomic analysis of the stress induced by capture-release health assessment studies in wild dolphins (Tursiops truncatus). Molecular Ecology, 17, 2581 2589.
29. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution, 18, 189 197.
30. Nicholls RJ, Wong PP, Burkett VR et al 2007) Coastal systems and low-lying areas. In : Climate Change 2007: Impacts, Adaptation and Vulnerability (eds Parry ML, Canziani OF, Palutikof JP, van der Linden PJ, Hanson CE), pp. 315 356. Cambridge Unversity Press, Cambridge, UK.
31. Obuchowski NA, Lieber ML, Wians FH Jr. (2004) ROC curves in clinical chemistry: uses, misuses, and possible solutions. Clinical Chemistry, 50, 1118 1125.
32. Oliver LM, Fisher WS, Winstead JT, Hemmer BL, Long ER (2001) Relationships between tissue contaminants and defense-related characteristics of oysters (Crassostrea virginica) from five Florida bays. Aquatic Toxicology, 55, 203 222.
33. r Development Core Team (2008) r: A Language and Environment for Statistical Computing. r Foundation for Statistical Computing, Vienna, Austria (http://www.R-project.org.).
34. Regoli F, Nigro M, Bertoli E, Principato G, Orlando E (1997) Defenses against oxidative stress in the Antarctic scallop Adamussium colbecki and effects of acute exposure to metals. Hydrobiologia, 355, 139 144.
35. Ringwood AH, Conners DE, Keppler CJ (1999) Cellular responses of oysters, Crassostrea virginica, to metal-contaminated sediments. Marine Environmental Research, 48, 427 437.
36. Ritchie ME, Silver J, Oshlack A et al 2007) A comparison of background correction methods for two-colour microarrays. Bioinformatics, 23, 2700 2707.
37. Sanger DM, Holland AF, Scott GI (1999a) Tidal creek and salt marsh sediments in South Carolina coastal estuaries. I. Distribution of trace metals. Archives of Environmental Contamination and Toxicology, 37, 445 457.
38. Sanger DM, Holland AF, Scott GI (1999b) Tidal creek and salt marsh sediments in South Carolina coastal estuaries. II. Distribution of organic contaminants. Archives of Environmental Contamination and Toxicology, 37, 458 471.
39. Smyth GK, Speed T (2003) Normalization of cDNA microarray data. Methods, 31, 265 273.
40. Smyth GK, Michaud J, Scott HS (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics, 21, 2067 2075.
41. Steinberg CEW, Sturzenbaum SR, Menzel R (2007) Genes and environment - striking the fine balance between sophisticated biomonitoring and true functional environmental genomics. Science of the Total Environment, 400, 142 161.
42. Stephan C, Wesseling S, Schink T et al 2003) Comparison of eight computer programs for receiver-operating characteristic analysis. Clinical Chemistry, 49, 433 439.
43. Van Dolah RF, Hyland JL, Holland AF, Rosen JS, Snoots TR (1999) A benthic index of biological integrity for assessing habitat quality in estuaries of the southeastern USA. Marine Environmental Research, 48, 269 283.
44. Wagner A (2005) Robustness and Evolvability in Living Systems. Princeton University Press, Princeton, New Jersey.
45. Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A (2003) Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. Environmental Health Perspectives, 111, 15 28.
46. White DL, Porter DE, Lewitus AJ (2004) Spatial and temporal analyses of water quality and phytoplankton biomass in an urbanized versus a relatively pristine salt marsh estuary. Journal of Experimental Marine Biology and Ecology, 298, 255 273.
47. Whitehead A, Crawford DL (2006) Neutral and adaptive variation in gene expression. Proceedings of the National Academy of Sciences of the United States of America, 103, 5425 5430.
48. Williams TD, Diab AM, George SG, Sabine V, Chipman JK (2007) Gene expression responses of European flounder (Platichthys flesus) to 17-β estradiol. Toxicology Letters, 168, 236 248.