Enchytraeus albidus microarray: Enrichment, design, annotation and database (enchyBASE)

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Novais, Sara C ^a   Arrais, Joel ^b   Lopes, Pedro ^b   Vandenbrouck, Tine ^c   de Coen, Wim ^c   Roelofs, Dick ^d   Soares, Amadeu M V M ^a   Amorim, Mónica J B ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

^b UNIVERSITY OF AVEIRO   (Portugal)

^c UNIVERSITY OF ANTWERP   (Belgium)

^d VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ENCHYTRAEUS; EXPRESSED SEQUENCE TAG; GENE LIBRARY; GENETIC DATABASE; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGOCHAETA; SEQUENCE ANALYSIS; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; UNINDEXED SEQUENCE; ANIMAL; BIOLOGY; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA MICROARRAY; DNA SEQUENCE; GENETICS; INTERNET; MOLECULAR GENETICS;

ENCHYTRAEIDAE; ENCHYTRAEUS ALBIDUS;

COMPLEMENTARY DNA; HEAVY METAL; PESTICIDE;

ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; INTERNET; METALS, HEAVY; MICROARRAY ANALYSIS; MOLECULAR SEQUENCE DATA; OLIGOCHAETA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PESTICIDES; SEQUENCE ANALYSIS, DNA;

EID: 84860441378     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034266     Document Type: Article

References (54)

1. Jeffrey S, Gardi C, Jones A, Montanarella L, Marmo L, et al. (2010) European Atlas of Soil Biodiversity. Luxembourg European Commission, Publications Office of the European Union.
2. ISO, (2004) Soil quality- Effects of pollutants on Enchytraeidae (Enchytraeus sp.)- Determination of effects on reproduction and survival. Guideline no. 16387. ISO (International Organization for Standardization). Geneve, Switzerland.
3. OECD, (2004) Guidelines for the testing of chemicals. Enchytraeid Reproduction Test. No. 220. OECD (Organization for Economic Cooperation and Development). Paris, France.
4. OECD, (2010) Guidelines for the testing of chemicals. Bioaccumulation in Terrestrial Oligochaete. No. 317. OECD (Organization for Economic Cooperation and Development). Paris, France.
5. Amorim MJB, Rombke J, Schallnass HJ, Soares AMVM, (2005) Effect of soil properties and aging on the toxicity of copper for Enchytraeus albidus, Enchytraeus luxuriosus, and Folsomia candida. Environ Toxicol Chem 24: 1875-1885.
6. Lock K, Janssen CR, (2001) Ecotoxicity of mercury to Eisenia fetida, Enchytraeus albidus and Folsomia candida. Biol Fertility Soils 34: 219-221.
7. Novais SC, Soares AMVM, Amorim MJB, (2010) Can avoidance in Enchytraeus albidus be used as a screening parameter for pesticides testing? Chemosphere 79: 233-237.
8. Amorim M, Rombke J, Soares A, (2005) Avoidance behaviour of Enchytraeus albidus: Effects of benomyl, carbendazim, phenmedipham and different soil types. Chemosphere 59: 501-510.
9. Loureiro S, Amorim MJB, Campos B, Rodrigues SMG, Soares AMVM, (2009) Assessing joint toxicity of chemicals in Enchytraeus albidus (Enchytraeidae) and Porcellionides pruinosus (Isopoda) using avoidance behaviour as an endpoint. Environ Pollut 157: 625-636.
10. Dodard SG, Sunahara GI, Kuperman RG, Sarrazin M, Gong P, et al. (2005) Survival and reproduction of enchytraeid worms, oligochaeta, in different soil types amended with energetic cyclic nitramines. Environ Toxicol Chem 24: 2579-2587.
11. Lock K, Janssen CR, (2001) Effect of clay and organic matter type on the ecotoxicity of zinc and cadmium to the potworm Enchytraeus albidus. Chemosphere 44: 1669-1672.
12. Amorim MJB, Novais S, Römbke J, Soares AMVM, (2008) Avoidance test with Enchytraeus albidus (Enchytraeidae): Effects of different exposure time and soil properties. Environ Pollut 155: 112-116.
13. Nota B, Timmermans MJTN, Franken C, Montagne-Wajer K, Marien J, et al. (2008) Gene expression analysis of collembola in cadmium containing soil. Environ Sci Technol 42: 8152-8157.
14. Heckmann LH, Sibly RM, Connon R, Hooper HL, Hutchinson TH, et al. (2008) Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna. Genome Biology 6: 25.
15. Nota B, Bosse M, Ylstra B, van Straalen NM, Roelofs D, (2009) Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene. BMC Genomics 10: 236.
16. Amorim MJB, Novais SC, Van der Ven K, Vandenbrouck T, Soares AMVM, et al. (2011) Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications. Environ Toxicol Chem 30: 1395-1402.
17. Poynton HC, Varshavsky JR, Chang B, Cavigiolio G, Chan S, et al. (2007) Daphnia magna ecotoxicogenomics provides mechanistic insights into metal toxicity. Environ Sci Technol 41: 1044-1050.
18. Owen J, Hedley BA, Svendsen C, Wren J, Jonker MJ, et al. (2008) Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics 9: 266.
19. Pirooznia M, Gong P, Guan X, Inouye L, Yang K, et al. (2007) Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. BMC Bioinformatics 8: S7.
20. Timmermans MJ, de Boer ME, Nota B, de Boer TE, Marien J, et al. (2007) Collembase: a repository for springtail genomics and soil quality assessment. BMC Genomics 8: 341.
21. Novais SC, Howcroft CF, Carreto L, Pereira PM, Santos MAS, et al. (2012) Differential gene expression analysis in Enchytraeus albidus exposed to natural and chemical stressors at different exposure periods. Ecotoxicology 21: 213-224.
22. Gomes SIL, Novais SC, Scott-Fordsmand JJ, de Coen W, Soares AMVM, et al. (2012) Effect of Cu-Nanoparticles versus Cu-salt in Enchytraeus albidus (Oligochaeta): differential gene expression through microarray analysis. Comparative Biochemistry and Physiology- Part C: Toxicology & Pharmacology 155: 219-227.
23. Gomes SIL, Novais SC, Soares AMVM, Amorim MJB, (2011) Effects of soil properties and time of exposure on gene expression of Enchytraeus albidus (Oligochaeta). Soil Biol Biochem 43: 2078-2084.
24. Diatchenko L, Lau YFC, Campbell AP, Chenchik A, Moqadam F, et al. (1996) Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A 93: 6025-6030.
25. Diatchenko L, Lukyanov S, Lau Y-FC, Siebert PD, (1999) Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes. Methods Enzymol 303: 349-380.
26. Løkke H, van Gestel CAM, (1998) Handbook of soil invertebrate toxicity tests. Chichester Wiley & Sons Ltd.
27. Novais SC, Gomes SIL, Gravato C, Guilhermino L, de Coen W, et al. (2011) Reproduction and biochemical responses in Enchytraeus albidus (Oligochaeta) to zinc or cadmium exposures. Environ Pollut 159: 1836-1843.
28. Lock K, Janssen CR, (2002) Ecotoxicity of nickel to Eisenia fetida, Enchytraeus albidus and Folsomia candida. Chemosphere 46: 197-200.
29. Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD, (2001) Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30: 892-897.
30. Rebrikov DV, Britanova OV, Gurskaya NG, Lukyanov KA, Tarabykin VS, et al. (2000) Mirror orientation selection (MOS): a method for eliminating false positive clones from libraries generated by suppression subtractive hybridization. Nucl Acids Res 28: e90.
31. Werle E, Schneider C, Renner M, Volker M, Fiehn W, (1994) Convenient single-step, one tube purification of PCR products for direct sequencing. Nucleic Acids Res 22: 4354-4355.
32. Lee MS, Cho SJ, Tak ES, Lee JA, Cho HJ, et al. (2005) Transcriptome analysis in the midgut of the earthworm (Eisenia andrei) using expressed sequence tags. Biochem Biophys Res Commun 328: 1196-1204.
33. Altschul S, Gish W, Miller W, Meyers E, Lipman D, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
34. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
35. Sturzenbaum SR, Parkinson J, Blaxter M, Morgan AJ, Kille P, et al. (2003) The earthworm Expressed Sequence Tag project. Pedobiologia 47: 447-451.
36. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27: 29-34.
37. Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, et al. (2004) PartiGene-constructing partial genomes. Bioinformatics 20: 1398-1404.
38. Deng W, Nickle DC, Learn GH, Maust B, Mullins JI, (2007) ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics 23: 2334-2336.
39. Gertz EM, (2005) BLAST Scoring Parameters.
40. Holmstrup M, Sorensen JG, Overgaard J, Bayley M, Bindesbol AM, et al. (2011) Body metal concentrations and glycogen reserves in earthworms (Dendrobaena octaedra) from contaminated and uncontaminated forest soil. Environ Pollut 159: 190-197.
41. Posthuma L, Van Straalen NM, (1993) Heavy-metal adaptation in terrestrial invertebrates- a review of occurrence, genetics, physiology and ecological consequences. Comparative Biochemistry and Physiology C-Pharmacology Toxicology & Endocrinology 106: 11-38.
42. Timmermans MJTN, Ellers J, Roelofs D, Van Straalen NM, (2005) Metallothionein mRNA expression and cadmium tolerance in metal-stressed and reference populations of the springtail Orchesella cincta. Ecotoxicology 14: 727-739.
43. Schill RO, Kohler HR, (2004) Energy reserves and metal-storage granules in the Hepatopancreas of Oniscus asellus and Porcellio scaber (Isopoda) from a metal gradient at Avonmouth, UK. Ecotoxicology 13: 787-796.
44. Vijver MG, Van Gestel CAM, Lanno RP, Van Straalen NM, Peijnenburg WJGM, (2004) Internal metal sequestration and its ecotoxicological relevance: A review. Environ Sci Technol 38: 4705-4712.
45. Roelofs D, Marien J, van Straalen NM, (2007) Differential gene expression profiles associated with heavy metal tolerance in the soil insect Orchesella cincta. Insect Biochem Mol Biol 37: 287-295.
46. Roelofs D, Janssens TKS, Timmermans MJTN, Nota B, Marien J, et al. (2009) Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta. Mol Ecol 18: 3227-3239.
47. Maraldo K, Ravn H, Slotsbo S, Holmstrup M, (2009) Responses to acute and chronic desiccation stress in Enchytraeus (Oligochaeta: Enchytraeidae). Journal of Comparative Physiology B-Biochemical Systemic and Environmental Physiology 179: 113-123.
48. Maraldo K, Holmstrup M, (2010) Enchytraeids in a changing climate: A mini-review. Pedobiologia 53: 161-167.
49. Slotsbo S, Maraldo K, Malmendal A, Nielsen NC, Holmstrup M, (2008) Freeze tolerance and accumulation of cryoprotectants in the enchytraeid Enchytraeus albidus (Oligochaeta) from Greenland and Europe. Cryobiology 57: 286-291.
50. Clark MS, Thorne MAS, Purac J, Grubor-Lajsic G, Kube M, et al. (2007) Surviving extreme polar winters by desiccation: clues from Arctic springtail (Onychiurus arcticus) EST libraries. BMC Genomics 8: 475.
51. Timmermans MJTN, Roelofs D, Nota B, Ylstra B, Holmstrup M, (2009) Sugar sweet springtails: on the transcriptional response of Folsomia candida (Collembola) to desiccation stress. Insect Mol Biol 18: 737-746.
52. de Boer TE, Holmstrup M, van Straalen NM, Roelofs D, (2010) The effect of soil pH and temperature on Folsomia candida transcriptional regulation. J Insect Physiol 56: 350-355.
53. de Boer TE, Birlutiu A, Bochdanovits Z, Timmermans MJTN, Dijkstra TMH, et al. (2011) Transcriptional plasticity of a soil arthropod across different ecological conditions. Mol Ecol 20: 1144-1154.
54. Amorim MJB, Novais S, Römbke J, Soares AMVM, (2008) Enchytraeus albidus (Enchytraeidae): A test organism in a standardised avoidance test? Effects of different chemical substances. Environ Int 34: 363-371.