Reference genes for QRT-PCR tested under various stress conditions in Folsomia candida and Orchesella cincta (Insecta, Collembola)

BMC Molecular Biology

Volumn 10, Issue , 2009, Pages

  de Boer, Muriel E ^a   de Boer, Tjalf E ^a   Mariën, Janine ^a   Timmermans, Martijn J T N ^a,b   Nota, Benjamin ^a   van Straalen, Nico M ^a   Ellers, Jacintha ^a   Roelofs, Dick ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ALPHA TUBULIN; BETA ACTIN; CADMIUM; CHAPERONE; CYCLOPHILIN A; ELONGATION FACTOR 1ALPHA; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HEAT SHOCK PROTEIN 70; INITIATION FACTOR 1A; INITIATION FACTOR 5A; METALLOTHIONEIN; RNA 28S; SUCCINATE DEHYDROGENASE; TYROSINE 3 MONOOXYGENASE; UBIQUITIN CONJUGATING ENZYME;

ARTICLE; CHEMICAL STRESS; CONTROLLED STUDY; DESICCATION; ENVIRONMENTAL EXPOSURE; FOLSOMIA CANDIDA; GLYCOLYSIS; HEAT SHOCK; NONHUMAN; NUCLEOTIDE SEQUENCE; ORCHESELLA CINCTA; PHYSICAL STRESS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS; REFERENCE DATABASE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SOIL ORGANISM; STARVATION; TEMPERATURE DEPENDENCE; ANIMAL; ECOLOGY; GENE; GENETICS; INSECT; PHYSIOLOGICAL STRESS; PHYSIOLOGY; SOIL; STANDARD;

COLLEMBOLA; EUKARYOTA; FOLSOMIA CANDIDA; INSECTA; ORCHESELLA CINCTA;

ANIMALS; ECOLOGY; GENES, INSECT; INSECTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SOIL; STRESS, PHYSIOLOGICAL;

EID: 67650917116     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-10-54     Document Type: Article

References (44)

1. Morrison T Hurley J Garcia J Yoder K Katz A Roberts D Cho J Kanigan T Ilyin SE Horowitz D Dixon JM Brenan C Nanoliter high throughput quantitative PCR Nucleic Acids Res 2006, 34(18):.
2. Snell TW Brogdon SE Morgan MB Gene Expression Profiling in Ecotoxicology Ecotoxicology 2003, 12(6):475-483. 10.1023/B:ECTX.0000003033.09923.a8 14680327
3. Ellers J Mariën J Driessen G Van Straalen NM Temperature-induced gene expression associated with different thermal reaction norms for growth rate J Exp Zool 2008, 310B(2):137-147. 10.1002/jez.b.21194
4. Muller WEG Grebenjuk VA Thakur NL Thakur AN Batel R Krasko A Muller IM Breter HJ Oxygen-controlled bacterial growth in the sponge Suberites domuncula: Toward a molecular understanding of the symbiotic relationships between sponge and bacteria Appl Environ Microbiol 2004, 70(4):2332-2341. 383090 15066829 10.1128/AEM.70.4.2332-2341.2004
5. Scharf ME Wu-Scharf D Pittendrigh BR Bennett GW Caste- and development-associated gene expression in a lower termite Genome Biol 2003, 4(10):11. 10.1186/gb-2003-4-10-r62
6. Zientz E Beyaert N Gross R Feldhaar H Relevance of the endosymbiosis of Blochmannia floridanus and carpenter ants at different stages of the life cycle of the host Appl Environ Microbiol 2006, 72(9):6027-6033. 1563639 16957225 10.1128/AEM.00933-06
7. Roelofs D Mariën J Van Straalen NM Differential gene expression profiles associated with heavy metal tolerance in the soil insect Orchesella cincta Insect Biochem Mol Biol 2007, 37(4):287-295. 10.1016/ j.ibmb.2006.11.013 17368192
8. Bustin SA Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): Trends and problems J Mol Endocrinol 2002, 29(1):23-39. 10.1677/jme.0.0290023 12200227
9. Applied_Biosystems Comparative CT Method (Separate Tubes) User Bulletin 2: Rev. B ABI Prism 7700 Sequence Detection System 2001, 2:11-15.
10. Pfaffl MW A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Res 2001, 29(9):2002-2007. 10.1093/nar/ 29.9.e45
11. Huggett J Dheda K Bustin S Zumla A Real-time RT-PCR normalisation; strategies and considerations Genes Immun 2005, 6(4):279-284. 10.1038/ sj.gene.6364190 15815687
12. Heckmann L-H Connon R Hutchinson T Maund S Sibly R Callaghan A Expression of target and reference genes in Daphnia magna exposed to ibuprofen BMC Genomics 2006, 7(1):175. 1523214 16827938 10.1186/ 1471-2164-7-175
13. Bas A Forsberg G Hammarstrom S Hammarstrom ML Utility of the Housekeeping Genes 18S rRNA, beta-Actin and Glyceraldehyde-3-Phosphate-Dehydrogenase for Normalization in Real-Time Quantitative Reverse Transcriptase-Polymerase Chain Reaction Analysis of Gene Expression in Human T Lymphocytes Scand J Immunol 2004, 59(6):566-573. 10.1111/j.0300-9475.2004.01440.x 15182252
14. Zhong H Simons JW Direct Comparison of GAPDH, beta-Actin, Cyclophilin, and 28S rRNA as Internal Standards for Quantifying RNA Levels under Hypoxia Biochem Biophys Res Commun 1999, 259(3):523-526. 10.1006/ bbrc.1999.0815 10364451
15. Vandesompele J De Preter K Pattyn F Poppe B Van Roy N De Paepe A Speleman F Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Genome Biol 2002, 3(7):rEsearch0034.0031 research0034.0011 10.1186/ gb-2002-3-7-research0034
16. Andersen CL Jensen JL Orntoft TF Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets Cancer Res 2004, 64(15):5245-5250. 10.1158/ 0008-5472.CAN-04-0496 15289330
17. Bergkvist A Forootan A Zoric N Strombom L Sjoback R Kubista M Choosing a Normalization Strategy for RT-PCR Genet Eng Biotechn N 2008, 28(13):1.
18. ISO ISO, Soil Quality. Inhibition of Reproduction of Collembola (Folsomia candida). ISO Guideline 11267 International Standardization Organization. Switzerland 1999:16.
19. Fountain MT Hopkin SP Folsomia candida (Collembola): A "standard" soil arthropod Annu Rev Entomol 2005, 50:201-222. 10.1146/annurev.ento.50.071803.130331 15355236
20. Timmermans MJTN De Boer ME Nota B De Boer TE Mariën J Klein-Lankhorst RM Van Straalen NM Roelofs D Collembase: A repository for springtail genomics and soil quality assessment BMC Genomics 2007, 8(341):10. 1783851 17212826
21. Timmermans MJTN Ellers J Van Straalen NM Allelic diversity of metallothionein in Orchesella cincta (L.): Traces of natural selection by environmental pollution Heredity 2007, 98(5):311-319. 10.1038/ sj.hdy.6800942 17314922
22. Nota B Timmermans MJTN Franken O Montagne-Wajer K Mariën J De Boer ME De Boer TE Ylstra B Van Straalen NM Roelofs D Gene Expression Analysis of Collembola in Cadmium Containing Soil Environ Sci Technol 2008, 42(21):8152-8157. 10.1021/es801472r 19031917
23. Bahrndorff S Holmstrup M Petersen H Loeschcke V Geographic variation for climatic stress resistance traits in the springtail Orchesella cincta J Insect Physiol 2006, 52(9):951-959. 10.1016/j.jinsphys.2006.06.005 16928381
24. Liefting M Ellers J Habitat-specific differences in thermal plasticity in natural populations of a soil arthropod Biol J Linn Soc 2008, 94(2):265-271. 10.1111/j.1095-8312.2008.00969.x
25. Roelofs D Overhein L De Boer ME Janssens TKS Van Straalen NM Additive genetic variation of transcriptional regulation: Metallothionein expression in the soil insect Orchesella cincta Heredity 2006, 96(1):85-92. 16304605
26. Spinsanti G Panti C Lazzeri E Marsili L Casini S Frati F Fossi C Selection of reference genes for quantitative RT-PCR studies in striped dolphin (Stenella coeruleoalba) skin biopsies BMC Mol Biol 2006, 7(1):32. 1599742 16984641 10.1186/1471-2199-7-32
27. Sinclair BJ Gibbs AG Roberts SP Gene transcription during exposure to, and recovery from, cold and desiccation stress in Drosophila melanogaster Insect Mol Biol 2007, 16(4):435-443. 10.1111/ j.1365-2583.2007.00739.x 17506850
28. Bustin SA Benes V Nolan T Pfaffl MW Quantitative real-time RT-PCR - a perspective J Mol Endocrinol 2005, 34(3):597-601. 10.1677/jme.1.01755 15956331
29. Stahlberg A Kubista M Pfaffl M Comparison of Reverse Transcriptases in Gene Expression Analysis Clin Chem 2004, 50(9):1678-1680. 10.1373/ clinchem.2004.035469 15331507
30. D'Haese CA Were the first springtails semi-aquatic? A phylogenetic approach by means of 28S rDNA and optimization alignment P Roy Soc Lond B-Bio 2002, 269(1496):1143-1151. 10.1098/rspb.2002.1981
31. Infante C Matsuoka MP Asensio E Canavate JP Reith M Manchado M Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR BMC Mol Biol 2008, 9(28):12. 2263068 18218142
32. Scharlaken B de Graaf DC Goossens K Brunain M Peelman LJ Jacobs FJ Reference gene selection for insect expression studies using quantitative real-time PCR: The head of the honeybee, Apis mellifera, after a bacterial challenge J Insect Sci 2008, 8(33):10.
33. Stürzenbaum SR Kille P Control genes in quantitative molecular biological techniques: The variability of invariance Comp Biochem Physiol B: Biochem Mol Biol 2001, 130(3):281-289. 10.1016/ S1096-4959(01)00440-7 11567890
34. Organisation for Economic Co-operation and Development Test no 207: Earthworm, acute toxicity tests OECD Guidelines for the testing of chemicals OECD: Paris, France; 1984.
35. Bayley M Holmstrup M Water vapor absorption in arthropods by accumulation of myoinositol and glucose Science 1999, 285:5435-1909. 1911 10.1126/science.285.5435.1909 10489369
36. Dröge STJ Paumen ML Bleeker EAJ Kraak MHS Van Gestel CAM Chronic toxicity of polycyclic aromatic compounds to the springtail Folsomia candida and the enchytraeid Enchytraeus crypticus Environ Toxicol Chem 2006, 25(9):2423-2431. 10.1897/05-628R.1 16986798
37. Van Gestel CAM Koolhaas JE Water-extractability, free ion activity, and pH explain cadmium sorption and toxicity to Folsomia candida (Collembola) in seven soil-pH combinations Environ Toxicol Chem 2004, 23(8):1822-1833. 10.1897/03-393 15352469
38. Bahrndorff S Petersen SO Loeschcke V Overgaard J Holmstrup M Differences in cold and drought tolerance of high arctic and sub-arctic populations of Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola) Cryobiology 2007, 55(3):315-323. 10.1016/j.cryobiol.2007.09.001 17959162
39. De Boer ME De Boer TE Nota B Timmermans MJTN Mariën J Roelofs D Van Straalen NM Application of real-time RT-QPCR to develop new biomarkers for soil quality assessment [abstract] Comp Biochem Physiol A Mol Integr Physiol 2008, 151(1):S21-S21. 10.1016/j.cbpa.2008.05.079
40. Bahrndorff S Loeschcke V Marien J Ellers J Dynamics of heat-induced thermal stress resistance and hsp70 expression in the springtail, Orchesella cincta Funct Ecol 2009, 23(2):233-239. 10.1111/ j.1365-2435.2009.01541.x
41. Sørensen JG Kristensen TN Loeschcke V The evolutionary and ecological role of heat shock proteins Ecol Lett 2003, 6(11):1025-1037. 10.1046/j.1461-0248.2003.00528.x
42. Coyle P Philcox JC Carey LC Rofe AM Metallothionein: The multipurpose protein Cell Mol Life Sci 2002, 59(4):627-647. 10.1007/s00018-002-8454-2 12022471
43. MultiD_Analyses_AB GenEx Light Software, version 4.3.5 MultiD Analyses AB Year of release 2008 http://www.multid.se
44. Online Statistics: An Interactive Multimedia Course of Study http://www.onlinestatbook.com