Development and Experimental Validation of a 20K Atlantic Cod (Gadus morhua) Oligonucleotide Microarray Based on a Collection of over 150,000 ESTs

Marine Biotechnology

Volumn 13, Issue 4, 2011, Pages 733-750

  Booman, Marije ^a   Borza, Tudor ^b   Feng, Charles Y ^a   Hori, Tiago S ^a   Higgins, Brent ^b   Culf, Adrian ^c   Léger, Daniel ^c   Chute, Ian C ^c   Belkaid, Anissa ^c   Rise, Marlies ^a,b   Gamperl, A Kurt ^a   Hubert, Sophie ^b   Kimball, Jennifer ^d   Ouellette, Rodney J ^c   Johnson, Stewart C ^e   Bowman, Sharen ^b   Rise, Matthew L ^a  

^a MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

^b Genome Atlantic   (Canada)

^c ATLANTIC CANCER RESEARCH INSTITUTE   (Canada)

^d NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^e PACIFIC BIOLOGICAL STATION   (Canada)

Author keywords

Aquaculture; Atlantic cod; Gene expression profiling; Microarray

Indexed keywords

AEROMONAS SALMONICIDA; ATLANTIC COD; BROAD SPECTRUM; CDNA LIBRARIES; DEVELOPMENT PROJECT; DEVELOPMENTAL STAGE; EXPERIMENTAL VALIDATIONS; EXPRESSED SEQUENCE TAGS; FUNCTIONAL GENOMICS; GENE EXPRESSION PROFILES; GENE EXPRESSION PROFILING; GENOMICS; IMMUNE RESPONSE; INNATE IMMUNE RESPONSE; OLIGONUCLEOTIDE MICROARRAY; QUANTITATIVE PCR; SUPPRESSION SUBTRACTIVE HYBRIDIZATION;

AQUACULTURE; FORMALDEHYDE; IMMUNOLOGY; INTERNET PROTOCOLS; LIBRARIES; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; TISSUE;

GENE EXPRESSION;

PRIMER DNA;

BACTERIUM; BIOTECHNOLOGY; BROOD STOCK; ENVIRONMENTAL STRESS; GADOID; GADOID FISHERY; GENE EXPRESSION; GENETIC ANALYSIS; GENOMICS; IMMUNE RESPONSE; NUCLEIC ACID; PATHOGEN; POLYMERASE CHAIN REACTION; PROBE; WILD POPULATION;

AEROMONAS SALMONICIDA; ANIMAL; ARTICLE; ATLANTIC COD; DNA MICROARRAY; EVALUATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; GENOMICS; IMMUNOLOGY; INNATE IMMUNITY; MASS SPECTROMETRY; METHODOLOGY; NODAVIRUS; OLIGONUCLEOTIDE PROBE; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPLEEN;

AEROMONAS SALMONICIDA; ANIMALS; DNA PRIMERS; EXPRESSED SEQUENCE TAGS; GADUS MORHUA; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOMICS; IMMUNITY, INNATE; MASS SPECTROMETRY; NODAVIRIDAE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPLEEN;

AEROMONAS SALMONICIDA; GADUS MORHUA;

EID: 79960453749     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-010-9335-6     Document Type: Article

References (47)

1. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573-580.
2. Borza T, Stone C, Gamperl AK, Bowman S (2009) Atlantic cod (Gadus morhua) hemoglobin genes: multiplicity and polymorphism. BMC Genet 10: 51.
3. Borza T, Stone C, Rise ML, Bowman S, Johnson SC (2010) Atlantic cod (Gadus morhua) CC chemokines: diversity and expression analysis. Dev Comp Immunol 34: 904-913.
4. Bowman S, Hubert S, Higgins B, Stone C, Kimball J, Borza T, Bussey JT, Simpson G, Kozera C, Curtis BA, Hall JR, Hori TS, Feng CY, Rise M, Booman M, Gamperl AK, Trippel E, Symonds J, Johnson SC, Rise ML (2010) An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua). Mar Biotechnol (NY). doi: 10. 1007/s10126-010-9285-z.
5. Bø TH, Dysvik B, Jonassen I (2004) LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Research 32: e34.
6. Brown JA, Minkoff G, Puvanendran V (2003) Larviculture of Atlantic cod (Gadus morhua): progress, protocols and problems. Aquaculture 227: 357-372.
7. Caipang CM, Lazado CC, Brinchmann MF, Kiron V (2010) Infection-induced changes in expression of antibacterial and cytokine genes in the gill epithelial cells of Atlantic cod, Gadus morhua during incubation with bacterial pathogens. Comp Biochem Physiol B Biochem Mol Biol 156: 319-325.
8. Celton M, Malpertuy A, Lelandais G, de Brevern AG (2010) Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. BMC Genomics 11: 15.
9. Edvardsen RB, Malde K, Mittelholzer C, Taranger GL, Nilsen F (2010) EST resources and establishment and validation of a 16k cDNA microarray from Atlantic cod (Gadus morhua). Comp Biochem Physiol Part D Genomics Proteomics. doi: 10. 1016/j. cbd. 2010. 06. 002.
10. Ewart KV, Belanger JC, Williams J, Karakach T, Penny S, Tsoi SC, Richards RC, Douglas SE (2005) Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology. Dev Comp Immunol 29: 333-347.
11. Fast MD, Johnson SC, Jones SR (2007) Differential expression of the pro-inflammatory cytokines IL-1beta-1, TNFalpha-1 and IL-8 in vaccinated pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon juveniles. Fish Shellfish Immunol 22: 403-407.
12. Feng CY, Johnson SC, Hori TS, Rise M, Hall JR, Gamperl AK, Hubert S, Kimball J, Bowman S, Rise ML (2009) Identification and analysis of differentially expressed genes in immune tissues of Atlantic cod stimulated with formalin-killed, atypical Aeromonas salmonicida. Physiol Genomics 37: 149-163.
13. Gollock MJ, Currie S, Petersen LH, Gamperl AK (2006) Cardiovascular and haematological responses of Atlantic cod (Gadus morhua) to acute temperature increase. J Exp Biol 209: 2961-2970.
14. Gudmundsdóttir S, Magnadóttir B, Björnsdóttir B, Arnadóttir H, Gudmundsdóttir BK (2009) Specific and natural antibody response of cod juveniles vaccinated against Vibrio anguillarum. Fish Shellfish Immunol 26: 619-624.
15. Halden Y, Rek A, Atzenhofer W, Szilak L, Wabnig A, Kungl AJ (2004) Interleukin-8 binds to syndecan-2 on human endothelial cells. Biochem J 377: 533-538.
16. Hansen T, Karlsen O, Taranger GL, Hemre GI, Holm JC, Kjesbu OS (2001) Growth, gonadal development and spawning time of Atlantic cod (Gadus morhua) reared under different photoperiods. Aquaculture 203: 51-67.
17. Hori TS, Gamperl AK, Afonso LO, Johnson SC, Hubert S, Kimball J, Bowman S, Rise ML (2010) Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques. BMC Genomics 11: 72.
18. Hubert S, Higgins B, Borza T, Bowman S (2010) Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics 11: 191.
19. Inagawa H, Honda T, Kohchi C, Nishizawa T, Yoshiura Y, Nakanishi T, Yokomizo Y, Soma G (2002) Cloning and characterization of the homolog of mammalian lipopolysaccharide-binding protein and bactericidal permeability-increasing protein in rainbow trout Oncorhynchus mykiss. J Immunol 168: 5638-5644.
20. Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T, Nederbragt AJ, Stenseth NC, Jakobsen KS (2009) Large-scale sequence analyses of Atlantic cod. N Biotechnol 25: 263-271.
21. Koski LB, Gray MW, Lang BF, Burger G (2005) AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 6: 151.
22. Lie KK, Lanzen A, Breilid H, Olsvik PA (2009) Gene expression profiling in Atlantic cod (Gadus morhua L.) from two contaminated sites using a custom-made cDNA microarray. Environ Toxicol Chem 28: 1711-1721.
23. Lucas PC, Yonezumi M, Inohara N, McAllister-Lucas LM, Abazeed ME, Chen FF, Yamaoka S, Seto M, Nunez G (2001) Bcl10 and MALT1, independent targets of chromosomal translocation in malt lymphoma, cooperate in a novel NF-kappa B signaling pathway. J Biol Chem 276: 19012-19019.
24. Lucas PC, McAllister-Lucas LM, Nunez G (2004) NF-kappaB signaling in lymphocytes: a new cast of characters. J Cell Sci 117: 31-39.
25. Lund V, Børdal S, Kjellsen O, Mikkelsen H, Schrøder MB (2006) Comparison of antibody responses in Atlantic cod (Gadus morhua L.) to Aeromonas salmonicida and Vibrio anguillarum. Dev Comp Immunol 30: 1145-1155.
26. Lund V, Børdal S, Schrøder MB (2007) Specificity and durability of antibody responses in Atlantic cod (Gadus morhua L.) immunised with Vibrio anguillarum O2b. Fish Shellfish Immunol 23: 906-910.
27. Magnadottir B, Gudmundsdottir S, Gudmundsdottir BK, Helgason S (2009) Natural antibodies of cod (Gadus morhua L.): specificity, activity and affinity. Comp Biochem Physiol B Biochem Mol Biol 154: 309-316.
28. Martin SA, Blaney SC, Houlihan DF, Secombes CJ (2006) Transcriptome response following administration of a live bacterial vaccine in Atlantic salmon (Salmo salar). Mol Immunol 43: 1900-1911.
29. Martin D, Galisteo R, Gutkind JS (2009) CXCL8/IL8 stimulates vascular endothelial growth factor (VEGF) expression and the autocrine activation of VEGFR2 in endothelial cells by activating NFkappaB through the CBM (Carma3/Bcl10/Malt1) complex. J Biol Chem 284: 6038-6042.
30. Miller KM, Kaukinen KH, Schulze AD (2002) Expansion and contraction of major histocompatibility complex genes: a teleostean example. Immunogenetics 53: 941-963.
31. Mulder IE, Wadsworth S, Secombes CJ (2007) Cytokine expression in the intestine of rainbow trout (Oncorhynchus mykiss) during infection with Aeromonas salmonicida. Fish Shellfish Immunol 23: 747-759.
32. Park KC, Osborne JA, Tsoi SC, Brown LL, Johnson SC (2005) Expressed sequence tags analysis of Atlantic halibut (Hippoglossus hippoglossus) liver, kidney and spleen tissues following vaccination against Vibrio anguillarum and Aeromonas salmonicida. Fish Shellfish Immunol 18: 393-415.
33. Persson AC, Stet RJ, Pilström L (1999) Characterization of MHC class I and beta(2)-microglobulin sequences in Atlantic cod reveals an unusually high number of expressed class I genes. Immunogenetics 50: 49-59.
34. Pérez-Casanova JC, Rise ML, Dixon B, Afonso LO, Hall JR, Johnson SC, Gamperl AK (2008) The immune and stress responses of Atlantic cod to long-term increases in water temperature. Fish Shellfish Immunol 24: 600-609.
35. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research 29: e45.
36. Pilstrom L, Warr GW, Stromberg S (2005) Why is the antibody response of Atlantic cod so poor? The search for a genetic explanation. Fisheries Science 71: 961-971.
37. Rise ML, Hall J, Rise M, Hori T, Gamperl AK, Kimball J, Hubert S, Bowman S, Johnson SC (2008) Functional genomic analysis of the response of Atlantic cod (Gadus morhua) spleen to the viral mimic polyriboinosinic polyribocytidylic acid (pIC). Dev Comp Immunol 32: 916-931.
38. Rise ML, Liu Z, Douglas SE, Brown LL, Nash JHE, McFall-Ngai MJ (2009) Aquaculture-related applications of DNA microarray technology. In: Overturf K (ed) Molecular research in aquaculture. Blackwell, Ames, pp 63-101.
39. Rise ML, Hall JR, Rise M, Hori TS, Browne MJ, Gamperl AK, Hubert S, Kimball J, Bowman S, Johnson SC (2010) Impact of asymptomatic nodavirus carrier state and intraperitoneal viral mimic injection on brain transcript expression in Atlantic cod (Gadus morhua). Physiol Genomics 42: 266-280.
40. Rorabacher DB (1991) Statistical treatment for rejection of deviant values: critical values of Dixon's "Q" parameter and related subrange ratios at the 95% confidence level. Anal Chem 63: 139-146.
41. Samuelsen OB, Nerland AH, Jørgensen T, Schrøder MB, Svåsand T, Bergh O (2006) Viral and bacterial diseases of Atlantic cod Gadus morhua, their prophylaxis and treatment: a review. Dis Aquat Organ 71: 239-254.
42. Schultz H, Weiss JP (2007) The bactericidal/permeability-increasing protein (BPI) in infection and inflammatory disease. Clin Chim Acta 384: 12-23.
43. Schwender H, Krause A, Ickstadt K (2006) Identifying interesting genes with siggenes. RNews 6: 45-50.
44. Solem ST, Stenvik J (2006) Antibody repertoire development in teleosts-a review with emphasis on salmonids and Gadus morhua L. Dev Comp Immunol 30: 57-76.
45. Stenvik J, Solstad T, Strand C, Leiros I, TØ JT (2004) Cloning and analyses of a BPI/LBP cDNA of the Atlantic cod (Gadus morhua L.). Dev Comp Immunol 28: 307-323.
46. Sturn A, Quackenbush J, Trajanoski Z (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18: 207-208.
47. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121.