Whole-genome transcriptional profiles of a novel marine fish iridovirus, Singapore grouper iridovirus (SGIV) in virus-infected grouper spleen cell cultures and in orange-spotted grouper, Epinephulus coioides

Virology

Volumn 377, Issue 1, 2008, Pages 39-48

  Teng, Yong ^a   Hou, Zhiwei ^a   Gong, Jie ^a   Liu, Hong ^b   Xie, Xiayang ^c   Zhang, Liang ^d   Chen, Xiaohong ^d   Qin, Qi Wei ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b Shenzhen Exit and Entry Inspection and Quarantine Bureau   (China)

^c MEDICAL COLLEGE OF GEORGIA   (United States)

^d NATIONAL ENGINEERING RESEARCH CENTER FOR BEIJING BIOCHIP TECHNOLOGY   (China)

Author keywords

cDNA microarrays; Expression pattern; Grouper; SGIV; Temporal kinetic class; Transcriptional profiles

Indexed keywords

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; DNA REPLICATION; EPINEPHULUS COIOIDES; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOME; IN VITRO STUDY; IRIDOVIRUS; NONHUMAN; OPEN READING FRAME; PERCIFORMES; PRIORITY JOURNAL; PROTEIN SYNTHESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SINGAPORE GROUPER IRIDOVIRUS; SPLEEN CELL; VIRUS GENE; VIRUS INFECTION;

ANIMALS; BASE SEQUENCE; BASS; CELLS, CULTURED; DNA PRIMERS; DNA VIRUS INFECTIONS; DNA, VIRAL; FISH DISEASES; GENE EXPRESSION PROFILING; GENOME, VIRAL; IRIDOVIRUS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TIME FACTORS;

EPINEPHELINAE; EPINEPHELUS COIOIDES; IRIDOVIRUS; SINGAPORE GROUPER IRIDOVIRUS;

EID: 44949090369     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2008.04.011     Document Type: Article

References (29)

1. Aguilar J.S., Devi-Rao G.V., Rice M.K., Sunabe J., Ghazal P., and Wagner E.K. Quantitative comparison of the HSV-1 and HSV-2 transcriptomes using DNA microarray analysis. Virology 348 (2006) 233-241
2. Ahne W.H.J., Schlotfeldt H.J., and Thomsen I. Fish viruses: isolation of an icosahedral cytoplasmic deoxyribovirus from sheatfish (Silurus glanis). J. Vet. Med. 36 (1989) 333-336
3. Cawley G.C., and Talbot N.L. Gene selection in cancer classification using sparse logistic regression with Bayesian regularization. Bioinformatics. 22 (2006) 2348-2355
4. Chen L.M., Wang F., Song W., and Hew C.L. Temporal and differential gene expression of Singapore grouper iridovirus. J. Gen. Virol. 87 (2006) 2907-2915
5. Chinchar V.G., Essbauer S., He J.G., Hyatt A., Miyazaki T., Seligy D., and Williams T. In: Fauqet C.M., Mayo M.A., Maniloff J., Desselberger U., and Ball L.A. (Eds). Iridovirade. Virus Taxonomy, VIIIth Report of the International Committee on Taxonomy of Viruses (2005), Academic Press, London 163-175
6. D'Costa S.M., Yao H.J., and Bilimoria S.L. Transcription and temporal cascade in Chilo iridescent virus infected cells. Arch. Virol. 146 (2001) 2165-2178
7. Gibson-Kueh S., Netto P., Ngoh-Lim G.H., Chang S.F., Ho L.L., Qin Q.W., Chua F.H., Ng M.L., and Ferguson H.W. The pathology of systemic iridoviral disease in fish. J. Comp. Pathol. 129 (2003) 111-119
8. Hsu A.L., Tang S.L., and Halgamuge S.K. An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data. Bioinformatics 19 (2003) 2131-2140
9. Huang C., Zhang X., Gin K.Y., and Qin Q.W. In situ hybridization of a marine fish virus, Singapore grouper iridovirus with a nucleic acid probe of major capsid protein. J. Virol. Methods 117 (2004) 123-128
10. Hyatt A.D., Gould A.R., Zupanovic Z., Cummingham A.A., Hengstberger S., Whittington R.J., Kattenbelt J., and Coupar B.E.H. Comparative studies of piscine and amphibian iridoviruses. Arch. Virol. 145 (2000) 301-331
11. Khadijah S., Neo S.Y., Hossain M.S., Miller L.D., Mathavan S., and Kwang J. Identification of white spot syndrome virus latency-related genes in specific-pathogen-free shrimps by use of a microarray. J. Virol. 77 (2003) 10162-10167
12. Lua D.T., Yasuike M., Hirono I., and Aoki T. Transcription program of red sea bream iridovirus as revealed by DNA microarrays. J. Virol. 79 (2005) 15151-15164
13. Lua D.T., Yasuike M., Hirono I., Kondo H., and Aoki T. Transcriptional profile of red seabream iridovirus in a fish model as revealed by viral DNA microarrays. Virus genes 35 (2007) 449-461
14. Marks H., Vorst O., van Houwelingen A.M., van Hulten M.C., and Vlak J.M. Gene-expression profiling of White spot syndrome virus in vivo. J. Gen. Virol. 86 (2005) 2081-2100
15. Martinez-Guzman D., Rickabaugh T., Wu T.T., Brown H., Cole S., Song M.J., Tong L., and Sun R. Transcription program of murine gammaherpesvirus 68. J. Virol. 77 (2003) 10488-10503
16. Nakano K., Sakaguchi Y., Isotani R., and Ohmori T. Self-organizing system obtaining communication ability. Primitive model for language generation. Biol. Cybern. 58 (1988) 417-425
17. Paulose-Murphy M., Ha N.K., Xiang C., Chen Y., Gillim L., Yarchoan R., Meltzer P., Bittner M., Trent J., and Zeichner S. Transcription program of human herpesvirus 8 (kaposi's sarcoma-associated herpesvirus). J. Virol. 75 (2001) 4843-4853
18. Piaskoski T.O., and Plumb J.A. Characterization of the largemouth bass virus in cell culture. J. Aquat. Anim. Health 11 (1999) 45-51
19. Qin Q.W., Lam T.J., Sin Y.M., Shen H., Chang S.F., Ngoh G.H., and Chen C.L. Electron microscopic observations of a marine fish iridovirus isolated from brown-spotted grouper, Epinephelus tauvina. J. Virol. Methods 98 (2001) 17-24
20. Qin Q.W., Chang S.F., Ngoh-Lim G.H., Gibson-Kueh S., Shi C., and Lam T.J. Characterization of a novel ranavirus isolated from grouper Epinephelus tauvina. Dis. Aquat. Organ 53 (2003) 1-9
21. Qin Q.W., Wu T.H., Jia T.L., Hegde A., and Zhang R.Q. Development and characterization of a new tropical marine fish cell line from grouper, Epinephelus coioides susceptible to iridovirus and nodavirus. J. Virol. Methods 131 (2006) 58-64
22. Reed L.J., and Muench H. A simple method of estimating fifty percent end points. Am. J. Hyg. 27 (1938) 493-497
23. Smith L., Underhill P., Pritchard C., Tymowska-Lalanne Z., bdul-Hussein S., Hilton H., Winchester L., Williams D., Freeman T., Webb S., and Greenfield A. Single primer amplification (SPA) of cDNA for microarray expression analysis. Nucleic Acids Res. 31 (2003) e9
24. Song W.J., Qin Q.W., Qiu J., Huang C.H., Wang F., and Hew C.L. Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis. J. Virol. 78 (2004) 12576-12590
25. Song W., Lin Q., Joshi S.B., Lim T.K., and Hew C.L. Proteomic studies of the Singapore grouper iridovirus. Mol. Cell Proteomics 5 (2006) 256-264
26. Stingley S.W., Ramirez J.J., Aguilar S.A., Simmen K., Sandri-Goldin R.M., Ghazal P., and Wagner E.K. Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray. J. Virol. 74 (2000) 9916-9927
27. Von K.A., and Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 22 (2006) 1930-1931
28. Wang Y.Q., Lu L., Weng S.P., Huang J.N., Chan S.M., and He J.G. Molecular epidemiology and phylogenetic analysis of a marine fish infectious spleen and kidney necrosis virus-like (ISKNV-like) virus. Arch. Virol. 152 4 (2007) 763-773
29. Ye R.W., Wang T., Bedzyk L., and Croker K.M. Applications of DNA microarrays in microbial systems. J. Microbiol. Methods 47 (2001) 257-272