Oligonucleotide microarray technology and its application to mycobacterium avium subsp. Paratuberculosis research

Molecular Biotechnology

Volumn 42, Issue 1, 2009, Pages 30-40

  Pribylova, Radka ^a   Kralik, Petr ^a   Pavlik, Ivo ^a  

^a VETERINARY RESEARCH INSTITUTE   (Czech Republic)

Author keywords

Chip; Crohn's disease; Expression; Genomics; Johne's disease; MAP; Potential zoonosis

Indexed keywords

CHIP; CROHN'S DISEASE; EXPRESSION; GENOMICS; JOHNE'S DISEASE; POTENTIAL ZOONOSIS;

MICROARRAYS; NUCLEIC ACIDS; OLIGONUCLEOTIDES; TECHNOLOGY;

RESEARCH;

BIOLOGICAL MARKER; COMPLEMENTARY DNA; GAMMA INTERFERON; INTERLEUKIN 1ALPHA; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR 1;

BACTERIAL STRAIN; COMPARATIVE GENOMIC HYBRIDIZATION; CROHN DISEASE; DNA HYBRIDIZATION; ENERGY METABOLISM; GENE EXPRESSION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; LIPID METABOLISM; MICROARRAY ANALYSIS; MYCOBACTERIUM AVIUM; MYCOBACTERIUM PARATUBERCULOSIS; NONHUMAN; NORTHERN BLOTTING; OLIGONUCLEOTIDE MICROARRAY TECHNOLOGY; PERIPHERAL BLOOD MONONUCLEAR CELL; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; ANIMAL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; METHODOLOGY; PARATUBERCULOSIS;

MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS;

ANIMALS; CROHN DISEASE; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARATUBERCULOSIS;

EID: 69149083530     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-008-9137-5     Document Type: Review

References (102)

1. HA Johne L Frothingham 1895 Ein eigenthümlicher fall von tuberculose beim rind Deutsche Zeitschrift fur Tiermedicin und Pathologie 21 438 454
2. EJ Manning MT Collins 2001 Mycobacterium avium subsp. paratuberculosis: Pathogen, pathogenesis and diagnosis Review of Science and Technology OIE 20 133 150 1:STN:280:DC%2BD3M7pvFKlsQ%3D%3D
3. Hermon-Taylor, J., & El-Zaatari, F. A. K. (2004). The Mycobacterium avium subspecies paratuberculosis problem and its relation to the causation of Crohn disease. In S. Pedley, J. Bartram, G. Rees, A. Dufour, & J. A. Cotruvo (Eds.), Pathogenic mycobacteria water: A guide to public health consequences, monitoring, management (pp. 74-94). London, UK: IWA Publishing.
4. IR Grant 2005 Zoonotic potential of Mycobacterium avium ssp paratuberculosis: The current position Journal of Applied Microbiology 98 1282 1293 10.1111/j.1365-2672.2005.02598.x 10.1111/j.1365-2672.2005.02598.x 1:STN:280:DC%2BD2M3nsVentA%3D%3D (Pubitemid 40813515)
5. J Hermon-Taylor T Bull 2002 Crohn's disease caused by Mycobacterium avium subspecies paratuberculosis: A public health tragedy whose resolution is long overdue Journal of Medical Microbiology 51 3 6 (Pubitemid 34060125)
6. TJ Bull EJ McMinn K Sidi-Boumedine A Skull D Durkin P Neild G Rhodes R Pickup J Hermon-Taylor 2003 Detection and verification of Mycobacterium avium subsp paratuberculosis (MAP) in fresh ileocolonic mucosal biopsy specimens from individuals with and without Crohn's disease Journal of Clinical Microbiology 41 2915 2923 10.1128/JCM.41.7.2915-2923.2003 10.1128/JCM.41.7.2915-2923.2003 1:CAS:528:DC%2BD3sXmsVWms7o%3D (Pubitemid 36842279)
7. SA Naser G Ghobrial C Romero JF Valentine 2004 Culture of Mycobacterium avium subspecies paratuberculosis from the blood of patients with Crohn's disease Lancet 364 1039 1044 10.1016/S0140-6736(04)17058-X 10.1016/S0140- 6736(04)17058-X (Pubitemid 39248662)
8. J Cheng TJ Bull P Dalton S Cen C Finlayson J Hermon-Taylor 2005 Mycobacterium avium subspecies paratuberculosis in the inflamed gut tissues of patients with Crohn's disease in China and its potential relationship to the consumption of cow's milk: A preliminary study World Journal of Microbiology & Biotechnology 21 1175 1179 10.1007/s11274-005-0809-z 10.1007/s11274-005- 0809-z (Pubitemid 41680543)
9. LA Sechi AM Scanu P Molicotti S Cannas M Mura G Dettori G Fadda S Zanetti 2005 Detection and isolation of Mycobacterium avium subspecies paratuberculosis from intestinal mucosal biopsies of patients with and without Crohn's disease in Sardinia The American Journal of Gastroenterology 100 1529 1536 10.1111/j.1572-0241.2005.41415.x 10.1111/j.1572-0241.2005.41415.x (Pubitemid 41032358)
10. H Nakase A Nishio H Tamaki M Matsuura M Asada T Chiba K Okazaki 2006 Specific antibodies against recombinant protein of insertion element 900 of Mycobacterium avium subspecies paratuberculosis in Japanese patients with Crohn's disease Inflammatory Bowel Diseases 12 62 69 10.1097/01.MIB.0000191671. 12229.47 10.1097/01.MIB.0000191671.12229.47 (Pubitemid 43032454)
11. J Hermon-Taylor TJ Bull JM Sheridan J Cheng ML Stellakis N Sumar 2000 Causation of Crohn's disease by Mycobacterium avium subspecies paratuberculosis Canadian Journal of Gastroenterology 14 521 539 1:STN:280:DC%2BD3czptlahsA%3D%3D (Pubitemid 30447224)
12. IR Grant HJ Ball MT Rowe 1999 Effect of higher pasteurization temperatures, and longer holding times at 72 degrees C, on the inactivation of Mycobacterium paratuberculosis in milk Letters in Applied Microbiology 28 461 465 10.1046/j.1365-2672.1999.00557.x 10.1046/j.1365-2672.1999.00557.x 1:STN:280:DyaK1MzhslCqtA%3D%3D (Pubitemid 29278300)
13. IR Grant LM O'Riordan HJ Ball MT Rowe 2001 Incidence of Mycobacterium paratuberculosis in raw sheep and goats' milk in England, Wales and Northern Ireland Veterinary Microbiology 79 123 131 10.1016/S0378-1135(00)00344-8 10.1016/S0378-1135(00)00344-8 1:STN:280:DC%2BD3MzlsVGmtQ%3D%3D (Pubitemid 32181849)
14. IR Grant EI Hitchings A McCartney F Ferguson MT Rowe 2002 Effect of commercial-scale high-temperature, short-time pasteurization on the viability of Mycobacterium paratuberculosis in naturally infected cows' milk Applied and Environmental Microbiology 68 602 607 10.1128/AEM.68.2.602-607.2002 10.1128/AEM.68.2.602-607.2002 1:CAS:528:DC%2BD38XhtV2gu7Y%3D (Pubitemid 34113047)
15. I Slana P Kralik A Kralova I Pavlik 2008 On-farm spread of Mycobacterium avium subsp. paratuberculosis in raw milk studied by IS900 and F57 competitive real time quantitative PCR and culture examination International Journal of Food Microbiology 128 250 257 10.1016/j.ijfoodmicro.2008.08.013 10.1016/j. ijfoodmicro.2008.08.013 1:CAS:528:DC%2BD1cXhtl2qtrvE
16. I Abubakar DJ Myhill AR Hart IR Lake I Harvey JM Rhodes R Robinson AJ Lobo CSJ Probert PR Hunter 2007 A case-control study of drinking water and dairy products in Crohn's disease - further investigation of the possible role of Mycobacterium avium paratuberculosis American Journal of Epidemiology 165 776 783 10.1093/aje/kwk067 10.1093/aje/kwk067 (Pubitemid 46434605)
17. Li, L.L., Bannantine, J.P., Zhang, Q., Amonsin, A., May, B.J., Alt, D., et al. (2005). The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proceedings of the National Academy of Sciences of the United States of America, 102, 12344-12349. doi: 10.1073/pnas.0505662102. (Pubitemid 41266361)
18. PR Marri JP Bannantine GB Golding 2006 Comparative genomics of metabolic pathways in Mycobacterium species: Gene duplication, gene decay and lateral gene transfer FEMS Microbiology Reviews 30 906 925 10.1111/j.1574-6976.2006.00041.x 10.1111/j.1574-6976.2006.00041.x 1:CAS:528:DC%2BD28XhtF2qs77F (Pubitemid 44583795)
19. M Gabig G Wegrzyn 2001 An introduction to DNA chips: Principles, technology, applications and analysis Acta Biochimica Polonica 48 615 622 1:CAS:528:DC%2BD3MXovVGjtbg%3D
20. JD Chaudhuri 2005 Genes arrayed out for you: The amazing world of microarrays Medical Science Monitor 11 RA52 RA62 1:CAS:528:DC%2BD2MXitlSmt70%3D
21. A Kumar G Goel E Fehrenbach AK Puniya K Singh 2005 Microarrays: The technology, analysis and application Engineering in Life Sciences 5 215 222 10.1002/elsc.200420075 10.1002/elsc.200420075 1:CAS:528:DC%2BD2MXmtF2gsL0%3D (Pubitemid 40932699)
22. A Ehrenreich 2006 DNA microarray technology for the microbiologist: An overview Applied Microbiology and Biotechnology 73 255 273 10.1007/s00253-006- 0584-2 10.1007/s00253-006-0584-2 1:CAS:528:DC%2BD28XhtlGiurvO (Pubitemid 350262603)
23. Jaluria, P., Konstantopoulos, K., Betenbaugh, M., & Shiloach, J. (2007). A perspective on microarrays: Current applications, pitfalls, and potential uses. Microbial Cell Factories, 6, Article 4 (1-14). doi: 10.1186/1475-2859-6-4. (Pubitemid 46306402)
24. MA Behr MA Wilson WP Gill H Salamon GK Schoolnik S Rane PM Small 1999 Comparative genomics of BCG vaccines by whole-genome DNA microarray Science 28 1520 1523 10.1126/science.284.5419.1520 10.1126/science.284.5419.1520 (Pubitemid 29291397)
25. JC Cho JM Tiedje 2002 Quantitative detection of microbial genes by using DNA microarrays Applied and Environmental Microbiology 68 1425 1430 10.1128/AEM.68.3.1425-1430.2002 10.1128/AEM.68.3.1425-1430.2002 1:CAS:528:DC%2BD38XitFSjsb4%3D (Pubitemid 34205385)
26. MJ Harriff M Wu ML Kent LE Bermudez 2008 Species of environmental mycobacteria differ in their abilities to grow in human, mouse, and carp macrophages and with regard to the presence of mycobacterial virulence genes, as observed by DNA microarray hybridization Applied and Environmental Microbiology 74 275 285 10.1128/AEM.01480-07 10.1128/AEM.01480-07 1:CAS:528: DC%2BD1cXnsVGqsg%3D%3D
27. AD Aho AM McNulty PM Coussens 2003 Enhanced expression of interleukin-1alpha and tumor necrosis factor receptor-associated protein 1 in ileal tissues of cattle infected with Mycobacterium avium subsp. paratuberculosis Infection and Immunity 71 6479 6486 10.1128/IAI.71.11.6479- 6486.2003 10.1128/IAI.71.11.6479-6486.2003 1:CAS:528:DC%2BD3sXoslensLc%3D (Pubitemid 37337708)
28. JA McGarvey D Wagner LE Bermudez 2004 Differential gene expression in mononuclear phagocytes infected with pathogenic and non-pathogenic mycobacteria Clinical and Experimental Immunology 136 490 500 10.1111/j.1365-2249.2004.02490. x 10.1111/j.1365-2249.2004.02490.x 1:CAS:528:DC%2BD2cXlt1Wrtbg%3D (Pubitemid 38703683)
29. Rosenow, C., Saxena, R. M., Durst, M., & Gingeras, T. R. (2001). Prokaryotic RNA preparation methods useful for high density array analysis: Comparison of two approaches. Nucleic Acids Research, 29, Article e112 (1-8).
30. R Diaz N Siddiqi EJ Rubin 2006 Detecting genetic variability among different Mycobacterium tuberculosis strains using DNA microarrays technology Tuberculosis (Edinburgh, Scotland) 86 314 318 10.1016/j.tube.2006.01.002 10.1016/j.tube.2006.01.002 1:CAS:528:DC%2BD28Xmtl2rsL4%3D
31. MF Templin D Stoll M Schrenk PC Traub CF Vohringer TO Joos 2002 Protein microarray technology Drug Discovery Today 7 815 822 10.1016/S1359-6446(00) 01910-2 10.1016/S1359-6446(00)01910-2 1:CAS:528:DC%2BD38XlvF2ks7Y%3D (Pubitemid 34879181)
32. JP Bannantine WR Waters JR Stabel MV Palmer LL Li V Kapur ML Paustian 2008 Development and use of a partial Mycobacterium avium subspecies paratuberculosis protein array Proteomics 8 463 474 10.1002/pmic.200700644 10.1002/pmic.200700644 1:CAS:528:DC%2BD1cXit1ygs78%3D (Pubitemid 351252005)
33. Bannantine, J. P., Bayles, D. O., Waters, W. R., Palmer, M. V., Stabel, J. R., & Paustian, M. L. (2008b). Early antibody response against Mycobacterium avium subspecies paratuberculosis antigens in subclinical cattle. Proteome Science, 6, Article 5 (1-12). doi: 10.1186/1477-5956-6-5.
34. RJ Lipshutz SPA Fodor TR Gingeras DJ Lockhart 1999 High density synthetic oligonucleotide arrays Nature Genetics 21 20 24 10.1038/4447 10.1038/4447 1:CAS:528:DyaK1MXltlWhsA%3D%3D (Pubitemid 29031487)
35. Dalma-Weiszhausz, D. D., Warrington, J., Tanimoto, E. Y., & Miyada, C. G. (2006). The affymetrix GeneChip platform: An overview. In R. A. Kimmel & B. Oliver (Eds.), Methods in Enzymology, vol. 410: DNA microarrays part A: Array platforms, wet-bench protocols (pp. 3-28). San DiegoUSA: Elsevier Academic Press Inc.
36. LM Fu 2006 Exploring drug action on Mycobacterium tuberculosis using affymetrix oligonucleotide genechips Tuberculosis (Edinburgh, Scotland) 86 134 143 10.1016/j.tube.2005.07.004 10.1016/j.tube.2005.07.004 1:CAS:528: DC%2BD28XivVWhsLk%3D (Pubitemid 43227438)
37. P Hegde R Qi K Abernathy C Gay S Dharap R Gaspard JE Hughes E Snesrud N Lee J Quackenbush 2000 A concise guide to cDNA microarray analysis BioTechniques 29 548 562 1:CAS:528:DC%2BD3cXmsFWgsb0%3D
38. CC Xiang YD Chen 2000 cDNA microarray technology and its applications Biotechnology Advances 18 35 46 10.1016/S0734-9750(99)00035-X 10.1016/S0734-9750(99)00035-X 1:CAS:528:DC%2BD3cXjtVamt7o%3D (Pubitemid 30300756)
39. YF Leung D Cavalieri 2003 Fundamentals of cDNA microarray data analysis Trends in Genetics 19 649 659 10.1016/j.tig.2003.09.015 10.1016/j.tig.2003.09. 015 1:CAS:528:DC%2BD3sXosVKrsrg%3D (Pubitemid 37338385)
40. A Brazma P Hingamp J Quackenbush G Sherlock P Spellman C Stoeckert J Aach W Ansorge CA Ball HC Causton T Gaasterland P Glenisson FCP Holstege IF Kim V Markowitz JC Matese H Parkinson A Robinson U Sarkans S Schulze-Kremer J Stewart R Taylor J Vilo M Vingron 2001 Minimum information about a microarray experiment (MIAME)-toward standards for microarray data Nature Genetics 29 365 371 10.1038/ng1201-365 10.1038/ng1201-365 1:CAS:528:DC%2BD3MXovFamurw%3D (Pubitemid 34326681)
41. Relogio, A., Schwager, C., Richter, A., Ansorge, W., & Valcarcel, J. (2002). Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Research, 30, Article e51 (1-10).
42. V Benes M Muckenthaler 2003 Standardization of protocols in cDNA microarray analysis Trends in Biochemical Sciences 28 244 249 10.1016/S0968-0004(03)00068-9 10.1016/S0968-0004(03)00068-9 1:CAS:528: DC%2BD3sXjvFWlt7k%3D (Pubitemid 36588666)
43. K Dheda JF Huggett SA Bustin MA Johnson G Rook A Zumla 2004 Validation of housekeeping genes for normalizing RNA expression in real-time PCR BioTechniques 37 112 119 1:CAS:528:DC%2BD2cXlvVagtrg%3D
44. EL Korn JK Habermann MB Upender T Ried LM McShane 2004 Objective method of comparing DNA microarray image analysis systems BioTechniques 36 960 967 1:CAS:528:DC%2BD2cXltVSltb8%3D
45. CL Yauk ML Berndt 2007 Review of the literature examining the correlation among DNA microarray technologies Environmental and Molecular Mutagenesis 48 380 394 10.1002/em.20290 10.1002/em.20290 1:CAS:528:DC%2BD2sXnvVWhs7k%3D (Pubitemid 47011767)
46. LS Zhang JN Kujis XH Liu 2008 Information visualization for DNA microarray data analysis: A critical review IEEE Transactions on Systems Man and Cybernetics Part C 38 42 54 10.1109/TSMCC.2007.906065 1:CAS:528: DC%2BD1cXhsVGhsb%2FF
47. IB Marsh JP Bannantine ML Paustian ML Tizard V Kapur RJ Whittington 2006 Genomic comparison of Mycobacterium avium subsp paratuberculosis sheep and cattle strains by microarray hybridization Journal of Bacteriology 188 2290 2293 10.1128/JB.188.6.2290-2293.2006 10.1128/JB.188.6.2290-2293.2006 1:CAS:528:DC%2BD28XisFKmsbc%3D (Pubitemid 43376484)
48. CW Wu SK Schmoller SJ Shin AM Talaat 2007 Defining the stressome of Mycobacterium avium subsp paratuberculosis in vitro and in naturally infected cows Journal of Bacteriology 189 7877 7886 10.1128/JB.00780-07 10.1128/JB.00780-07 1:CAS:528:DC%2BD2sXht1Knu7%2FF (Pubitemid 350035096)
49. Paustian, M. L., Zhu, X., Sreevatsan, S., Robbe-Austerman, S., Kapur, V., & Bannantine, J. P. (2008). Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species. BMC Genomics, 20, Article 135 (1-15). doi: 10.1186/1471-2164-9-135. (Pubitemid 351566950)
50. L Bodrossy A Sessitsch 2004 Oligonucleotide microarrays in microbial diagnostics Current Opinion in Microbiology 7 245 254 10.1016/j.mib.2004.04.005 10.1016/j.mib.2004.04.005 1:CAS:528:DC%2BD2cXkvV2ns7Y%3D (Pubitemid 38758065)
51. DR Call 2005 Challenges and opportunities for pathogen detection using DNA microarrays Critical Reviews in Microbiology 31 91 99 10.1080/ 10408410590921736 10.1080/10408410590921736 1:CAS:528:DC%2BD2MXjvVOltr4%3D (Pubitemid 40762632)
52. Ojha, S., & Kostrzynska, M. (2008). Examination of animal and zoonotic pathogens using microarrays. Veterinary Research, 39, Article 4 (1-22). doi: 10.1051/vetres:2007042.
53. A Troesch H Nguyen CG Miyada S Desvarenne TR Gingeras PM Kaplan P Cros C Mabilat 1999 Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays Journal of Clinical Microbiology 37 49 55 1:CAS:528:DyaK1MXks1ynuw%3D%3D
54. NE Tobler M Pfunder K Herzog JE Frey M Altwegg 2006 Rapid detection and species identification of Mycobacterium spp. using real-time PCR and DNA Microarray Journal of Microbiological Methods 66 116 124 10.1016/j.mimet.2005. 10.016 10.1016/j.mimet.2005.10.016 1:CAS:528:DC%2BD28XltFOntLw%3D (Pubitemid 43786436)
55. M Fukushima K Kakinuma H Hayashi H Nagai K Ito R Kawaguchi 2003 Detection and identification of Mycobacterium species isolates by DNA microarray Journal of Clinical Microbiology 41 2605 2615 10.1128/JCM.41.6.2605-2615.2003 10.1128/JCM.41.6.2605-2615.2003 1:CAS:528:DC%2BD3sXlsValtL4%3D
56. H Park HJ Jang E Song CL Chang M Lee S Jeong J Park B Kang C Kim 2005 Detection and genotyping of Mycobacterium species from clinical isolates and specimens by oligonucleotide array Journal of Clinical Microbiology 43 1782 1788 10.1128/JCM.43.4.1782-1788.2005 10.1128/JCM.43.4.1782-1788.2005 1:CAS:528:DC%2BD2MXjvF2lu7c%3D
57. B Heym Y Zhang S Poulet D Young ST Cole 1993 Characterization of the katG gene encoding a catalase-peroxidase required for the isoniazid susceptibility of Mycobacterium tuberculosis Journal of Bacteriology 175 4255 4259 1:CAS:528:DyaK3sXlvFKqtrw%3D
58. A Telenti P Imboden F Marchesi D Lowrie S Cole MJ Colston L Matter K Schopfer T Bodmer 1993 Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis Lancet 341 647 650 10.1016/0140-6736(93)90417-F 10.1016/0140-6736(93)90417-F 1:CAS:528:DyaK3sXkvFWjsbo%3D (Pubitemid 23083244)
59. M Semret G Zhai S Mostowy C Cleto D Alexander G Cangelosi D Cousins DM Collins D van Soolingen MA Behr 2004 Extensive genomic polymorphism within Mycobacterium avium Journal of Bacteriology 186 6332 6334 10.1128/JB.186.18. 6332-6334.2004 10.1128/JB.186.18.6332-6334.2004 1:CAS:528:DC%2BD2cXns1eit7c%3D (Pubitemid 39187025)
60. ML Paustian V Kapur JP Bannantine 2005 Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates Journal of Bacteriology 187 2406 2415 10.1128/JB.187.7.2406-2415.2005 10.1128/JB.187.7. 2406-2415.2005 1:CAS:528:DC%2BD2MXjt1Kqs70%3D (Pubitemid 40389139)
61. M Semret DC Alexander CY Turenne P de Haas P Overduin D van Soolingen D Cousins MA Behr 2005 Genomic polymorphisms for Mycobacterium avium subsp. paratuberculosis diagnostics Journal of Clinical Microbiology 43 3704 3712 10.1128/JCM.43.8.3704-3712.2005 10.1128/JCM.43.8.3704-3712.2005 1:CAS:528:DC%2BD2MXpvVCrt7Y%3D (Pubitemid 41129649)
62. CW Wu J Glasner M Collins S Naser AM Talaat 2006 Whole-genome plasticity among Mycobacterium avium subspecies: Insights from comparative genomic hybridizations Journal of Bacteriology 188 711 723 10.1128/JB.188.2.711-723.2006 10.1128/JB.188.2.711-723.2006 1:CAS:528:DC%2BD28Xms1Ohtg%3D%3D (Pubitemid 43100559)
63. M Semret D Bakker N Smart I Olsen K Haslov MA Behr 2006 Genetic analysis of Mycobacterium avium complex strains used for producing purified protein derivatives Clinical and Vaccine Immunology; CVI 13 991 996 10.1128/CVI.00217-06 10.1128/CVI.00217-06 1:CAS:528:DC%2BD28XhtVWgt73J (Pubitemid 44518966)
64. TJ Gentry GS Wickham CW Schadt Z He J Zhou 2006 Microarray applications in microbial ecology research Microbial Ecology 52 159 175 10.1007/s00248-006- 9072-6 10.1007/s00248-006-9072-6 1:CAS:528:DC%2BD28XpsVaisLw%3D (Pubitemid 44392971)
65. T Kostic A Weilharter S Rubino G Delogu S Uzzau K Rudi A Sessitsch L Bodrossy 2007 A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens Analytical Biochemistry 360 244 254 10.1016/j.ab.2006.09.026 10.1016/j.ab.2006.09.026 1:CAS:528:DC%2BD2sXht1Wisw%3D%3D (Pubitemid 44958320)
66. JL Sebat FS Colwell RL Crawford 2003 Metagenomic profiling: Microarray analysis of an environmental genomic library Applied and Environmental Microbiology 69 4927 4934 10.1128/AEM.69.8.4927-4934.2003 10.1128/AEM.69.8.4927- 4934.2003 1:CAS:528:DC%2BD3sXmsFWrtbc%3D (Pubitemid 36992958)
67. Alwine, J.C., Kemp, D.J., & Stark, G.R. (1977). Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proceedings of the National Academy of Sciences of the United States of America, 74, 5350-5354. doi: 10.1073/pnas.74.12.5350.
68. AJ Berk PA Sharp 1977 Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids Cell 12 721 732 10.1016/0092-8674(77)90272-0 10.1016/0092-8674(77)90272-0 1:CAS:528: DyaE1cXhvV2hsQ%3D%3D
69. K Okubo N Hori R Matoba T Niiyama A Fukushima Y Kojima K Matsubara 1992 Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression Nature Genetics 2 173 179 10.1038/ng1192-173 10.1038/ng1192-173 1:CAS:528:DyaK3sXjtlKmsA%3D%3D
70. VE Velculescu L Zhang B Vogelstein KW Kinzler 1995 Serial analysis of gene expression Science 270 484 487 10.1126/science.270.5235.484 10.1126/science.270.5235.484 1:CAS:528:DyaK2MXovVersb8%3D
71. HC King AA Sinha 2001 Gene expression profile analysis by DNA microarrays-Promise and pitfalls Journal of the American Medical Association 286 2280 2288 10.1001/jama.286.18.2280 10.1001/jama.286.18.2280 1:CAS:528:DC%2BD3MXosFCktrs%3D
72. ZY Xiang YN Yang XJ Ma W Ding 2003 Microarray expression profiling: Analysis and applications Current Opinion in Drug Discovery 6 384 395 1:CAS:528:DC%2BD3sXkslCnsrw%3D
73. FH Sharkey IM Banat R Marchant 2004 Detection and quantification of gene expression in environmental bacteriology Applied and Environmental Microbiology 70 3795 3806 10.1128/AEM.70.7.3795-3806.2004 10.1128/AEM.70.7.3795-3806.2004 1:CAS:528:DC%2BD2cXmtFWnsL0%3D (Pubitemid 38969714)
74. Dallas, P. B., Gottardo, N. G., Firth, M. J., Beesley, A. H., Hoffmann, K., Terry, P. A., Freitas, J. R., Boag, J. M., Cummings, A. J., & Kees, U. R. (2005). Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR-how well do they correlate? BMC Genomics, 6, Article 59 (1-10). doi: 10.1186/1471-2164-6-59. (Pubitemid 41357676)
75. R Manganelli E Dubnau S Tyagi FR Kramer I Smith 1999 Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis Molecular Microbiology 31 715 724 10.1046/j.1365-2958.1999.01212.x 10.1046/j.1365-2958. 1999.01212.x 1:CAS:528:DyaK1MXhtFygs78%3D (Pubitemid 29046111)
76. R Manganelli R Provvedi S Rodrigue J Beaucher L Gaudreau I Smith 2004 Sigma factors and global gene regulation in Mycobacterium tuberculosis Journal of Bacteriology 186 895 902 10.1128/JB.186.4.895-902.2004 10.1128/JB.186.4.895- 902.2004 1:CAS:528:DC%2BD2cXhsVWjsbY%3D (Pubitemid 38209448)
77. PH Vary PR Andersen E Green J Hermon-Taylor JJ McFadden 1990 Use of highly specific DNA probes and the polymerase chain reaction to detect Mycobacterium paratuberculosis in Johne's disease Journal of Clinical Microbiology 28 933 937 1:CAS:528:DyaK3cXitlajsrk%3D
78. M Bartos P Hlozek P Svastova L Dvorska T Bull L Matlova I Parmova I Kuhn J Stubbs M Moravkova J Kintr V Beran I Melicharek M Ocepek I Pavlik 2006 Identification of members of Mycobacterium avium species by Accu-Probes, serotyping, and single IS900, IS901, IS1245 and IS901-flanking region PCR with internal standards Journal of Microbiological Methods 64 333 345 10.1016/j.mimet.2005.05.009 10.1016/j.mimet.2005.05.009 1:CAS:528: DC%2BD28XhtlCksrs%3D (Pubitemid 43212810)
79. M Bhide E Chakurkar L Tkacikova S Barbuddhe M Novak I Mikula 2006 IS900-PCR-based detection and characterization of Mycobacterium avium subsp paratuberculosis from buffy coat of cattle and sheep Veterinary Microbiology 112 33 41 10.1016/j.vetmic.2005.10.004 10.1016/j.vetmic.2005.10.004 1:CAS:528:DC%2BD2MXhtlCrsL%2FO (Pubitemid 41814712)
80. E Vansnick P De Rijk F Vercammen D Geysen L Rigouts F Portaels 2004 Newly developed primers for the detection of Mycobacterium avium subspecies paratuberculosis Veterinary Microbiology 100 197 204 10.1016/j.vetmic.2004.02. 006 10.1016/j.vetmic.2004.02.006 1:CAS:528:DC%2BD2cXktVCiur8%3D (Pubitemid 38625690)
81. CA Speer MC Scott JP Bannantine WR Waters Y Mori RH Whitlock S Eda 2006 A novel enzyme-linked immunosorbent assay for diagnosis of Mycobacterium avium subsp. paratuberculosis infections (Johne's disease) in cattle Clinical and Vaccine Immunology; CVI 13 535 540 10.1128/CVI.13.5.535-540.2006 10.1128/CVI.13.5.535-540.2006 1:CAS:528:DC%2BD28XkvFKksL0%3D (Pubitemid 43736452)
82. G Jungersen A Huda JJ Hansen P Lind 2002 Interpretation of the gamma interferon test for diagnosis of subclinical paratuberculosis in cattle Clinical and Diagnostic Laboratory Immunology 9 453 460 10.1128/CDLI.9.2.453-460.2002 10.1128/CDLI.9.2.453-460.2002 1:STN:280:DC%2BD387jvV2gsQ%3D%3D (Pubitemid 34226046)
83. K McGuire EJ Glass 2005 The expanding role of microarrays in the investigation of macrophage responses to pathogens Veterinary Immunology and Immunopathology 105 259 275 10.1016/j.vetimm.2005.02.001 10.1016/j.vetimm.2005. 02.001 1:CAS:528:DC%2BD2MXivV2htLg%3D (Pubitemid 40460950)
84. MS Gomes S Paul AL Moreira R Appelberg M Rabinovitch G Kaplan 1999 Survival of Mycobacterium avium and Mycobacterium tuberculosis in acidified vacuoles of murine macrophages Infection and Immunity 67 3199 3206 1:CAS:528:DyaK1MXktFaiu7Y%3D
85. L Nguyen J Pieters 2005 The Trojan horse: Survival tactics of pathogenic mycobacteria in macrophages Trends in Cell Biology 15 269 276 10.1016/j.tcb.2005.03.009 10.1016/j.tcb.2005.03.009 1:CAS:528: DC%2BD2MXjslKhsbw%3D (Pubitemid 40603896)
86. SR Woo CJ Czuprynski 2008 Tactics of Mycobacterium avium subsp. paratuberculosis for intracellular survival in mononuclear phagocytes Journal of Veterinary Science (Suwon-si, Korea) 9 1 8
87. PM Coussens CJ Colvin K Wiersma A Abouzied S Sipkovsky 2002 Gene expression profiling of peripheral blood mononuclear cells from cattle infected with Mycobacterium paratuberculosis Infection and Immunity 70 5494 5502 10.1128/IAI.70.10.5494-5502.2002 10.1128/IAI.70.10.5494-5502.2002 1:CAS:528:DC%2BD38XnsV2ls7s%3D (Pubitemid 35050983)
88. PM Coussens CJ Colvin GJM Rosa JP Laspiur MD Elftman 2003 Evidence for a novel gene expression program in peripheral blood mononuclear cells from Mycobacterium avium subsp paratuberculosis-infected cattle Infection and Immunity 71 6487 6498 10.1128/IAI.71.11.6487-6498.2003 10.1128/IAI.71.11.6487- 6498.2003 1:CAS:528:DC%2BD3sXoslensb4%3D (Pubitemid 37337709)
89. PM Coussens CB Pudrith K Skovgaard XN Ren SP Suchyta JR Stabel PMH Heegaard 2005 Johne's disease in cattle is associated with enhanced expression of genes encoding IL-5, GATA-3, tissue inhibitors of matrix metalloproteinases 1 and 2, and factors promoting apoptosis in peripheral blood mononuclear cells Veterinary Immunology and Immunopathology 105 221 234 10.1016/j.vetimm.2005.02. 009 10.1016/j.vetimm.2005.02.009 1:CAS:528:DC%2BD2MXivV2htL0%3D (Pubitemid 40460947)
90. DJ Weiss OA Evanson A Moritz MQ Deng MS Abrahamsen 2002 Differential responses of bovine macrophages to Mycobacterium avium subsp paratuberculosis and Mycobacterium avium subsp avium Infection and Immunity 70 5556 5561 10.1128/IAI.70.10.5556-5561.2002 10.1128/IAI.70.10.5556-5561.2002 1:CAS:528:DC%2BD38XnsV2lsLw%3D (Pubitemid 35050990)
91. DJ Weiss OA Evanson MQ Deng MS Abrahamsen 2004 Sequential patterns of gene expression by bovine monocyte-derived macrophages associated with ingestion of mycobacterial organisms Microbial Pathogenesis 37 215 224 10.1016/j.micpath.2004.07.001 10.1016/j.micpath.2004.07.001 1:CAS:528: DC%2BD2cXotF2nt7k%3D (Pubitemid 39349045)
92. DJ Weiss OA Evanson M Deng MS Abrahamsen 2004 Gene expression and antimicrobial activity of bovine macrophages in response to Mycobacterium avium subsp. paratuberculosis Veterinary Pathology 41 326 337 10.1354/vp.41-4-326 10.1354/vp.41-4-326 1:CAS:528:DC%2BD2cXmtl2rtbw%3D (Pubitemid 39091021)
93. JT Murphy S Sommer EA Kabara N Verman MA Kuelbs P Saama R Halgren PM Coussens 2006 Gene expression profiling of monocyte-derived macrophages following infection with Mycobacterium avium subspecies avium and Mycobacterium avium subspecies paratuberculosis Physiological Genomics 28 67 75 10.1152/physiolgenomics.00098.2006 10.1152/physiolgenomics.00098.2006 1:CAS:528:DC%2BD28XhtlCmtrzI (Pubitemid 46702018)
94. RN Streeter GF Hoffsis S Bechnielsen WP Shulaw M Rings 1995 Isolation of Mycobacterium paratuberculosis from colostrum and milk of subclinically infected cows American Journal of Veterinary Research 56 1322 1324 1:STN:280: BymC3M7gs1Q%3D
95. SA Naser D Schwartz I Shafran 2000 Isolation of Mycobacterium avium subsp paratuberculosis from breast milk of Crohn's disease patients The American Journal of Gastroenterology 95 1094 1095 10.1111/j.1572-0241.2000.01954.x 10.1111/j.1572-0241.2000.01954.x 1:STN:280:DC%2BD3c3isFSntw%3D%3D
96. D Patel L Danelishvili Y Yamazaki M Alonso ML Paustian JP Bannantine L Meunier-Goddik LE Bermudez 2006 The ability of Mycobacterium avium subsp paratuberculosis to enter bovine epithelial cells is influenced by preexposure to a hyperosmolar environment and intracellular passage in bovine mammary epithelial cells Infection and Immunity 74 2849 2855 10.1128/IAI.74.5.2849-2855. 2006 10.1128/IAI.74.5.2849-2855.2006 1:CAS:528:DC%2BD28XksFagu78%3D (Pubitemid 43672995)
97. K Skovgaard SN Grell PMH Heegaard G Jungersen CB Pudrith PM Coussens 2006 Differential expression of genes encoding CD30L and P-selectin in cattle with Johne's disease: Progress toward a diagnostic gene expression signature Veterinary Immunology and Immunopathology 112 210 224 10.1016/j.vetimm.2006.02. 006 10.1016/j.vetimm.2006.02.006 1:CAS:528:DC%2BD28Xms1Glsb0%3D (Pubitemid 43975143)
98. C Csillag OH Nielsen R Borup FC Nielsen 2005 Microarrays and Crohn's disease: Collecting reliable information Scandinavian Journal of Gastroenterology 40 369 377 10.1080/00365520510012226 10.1080/00365520510012226 (Pubitemid 40552884)
99. W Chamberlin DY Graham K Hulten HMT El-Zimaity MR Schwartz S Naser I Shafran FAK El-Zaatari 2001 Review article: Mycobacterium avium subsp. paratuberculosis as one cause of Crohn's disease Alimentary Pharmacology & Therapeutics 15 337 346 10.1046/j.1365-2036.2001.00933.x 10.1046/j.1365-2036. 2001.00933.x 1:STN:280:DC%2BD3M3jsFOjug%3D%3D (Pubitemid 32187555)
100. JC Uzoigwe ML Khaitsa PS Gibbs 2007 Epidemiological evidence for Mycobacterium avium subspecies paratuberculosis as a cause of Crohn's disease Epidemiology and Infection 135 1057 1068 10.1017/S0950268807008448 10.1017/S0950268807008448 1:STN:280:DC%2BD2srmtlWrug%3D%3D (Pubitemid 47487591)
101. MA Behr V Kapur 2008 The evidence for Mycobacterium paratuberculosis in Crohn's disease Current Opinion in Gastroenterology 24 17 21 10.1097/MOG.0b013e3282f1dcc4 (Pubitemid 350190892)
102. AS Motiwala HK Janagama ML Paustian XC Zhu JP Bannantine V Kapur S Sreevatsan 2006 Comparative transcriptional analysis of human macrophages exposed to animal and human isolates of Mycobacterium avium subspecies paratuberculosis with diverse genotypes Infection and Immunity 74 6046 6056 10.1128/IAI.00326-06 10.1128/IAI.00326-06 1:CAS:528:DC%2BD28Xht1KhurbL (Pubitemid 44657382)