Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology

Clinical Microbiology Reviews

Volumn 13, Issue 3, 2000, Pages 408-427

  Sturtevant, Joy ^a  

^a GEORGETOWN UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MYCOSIS; NONHUMAN; PATHOGENESIS; POLYMERASE CHAIN REACTION; REVIEW; RNA FINGERPRINTING;

ANIMALS; CELL CYCLE; CELL DIFFERENTIATION; CLONING, MOLECULAR; GENE EXPRESSION; HUMANS; MYCOLOGY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; VIRULENCE;

AJELLOMYCES; AJELLOMYCES CAPSULATUS; CANDIDA ALBICANS; FUNGI; MAMMALIA;

EID: 0033924256     PISSN: 08938512     EISSN: None     Source Type: Journal    
DOI: 10.1128/CMR.13.3.408-427.2000     Document Type: Review

References (156)

1. Abu Kwaik, Y., and L. L. Pederson. 1996. The use of differential display-PCR to isolate and characterize a Legionella pneumophila locus induced during the intracellular infection of macrophages. Mol. Microbiol. 21:543-556.
2. Afonina, I., M. Zivarts, I. Kutyavin, E. Lukhtanov, H. Gamper, and R. B. Meyer. 1997. Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder. Nucleic Acids Res. 25:2657-2660.
3. An, G., G. Luo, R. W. Veltri, and O. H. SM. 1996. Sensitive, nonradioactive differential display method using chemiluminescent detection. BioTechniques. 20:342-324, 346.
4. Appleyard, V. C., S. E. Unkles, M. Legg, and J. R. Kinghorn. 1995. Secondary metabolite production in filamentous fungi displayed. Mol. Gen. Genet. 247:338-342.
5. Baudet, C., E. Perret, B. Delpech, M. Kaghad, P. Brachet, D. Wion, and D. Caput. 1998. Differentially expressed genes in C6.9 glioma cells during vitamin D-induced death program. Cell Death Differ. 5:116-125.
6. Benito, E. P., T. Prins, and J. A. van Kan. 1996. Application of differential display RT-PCR to the analysis of gene expression in a plant-fungus interaction. Plant Mol. Biol. 32:947-957.
7. Bertioli, D. J., U. H. Schlichter, M. J. Adams, P. R. Burrows, H. H. Steinbiss, and J. F. Antoniw. 1995. An analysis of differential display shows a strong bias towards high copy number mRNAs. Nucleic Acids Res. 23: 4520-4523.
8. Birch, P. R. 1998. Targeted differential display of abundantly expressed sequences from the basidiomycete Phanerochaete chrysosporium which contain regions coding for fungal cellulose-binding domains. Curr Genet. 33:70-76.
9. Birse, C., M. Irwin, W. Fonzi, and P. Sypherd. 1993. Cloning and characterization of ECE1, a gene expressed in association with cell elongation of the dimorphic pathogen Candida albicans. Infect. Immun. 61:3648-3655.
10. Bonnet, S., G. Prevot, and C. Bourgouin. 1998. Efficient reamplification of differential display products by transient ligation and thermal asymmetric PCR. Nucleic Acids Res. 26:1130-1131.
11. Brenz Verca, M. S., S. Brenz Verca, S. Rusconi, and J. L. Dreyer. 1998. Modification of primer design facilitates the use of differential display. BioTechniques 24:374-376, 378-380.
12. Broude, N. E., A. Chandra, and C. L. Smith. 1997. Differential display of genome subsets containing specific interspersed repeats. Proc. Natl. Acad. Sci. USA 94:4548-4553.
13. Brown, A. J., C. Hutchings, J. F. Burke, and L. V. Mayne. 1999. Application of a rapid method (targeted display) for the identification of differentially expressed mRNAs following NGF-induced neuronal differentiation in PC12 cells. Mol. Cell. Neurosci. 13:119-130.
14. Carter, D., J. R. Goepel, P. R. Winship, and M. H. Goyns. 1999. Identification of different gene expression patterns in low and high grade non-Hodgkin's lymphomas by differential display. Leuk. Lymphoma 33:343-350.
15. Carulli, J. P., M. Artinger, P. M. Swain, C. D. Root, L. Chee, C. Tulig, J. Guerin, M. Osborne, G. Stein, J. Lian, and P. T. Lomedico. 1998. High throughput analysis of differential gene expression. J. Cell. Biochem. Suppl. 30-31:286-296.
16. Castles, C. G., D. C. Allred, S. L. Krieg, M. G. Benedix, and S. A. Fuqua. 1996. RNA from air-dried frozen sections for RT-PCR and differential display. BioTechniques 21:425-428.
17. Cataldo, L. M., Y. Zhang, J. Lu, and K. Ravid. 1999. Rat NAP1: cDNA cloning and upregulation by Mp1 ligand. Gene 226:355-364.
18. Chaffin, W. L., J. L. Lopez-Ribot, M. Casanova, D. Gozalbo, and J. P. Martinez. 1998. Cell wall and secreted proteins of Candida albicans: identification, function, and expression. Microbiol. Mol. Biol. Rev. 62:130-180.
19. Chen, B., S. Gao, G. H. Choi, and D. L. Nuss. 1996. Extensive alteration of fungal gene transcript accumulation and elevation of G-protein-regulated cAMP levels by a virulence-attenuating hypovirus. Proc. Natl. Acad. Sci. USA 93:7996-8000.
20. Chen, J. J., and K. Peck. 1996. Non-radioisotopic differential display method to directly visualize and amplify differential bands on nylon membrane. Nucleic Acids Res. 24:793-794.
21. Chen, J. J., R. Wu, P. C. Yang, J. Y. Huang, Y. P. Sher, M. H. Han, W. C. Kao, P. J. Lee, T. F. Chiu, F. Chang, Y. W. Chu, C. W. Wu, and K. Peck. 1998. Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. Genomics 51:313-324.
22. 35S-labeled gas released from reaction tubes during differential display PCR. BioTechniques 19:798-799.
23. Colonna-Romano, S., A. Porta, A. Franco, G. S. Kobayashi, and B. Maresca. 1998. Identification and isolation by DDRT-PCR of genes differentially expressed by Histoplasma capsulatum during macrophages infection. Microb. Pathog. 25:55-66.
24. Consalez, G. G., A. Corradi, S. Ciarmatori, M. Bossolasco, N. Malgaretti, and C. L. Stayton. 1996. A new method to screen clones from differential display experiments prior to RNA studies. Trends Genet. 12:455-456.
25. Corton, J. C., and J. A. Gustafsson. 1997. Increased efficiency in screening large numbers of cDNA fragments generated by differential display. BioTechniques 22:802-804, 806, 808.
26. Crauwels, M., J. Winderickx, J. H. de Winde, and J. M. Thevelein. 1997. Identification of genes with nutrient-controlled expression by PCR-mapping in the yeast Saccharomyces cerevisiae. Yeast 13:973-984.
27. Diatchenko, L. B., J. Ledesma, A. A. Chenchik, and P. D. Siebert. 1996. Combining the technique of RNA fingerprinting and differential display to obtain differentially expressed mRNA. Biochem. Biophys. Res. Commun. 219:824-828.
28. Diatchenko, L., S. Lukyanov, Y. F. Lau, and P. D. Siebert. 1999. Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes. Methods Enzymol. 303:349-380.
29. Dimopoulos, G., A. Richman, A. della Torre, F. C. Kafatos, and C. Louis. 1996. Identification and characterization of differentially expressed cDNAs of the vector mosquito, Anopheles gambiae. Proc. Natl. Acad. Sci. USA 93:13066-13071.
30. Domachowske, J. B., and H. L. Malech. 1997. Reamplification of differential display products: more is not better. Front. Biosci. 2:C12-C14.
31. Dominguez, O., Y. Ashhab, L. Sabater, E. Belloso, P. Caro, and R. Pujol-Borrell. 1998. Cloning of ARE-containing genes by AU-motif-directed display. Genomics 54:278-286.
32. Edwards, W. D., H. L. Jessop, and A. Cryer. 1994. Using differential display in the study of adipocyte differentiation. Biochem. Soc. Trans. 22:247S.
33. Fanciulli, M., T. Bruno, C. Cerboni, F. Bonetto, C. Iacobini, L. Frati, M. Piccoli, A. Floridi, A. Santoni, and A. Punturieri. 1996. Cloning of a novel human RNA polymerase II subunit downregulated by doxorubicin: new potential mechanisms of drug related toxicity. FEBS Lett. 384:48-52.
34. Ferrer, J., J. Wasson, K. D. Schoor, M. Mueckler, H. Donis-Keller, and M. A. Permutt. 1997. Mapping novel pancreatic islet genes to human chromosomes. Diabetes 46:386-392.
35. Fischer, A., H. Saedler, and G. Theissen. 1995. Restriction fragment length polymorphism-coupled domain-directed differential display: a highly efficient technique for expression analysis of multigene families. Proc. Natl. Acad. Sci. USA 92:5331-5335.
36. Fislage, R., M. Berceanu, Y. Humboldt, M. Wendt, and H. Oberender. 1997. Primer design for a prokaryotic differential display RT-PCR. Nucleic Acids Res. 25:1830-1835.
37. Fleming, J. T., W. H. Yao, and G. S. Sayler. 1998. Optimization of differential display of prokaryotic mRNA: application to pure culture and soil microcosms. Appl. Environ. Microbiol. 64:3698-3706.
38. Gery, S., and S. Lavi. 1997. Purification and cloning of differential display products. BioTechniques 23:198-200, 202.
39. Godovac-Zimmerman, J., V. Soskic, S. Poznanovic, and F. Brianza. 1999. Functional proteomics of signal transduction by membrane receptors. Electrophoresis 20:952-961.
40. Goormachtig, S., M. Valerio-Lepiniec, K. Szczyglowski, M. Van Montagu, M. Holsters, and F. J. de Bruijn. 1995. Use of differential display to identify novel Sesbania rostrata genes enhanced by Azorhizobium caulinodans infection. Mol. Plant-Microbe Interact. 8:816-824.
41. Gottschlich, S., T. Goeroegh, B. J. Folz, B. M. Lippert, and J. A. Werner. 1997. Optimized differential display and reamplification parameters for silver staining. Res. Commun. Mol. Pathol. Pharmacol. 97:237-240.
42. Graf, D., A. G. Fisher, and M. Merkenschlager. 1997. Rational primer design greatly improves differential display-PCR (DD-PCR). Nucleic Acids Res. 25:2239-2240.
43. Green, C. B., and J. C. Besharse. 1996. Use of a high stringency differential display screen for identification of retinal mRNAs that are regulated by a circadian clock. Brain Res. Mol. Brain Res. 37:157-165.
44. Gromova, I., P. Gromov, and J. E. Celis. 1999. Identification of true differentially expressed mRNAs in a pair of human bladder transitional cell carcinomas using an improved differential display procedure. Electrophoresis 20:241-248.
45. Gross, C., and K. Watson. 1998. Application of mRNA differential display to investigate gene expression in thermotolerant cells of Saccharomyces cerevisiae. Yeast 14:431-442.
46. Guimaraes, M. J., F. Lee, A. Zlotnik, and T. McClanahan. 1995. Differential display by PCR: novel findings and applications. Nucleic Acids Res. 23:1832-1833.
47. Gupta, R., P. Thomas, R. S. Beddington, and P. W. Rigby. 1998 Isolation of developmentally regulated genes by differential display screening of cDNA libraries. Nucleic Acids Res. 26:4538-4539.
48. Haag, E., and V. Raman. 1994. Effects of primer choice and source of Taq DNA polymerase on the banding patterns of differential display RT-PCR. BioTechniques 17:226-228.
49. Hadman, M., B. L. Adam, G. L. Wright, Jr., and T. J. Bos. 1995. Modifications to the differential display technique reduce background and increase sensitivity. Anal. Biochem. 226:383-386.
50. Harris, E. D. 1996. Differential display PCR: a new age in nutrition investigation. Nutr. Rev. 54:287-289.
51. Heard, P. L., C. S. Lewis, and G. Chaudhuri. 1996. Leishmania mexicana amazonensis: differential display analysis and cloning of mRNAs from attenuated and infective forms. J. Eukaryot. Microbiol. 43:409-415.
52. Hershkovits, G., Z. Dubinsky, and D. J. Katcoff. 1997. A novel homologue of the prokaryotic htrA gene is differentially expressed in the alga Haematococcus pluvialis following stress. Mol. Gen. Genet. 254:345-350.
53. Hipfel, R., C. Garbe, and B. Schittek. 1998. RNA isolation from human skin tissues for colorimetric differential display. J. Biochem. Biophys. Methods 37:131-135.
54. Hogan, L. H., B. S. Klein, and S. M. Levitz. 1996. Virulence factors of medically important fungi. Clin. Microbiol. Rev. 9:469-488.
55. Hong, Y. M., S. W. Park, and S. Y. Choi. 1998. Expression of the CIP1 gene induced under cadmium stress in Candida sp. Mol. Cells 8:84-89.
56. Hoyer, L. L., S. Scherer, A. R. Shatzman, and G. P. Livi. 1995. Candida albicans ALS1: domains related to a Saccharomyces cerevisiae sexual agglutinin separated by a repeating motif. Mol. Microbiol. 15:39-54.
57. Hung, H. L., F. Song, and A. Gewirtz. 1999. A method for identifying differentially expressed genes in rare populations of primary human hematopoietic cells. Leukemia 13:295-297.
58. Iimura, Y., and K. Tatsumi. 1997. Isolation of mRNAs induced by a hazardous chemical in white-rot fungus, Coriolus versicolor, by differential display. FEBS Lett. 412:370-374.
59. Ikonomov, O. C., and M. H. Jacob. 1996. Differential display protocol with selected primers that preferentially isolates mRNAs of moderate-to low-abundance in a microscopic system. BioTechniques 20:1030-1034, 1036-1038, 1040-1042.
60. Ito, T., K. Kito, N. Adati, Y. Mitsui, H. Hagiwara, and Y. Sakaki. 1994. Fluorescent differential display: arbitrarily primed RT-PCR fingerprinting on an automated DNA sequencer. FEBS Lett. 351:231-236.
61. Ito, T., and Y. Sakaki. 1997. Fluorescent differential display. Methods Mol. Biol. 85:37-44.
62. Johnson, S. W., N. A. Lissy, P. D. Miller, J. R. Testa, R. F. Ozols, and T. C. Hamilton. 1996. Identification of zinc finger mRNAs using domain-specific differential display. Anal. Biochem. 236:348-352.
63. Jones, S. W., D. Cai, O. S. Weislow, and B. Esmaeli-Azad. 1997. Generation of multiple mRNA fingerprints using fluorescence-based differential display and an automated DNA sequencer. BioTechniques 22:536-540, 542-543.
64. Jorgensen, M., M. Bevort, T. S. Kledal, B. V. Hansen, M. Dalgaard, and H. Leffers. 1999. Differential display competitive polymerase chain reaction: an optimal tool for assaying gene expression. Electrophoresis 20:230-240.
65. Joshi, L., and R. J. St Leger. 1999. Cloning, expression, and substrate specificity of MeCPA, a zinc carboxypeptidase that is secreted into infected tissues by the fungal entomopathogen Metarhizium anisopliae. J. Biol. Chem. 274:9803-9811.
66. Joshi, L., R. J. St. Leger, and D. W. Roberts. 1997. Isolation of a cDNA encoding a novel subtilisin-like protease (PrlB) from the entomopathogenic fungus, Metarhizium anisopliae using differential display-RT-PCR. Gene 197:1-8.
67. Jurecic, R., R. G. Nachtman, S. M. Colicos, and J. W. Belmont. 1998. Identification and cloning of differentially expressed genes by long-distance differential display. Anal. Biochem. 259:235-244.
68. Jurecic, R., T. Nguyen, and J. W. Belmont. 1996. Differential mRNA display using anchored oligo-dT and long sequence-specific primers as arbitrary primers. Trends Genet. 12:502-504.
69. Kim, S. J., J. Zheng, S. T. Hiremath, and G. K. Podila. 1998. Cloning and characterization of a symbiosis-related gene from an ectomycorrhizal fungus Laccaria bicolor. Gene 222:203-212.
70. Kociok, N., K. Unfried, P. Esser, R. Krott, U. Schraermeyer, and K. Heimann. 1998. The nonradioisotopic representation of differentially expressed mRNA by a combination of RNA fingerprinting and differential display. Mol. Biotechnol. 9:25-33.
71. Lashkari, D. A., J. L. DeRisi, J. H. McCusker, A. F. Namath, C. Gentile, S. Y. Hwang, P. O. Brown, and R. W. Davis. 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 94:13057-13062.
72. Lee, J. S., S. Scala, Y. Matsumoto, B. Dickstein, R. Robey, Z. Zhan, G. Altenberg, and S. E. Bates. 1997. Reduced drug accumulation and multi-drug resistance in human breast cancer cells without associated P-glycoprotein or MRP overexpression. J. Cell. Biochem. 65:513-526.
73. Liang, P., L. Averboukh, and A. B. Pardee. 1993. Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimization. Nucleic Acids Res. 21:3269-3275.
74. Liang, P., and A. B. Pardee. 1992. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967-971.
75. Liang, P., and A. B. Pardee. 1994. Differential display of mRNA by PCR, p. 15.8.1-15.8.8. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), Current protocols in molecular biology, suppl. 26. Greene Publishing Associates, Inc., New York, N.Y.
76. 35S as a label for the differential display of eukaryotic messenger RNA. Science 267:1186-1187.
77. Liang, P., W. Zhu, X. Zhang, Z. Guo, O. C. RP, L. Averboukh, F. Wang, and A. B. Pardee. 1994. Differential display using one-base anchored oligo-dT primers. Nucleic Acids Res. 22:5763-5764.
78. Lim, J. S., S. H. Lee, E. Lee, Y. Kang, J. W. Kim, J. K. Kim, H. H. Kim, C. Lee, S. J. Kim, G. H. Bai, H. G. Lee, K. D. Kim, T. W. Chung, and Y. K. Choe. 1997. Differential expression of ferritin heavy chain in THP-1 cells infected with Mycobacterium bovis BCG. Biochem. Mol. Biol. Int. 43:981-988.
79. Linskens, M. H., J. Feng, W. H. Andrews, B. E. Enlow, S. M. Saati, L. A. Tonkin, W. D. Funk, and B. Villeponteau. 1995. Cataloging altered gene expression in young and senescent cells using enhanced differential display. Nucleic Acids Res. 23:3244-3251.
80. Livesey, F. J., and S. P. Hunt. 1996. Identifying changes in gene expression in the nervous system: mRNA differential display. Trends Neurosci. 19:84-88.
81. Lohmann, J., H. Schickle, and T. C. Bosch. 1995. REN display, a rapid and efficient method for nonradioactive differential display and mRNA isolation. BioTechniques 18:200-202.
82. Loros, J., S. A. Denome, and J. C. Dunlap. 1989. Molecular cloning of genes under control of the circadian clock in Neurospora. Science 243:385-388.
83. Luce, M. J., and P. D. Burrows. 1998. Minimizing false positives in differential display. BioTechniques 24:766-768, 770.
84. Luehrsen, K. R., L. L. Marr, E. van der Knaap, and S. Cumberledge. 1997. Analysis of differential display RT-PCR products using fluorescent primers and GENESCAN software. BioTechniques 22:168-174.
85. Lurton, J., T. M. Rose, G. Raghu, and A. S. Narayanan. 1999. Isolation of a gene product expressed by a subpopulation of human lung fibroblasts by differential display. Am. J. Respir. Cell Mol. Biol. 20:327-331.
86. Malhotra, K., L. Foltz, W. C. Mahoney, and P. A. Schueler. 1998. Interaction and effect of annealing temperature on primers used in differential display RT-PCR. Nucleic Acids Res. 26:854-856.
87. Martin, K. J., C. P. Kwan, O. H. MJ, A. B. Pardee, and R. Sager. 1998. Identification and verification of differential display cDNAs using gene-specific primers and hybridization arrays. BioTechniques 24:1018-1026.
88. Martin, K. J., and A. B. Pardee. 1999. Principles of differential display. Methods Enzymol. 303:234-257.
89. Martin-Laurent, F., P. Franken, and S. Gianinazzi. 1995. Screening of cDNA fragments generated by differential RNA display. Anal. Biochem. 228:182-184.
90. Maser, R. L., and J. P. Calvet. 1995. Analysis of differential gene expression in the kidney by differential cDNA screening, subtractive cloning, and mRNA differential display. Semin. Nephrol. 15:29-42.
91. Mathieu-Daude, F., R. Cheng, J. Welsh, and M. McClelland. 1996. Screening of differentially amplified cDNA products from RNA arbitrarily primed PCR fingerprints using single strand conformation polymorphism (SSCP) gels. Nucleic Acids Res. 24:1504-1507.
92. Mathieu-Daude, F., T. Trenkle, J. Welsh, B. Jung, T. Vogt, and M. McClelland. 1999. Identification of differentially expressed genes using RNA fingerprinting by arbitrarily primed polymerase chain reaction. Methods Enzymol. 303:309-324.
93. Matz, M., N. Usman, D. Shagin, E. Bogdanova, and S. Lukyanov. 1997. Ordered differential display: a simple method for systematic comparison of gene expression profiles. Nucleic Acids Res. 25:2541-2542.
94. McClelland, M., F. Mathieu-Daude, and J. Welsh. 1995. RNA fingerprinting and differential display using arbitrarily primed PCR. Trends Genet. 11:242-246.
95. Miele, G., L. MacRae, D. McBride, J. Manson, and M. Clinton. 1998. Elimination of false positives generated through PCR re-amplification of differential display cDNA. BioTechniques 25:138-144.
96. Miller, F. R., N. Barnbabas, X. Liu, B. Wang, and J. Park. 1999. Differential display, subtractive hybridization, and application of methodology to search for point mutations to identify genetic defects responsible for progression in MCF10AT model of human breast disease. Electrophoresis 20:256-260.
97. Mirbod, F., S. Nakashima, Y. Kitajima, M. A. Ghannoum, R. D. Cannon, and Y. Nozawa. 1996. Molecular cloning of a gene encoding translation initiation factor (TIF) from Candida albicans. J. Med. Vet. Mycol. 34:393-400.
98. Mohr, S., P. Cullen, R. Schmidt, A. Cignarella, and G. Assmann. 1997. Avoidance of false positives in PCR-based mRNA differential display during investigation of nonstandardized tissues or cells. Clin. Chem. 43:182-184.
99. Muhlschlegel, F. A., W. A. Fonzi, L. Hoyer, T. Payne, F. M. Poulet, J. Clevenger, J.-P. Latge, A. Beauvais, S. Paris, M. Monod, J. Sturtevant, M. Ghannoum, Y. Nozawa, and R. Calderone, 1998. Molecular mechanisms of virulence in fungus-host interactions. J. Med. Vet. Mycol. 36(Suppl. 1):238-248.
100. Munoz, C. I., and A. M. Bailey. 1998. A cutinase-encoding gene from Phytophthora capsici isolated by differential-display RT-PCR. Curr. Genet. 33:225-230.
101. Nag, D. K., and J. Axelrod. 1998. Identification of yeast meiosis-specific genes by differential display. Methods 16:423-433.
102. Ofir, R., S. Horowitz, Q. Wu, and Y. Weinstein. 1998. The ftsZ gene as a tool for detection of Mycoplasma fermentans. Mol. Cell. Probes 12:85-92.
103. Pardinas, J. R., N. J. Combates, S. M. Prouty, K. S. Stenn, and S. Parimoo. 1998. Differential subtraction display: a unified approach for isolation of cDNAs from differentially expressed genes. Anal. Biochem. 257:161-168.
104. Park, K. S., J. Kwon, and S. Y. Choi. 1998. Cloning, characterization, and expression of the CIP2 gene induced under cadmium stress in Candida sp. FEMS Microbiol. Lett. 162:325-330.
105. Perfect, J. R., B. Wong, Y. C. Chang, K. J. Kwon-Chung, and P. R. Williamson. 1999. Cryptococcus neoformans: virulence and host defences. Med. Mycol. 36:79-86.
106. Pesole, G., S. Liuni, G. Grillo, P. Belichard, T. Trenkle, J. Welsh, and M. McClelland. 1998. GeneUp: a program to select short PCR primer pairs that occur in multiple members of sequence lists. BioTechniques 25:112-117, 120-123.
107. Pienkowska, M., J. Dimitroulakos, M. Zielenska, P. Thorner, N. Plavsic, H. Yeger, and J. A. Squire. 1996. Selection of probes for fluorescence in situ hybridization analysis by differential display polymerase chain reaction of mRNA from rhabdomyosarcoma. Cancer Genet. Cytogenet. 92:58-65.
108. Planitzer, S. A., A. W. Machl, D. Schindler, and M. Kubbies. 1998. Small deletions in the regulatory 3′ UTR of the human alpha-tropomyosin gene identified by differential display. Mol. Cell. Probes 12:35-40.
109. Porta, A., S. Colonna-Romano, I. Callebaut, A. Franco, L. Marzullo, G. S. Kobayashi, and B. Maresca. 1999. An homologue of the human 100-kDa protein (p100) is differentially expressed by Histoplasma capsulatum during infection of murine macrophages. Biochem. Biophys. Res. Commun. 254: 605-613.
110. Prashar, Y., and S. M. Weissman. 1996. Analysis of differential gene expression by display of 3′ end restriction fragments of cDNAs. Proc. Natl. Acad. Sci. USA 93:659-663.
111. Prashar, Y., and S. M. Weissman. 1999. READS: A method for display of 3′-end fragments of restriction enzyme-digested cdnas for analysis of differential gene expression. Methods Enzymol. 303:258-271.
112. Ragno, S., I. Estrada, R. Butler, and M. J. Colston. 1997. Regulation of macrophage gene expression following invasion by Mycobacterium tuberculosis. Immunol. Lett. 57:143-146.
113. Ragno, S., I. Estrada-Garcia, R. Butler, and M. J. Colston. 1998. Regulation of macrophage gene expression by Mycobacterium tuberculosis: down-regulation of mitochondrial cytochrome c oxidase. Infect. Immun. 66:3952-3958.
114. Rajeevan, M. S., I. M. Dimulescu, E. R. Unger, and S. D. Vernon. 1999. Chemiluminescent analysis of gene expression on high-density filter arrays. J. Histochem. Cytochem. 47:337-342.
115. Reed, M. B., T. W. Spithill, R. A. Strugnell, and M. Panaccio. 1998. Fasciola hepatica: stage-specific expression of novel gene sequences as identified by differential display. Exp. Parasitol. 89:169-179.
116. Reeves, S. A., M. P. Rubio, and D. N. Louis. 1995. General method for PCR amplification and direct sequencing of mRNA differential display products. BioTechniques 18:18-20.
117. Renner, C., L. Trumper, J. P. Pfitzemmeier, U. Loftin, K. Gerlach, I. Stehle, A. Wadle, and M. Pfreundschuh. 1998. Differential mRNA display at the single-cell level. BioTechniques 24:720-722, 724.
118. Rindi, L., N. Lari, and C. Garzelli. 1999. Search for genes potentially involved in Mycobacterium tuberculosis virulence by mRNA differential display. Biochem. Biophys. Res. Commun. 258:94-101.
119. Rivera-Marrero, C. A., M. A. Burroughs, R. A. Masse, F. O. Vannberg, D. L. Leimbach, J. Roman, and J. J. Murtagh, Jr. 1998. Identification of genes differentially expressed in Mycobacterium tuberculosis by differential display PCR. Microb. Pathog. 25:307-316.
120. Robinson, L., A. Panayiotakis, T. S. Papas, I. Kola, and A. Seth. 1997. ETS target genes: identification of egr1 as a target by RNA differential display and whole genome PCR techniques Proc. Natl. Acad. Sci. USA 94:7170-7175.
121. Rohrwild, M., R. S. Alpan, P. Liang, and A. B. Pardee. 1995. Inosine-containing primers for mRNA differential display. Trends Genet. 11:300.
122. Rompf, R., and G. Kahl. 1997. mRNA differential display in agarose gels. BioTechniques 23:28, 30, 32.
123. Rosok, O., J. Odeberg, M. Rode, T. Stokke, S. Funderud, E. Smeland, and J. Lundeberg. 1996. Solid-phase method for differential display of genes expressed in hematopoietic stem cells. BioTechniques 21:114-121.
124. Ross, R., K. Kumpf, and A. B. Reske-Kunz. 1997. PCR-amplified cDNA probes for verification of differentially expressed genes. BioTechniques 22:894-897.
125. Russell, M. E., A. Raisanen-Sokolowski, and U. Utans. 1997. Differential mRNA display. Adaption for in vivo studies of diseased tissues. Methods Mol. Biol. 85:233-247.
126. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
127. Saporito-Irwin, S. M., C. E. Birse, P. S. Sypherd, and W. A. Fonzi. 1995. PHR1, a pH-regulated gene of Candida albicans, is required for morphogenesis. Mol. Cell. Biol. 15:601-613.
128. Saravitz, D. M., and J. N. Siedow. 1996. The differential expression of wound-inducible lipoxygenase genes in soybean leaves. Plant Physiol. 110: 287-299.
129. Schena, M., D. Shalon, R. W. Davis, and P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA mi-croarray. Science 270:467-470.
130. Schwiebert, L. M., J. L. Mooney, S. Van Horn, A. Gupta, and R. P. Schleimer. 1997. Identification of novel inducible genes in airway epithelium. Am. J. Respir. Cell Mol. Biol. 17:106-113.
131. Seehaus, K., and R. Tenhaken. 1998. Cloning of genes by mRNA differential display induced during the hypersensitive reaction of soybean after inoculation with Pseudomonas syringae pv. glycinea. Plant Mol. Biol. 38: 1225-1234.
132. Shepard, B. D., and M. S. Gilmore. 1997. Identification of virulence genes in Enterococcus faecalis by differential display polymerase chain reaction. Adv. Exp. Med. Biol. 418:777-779.
133. Shoham, N. G., T. Arad, R. Rosin-Abersfeld, P. Mashiah, A. Gazit, and A. Yaniv. 1996. Differential display assay and analysis. BioTechniques 20:182-184.
134. Smith, N. R., M. Aldersley, A. Li, A. S. High, T. P. Moynihan, A. F. Markham, and P. A. Robinson. 1997. Automated differential display using a fluorescently labeled universal primer. BioTechniques 23:274-279.
135. Smith, N. R., A. Li, M. Aldersley, A. S. High, A. F. Markham, and P. A. Robinson. 1997. Rapid determination of the complexity of cDNA bands extracted from DDRT-PCR polyacrylamide gels. Nucleic Acids Res. 25: 3552-3554.
136. Sompayrac, L., S. Jane, T. C. Burn, D. G. Tenen, and K. J. Danna. 1995. Overcoming limitations of the mRNA differential display technique. Nucleic Acids Res. 23:4738-4739.
137. Tawe, W. N., M. L. Eschbach, R. D. Walter, and K. Henkle-Duhrsen. 1998. Identification of stress-responsive genes in Caenorhabditis elegans using RT-PCR differential display. Nucleic Acids Res. 26:1621-1627.
138. Thelu, J., J. Burnod, V. Bracchi, and P. Ambroise-Thomas. 1994. Identification of differentially transcribed RNA and DNA helicase-related genes of Plasmodium falciparum. DNA Cell Biol. 13:1109-1115.
139. 33P-labeled primer increases the sensitivity and specificity of mRNA differential display. BioTechniques 18: 424-425.
140. Trentmann, S. M., E. van der Knaap, and H. Kende. 1995. Alternatives to 35S as a label for the differential display of eukaryotic messenger RNA. Science 267:1186-1187.
141. VanBogelen, R., E. Schiller, J. Thomas, and F. Neidhardt. 1999. Diagnosis of cellular states of microbial organisms using proteomics. Electrophoresis 20:2149-2159.
142. Vanden Bossche, H., F. Dromer, I. Improvisi, M. Lozano-Chiu, J. H. Rex, and D. Sanglard. 1999. Antifungal drug resistance in pathogenic fungi. Med. Mycol. 36:119-128.
143. Velculescu, V. E., L. Zhang, B. Vogelstein, and K. W. Kinzler. 1995. Serial analysis of gene expression. Science 270:484-487.
144. Verweij, P. E., D. Poulain, T. Obayashi, T. F. Patterson, D. W. Denning, and J. Ponton. 1999. Current trends in the detection of antigenaemia, metabolites and cell wall markers for the diagnosis and therapeutic monitoring of fungal infections. Med. Mycol. 36:146-155.
145. Viviani, M. A., S. De Mareie, J. R. Graybill, H. Yamaguchi, E. Anaissie, and D. Caillot. 1999. New approaches in antifungal chemotherapy. Med. Mycol. 36:194-206.
146. Vogeli-Lange, R., N. Burckert, T. Boller, and A. Wiemken. 1996. Rapid selection and classification of positive clones generated by mRNA differential display. Nucleic Acids Res. 24:1385-1386.
147. von der Kammer, H., C. Albrecht, M. Mayhaus, B. Hoffmann, G. Stanke, and R. M. Nitsch. 1999. Identification of genes regulated by muscarinic acetylcholine receptors: application of an improved and statistically comprehensive mRNA differential display technique. Nucleic Acids Res. 27: 2211-2218.
148. Wang, X., and G. Z. Feuerstein. 1995. Direct sequencing of DNA isolated from mRNA differential display. Biotechniques 18:448-453.
149. Wang, X., and G. Z. Feuerstein. 1997. The use of mRNA differential display for discovery of novel therapeutic targets in cardiovascular disease. Cardiovasc. Res. 35:414-421.
150. Wang, X., X. Li, and G. Z. Feuerstein. 1998. Use of novel downstream primers for differential display RT-PCR. BioTechniques 24:382-384, 386.
151. Welburn, S. C., S. Lillico, and N. B. Murphy. 1999. Programmed cell death in procyclic form Trypanosoma brucei rhodesiense - identification of differentially expressed genes during con A induced death. Mem. Inst. Oswaldo Cruz 94:229-234.
152. Wong, L., M. Y. Lue, C. A. Chang, Y. L. Lin, and E. C. Chan. 1996. Helicobacter pylori induces gene expression in human gastric cells identified by mRNA differential display. Biochem. Biophys. Res. Commun. 228: 484-488.
153. Zehntner, S. P., A. Mackay-Sim, and G. R. Bushell. 1998. Differentiation in an olfactory cell line. Analysis via differential display. Ann. N. Y. Acad. Sci. 855:235-239.
154. Zhao, S., G. Molnar, J. Zhang, L. Zheng, L. Averboukh, and A. B. Pardee. 1998. 3′-end cDNA pool suitable for differential display from a small number of cells. BioTechniques 24:842-850, 852.
155. Zhao, S., S. L. Ooi, and A. B. Pardee. 1995. New primer strategy improves precision of differential display. BioTechniques 18:842-846, 848, 850.
156. Zhao, X. J., J. T. Newsome, and R. L. Cihlar. 1998. Up-regulation of two Candida albicans genes in the rat model of oral candidiasis detected by differential display. Microb. Pathog. 25:121-129.