Department of Molecular Microbiology, Washington University in St. Louis, School of Medicine

 

 

 

Douglas E. Berg

Professor
Phone, office: (314)-362-2772
Phone, lab: (314)-362-2771
FAX: (314)-362-1232
email: berg@borcim.wustl.edu

8220 McDonnell Pediatric Research Building
Box 8230 Department of Molecular Microbiology
Washington University School of Medicine
660 South Euclid Avenue
St. Louis, MO 63110-1093

 

Research Interests | CV | Publications | Technology for licensing

Research Interests

We study Helicobacter pylori (Hp), a genetically diverse species that chronically infects the gastric mucosa of billions of people worldwide. It constitutes a major cause of peptic ulcers and gastric cancer, even though most infections are asymptomatic. Infections seem poised on a “knife edge”, always provoking some inflammation, which provides nutrients for bacterial growth while being insufficient for pathogen clearance. The following three projects illustrate our current research directions.

1) Hp population genetics. Our analysis of housekeeping gene sequences of Hp from different human populations showed that East Asian and Spanish strains are distinct, whereas strains from urban Peruvian Amerindians (collected by collaborator Dr. Robert Gilman) are mostly Spanish-like, whereas strains from a remote Amazonian population are Asian-like. Perhaps Hp brought to the Americas by European conquerors were more robust than ancestral Amerindian strains, and outcompeted them during mixed infection.

2) Interplay with host. We found that many Hp strains can infect mice, and that “specialist” Hp strains can infect some inbred mouse lines (e.g., DBA/2) far better than others (e.g. BALB/c). Certain pairs of mouse-colonizing H. pylori strains differ in preferred sites of stomach colonization, and thus can coexist during chronic infection. Among strains that do not differ in gastric tropism, some are more vigorous than others. This mouse infection model should allow experimental tests of interpretations gleaned from human population studies (1, above). Selection and analysis of increased-vigor or expanded-host-range Hp mutants or recombinants should allow definition of bacterial factors important in vivo.

3) Evolution in real time. In collaboration with Dr. Tom Albert, we implemented a very efficient microarray-hybridization method for finding point mutations anywhere in a bacterial genome. Using this and new genetic analysis strategies, we are analyzing mutations in the multiple genes that allow stepwise emergence of high level resistance to the important anti-Hp agent metronidazole (Mtz). Many of these mutations diminish the ability of cells to convert Mtz from prodrug to bactericidal agent (chemical reduction). One special class alters Hp’s novel “Fur” [iron and pH responsive] regulatory protein. These analyses should give valuable insights into protein structure-function and regulatory circuitry, serve as a general model for studies and understanding of complex, important genetic traits, with implications for the new discipline of “systems biology”.



  • Field of specializtion: Microbial Genetics and Pathogenesis

    CV


    Date and place of birth: September 21, 1943; Mt. Vernon, New York
    Citizenship: U.S.A.

    Education
    1964B.S. Botany, Cornell University, Ithaca, New York
    1969 Ph.D. Genetics, University of Washington, Seattle

    Professional Experience and Appointments
    1991-Present Alumni Endowed Professor of Molecular Microbiology
    Professor of Genetics, and Professor of Medicine
    Washington University School of Medicine. St. Louis, Missouri, 63110
    1964-1969Graduate Fellow and Teaching Assistant (Genetics),
    University of Washington (with Dr. Jonathan A. Gallant) Thesis: Berg, D. E. 1969. Recombinant formation in partially diploid strains of Escherichia coli. Ph.D. dissertation, University of Washington.
    1969-1971 USPHS Postdoctoral Fellow,
    Stanford University Medical School, Department of Biochemistry (with Dr. A. Dale Kaiser).
    1971-1975 Research Associate,
    University of Geneva, Department of Molecular Biology (with Dr. Lucien G. Caro).
    1975-1977 Research Associate,
    University of Wisconsin, Department of Biochemistry (with Dr. Julian Davies).
    1977-1981 Assistant Professor,
    Washington University School of Medicine, Departments of Microbiology & Immunology and of Genetics
    1981-1983 Associate Professor,
    Washington University School of Medicine, Departments of Microbiology & Immunology and of Genetics
    1984-1990 Professor,
    Washington University School of Medicine, Departments of Microbiology & Immunology and of Genetics
    1990-Present Alumni Endowed Professor of Molecular Microbiology
    Washington University School of Medicine
    2004-Present Professor, Department of Medicine
    Washington University School of Medicine

    Editorial service
    1985-1990Associate Editor, Genetics
    Jan. 1991-1993 Associate Editor, Plasmid
    Jan. 1992-present Editorial Board, Journal of Bacteriology
    Jan. 1995-present Journal of Clinical Microbiology

    Honors
      Honorary Doctor of Medicine, University of Umeå, Sweden
      Membership in American Academy of Microbiology

    Publications

    1. Berg, D.E. 1971. Regulation of phage with duplications of the immunity region. In "The Bacteriophage Lambda" (ed. by A.D. Hershey), Cold Spring Harbor Press, pp. 667-678.

    2. Berg, D.E. and J.A. Gallant.  1971.  Tests of reciprocality in crossingover in partially diploid F' strains of Escherichia  coli.  Genetics 68: 457-472.

    3. Berg, D.E.  1974.  Genetic evidence for two types of gene arrangements in new ldv plasmid mutants.  J. Mol. Biol. 86:  59-68.

    4. Chow, L.T., Davidson, N. and Berg, D. 1974.  Electron microscope study of the structure of  ldv DNAs.  J. Mol. Biol. 86: 69-89.

    5. Kellenberger-Gujer, G., Boy de la Tour, E. and Berg, D.E. 1974.  Transfer of the ldv plasmid to new bacterial hosts.  Virology 58: 576-585.

    6. Berg, D.E. 1974.  Genes of phage l essential for ldv plasmids.  Virology 62: 224-233.

    7. Berg, D.E., Jackson, D.A. and Mertz, J.E. 1974.  Isolation of a ldv plasmid carrying the bacterial gal  operon.  J. Virology 14: 1063-1069.

    8. Berg, D.E. and Kellenberger-Gujer, G. 1974.  N protein causes the ldv plasmid to inhibit heteroimmune phage limm434 growth and stimulates ldv replication.  Virology 62: 234-241, 1974.

    9. Matsubara, K. and Berg, D. 1974.  The regulation of replication of ldv plasmid.  In"Proceedings First Intersectional Congress of the International Association Microbiological Societies", Tokyo, Japan, pp. 223-228.

    10. Berg, D.E., J. Davies, B. Allet and J. -D. Rochaix. 1975.  Transposition of R factor genes to bacteriophage l.  Proc. Natl. Acad. Sci. USA 72: 3628-3632.

    11. Berg, D.E. 1977.  Insertion and excision of the transposable kanamycin resistance determinant Tn5.  In "DNA Insertion Elements, Plasmids and Episomes" (ed. by A.I. Bukhari, J.A. Shapiro and S.L. Adhya), Cold Spring Harbor Press. pp.205-212.

    12. Berg, D.E. 1977.  Detection of transposable antibiotic resistance determinants using phage lambda.  In"DNA Insertion Elements, Plasmids, and Episomes" (ed. by A.I. Bukhari, J.A. Shapiro, and S.L. Adhya,), Cold Spring Harbor Press, pp.555-558.

    13. Campbell, A., Berg, D.E., Botstein, D., Novick, R. and Starlinger, P. 1977.  Nomenclature of transposable elements in prokaryotes.  In"DNA Insertions" (ed. by S. Adhya, A. Bukhari, and J. Shapiro).  Cold Spring Harbor Press, pp.15-22.

    14. Davies, J., Courvalin, P. and Berg, D.E. 1977.  Thoughts on the origins of resistance plasmids.  J. Antimicrob. Chemotherapy 3: (Suppl. c) 7-17.

    15. Davies, J., Berg, D., Jorgensen, R., Fiandt, M.T., Huang, S.R., Courvalin, P. and Schloff, J. 1977.  Transposable neomycin phosphotransferases.  In"Vienna Symposium on R Factors: Their Properties and Possible Control" (ed. by J. Drews and G. Hogenauer), Springer-Verlag, pp.101-114.

    16. Berg, D.E., Jorgensen, R. and Davies, J. 1978.  Transposable kanamycin-neomycin resistance determinants.  In"Microbiology 1978" (ed. by D. Schlessinger), ASM Publications, pp. 13-15.

    17. Jorgensen, R., Berg, D.E. and Reznikoff, W. 1978.  Genetic organization in the transposable tetracycline  resistance  determinant  Tn10.  In"Microbiology 1978" (ed. by D. Schlessinger),ASM Publications, pp. 181-183.

    18. Berg, D.E. and Drummond, M. 1978.  Absence of DNA sequences homologous to transposable element Tn5 (Kan) in the chromosome of Escherichia  coli K-12.  J. Bacteriol. 136: 419-422.

    19. Jorgensen, R.A., Berg, D.E., Allet, B. and Reznikoff, W. 1979.  A restriction endonuclease map of Tn10, a transposon which encodes tetracycline resistance. J. Bacteriol. 137: 681-685.

    20. Campbell, A., Berg, D.E., Botstein, D., Lederberg, E.M., Novick, R.P., Starlinger, P. and Szybalski, W. 1979.  Nomenclature of transposable elements in bacteria.  Gene 5: 197-206, and Plasmid 2: 466-473.

    21. Berg, D.E., Weiss, A. and Crossland, L. 1980.  The polarity of Tn5  insertion mutations in Escherichia  coli.  J. Bacteriol. 142:  439-446. 

    22. Berg, D.E. 1980.  Control of gene expression by a mobile recombinational switch.  Proc. Natl. Acad. Sci. USA 77: 4880-4884.

    23. Berg, D.E., Egner, C., Hirschel, B.J., Howard, J., Jorgensen, R.A. and Tlsty, T.D. 1980.  Insertion, excision and inversion of transposon Tn5.  Cold Spring Harbor Symposium Quantitative Biology  45:  115-123.

    24. Berg, C., Shaw, K., and Berg, D. 1980.  IlvG is expressed in Escherichia  coli K-12.  Gene 12: 324-333.

    25. Egner, C. and Berg, D. 1981.  Excision of transposon Tn5 dependent on the inverted repeats but not the transposase function of Tn5.  Proc. Natl. Acad. Sci. USA.  78: 459-463.

    26. Kuner, J.M., Avery, L.M., Berg, D.E. and Kaiser, A.D. 1981.  Uses of transposon Tn5 in the genetic analysis of Myxococcusxanthus.  In"Microbiology 1981" (ed. by D. Schlessinger), ASM Publications, pp. 128-132.

    27. Berg, C.M. and Berg, D.E. 1981.  Transposons as tools in microbial genetics.  In"Microbiology 1981" (ed. by D. Schlessinger), ASM Publications, pp. 107-116.

    28. Berg, C.M., Shaw, K.J., Sarokin, L.J. and Berg, D.E. 1981.  Probing the organization of bacterial operons with transposons.  In"Microbiology 1981" (ed. by D. Schlessinger), ASM Publications, pp.121-123.

    29. Berg, D.E., Sasakawa, C., Hirschel, B.J., Johnsrud, L., McDivittt, L., Egner, C. and Ramabhadran, R. 1981.  Transposition of the long inverted repeats of Tn5.  In"Molecular Biology, Pathogenicity and Ecology of Bacterial Plasmids".  (ed. by S. Levy, R. Clowes and E. Koenig), Plenum Press, pp. 381-390.

    30. Hirschel, B.J. and Berg, D.E. 1982.  A derivative of Tn5 with direct terminal repeats can transpose.  J. Mol. Biol. 155:  105-120.

    31. Berg, D.E., Johnsrud, L., McDivitt, L., Ramabhadran, R. and Hirschel, B.J. 1982.  The inverted repeats of Tn5  are transposable elements.  Proc. Natl. Acad. Sci. USA 79: 2632-2635.

    32. Sasakawa, C. and Berg, D.E. 1982.  IS50 mediated inverse transposition: Discrimination between the two ends of an IS element.  J. Mol. Biol. 159: 257-271.

    33. Hirschel, B.J., Galas, D.J., Berg, D.E. and Chandler, M. 1982.  Structure and stability of transposon 5-mediated cointegrates.  J. Mol. Biol. 159: 557-580.

    34. Sasakawa, C., Lowe, J.B., McDivitt, L. and Berg, D.E. 1982.  Control of transposon Tn5 transposition in  Escherichia  coli.  Proc. Natl. Acad. Sci. USA 79: 7450-7454.

    35. Berg, D.E., Lowe, J.B., Sasakawa, C., and McDivitt, L. 1982.  The mechanism and control of Tn5 transposition.  In:  Fourteenth Stadler Genetics Symposium (ei) University of Missouri Press  pp. 5-28.

    36. Berg, D.E. 1983.  Structural requirement for IS50-mediated gene transposition.  Proc. Natl. Acad. Sci. USA 79: 792-796.

    37. Berg, D.E., Egner, C. and Lowe, J.B. 1983.  Mechanism of F factor enhanced excision of transposon Tn5.  Gene 22: 1-7.

    38. Lowe, J.B. and Berg, D.E. 1983.  A product of the transposase gene of Tn5 inhibits Tn5 transposition.  Genetics 103: 581-592.

    39. Berg, D.E. and Berg, C.M. 1983.  The prokaryotic transposable element Tn5.  Biotechnology 1: 417-435.

    40. Berg, C.M., Grullon, C., Wang, A., Whalen, W. and Berg, D.E. 1983.  Generalized and specialized transduction of Tn5 by bacteriophage P1. Genetics 105: 252-263.

    41. Hartl, D., Dyhuizen, D. and Berg. D.E. 1983.  Accessory DNAs in bacteria: Playground for coevolution.  In "The Origins and Development of Adaptation".  CIBA Foundation Symposium No. 102:  233-245.

    42. Berg, D.E., Schmandt, M. and Lowe, J.B. 1983.  Specificity of transposon Tn5 insertion.  Genetics 105: 813-828.

    43. Sasakawa, C., Carle, G. and Berg, D.E. 1983.  Sequences essential for transposition at the termini of IS50.  Proc. Natl. Acad. Sci. USA 80: 7293-7297.

    44. Berg, D.E., Berg, C.M., and Sasakawa, C. 1984.  The bacterial transposon Tn5: Evolutionary inferences.  Molecular Biology and Evolution 1: 411-422.

    45. Biel, S.W., Adelt, G. and Berg, D.E. 1984.  Transcriptional control of IS1 transposition. J.Mol. Biol. 174: 251-264.

    46. Berg, C.M. and Berg, D.E. 1984.  Jumping genes:  The transposable DNAs of bacteria.  The American Biology Teacher 46: 431-439.

    47. Berg, D.E., Phadnis, S.H. and Biel, S.W. 1984.  Conservative and replicative transposition in bacteria.  Proc. XV Int'l Congress Genetics.  Vol. 1: 119-130.

    48. Biel. S.W. and Berg, D.E. 1984.  Mechanism of IS1 transposition in E. coli : Choice between simple insertion and cointegration.  Genetics 108: 319-330.

    49. Berg, D.E. 1984.  Mechanisms of transposition in bacteria.  InPlasmids in Bacteria (ed. by D.R. Helinski, S.N. Cohen, D.B. Clewell, D.A. Jackson, and A.E. Hollaender) Plenum Press, New York, pp. 33-44.

    50. Berg, D.E., Lodge, J.K., Sasakawa, C., Nag, D. K., Phadnis, S.H., Weston, K., and Carle, G.F. 1984.  Transposon Tn5: Specific sequence recognition and conservative transposition.  Cold Spring Harbor Symposium Quant. Biol. 49: 215-226.

    51. Lodge, J.K., Weston-Hafer, K., Lowe, J.B., Dodson, K.W. and Berg, D.E. 1984.  Determinants of Tn5 insertion specificity.  "Genome Rearrangement", UCLA Symposia on Molecular Biology 20: 37-42.

    52. Phadnis, S.H., and Berg, D.E. 1985.  RecA-independent recombination between repeated IS50 elements is not due to an IS50--encoded resolvase. J. Bacteriol. 161: 928-932.

    53. Nag, D.K., DasGupta, U., Adelt, G., and Berg, D.E. 1985.  IS50-mediated inverse transposition:  Specificity and precision.  Gene 34: 17-26.

    54. Sasakawa, C., Phadnis, S.H., Carle, G.F., and Berg, D.E. 1985.  Sequences essential for IS50 transposition:  The first base pair.  J. Mol. Biol. 182: 487-493.

    55. Phadnis, S.H., Sasakawa, C. and Berg, D.E. 1986.  Localization of action of the IS50-encoded transposase protein.  Genetics 112: 421-427.

    56. Berg, C.M. and Berg, D.E. 1987.  Uses of transposable elements and maps of known insertions.  In "Escherichia  coliandSalmonella  typhimurium:  Cellular and Molecular Biology" (ed. by Neidhardt, F.C., Ingraham, J. Low, K.B., Magasanik, B., Schaechter, M., and Umbarger, H.E.) American Society for Microbiology, Washington, D.C., pp 1071-1109.

    57. Nag, D.K. and Berg, D.E. 1987.  Specificity of bacteriophage Mu excision.  Molecular and General Genetics 207:  395-401.

    58. Dasgupta, U., Weston-Hafer, K. and Berg, D.E. 1987.  Local DNA sequence control of deletion formation in Escherichia  coli  plasmid pBR322. Genetics 115: 41-49.

    59. Phadnis, S.H. and Berg, D.E. 1987.  Identification of base pairs in the IS50  O end needed for IS50 and Tn5 transposition.  Proc Natl Acad Sci 84:  9118-9122.

    60. Berg, D.E., Kazic, T., Phadnis, S.H. Dodson, K.W. and Lodge, J.K. 1988.  Mechanism and regulation of transposition.  In:  Transposition (ed. by Kingsman, A., Kingsman, S. and Chater, K.)  Society for General Microbiology 34: 107-129.  Cambridge University Press.

    61. Nag, D.K., Huang, H.V. and Berg, D.E. 1988.  Bidirectional chain termination DNA sequencing:  Transposon Tn5-seql as a mobile source of primer sites.  Gene 64: 135-145.

    62. Chow, W.-Y., W. and Berg, D.E. 1988.  Tn5tacl, a derivative of transposon Tn5 that generates conditional mutations.  Proc Natl Acad Sci 85:  6468-6472.

    63. Lodge, J.K., Weston-Hafer, K., and Berg, D.E. 1988. Transposon Tn5 target specificity:  Preference for insertion at GC pairs.  Genetics 20: 645-650.

    64. Berg, D.E. 1989.  Transposon Tn5.  In:  "Mobile DNA" (ed. by Berg, D.E. and Howe, M.M.) American Society for Microbiology, Washington, D.C. pp. 185-210.

    65. Berg, C.M., Berg, D.E., and Groisman, E. 1989.  Transposable elements and genetic engineering of bacteria.  In:  "Mobile DNA" (ed. by Berg, D.E. and Howe, M.M.) American Society for Microbiology, Washington, D.C. pp. 879-925.

    66. Berg, D.E. 1989.  Transposable elements in prokaryotes.  In:  "Gene Transfer in the Environment":(ed. by Levy, S.B. and Miller, R.) McGraw-Hill, New York.  pp. 99-137.

    67. Dodson, K.W. and Berg, D.E. 1989.  Factors affecting the use of IS50 ends during transposition.  Gene 76: 206-213.

    68. Weston-Hafer, K., and Berg, D.E. 1989.  Palindromy and the location of deletion endpoints in E. coli.  Genetics121: 651-658.

    69. Lodge, J.K., Kazic, T., and Berg, D.E. 1989.  Formation of supercoiling domains in plasmid pBR322. J. Bacteriol.171: 2181-2187.

    70. Berg, C.M., Liu, L., Coon, M., Strausbaugh, L.D., Gray, P., Vartak, N.B., Brown, M., Talbot, D., and Berg, D.E. 1989.  pBR322-derived multicopy plasmids harboring large inserts are often dimers in Escherichia  coli  K-12.  Plasmid 21: 138-141.

    71. Weston-Hafer, K., and Berg, D.E. 1989. Specificity of deletion events in pBR322. Plasmid 21: 251-253.

    72. Phadnis, S.H., Huang, H.V., and Berg, D.E. 1989. Tn5supF, a 264 bp transposon derived from Tn5 for insertion mutagenesis and sequencing of DNAs cloned in phage l.  Proc. Natl. Acad. Sci., USA 86:5908-5912.

    73. Tomcsanyi, T., and Berg, D.E. 1989.  Mutations in the O end of insertion sequence IS50 (Tn5):  Effect of adenine (dam) methylation. J Mol Biol209 191-193.

    74. Dodson, K.W. and Berg, D.E. 1989.  Saturation mutagenesis of the inside end of IS50.  Gene85:75-81.

    75. Berg, D.E. 1990.  Conditional mutations in procaryotes.  In The Bacterial Chromosome (ed. Drlica, K. and Riley, M.).  American Soc. Microbiol., Washington D.C.  pp. 15-26.

    76. Berg, D.E., 1990.  DNA rearrangements in prokaryotes.  In "Frontiers in Molecular Biology: Genome Rearrangement and Amplification" (ed. Hames, B.D. and Glover, D.) IRL Press, Oxford. pp. 1-50.

    77. Cookson, B. T., Berg, D. E. and Goldman, W. E. 1990.  Mutagenesis of Bordetella pertussis with transposon Tn5tac1: conditional expression of virulence-associated genes. J. Bacteriol.172:1681-1687.

    78. Kazic, T., and Berg, D. E. 1990. Context effects in the formation of deletions in Escherichia coli.. Genetics126:17-24.

    79. Lodge, J.K. and Berg, D.E. 1990. Mutations that affect Tn5 insertion into pBR322: Importance of Local DNA supercoiling  J. Bact. 172: 5956-5960.

    80. Tomcsanyi, T., Berg, C. M., Phadnis, S. H. and Berg, D. E.  1990. Intramolecular transposition by a synthetic IS50 (Tn5) derivative. J. Bact. 172:6348-6354

    81. Cookson, B.T., Tomcsanyi, T., Berg, D. E. and Goldman, W. E. 1990. A strategy for studying pathogenic mechanisms: Transposon insertion mutations with conditional phenotypes. In C. R. Manclark (ed.), Proceedings of the Sixth International Symposium on Pertussis. Department of Health and Human Services, U.S. Public Health Service, Bethesda, MD [DHHS Publication (FDA) 90-1163] pp. 243-250.

    82. Weston-Hafer, K. and Berg, D. E.  1991. Limits to the role of palindromy in deletion formation. J. Bact.  173:315-318

    83. Phadnis, S. H., Kulakauskas, S., Krishnan, B. R., Hiemstra, J. and Berg,  D. E.  1991. Transposon Tn5supF-based reverse genetic method for mutational analysis of Escherichia coli with DNAs cloned in l phage. J. Bact. 173:896-899.

    84. Weston-Hafer, K. and Berg, D.E.  1991. Deletions in plasmid pBR322: replication slippage involving leading and lagging strands. Genetics127:649-655

    85. Dodson, K. W., and Berg, D.E. 1991. A sequence at the inside end of IS50 down regulates transposition. Plasmid25:145-148.

    86. Krishnan, B.R., Blakesley, R.W. and Berg, D.E. 1991. Linear amplification sequencing of DNAs in single phage plaques and bacterial colonies. Nucleic Acids Res. 19:1153.

    87. Kulakauskas, S., Wikström, P.M. and Berg, D.E.  1991. Efficient introduction of cloned mutant alleles into the E. coli chromosome. J. Bact.173: 2633-2638.

    88. Lodge, J. K., Weston-Hafer, K., and Berg, D. E. 1991.  Tn5 insertion specificity is not influenced by IS50 end sequences in target DNA.  Molec. Gen Genet. 228:312-315.

    89. Berg, D. E., Kersulyte, D., Krishnan, B. R., and Berg, C. M. 1991. Transposon Tn5 and its use in genome analysis. Proceedings of the First Taiwan Symposium on Transposable Elements.

    90. Berg, C.M., Wang, G. and Berg, D. E. 1991. Transposon gd (Tn1000): useful for large-scale sequencing of cloned DNAs. Proceedings of the First Taiwan Symposium on Transposable Elements.

    91. Krishnan, B. R., Kersulyte, D., Brikun, I., Berg, C. M. and Berg, D. E. 1991. Direct and crossover PCR amplification to facilitate Tn5supF-based sequencing of l phage clones. Nucleic Acids Res. 19:6177-6182

    92. Neuwald, A. F., Krishnan, B. R., Brikun, I., Kulakauskas, S., Suziedelis, K., Tomcsanyi, T., Leyh, T. S. and Berg, D. E.  1992. cysQ, a gene needed for cysteine synthesis in Escherichia coli K-12 only during aerobic growth. J. Bacteriol. 174:415-425.

    93. Berg, C.M., Vartak, N. B., Wang, G., Xu, X.-X., Liu, L., MacNeil, D. J., Gewain, K., M., Wiater, L. A., and Berg, D. E.  1992. mgd-1, a small gd (Tn1000) derivative useful for plasmid mutagenesis, allele replacement and DNA sequencing.  Gene113:9-16.

    94. Krishnan, B. R., Kersulyte, D., Brikun, I., Huang, H. V., Berg, C. M. and Berg, D. E. 1993. Transposon-facilitated sequencing of DNAs cloned in phage l. Methods in Enzymology  (ed. by R. Wu)  218:258-279.

    95. Berg, C. M., Wang, G., Strausbaugh, L. D. and Berg, D. E. 1993. Transposon-facilitated sequencing of DNAs cloned in plasmids Methods in Enzymology (ed. by R. Wu)  218:279-306.

    96. Persson, B. C., Gustafsson, C., Berg, D. E. and Bjork, G. R. 1992 The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli . Proc. Natl. Acad. Sci., USA 89:3995-3998.

    97. Neuwald, A. F., Berg, D. E., and Stauffer, G. V. 1992. Mutational analysis of the Escherichia coli serB gene promoter region reveals transcriptional linkage to a downstream gene. Gene 120:1-9

    98. Wikström, P. M., Lind, L. K., Berg, D. E. and Björk, G. R. 1992. The importance of mRNA folding and start codon accessibility in the expression of genes in a ribosomal protein operon of Excherichia coli   J. Mol. Biol.224:949-966.

    99. Kersulyte, D., Krishnan, B. R. and Berg, D. E. 1992.  Nonrandom orientation of transposon Tn5supF insertions in phage lambda.  Gene 114:91-96.

    100. Akopyanz, N., Bukanov, N. O., Westblom, T. U., Kresovich, S. and Berg, D. E.  1992.  DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting.  Nuc Acids Res. 20:5137-5142.

    101. Kersulyte, D., Woods, J. P.,  Keath, E. J., Goldman, W. E. and Berg, D. E. 1992. Diversity among clinical isolates of Histoplasma capsulatum detected by RAPD  DNA fingerprinting. J. Bacteriol.174:7075-7079.     

    102. Akopyanz, N., Bukanov, N. O., Westblom, T. U., and Berg, D. E.  1992. PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nuc. Acids Res. 20:6221-6225.

    103. Kasai, H., Isono, S., Kitakawa, M., Mineno, J., Akiyama, H., Kurnit, D., Berg, D.E. and Isono, K. 1992.Efficient large scale sequencing of the Escherichia coli genome: Implementation of  a transposon- and PCR-based strategy for the analysis of overlapping _ phage clones. Nuc Acids Res 20:6509-6515.

    104. Krishnan, B. R. and Berg, D. E. 1993. Viability of folA-null derivatives of wild type (thyA+) Escherichia coli K-12. J. Bacteriol. 175:909-911.

    105. Neuwald, A. F., Krishnan, B. R., Ahrweiler, P. M., Frieden, C. and and Berg, D. E. 1993. Conditional dihydrofolate reductase deficiency due to transposon Tn5tac1 insertion downstream of the folA gene in Escherichia coli. Gene125:69-73.

    106. Woods, J. P., Kersulyte, D., Goldman, W. E. and Berg, D. E. 1993.  Fast DNA isolation from Histoplasma capsulatum: Methodology for arbiotrary primer PCR-based epidemiological and clinical studies. J. Clin. Microbiol.31:463-464.

    107. Berg, C. M., Wang, G., Isono, K., Kasai, H. and Berg, D. E. 1993. Transposon-facilitated large scale DNA sequencing. In "Automated DNA Sequencing and Analysis Techniques" (ed. C. Venter). Academic Press, London  pp. 51-59.

    108. Wang, G., Berg, C. M., Chen, J.-M., Yong, A. C., Blakesley, R. W., Lee, L.-Y. and Berg, D. E. 1993. Creating nested deletions for sequencing cosmid DNAs. Focus 15:47-49.

    109. Wang, G., Blakesley, R. W., Berg, D. E. and Berg, C. M. 1993. pDUAL: a transposon-based cosmid cloning vector for generating nested deletions and DNA sequencing templates in vivo. Proc. Natl. Acad. Sci. USA 90:7874-7878.

    110. Wang, G., Whittam, T.S., Berg, C.M. and Berg, D.E.   1993.  RAPD (arbitrary primer) PCR is more sensitive than multilocus enzyme electrophoresis for distinguishing related bacterial strains. Nuc. Acids Res21:5930-5933.

    111. Brikun, I., Suziedelis, K. and Berg, D.E.  1994. DNA sequence diversity among historic strains of Escherichia coli K-12 detected by arbitrary primer PCR (random amplified polymorphic DNA) fingerprinting. J. Bacteriol. 176:1673-1682.

    112. Bukanov, N.O.  and Berg, D.E.  1994. Ordered cosmid library and high resolution physical-genetic map of Helicobacter pylori strain NCTC11638.  Molec. Microbiol. 11:509-523.

    113. Wang, G., Xu, X, Chen, J.-M., Berg, D.E, and Berg, C.M. 1994. Inversions and deletions generated by a mini-gd (Tn1000) transposon. J. Bacteriol. 176:1332-1338 .

    114. Woods, J.P., Kersulyte, D., Tolan, R.W.,  Berg, C.M. and Berg, D.E. 1994. Use of arbitrarily primed polymerase chain reaction analysis to type disease and carrier strains of Neisseria meningitidis isolated during a university outbreak.  J. Inf. Dis. 169:1384-1389.

    115. Berg, C. M. and Berg, D. E. 1994. Transposable elements as tools for molecular analyses in bacteria.  In "Mobile Genetic Elements: Frontiers in Molecular Biology" (ed.  D. Sherratt). Oxford University Press, Oxford, UK. pp. 38-68.

    116. Geary, S. J., Forsyth, M. H., Aboul, Saoud, S., Wang, G., Berg, D. E. and Berg, C. M. 1994. Mycoplasma gallisepticum strain differentiation by arbitrary primer PCR (RAPD) fingerprinting. Molec. Cell. Probes8:311-316.

    117. Berg, D. E., Akopyants, N. and Kersulyte, D. 1994. Fingerprinting microbial genomes using the RAPD or AP-PCR method. Methods inMolec. Cell. Biology 5:13-24.

    118. Bukanov, N., Ravi, N., Miller, D., Srivastava, K. and Berg, D.E. 1994. Pseudomonas aeruginosa  isolates from corneal ulcers distinguished using the arbitrarily primed PCR DNA fingerprinting method. Current Eye Res.13:783-790.

    119. Akopyants, N. S., Eaton, K. A. and Berg, D. E. 1995. Adaptive mutation and co-colonization during Helicobacter pylori infection of gnotobiotic piglets. Infect Immun. 63:116-121

    120. Krishnan, B.R., Jamry, I. Berg, D. E., Berg, C. M. and Chaplin, D.D. 1995.  Construction of a genomic DNA "Feature Map" by sequencing from nested deletions: Application to the HLA class I region. Nucl. Acids Res. 23:117-122.

    121. Taylor, N. S., Fox, J. G.,  Akopyants, N.S., Berg, D. E., Thompson, N., Shames, B., Yan, L., Fontham, E., Janney, F., Hunter, F. M., and Correa, P. 1995. Long term colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting. J. Clin. Microbiol. 33:918-923.

    122. Madico, G., N. S. Akopyants and D. E. Berg, 1995.  Arbitrarily primed PCR DNA fingerprinting of Escherichia coli O157:H7 strains using templates from boiled cultures.   J. Clin. Microbiol. 33:1534-1536.

    123. Kersulyte, D., M. J. Struelens, A. Deplano and D. E. Berg.  1995.  Comparison of arbitrarily primed PCR and macrorestriction (pulsed field gel electrophoresis) typing of Pseudomonas aeruginosa strains from cystic fibrosis patients. J. Clin. Microbiol. 33: 2216-2219

    124. Persson, B. C., G. O. Bylund, D. E. Berg and P. M. Wikström. 1995.  A functional analysis of the ffh-trmD region of the Escherichia coli chromosome using reverse genetics.   J. Bacteriol. 177:5554-5560.

    125. Drazek, E. S., A. Dubois, R. K. Holmes, D. Kersulyte, N.S. Akopyants, D. E. Berg and R. L. Warren. 1995.  Cloning and characterization of hemolytic genes from Helicobacter pylori.  Infect. Immun. 63: 4345-4349.

    126. LaBanca, F., Krishnan, B.R., Chaplin, D.D., Berg, D. E. and Berg, C. M. 1995. "Drop-out" restriction mapping: construction of a 35 kb restriction map using nested deletions. Gene164:335-339

    127. Berg, D. E. 1995. Genética molecular de Helicobacter pylori.  In "Helicobacter pylori: Microbiologia clinica y tratamiento". (edited and translated by M. Lopez-Brea) Mosby/Doyma Libros, Madrid. pp. 84-116.

    128. Berg, C. M. and D. E. Berg 1996. Transposable element tools for microbial genetics.  In "Escherichia  coliandSalmonella  typhimurium: Cellular and Molecular Biology II" (ed. by Neidhardt, F.C., Curtiss, R. III, Gross, C., Ingraham, J., Lin, E. C. C., Low, K.B., Magasanik, B., Reznikoff, W. S., Riley, M., Schaechter, M., and Umbarger, H.E.) American Society for Microbiology, Washington, D.C., pp 2588-2612.

    129. Brikun, I., K. Suziedelis, O. Stemmann, R. Zhong, L. Alikhanian, E. Linkova, A. Mironov and D. E. Berg. 1996. Analysis of crp-cytR interactions at the Escherichia coli udp promoter.  J. Bacteriol. 178:1614-1622.

    130. Vasquez, A., Y. Valdez, R. H. Gilman, J. J. McDonald, T. U. Westblom, D. Berg, H. Kayta, V. Gutierrez and the Gastrointestinal Physiology Working Group of Universidad Peruana Cayetano Heredia and The Johns Hopkins University. 1996. Metronidazole and clarithromycin resistance in Helicobacter pylori determined by measuring MICs of antimicrobial agents in color indicator egg yolk agar in a miniwell format. J. Clin. Microbiol. 34:1232-1234.

    131. Dubois, A., D. E. Berg, E. T. Incecik, N. Fiala, L. M. Heman-Ackah, G. I. Perez-Perez, and M. J. Blaser. 1996. Transient and persistent infection of nonhuman primates with Helicobacter pylori: implications for human disease.  Inf & Immun 64:2885-2891. 

    132. Lebedev, Y., Akopyants, N., Azhikina, T., Shevchenko, Y., Potapov, V., Stecenko, D, Berg, D. and Sverdlov, E. 1996. Oligonucleotides containing 2-aminoadenine and 5-methylcytosine are more effective as primers for PCR amplification than their nonmodified counterparts. Genetic Analysis: Biomolecular Engineering 13:15-21.

    133. Azhikina, T., Kostina, M., Skaptsova, N., Potapov, V., Berg, D. and Sverdlov, E. 1996.  Factors affecting priming efficiency of short contiguous oligonucleotide strains in the primer walking strategy of DNA sequencing. DNA sequence: the journal of sequencing and mapping. 6: 211-216.

    134. Swenson, DL, Bukanov, NO, Berg, DE and Welch, RA. 1996. Two pathogenicity islands in uropathogenic Escherichia coli J96: cosmid cloning and sample sequencing. Inf. & Immun. 64:3736-3743.

    135. Logan, R. P. H. and Berg, D. E. 1996. Genetic diversity of Helicobacter pylori. Lancet 348:1462-1463.

    136. Berg, D. E. J. Lelwala-Guruge, E. T. Incecik, K. Srivastava and N. S. Akopyants. 1997. Helicobacter pylori DNA fingerprinting using the arbitrarily primed PCR (AP-PCR) or random amplified polymorphic DNA (RAPD) method.  In "Methods in Molecular Medicine: Helicobacter pylori"(ed. by C. Clayton and H. Mobley) Humana Press, Totowa, NJ pp. 117-132.

    137. Dubois, A., and D. E. Berg. 1997. The non-human primate model for H. pylori infection.  In "Methods in Molecular Medicine: Helicobacter pylori"(ed. by C. Clayton and H. Mobley) Humana Press, Totowa, NJ pp 253-269.

    138. Akopyants, NS, Jiang, Q, Taylor, DE and Berg, DE. 1997. Corrected identity of isolates of Helicobacter pylori strain NCTC11637.  Helicobacter.  2:48-52

    139. Berg, D. E. and Logan, R. P. H. 1997. Helicobacter pylori, individual host specificity and human disease. Bioessays 19:86-90.

    140. Woods, JP, Berg, DE, and Fisher, KL. 1997 Extraction of Histoplasma capsulatum DNA for PCR. In Fingerprinting Methods Based on PCR, M.R. Micheli and R. Bova (eds), Heidelberg, Springer-Verlag, in press.

    141. Cover, T, Berg, D.E., and Blaser, M. J. 1997. VacA and the cag pathogenicity island of Helicobacter pylori. In "The Immunobiology of H. pylori: from pathogenesis to prevention. In Ernst, P.B., Michetti, P., and Smith, P.D.  Lippincott-Raven, Philadelphia, PA  pp 75-90.

    142. Tomb, J.F. White, O.,Kerlavage, A.R., Clayton, R.A., Sutton, G.G., Fleischmann, R.D., Ketchum, K.A. Klenk, H.P., Gill, S., Dougherty, B.A., Nelson, K., Quackenbush, J., Zhou, L., Kirkness, E.F., Peterson, S., Loftus, B., Richardson, D., Dodson, R.,Khalak, H.G., Glodek, A., McKenney, K., Fitzegerald, L.M., Lee, N., Adams, M.D., Hickey, E.K., Berg, D.E., Gocayne, J.D., Utterback,T.R., Peterson, J.D., Kelley, J.M., Cotton, M.D., Weidman, J.M., Fujii, C., Bowman, C., Watthey, L., Wallin, E., Hayes, W.S., Borodovsky, M., Karp, P.D., Smith, H.O., Fraser, C.M. and Venter, J.C. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori   Nature 388, 539-547.

    143. Berg DE, Gilman RH, Lelwala-Guruge J, Srivastava K, Valdez Y, Watanabe J, Miyagi J, Akopyants NS, Ramirez-Ramos A, Yoshiwara TH, Recavarren S, Leon-Barua R. 1997 Helicobacter pylori Populations in Individual Peruvian Patients. Clin. Inf. Dis.  25:996-1002.

    144. Berg, D.E., Hoffman, P. S., Appelmelk, B.J. and Kusters, J.G. 1997. The Helicobacter pylori genome sequence: genetic factors for long life in the gastric mucosa. Trends Microbiol. 5:468-474

    145. Gzyl, A., Berg, D. E. and Dzierzanowska. 1997 Epidemiology of cagA/vacA genes in H. pylori isolated from children and adults in Poland. J. Physiol Pharmac. 48:333-343.

    146. Ilver, D., Arnqvist, A., Ogren, J., Frick, I-M., Kersulyte, D., Incecik, E. T., Berg, D. E., Covacci, A., Engstrand, L. and Boren, T. 1998 The Helicobacter pylori Lewis b blood group antigen binding adhesin revealed by retagging. Science 279: 373-377

    147. Dubois, A., Berg, D.E., Fiala, N., Heman-Ackah, L.M., Perez-Perez, G. and Blaser, M.J.  1998 Cure of Helicobacter pylori infection by omeprazole-clarithromycin-based therapy in non-human primates. J. Gastro. 33:18-22.

    148. Akopyants, N. S., Clifton, S. W., Kersulyte, D., Crabtree, J.E., Youree, B.E., Reece, C.A.,  Bukanov, N. O., Drazek, E. S., Roe, B. A. and Berg, D. E. 1998 Analyses of the cag pathogenicity island of Helicobacter pylori. Molec. Microbiol. 28:37-54

    149. Goodwin, A., Kersulyte, D., Sisson, G., Veldhuyzen van Zanten, S. J. O.,  Berg, D. E. and Hoffman, P. S. 1998. Metronidazole-Resistance in Helicobacter pylori is caused by null mutations in a gene (rdxA) that encodes an NADPH Linked Flavin Nitroreductase Activity. Molec. Microbiol. 28:383-393.

    150. Kersulyte, D., Akopyants, N.S., Clifton, S.W., Roe, B.A. and Berg, D. E. 1998. Novel sequence organization and insertion specificity of IS605 and IS606: chimaeric transposable elements of Helicobacter pylori. GENE 223:175-186

    151. Höök-Nikanne, J., Berg, D. E., Peek, R. R., Kersulyte, D. Tummuru, M. K. R. and Blaser, M.J.. DNA sequence conservation and diversity in transposable element IS605 of Helicobacter pylori. Helicobacter 3:79-85.

    152. Guruge, J. L., Falk, P. G., Lorenz, R. G., Dans, M., Wirth, H.-P., Blaser, M. J., Berg, D. E. and Gordon, J. I. 1998 Epithelial attachment alters the outcome of Helicobacter pylori infection   Proc. Natl. Acad. Sci., USA 95: 3925-3930.

    153. Pan, Z.-J., Berg, D.E., van der Hulst, R.W.M., Su, W.-W., Raudonikiene, A., Xia, S.-D., Dankert, J., Tytgat, G.N.J. and van der Ende, A.  1998. High prevalence of vacuolating cytotoxin production and unusual distribution of vacA alleles in Helicobacter pylori from China. J. Inf. Dis.178:220-226

    154. McAtee, C.P., Lim M.Y., Fung, K., Velligan, M., Fry, K. and Berg, D.E. Identification of potential diagnostic and vaccine candidates of Helicobacter pylori by two-dimensional gel electrophoresis, sequence analysis and serum profiling. Clin Diagn Lab Immunol. 5:537-42.

    155. McAtee, C.P., Young, M.L., Fung, K., Velligan, M., Fry, K. and Berg, D.E. 1998. Characterization of a Helicobacter pylori vaccine candidate by proteome techniques. J. Chromatog B Biomed Sci Appl 714:325-33.

    156. Zakharova, N., Hoffman, P.S., Berg, D.E. and Severinov, K. 1998. The largest subunits of RNA polymerase from gastric Helicobacters are tethered. J. Biol. Chem 273:19371-19374.

    157. McAtee, C.P. and Berg, D. E. 1998. Identification of potential diagnostic and vaccine candidates of Helicobacter pylori by "proteome" technologies. Helicobacter 3:163-169.

    158. Chalkauskas, H., Kersulyte, D., Cepuliene, I., Urbonas, V., Ruzeviciene, D., Barakauskiene, A., Raudonikiene, A., and Berg, D. E.  1998. Genotypes of Helicobacter pylori in Lithuanian families.  Helicobacter 3: 296-302.

    159. Akopyants,NS, Fradkov, A, Diatchenko,L, Siebert, PD, Lukyanov, S, Sverdlov, ED and Berg, DE. 1998. PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc. Natl. Acad. Sci., USA 95:13108-13113.

    160. Kersulyte, D., Chalkauskas, H. and Berg, D. E.  1999. Emergence of recombinant strains of Helicobacter pylori during human infection. Molec. Microb. 31:31-43.

    161. Dubois, A., Berg, D.E., Incecik, E.T., Fiala, N., Heman-Ackah, L. M., Del Valle, J., Yang, M, Wirth, H.-P., Perez-Perez, G.I. and Blaser, M.J.  1999. Individual host specificity of Helicobacter pylori strains and host responses in experimentally challenged non-human primates. Gastroenterology, 116:90-96.

    162. Gzyl, A., Dzierzanowska, Roznyek, E., Celinska-Cedro, D, Dura, W. and Berg, D. E. 1999. PCR-based diagnosis of Helicobacter pylori in Polish children and adults. J. Med. Micro. 48:349-356.

    163. Raudonikiene, A., Zakharova, N. Su, WW, Jeong, JY, Bryden, L., Hoffman, PS, Berg, D. E. and Severinov, K. 1999 Helicobacter pylori with separate b and b' subunits of RNA polymerase is viable and can colonize mice. Molec Microbiol  32:131-138

    164. Berg, D.E. 1999. Variabilité génomique chez Helicobacter pylori: étendue, signification.  Lettre de l'infectiologue 14 (suppl 1):9-15.

    165. Achtman, M., Azuma, T., Berg, D. E., Ito, Y., Morelli, G., Pan, Z.-J., Suerbaum, S., Thompson, S. A., van der Ende, A. and van Doorn, L.J.  1999. Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Molec. Microbiol. 32:459-470.

    166. Zakharova, N., Wesley, I., Dewhirst, F.E., Paster. B.J., Berg, D.E., and Severinov, K.J. 1999 Fused and overlapping rpoB and rpoC genes in Helicobacters, Campylobacters and related bacteria. J. Bacteriol. 181: 3857-3859

    167. Li, S.D., Kersulyte, D., Lindley, I.J.D., Neelam, B., Berg, D. E. and Crabtree, J. E. 1999. Multiple genes in the cag pathogenicity island of Helicobacter pylori are required for tyrosine kinase dependent transcription of interleukin-8 in gastric epithelial cells. Inf. Immun. 67:3893-3899

    168. Crabtree, J.E., Kersulyte, D., Li, S.D., Lindley, I.J.D., and Berg, D. E. 1999 Modulation of Helicobacter pylori induced IL-8 synthesis in gastric epithelial cells mediated by cag PAI-encoded VirD4 homologue. J. Clin Path.  52:653-657

    169. Debets-Ossenkopp, Y.J., Pot, R.G.J., van Weserloo, D.J., Goodwin, A., Vandenbroucke-Grauls, C.M.J.E., Berg, D.E., Hoffman, P.S. and Kusters, J.G. 1999. Insertion of mini-IS605 and deletion of adjacent sequences in the nitroreductase (rdxA) gene cause metronidazole resistance in Helicobacter pylori NCTC11637.  Antimicrob Agents Chemo. 43:2657-2662.

    170. Dubois, A., Welch, A., Berg, D. E. and Blaser, M. J. 2000 Helicobacter pylori. In "Persistent Bacterial Infections" J.P. Nataro, MJ Blaser and S Cunningham-Rundles eds.  ASM Press, Washington DC.,  pp 263-280.

    171. Monteiro, M. A., MacLean, L. L., Chan, K. H. Pan, Z. J., Yokota, S., Amano, K., Berg, D. E. and Perry, D. E. 2000. Production of histo-blood group antigens by lipopolysaccharides isolated from Chinese and Japanese hosts: comparison of Asian and Western H. pylori lipopolysaccharide molecules. Glycobiology 10:701-713

    172. Mitra, R., Figueroa, P., Mukhopadhyay, A. K., Shimada, T., Takeda, Y., Berg, D. E., and Nair, G. B.  2000. Cell vacuolation, a manifestation of the hemolysin of Vibrio cholerae. Infection and Immunity 68:1928-1933.

    173. Caviedes, L., Lee, T.-S., Gilman, R. H., Sheen, P., Berg, D. E., Montenegro-James, S. and the Tuberculosis Working Group in Peru.  2000 Fast and efficient detection and drug susceptibility testing of Mycobacterium tuberculosis in sputum by microscopic observation of broth cultures. J. Clin Micro. 38:1203-1208

    174. Kersulyte, D., Mukhopadhyay, A. K., Velapatiño, B., Valdez, Y., Su, WW, Pan, ZJ, Hernandez, V., Garcia, C., Gilman, R. H., Kersulyte, D. Mukhopadhyay, A. K., Velapatiño, B., Valdez, Y., Su, WW., Pan, ZJ., Hernandez, V., Garcia, C., Gilman, R. H., Yuan, Y., Gao, H. Watanabe, J., Rodriguez, C., Nair, G. B., Chowdhury, A., Dutta, S., Shirai, M., Nakazawa, T., Alarcon, T., Lopez-Brea, M., Mistry, R. S., Ally, R., Segal, I., Wong, B. C. Y., Lam, S. K., Ogren, J., Engstrand, L., Boren, T., Torres, O., Schneider, R., Thomas, J. E., Czinn, S., and Berg, D. E. 2000 Differences in Genotypes of Helicobacter pylori from Different Human Populations. J. Bacteriol. 182:3210-3218

    175. Mukhopadhyay, A.K., D. Kersulyte, S. Datta, A. Chowdhury, S. Chowdhury, A. Santra, S.K. Bhattacharya, G. B. Nair, and D.E. Berg. 2000 Distinctiveness of genotypes of Helicobacter pylori in Calcutta, India. J. Bacteriol. 182:3219-3227

    176. Wang, W.H., B.C.Y. Wong, A.K. Mukhopadhyay, D.E. Berg, C.H. Cho, K.C. Lai, W.H.C. Hu, F.M.Y. Fung, W.M. Hui, and S.K. Lam, 2000. High prevalence of Helicobacter pylori infection with dual resistance to metronidazole and clarithromycin in Honk Kong. Aliment Pharmacol. Ther. 14: 901-910.

    177. Jeong, J.Y., A.K. Mukhopadhyay, D. Dailidiene, Y. Wang, B. Velapatiño, R.H. Gilman, A.J. Parkinson, G.B. Nair, B.C.Y. Wong, S.K. Lam, R. Mistry, I. Segal, Y. Yuan, H. Gao, T. Alarcon, M. Lopez Brea, Y. Ito, D. Kersulyte, H.K. Lee, Y. Gong, A. Goodwin, P.S. Hoffman, and D.E. Berg.  2000. Sequential inactivation of rdxA (HP0954) and frxA (HP0642) nitroreductase genes cause moderate and high level metronidazole resistance in Helicobacter pylori  J. Bacteriol. 182: 5082-5090.

    178. Sisson, G., J-Y. Jeong, A. Goodwin, L. Bryden, N. Rossler, S. Lim-Morrison, A. Raudonikiene, D.E. Berg, and P.S. Hoffman. 2000. Metronidazole Activation is Mutagenic and Causes DNA Fragmentation in Helicobacter pylori and in Escherichia coli Containing a Cloned H. pylori rdxA (Nitroreductase) Gene. J. Bacteriol. 182:5091-5096

    179. Kersulyte, D., A.K. Mukhopadhyay, M. Shirai, T. Nakazawa, and D.E. Berg. 2000 Functional organization and insertion specificity of IS607, a chimaeric element of Helicobacter pylori.  J. Bacteriol., 182:5300-5308

    180. Kostina M., T. Azhikina, T. Gorodentseva, D. Berg, E. Sverdlov. 2000. Contiguous strings of strongly binding short oligonucleotides as a useful tool for completing sequencing experiments. DNA Seq 10:355-64
    181. Jeong, J. Y. and D.E. Berg. 2000. Mouse colonizing Helicobacter pylori strain SS1 is unusually susceptible to metronidazole due to two complementary reductase activities. Antimicrob. Agents Chemoth. 44:3127-3132.

    182. Cover, T. L., Berg, D. E., Blaser, M. J., and Mobley, H. L. T. 2001. H. pylori pathogenesis.  In "Principles of bacterial pathogensis" (E. A. Groisman, ed.)  Academic Press, NY, pp. 509-558.

    183. Blaser, M. J. and Berg, D. E. 2001. Helicobacter pylori genetic diversity and risk of human disease.  Perspectives.  J. Clin. Investig. 107:767-773.

    184. Figueroa-Arredondo, P., Heuser, J. E., Akopyants, N. S., Morisaki, J. H., Giono-Cerezo, S., Enríquez-Rincón, F., and Berg, D. E. 2001. Cell vacuolation caused by the hemolysin of Vibrio cholerae. Inf. Immun. 69:1613-1624.

    185. Vitkute, J., Stankevicius, K., Tamulaitiene, G., Maneliene, Z., Timinskas, A., Berg, D.E. and Janulaitis, A. 2001. Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695. J. Bact. 183:443-450.

    186. Wong, B.C.Y., Wang, W.H., Berg, D.E., Fung, F.M.Y.,  Wong, K.W., Wong, W.M., Lai, K.C., Cho, C.H., Hui, W.M., and Lam, S.K. 2001. High prevalence of mixed infections by Helicobacter pylori in Hong Kong: Metronidazole sensitivity and overall genotype  Aliment Pharmacol. Ther.  15:493-503

    187. Eaton, K. A., Kersulyte, D., Mefford, M., Danon, S. J., Krakowka, S. and Berg, D. E. 2001. Role of Helicobacter pylori cag region genes in colonization and gastritis in two animal models. Inf and Immun. 69:2902-2908.
    188. McAtee, C. P. Hoffman, P. S. and Berg, D. E. 2001. Identification of differentially regulated proteins in metronidazole resistant Helicobacter pylori by proteome techniques. Proteomics 1:516-521.

    189. Wong, BCY, Yin, Y, Berg, DE, Xia, HHX, Zhang, JZ, Wang, WH, Wong, WM, Huang, XR, Tang, VSY, Lam, SK. 2001. Distribution of distinct vacA, cagA and iceA alleles in Helicobacter pylori in Hong Kong. Helicobacter 6:317-324.

    190. Mukhopadhyay, A.K., Chakraborty, S., Takeda, Y., Nair, G.B., and Berg, D.E. Characterization of VPI pathogenicity island and CTXf prophage in environmental strains of Vibrio cholerae  J. Bact. 183:4737-4746.

    191. Jeong, J. Y., A. K. Mukhopadhyay, J. K. Akada, D. Dailidiene, P. S. Hoffmanand D. E. Berg. 2001. Roles of FrxA and RdxA nitroreductases of Helicobacter pylori in susceptibility and resistance to metronidazole. J. Bact. 183:5155-5162.

    192. Roth DE, Velapatino B, Gilman RH, Su WW, Berg DE, Cabrera L, Garcia. 2001. A comparison of a string test-PCR assay and a stool antigen immunoassay (HpSA) for Helicobacter pylori screening in Peru. Trans R Soc Trop Med Hyg 2001 95:398-399

    193. Datta S, Kurazono H, Chattopadhyay S, Chowdhury A, Chaudhuri S, Bhattacharya SK, Mukhopadhyay AK, Berg DE, Hirayama T, Nair GB. 2001. Estimation of vacuolating cytotoxin secreted by different strains of Helicobacter pylori using bead enzyme-linked immunosorbent assay & its correlation with bacterial genotype. Indian J Med Res. 114:192-8.

    194. Kersulyte, D., Velapatiño, B., Dailide, G., Mukhopadhyay, A. K., Ito, Y., Cahuayme, L., Parkinson, A. J.,  Gilman, R. H. and Berg, D. E.  2002 Transposable element ISHp608 of Helicobacter pylori: non-random geographic distribution, functional organization and insertion specificity. J. Bacteriol 184:992-1002

    195. Chowdhury, A., Berg, D.E., Jeong, J.-Y, Mukhopadhyay, A.K. Nair, G. B. 2002. Metronidazole Resistance in Helicobacter pylori : Magnitude, Mechanism and Implications for India. Indian J. Gastro. 21:23-28.

    196. Datta, S, Chowdhury, A., Mukhopadhyay, AK., Bhattacharya, SK, Berg DE and Nair, GB. Molecular and evolutionary genetics and drug resistance of the gastric pathogen, Helicobacter pylori. 2002. Indian J Med Res115:73-101

    197. Sisson, G, Goodwin, A, Raudonikiene, A, Hughes, NJ, Mukhopadhyay, AK, Berg, DE and Hoffman, PS. 2002. Enzymes associated with reductive activation and action of nitazoxanide, nitrofurans and metronidazole in Helicobacter pylori. Antimicrob Agents Chemotherapy. 46:2116-2123.

    198. Chattopadhyay, S,  Datta,S., Chowdhury, A., Chowdhury, S., Mukhopadhyay, A. K.,  Rajendran, K., Bhattacharya, S. K., Berg, D. E., and Nair, G. B. 2002. Virulence genes in Helicobacter pylori strains from West Bengal residents with overt H. pylori-associated disease and healthy volunteers. J. Clin Microbiol. 40:2262-2625.

    199. Mahdavi, J., Sondén, B., Hurtig, M., Olfat, F., Forsberg, L., Roche, N., Ångström, J., Larsson, T., Teneberg, S., Karlsson, K. A., Altraja, S., Wadström, T., Kersulyte, D., Berg, D. E., Dubois, Petersson, C., Magnusson, K.E., Norberg, T., Lindh, F., Lundskog, B. B. Arnqvist, A., Hammarström, L., and Borén, T. 2002. Helicobacter pylori SabA adhesin in persistent infection and chronic inflammation. Science. 297:573-578.

    200. Dailidiene, D, Bertoli, MT, Miciuleviene, J, Mukhopadhyay, AK, Dailide, G., Pascasio, MA., Kupcinskas, L. and Berg, DE. 2002. Emergence of tetracycline resistance in Helicobacter pylori: multiple mutational changes in 16S rDNA and other genetic loci. Antimicrob Agents Chemotherapy 46:3940-3946.

    201. Wang, W-H, Hu, F-L, Wong, BCY, Berg, DE and Lam S-K. 2002. Inhibitory effects of aspirin and indometacin on the growth of Helicobacter pylori in vitro. Chin. J. Digestive Disease 3:172-177.

    202. Chaudhuri, S., Chowdhury, A., Datta, S. Mukhopadhyay, A. K., Chattopadhya, S., Saha, D. R., Dhali, G., Santra, A., Nair, G.B. Bhattacharya, S. Berg, D. E. 2003.  Anti-Helicobacter pylori therapy in India: differences in eradication efficiency associated with particular alleles of vacuolating cytotoxin (vacA) gene. J. Gastro Hepat. 18:190-195.

    203. Wang, W-H, Wong, WM, Dailidiene, D., Berg, DE, Gu, Q, Lai, K-C, Lam, S-K, Wong, B C-Y. 2003. Aspirin inhibits the growth of Helicobacter pylori and enhances its susceptibility to antimicrobial agents. GUT 52:490-495.

    204. Rahman, M., Mukhopadhyay, A. K., Nahar, S., Datta, S., Mian, M. Sarker. S., Masud, I. M., Engstrand, L., Albert, J. M., Nair, G. B., and Berg, D. E. 2003. DNA level characterization of Helicobacter pylori strains from patients with overt disease and with benign infections in Bangladesh. J. Clin Microbiol. 41:2008-2014.

    205. Mukhopadhyay, A. K. Jeong, J.-Y. Dailidiene, D., Hoffman, P. S. and Berg, D. E. 2003. The fdxA ferredoxin gene can down-regulate frxA nitroreductase gene expression and is essential in many strains of Helicobacter pylori. J. Bact. 185:2927-2935.

    206. Straubinger, R.K., A. Greiter, S. P. McDonough, A. Gerold, E. Scanziani, S. Soldati, D. Dailidiene, G. Dailide, D. E. Berg and K. W. Simpson. 2003. Quantitative evaluation of inflammatory and immune responses in the early stages of Helicobacter pylori infection. Inf Immun. 71:2693-2703.

    207. Akada JK, Ogura K, Dailidiene D, Dailide G, Cheverud JM, and Berg DE. 2003. Helicobacter pylori tissue tropism: Mouse colonizing strains can target different gastric niches. Microbiology, 149:1901-1909.

    208. Kersulyte, D., B. Velapatiño, A. K. Mukhopadhyay, L. Cahuayme, A. Bussalleu, J. Combe, R. H. Gilmanand D. E. Berg. 2003. Cluster of type IV secretion genes in Helicobacter pylori's plasticity zone.  J. Bacteriol. 185:3764-3772

    209. Soto, G., Bautista, C. T. Gilman, R. H., Roth, D. E., Velapatiño, B, Ogura, M., Dailide, G., Razuri, M., Meza, R., Katz, U., Monath, T. P. Berg, D. E. Taylor, D. N. and the Gastrointestinal Physiology Working Group in Peru. 2003. Helicobacter pylori reinfection is common in Peruvian adults following antibiotic eradication therapy.  J. Inf Dis. 188:1263-1275.

    210. Datta, S., Chattopadhyay, S., Nair, GB, Mukhopadhyay, A.K. Hembram, J., Berg, D. E. Saha, D. R., Khan, A., Santra, A., Bhattacharya, S. K. and Chowdhury, A. 2003. Virulence genes and neutral DNA markers of Helicobacter pylori isolated from different ethnic communities of West Bengal, India. J. Clin Microbiol. 41: 3747-3743.

    211. Bury-Moné, S., Skouloubris, S., Dauga, C., Thiberge, J.-M., Dailidiene, D., Berg, D. E., Labigne, A. and Reuse, H. D. 2003. Presence of active aliphatic amidases in Helicobacter species able to colonize the stomach. Inf Immun. 71:5613-5622. 

    212. Wong WM, Gu Q, Wang WH, Fung FM, Berg DE, Lai KC, Xia HH, Hu WH, Chan CK, Chan AO, Yuen MF, Hui CK, Lam SK, Wong BC. 2003. Effects of Primary Metronidazole and Clarithromycin Resistance to Helicobacter pylori on Omeprazole, Metronidazole, and Clarithromycin Triple-Therapy Regimen in a Region with High Rates of Metronidazole Resistance. Clin Infect Dis. 37:882-9.

    213. Dailidiene, D., G. Dailide, K. Ogura, M. Zhang, A. K. Mukhopadhyay, K. A. Eaton, G. Cattoli, J. G. Kustersand D. E. Berg. 2004. Helicobacter acinonychis: genetic and rodent infection studies of an H. pylori-like gastric pathogen of cheetahs and other big cats. J. Bact 186:356-365.

    214. Tan S. and Berg DE. 2004. The motility of urease deficient derivatives of Helicobacter pylori. J. Bact. 186:885-888.

    215. Chattopadhyay S, Patra R, Ramamurthy T, Chowdhury A, Santra A, Dhali GK, Bhattacharya SK, Berg DE, Nair GB, and Mukhopadhyay AK. 2004. Multiplex PCR assay for rapid detection and genotyping of Helicobacter pylori directly from biopsy specimens. J. Clin. Microbiol. 42: 2821-2824.

    216. Aspholm-Hurtig M, Dailide G, Lahmann M, Kalia A, Ilver D, Roche N, Vikström S, Sjöström R, Lindén S, Lundberg C, Bäckström A, Arnqvist A, Mahdavi J, Nilsson UJ, Velapatiño B, Gilman RH, Gerhard M, Alarcon T, López-Brea M, Nakazawa T, Fox JG, Correa, P, Dominguez-Bello MG, Perez-Perez GI, Blaser MJ, Normark S, Carlstedt I, OscarsonS, Teneberg S, Berg DE, Borén T. Functional adaptation of the Helicobacter pylori ABO blood-group antigen-binding adhesin. Science 305:519-522.

    217. Nahar S, Mukhopadhyay AK, Khan R, Mashhud Ahmad M, Datta S, Chattopadhyay S, Sarker S, Engstrand L, Ahmed S, Berg DE, Nair GB, Rahman M. 2004. Antimicrobial susceptibility of Helicobacter pylori strains isolated from Bangladesh. J. Clin. Microbiol. 42:4856-4858.

    218. Kalia A, Mukhopadhyay AK, Dailide G, Ito Y, Azuma T, Wong BCY, and Berg DE. 2004. Evolutionary Dynamics of Insertion Sequences IS605 and IS607 in Helicobacter pylori. J. Bacteriol 186:7508-7520.

    219. Kersulyte D, Kalia A, Zhang M, Lee HK, Subramaniam D, Kiuduliene L, Chalkauskas H, and Berg DE. 2004. Sequence organization and insertion specificity of the novel chimaeric ISHp609 transposable element of Helicobacter pylori. J. Bacteriol. 186: 7521-7528.

    220. McNulty, S. L., Mole, B. M., Dailidiene, D., Segal, S., Ally, R., Secka, O., Adegbola, R. A., Thomas, J. E., Lenarcic, E. M., Peek, Jr., R. M., Berg, D. E., and Forsyth, M. H.. 2004. Novel 180bp and 480 bp insertion/deletions Associated with African and African-American strains of Helicobacter pylori. J. Clin Micro.42:5658-5663.

    221. Bäckström, A., Lundberg, C. Kersulyte, D., Berg, D. E. Borén, T. and Arnqvist, A. 2004. Metastability of Helicobacter pyloribab adhesin genes and dynamics in Lewis b antigen binding. PNAS 101:16923-16928

    222. Suto, H, Zhang, M, and Berg DE. 2005. Age-dependent changes in susceptibility of  suckling mice to individual strains of Helicobacter pylori. Inf Imm 73:1232-1234.

    223. Xia HH, Lam SK, Chan AO, Lin MC, Kung HF, Ogura K, Berg DE, Wong BC. Macrophage migration inhibitory factor stimulated by Helicobacter pylori increases proliferation of gastric epithelial cells.  World J Gastroenterol. 2005 Apr 7;11(13):1946-50.

    224. Datta S, Chattopadhyay S, Patra R, DE R, Ramamurthy T, Hembram J, Chowdhury A, Bhattacharya SK, Berg DE, Nair GB, Mukhopadhyay AK. Most Helicobacter pylori strains of Kolkata in India are resistant to metronidazole but susceptible to other drugs commonly used for eradication and ulcer therapy. Aliment Pharmacol Ther. 2005 22:51-7.

    225. Morris JM, Reasonover AL, Bruce MG, Bruden DL, McMahon BJ, Sacco FD, BergDE, Parkinson AJ. Evaluation of seaFAST, a Rapid Fluorescent In Situ Hybridization Test, for Detection of Helicobacter pylori and Resistance to Clarithromycin in Paraffin-Embedded Biopsy Sections. J Clin Microbiol. 2005 43:3494-6.

    226. Tan, S., Fraley, C. D., Zhang, M., Dailidiene, D., Kornberg, A. and Berg, D. E. 2005 Diverse phenotypes resulting from polyphosphate kinase gene (ppk1) inactivation in different strains of Helicobacter pylori. J. Bacteriol. 187:7687-7695.

    227. Albert TJ, Dailidiene D, DailideG, Norton JE, Kalia A, Richmond TA, Molla M, Singh J, GreenRD, BergDE. 2005. Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori. Nature Methods. 2:951-953.

    228. Velapatiño B, Balqui J, Gilman RH, Bussalleu A, Quino W, Finger SA, Santivañez L, Herrera P, Piscoya A, Valdivia J, Cok J and Berg DE. 2006. Validation of string test for Helicobacter pylori diagnosis. J Clin Micro 44:976-980.

    229. Li GQ, Hua-Xiang Xia H, Chen MH, Gu Q, Wang JD, Peng JZ, Chan AO, Cho CH, So HL, Lam SK, Hu PJ, Liang YJ, Lin HL, Berg DE, Feng ZH, Langenbach R, Wong BC. 2006  Effects of Cyclooxygenase-1 and -2 Gene Disruption on Helicobacter pylori-Induced Gastric Inflammation. J Infect Dis. 193:1037-1046

    230. McMahon, BJ, Bruce MG, Hennessey TW, Bruden DL, Sacco F, Hurlburt DA, Morris JM, Reasonover AL, Dailide G, Berg DE and Parkinson, AJ. 2006. Reinfection after successful eradication of Helicobacter pylori: a two-year prospective study in Alaska Natives. Aliment Pharm Ther, 23:1215-1223.

    231. Wirth, HP, Yang, M, Sanabria-Valentin, E, Berg, DE Dubois, A., Blaser, MJ. 2006. Host Lewis phenotype-dependent Lewis antigen expression in rhesus monkeys. FASEB J (epub May 2006).

    232. Aspholm, M, Kalia, A, Ruhl, S, Schedin, S, Arnqvist, A, Lindén, S, Sjöström, R, Gerhard, M, Semino-Mora, C, Dubois, A, Unemo, M, Danielsson, D, Teneberg, S, Lee, WK, Berg, DE, Borén, T. 2006. Helicobacter pylori adhesion to carbohydrates. Methods in Enzymology (in press).

    233. Finger, S. A., Velapatiño, B. Kosek, M., Santivañez, L., Dailidiene, D., Quino, W., Balqui, J., Herrera, P., Berg, D. E., and Gilman, R. H. 2006. Effectiveness of ERIC-PCR and RAPD fingerprinting for Helicobacter pylori strain differentiation. Appl Env Micro 72:4713-4716

    234. Dailidiene, D., Dailide, G., Kersulyte, D., and Berg, D. E. 2006. Contraselectable streptomycin susceptibility determinant for genetic manipulation and analysis of Helicobacter pylori. Appl. Env. Microbiol 72:5908-5914.

    235. Simpson KW, Dogan B, Rishniw M, Goldstein RE, Klaessig S, McDonough PL, German AJ, Yates RM, Russell DG, Johnson SE, Berg DE, Harel J, Bruant G, McDonough SP, Schukken YH. 2006. Adherent and Invasive Escherichia coli Is Associated with Granulomatous Colitis in Boxer Dogs. Infect Immun. 74:4778-92.

    236. Lee, WK, Ogura K, Loh, JT, Cover, TL, and Berg DE. 2006. Quantitative effect of luxS gene inactivation on Helicobacter pylori fitness. Appl Env Microbiol, in press.

    237. Kundu P, Mukhopadhyay AK, Patra R, Bannerjee A, Berg DE, Swarnakar S. 2006. Cag pathogenicity island independent upregulation of matrix metalloproteinases-9 and -2 secretion and expression in mice by Helicobacter pylori infection. J. Biol. Chem. In press238. Bruce, MG, Bruden DL, McMahon BS, Hennessy TW, Reasonover A, Morris J,Hurlburt DA, PetersH, Sacco F, Martinez P, Swenson M, BergDE, ParksD, ParkinsonAJ. 2006. Alaska Sentinel Surveillance for Antimicrobial Resistance in Helicobacter pylori
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