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БЕСПЛАТНАЯ ЭЛЕКТРОННАЯ БИБЛИОТЕКА - Научные публикации
 


«Peer Reviewed Papers In review: 1. Chris Stockmann, Krow Ampofo, Andrew T. Pavia, Anne J. Blaschke, Benjamin Chan, ...»

Publications

Peer Reviewed Papers

In

review:

1. Chris Stockmann, Krow Ampofo, Andrew T. Pavia, Anne J. Blaschke, Benjamin Chan,

Edwards O. Mason, Larry J. Forney, Carrie L. Byington. (2012). Evidence for Red

Queen Dymanics in Invasive Streptococcus pneumonia Serotypes Following the

Introduction of a Pneumococcal Conjugate Vaccine.

2. Tyerman, JG, JM Ponciano, P. Joyce, LJ Forney, and LJ Harmon. (2012). The

evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms.

In press:

3. Hickey, Roxana J., Z. Abdo, X. Zhou, K. Nemeth, M. Hansmann, TW Osborn III, F.

Wang, L.J. Forney. (2012). Effects of tampons and menses on the temporal dynamics of vaginal microbiota. British Journal of Obstetrics and Gynecology.

4. Witkin, S.S., X. Zhou, G.E. Reya, W.J. Ledger, L.J. Forney. (2012). Bacterial Characterization of Paired Vaginal and Vestibular Samples From women with Vulvar Vestibulitis Syndrome. American Journal of Obstetrics and Gynecology.

Published:

5. Ma, B., L.J. Forney, J. Ravel. (2012). The Vaginal Microbiome: Rethinking Health and Disease. Annual Review of Microbiology, 66(1):d371-89. PMID: 22746335

6. Human Microbiome Project Consortium. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486(7402):207–214. PMID: 22699609

7. Human Microbiome Project Consortium. (2012). A framework for human microbiome research. Nature, 486(7402):215–221. PMID: 22699610

8. Gajer, P., R. M. Brotman, G. Bail, J. Sakamoto, U. M. E. Shutte, X. Zhong, S. S.

Koeng, L. Fu, Z. Ma, X. Zhou, Z. Abdo, L. J. Forney and J. Ravel. (2012). Temporal Dynamics of the Human Vaginal Microbiota. Science Translational Medicine, 4(132):132ra52. PMID: 22553250

9. Hickey, Roxana J., X. Zhou, J.D. Pierson, J.Ravel, L.J. Forney. (2012). Understanding vaginal microbiome complexity from an ecological perspective. Translational Research, 160(4):267-82. PMID: 22683415

10. Ma Z., J. Geng, Z. Abdo and L.J. Forney. (2012). A bird’s eye view of microbial community dynamics. Book chapter in Microbial Ecological Theory: Current Perspectives. Editors: Lesley A. Ogilvie and Penny R. Hirsch. ISBN: 978-1-908230Yuan, S., D. B. Cohen, J. Ravel, Z. Abdo and L. J. Forney. (2012). Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One, 7(3):e33865. PMID: 22457796.

12. Hunt, K. M., Foster, J. A., Forney, L. J., Schtte, U. M. E., Beck, D. L., Abdo, Z., Fox, L. K., et al. (2011). Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS ONE, 6(6):e21313. PMID: 21695057.

13. Copland, W.K., V. Krishnan, D. Beck, M. Settles, J. Foster, KC Cho, M. Day, R.

Hickey, U.M.E. Schutte, X. Zhou, C.J. Williams, L.J. Forney and Z. Abdo. (2011).

mcaGUI: a graphical user interface (GUI) to facilitate analysis of microbial community data. Bioinformatics, 28(16):2198-9. PMID: 22692220.

14. Eastman, J. M., Harmon, L. J., La, H.-J., Joyce, P. and Forney, L. J. (2011). The onion model, a simple neutral model for the evolution of diversity in bacterial biofilms.

Journal of Evolutionary Biology, 24: 2496–2504. PMID: 21929684.

15. Forney, L., Koutchma, T. and Ye, Z. (2011). Characterization and Simulation of Ultraviolet Processing of Liquid Foods Using Computational Fluid Dynamics, in Innovative Food Processing Technologies: Advances in Multiphysics Simulation (eds K. Knoerzer, P. Juliano, P. Roupas and C. Versteeg), Blackwell Publishing Ltd., Oxford, UK. doi: 10.1002/9780470959435.ch14

16. Ma Z., Z. Abdo and L. J. Forney. (2011). Caring about trees in the forest:

incorporating frailty in risk analysis for personalized medicine. Future Medicine, 8: 681PMID: 22754581.

17. Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., et al. (2011). Vaginal microbiome of reproductive-age women.

Proceedings of the National Academy of Sciences, 108 Suppl 1, 4680–4687. PMID:

20534435.

18. Brotman, RM, LL Jones, J. Sakamoto, P. Gajer, K Ault, L Peralta, LJ Forney, Z. Abdo, and J Ravel. (2011). Association between Trichomonas vaginalis and the vaginal microbiota among asymptomatic reproductive-age women in the United States.

Sexually Transmitted Diseases, 39(10), 807-812.

19. Zhou, X., Brotman, R. M., Gajer, P., Abdo, Z., Schette, U., Ma, S., Ravel, J., et al.

(2010). Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth Infectious Diseases in Obstetrics & Gynecology, 2010:737425. PMID: 21197076.

20. Forney, L.J., P. Gajer, C.J. Williams, G.M. Schneider, S. McCulle, S. Karlebach, R.

Brotman, C.C. Davis, K. Ault and J. Ravel. (2010). Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis. J. Clin. Microbiol, 48(5):1741-8. PMID: 20200290.

21. Schtte, U.M.E., Z. Abdo, J. Foster, J. Ravel, J. Bunge, B. Solheim, and L.J. Forney.

(2010). Bacterial diversity in a glacier foreland of the High Arctic. Mol. Ecol. 19:54–66.

PMID: 20331770.

22. Ravel, J., L.J. Forney. (2010). The Microbial Ecology of Bacterial Vaginosis: A Fine Scale Resolution Metagenomic Analysis. Nature Precedings.

http://dx.doi.org/10.1038/npre.2010. 5062.1

23. Sota, M., H. Yano, J. Hughes, G.W. Daughdrill, Z. Abdo, L.J. Forney, and E.M. Top.

(2010). Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J. 4(12):1568-1580. PMID: 20510653.

24. Lim, J.Y., H-J. La, H. Sheng, L.J. Forney, and C.J. Hovde. (2010). Plasmid O157 Influences Escherichia coli O157:H7 Sakai biofilm formation. Appl. Environ. Microbiol.

76(3):963-6. PMID: 19966025.

25. Zhou, X, M.A. Hansmann, H. Suzuki, C.C. Davis, C.J. Brown, U. Schtte, J.D.

Pierson and L.J. Forney. (2010). The vaginal bacterial communities of Japanese women resemble those of women in other racial groups. FEMS Immunol and Med.

Microbiol. 58(2):169-181. PMID: 19912342.

26. Ponciano, J.M., H.J. La, P. Joyce and L.J. Forney. (2009). Evolution of Diversity in Spatially Structured Escherichia coli Populations. Appl. Environ. Microbiol.

75(19):6047-6054. PMID: 19648364.

27. Schtte, U.M.E., Z. Abdo, S.J. Bent, C.J. Williams, G.M. Schneider, B. Solheim, and L.J. Forney. (2009). Bacterial succession in a glacial foreland of the High Arctic. ISME J., 3(11):1258-1268. PMID: 19587774.

28. Hu, B., X. Zhou, L.J. Forney, S. Chen. (2009). Changes in microbial community composition following treatment of methanogenic granules with chloroform.

Environmental Progress and Sustainable Energy 28(1):60-71. doi: 10.1002/ep.10338.

29. Pierson, J.D., M.A. Hansmann, C.C. Davis, and L.J. Forney. (2009). Vaginal microbial communities do not preclude colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1). Thesis. Print

30. Zhou, X, R. Westman, R. Hickey, M.A. Hansmann, C. Kennedy, T.W. Osborn, and L.J. Forney. (2009). Vaginal microbiota of women with frequent vulvovaginal candidiasis. Infect. Immun. 77(9):4130-4135. PMID: 19528218.

31. Yamamoto, T., X. Zhou, A. Hochwalt, L.J. Forney. (2009). Bacterial populations in the vaginas of healthy adolescent women. J. Pediatr Adolesc Gynecol. 22(1):11-18.

PMID: 19232297.

32. Noguez, A.M., A.E. Escalante, L.J. Forney, M. Nava-Mendoza, I. Rosas, V. Souza, F.

Garcia-Oliva. (2008). Soil aggregates in a tropical deciduous forest: effects on C and N dynamics, and microbial communities as determined by t-RFLPs. Biogeochemistry 89: 209-220. doi: 10.1007/s10533-008-9214-7.

33. Suzuki, H., C.J. Brown, L.J. Forney, and E.M. Top. (2008). Comparison of correspondence analysis methods for synonymous codon usage in bacteria. DNA Res., 15(6):357-65. PMID: 18940873.

34. Foster, L., S. Krone, L.J. Forney. (2008). Application of ecological network theory to

the human microbiome. Interdiscip. Perspect Infect Dis., 2008:839501. PMID:

19259330..

35. Schuette, U.M.E., Z. Abdo, S.J. Bent, C. Shyu, C.J. Williams, J.D. Pierson, L.J.

Forney. (2008). Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl. Microbiol. Biotechnol. 80(3):365-380. PMID: 18648804.

36. Escalante, A.E., L.E. Eguiarte, L. Espinosa-Asuar, L.J. Forney, A.M. Noguez and V.

Souza. (2008). Diversity of aquatic prokaryotic communities in the Cuatro Cinegas basin: evidence of highly structured communities. FEMS Microbial Ecol. 65(1):50-60.

PMID: 18479448.

37. Heijs, S.K., A. M. Laverman, L.J. Forney, P.R. Hardoim, and J.D. van Elsas. (2008).

Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol Ecol, 64(3):362–377. PMID: 18422633.

38. Bent, S.J. and L.J. Forney. (2008). The tragedy of the uncommon: understanding

limitations in the analysis of microbial diversity. ISME J 2(7):689-695. PMID:

18463690.

39. Zhou, X., C.J. Brown, Z. Abdo, C.C. Davis, M.A. Hansmann, P. Joyce, J.A. Foster, and L.J. Forney. (2007). Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J, 1(2):121-133.

PMID: 18043622.

40. Shyu, C., T. Soule, T., S.J. Bent, J.A. Foster, and L.J. Forney. (2007). MiCA: A webbased tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb Ecol. 53(4):562PMID:17406775.

41. Brown, C.J., M. Wong, C. Davis, A. Kanti, X. Zhou, and L.J. Forney. (2007).

Preliminary characterization of the normal microbiota of the human vulva using cultivation-independent methods. J Med Microbiol. 56(2):271-276. PMID: 17244812.

42. Bent, S.J., J.D. Pierson, L.J. Forney. (2007). Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl Environ Microbiol.

73(7):2399–2401. PMID: 17403942.

43. Sota, M. M. Tsuda, H. Yano, H. Suzuki, L. J. Forney, and E. M. Top. (2007). RegionSpecific Insertion of Transposons in Combination with Selection for High Plasmid Transferability and Stability Accounts for the Structural Similarity of IncP-1 Plasmids. J Bacteriol. 189(8):3091–3098. PMID: 17277066.

44. Heijs, S.K., G. Alosi. I. Bouloubassi, R.D. Pancost, C. Pierre, J.S. Sinninghe Damste, J.C. Gottschal, J.D. van Elsas, and L.J. Forney. (2006). Microbial community structure in three deep-sea carbonate crusts. Microb Ecol 52(3):451-462. PMID: 16909345.

45. Forney, L.J., J.A. Foster, W. Ledger. (2006). The vaginal flora of healthy women is not always dominated by Lactobacillus sp. J. Infect. Dis. 194(10):1468-1469 [Correspondence]

46. H.-J. Ahn, H.-J.La, and L. J. Forney. (2006). System for measuring differences in fitness among bacterial populations without using selective markers. Appl. Environ.

Microbiol. 72(11):7383–7385. PMID: 16963557.

47. Wu, X.-L. L.J. Forney, and P. Joyce. (2006). Comments on ‘Bayesian hierarchical error model for analysis of gene expression data’. Bioinformatics, 22(19):2446-2451.

PMID: 16731698.

48. Souza, V., L. Espinosa-Asuar, A. Escalante, L. E. Eguiarte, J. Farmer, L. Forney, L.

Lloret, J. M. Rodrguez Martnez, X. Sobern, R. Dirzo and J. J. Elser. (2006). Marine Jurassic microbes in a continental karst setting: evolutionary and conservation implications. Proc. Natl. Acad. Sci (USA) PNAS 103: 6565– 6570.

49. Abdo, Z., U.M.E. Schette, S.J. Bent, C.J. Williams, L.J. Forney, and P. Joyce.

(2006). Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes.

Environ. Microbiol. 8(5): 929–938. PMID: 16623749.

50. De Gelder, L., F.P.J. Vandecasteele, C. J. Brown, L. J. Forney, and E. M. Top. (2005).

Plasmid donor affects host range of the promiscuous IncP-1 plasmid pB10 in an activated sludge microbial community. Appl. Environ. Microbiol. 71(9):5309-5317.

PMID: 16151119.

51. Coolen, M.J., E. Post, C.C. Davis, and L.J. Forney. (2005). Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms (T-RFLPs) of 16S rRNA genes. Appl. Environ.

Microbiol. 71(12):8729-8737. PMID: 16332868.

52. Heijs S.K., J.S. Damste, and L.J. Forney. (2005) Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea. FEMS Microbiol Ecol. 54(1):47-56. PMID: 16329971.

53. Noguez, A. M., H. T. Arita, A. E. Escalante, L. J. Forney, F. Garca-Oliva, and V.

Souza. (2005). Microbial macroecology: Highly structured prokaryotic soil assemblages in a tropical deciduous forest. Global Ecology and Biogeography, 14(3):241-248. doi: 10.1111/j/1466-822X.2005.00156.x.

54. Ponciano, J.M., F. P.J. Vandecasteele, T.F. Hess, L.J. Forney, R.L. Crawford, and P.

Joyce. (2005). Use of stochastic models to assess the effect of environmental factors on microbial growth. Appl. Environ. Microbiol. 71(5):2355-2364. PMID: 15870322.

55. Joyce P., Z. Abdo, J.M. Ponciano, L. De Gelder, L.J. Forney, and E.M. Top. (2005).

Modeling the impact of periodic bottlenecks, unidirectional mutation, and

observational error in experimental evolution. J Math Biol. 50(6):645-662. PMID:

15614551.

56. De Gelder, L., J. M. Ponciano, Z. Abdo, P. Joyce, L. J. Forney, and E. M. Top. (2004).

Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic sensitive mutants in a population of resistant bacteria during experimental evolution. Genetics 168(3):1131-1144. PMID: 15579675.

57. Zhou, X., S.J. Bent, M.G. Schneider, C.C. Davis, M.R. Islam, and L.J. Forney. (2004).

Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology 150(8):2565–2573. PMID: 15289553.

58. Forney, L.J., X. Zhou, and C.J. Brown. (2004). Molecular microbial ecology: land of the one-eyed king. Curr. Opin. Microbiol. 7(3):210–220. PMID: 15196487.

59. Werne, J.P., R.R. Haese, T. Zitter, G. Aloisi, I. Bouloubassi, S. Heijs, A.F. Medioni, R.D. Pancost, J.S. Damste, G. de Lange, LJ. Forney, J.C. Gottschalf, J-P. Foucher, J. Mascle, J. Woodside, and the MEDINAUT and MEDINETH Shipboard Scientific Parties. (2004). Life at cold seeps: a synthesis of biogeochemical and ecological data from Kazan mud volcano, eastern Mediterranean Sea. Chemical Geology 205(3):67– 390.

60. Haack, S.K., L.R. Fogarty, T.G. West, E.W. Alm, J.T. McGuire, D.T. Long,, D.W.

Hyndman, and L.J. Forney. (2004). Changes in microbial community structure over spatial and temporal chemical gradients in a contaminated aquifer. Environ.

Microbiol. 6(5):438–448. PMID: 15049917.

61. Oda, Y. W.G. Meijer, J.L. Gibson, J.C. Gottschal, and L.J. Forney. (2004). Analysis of diversity among 3-chlorobenzoate-degrading strains of Rhodopseudomonas palustris Microbial Ecology 47(1):68–79. PMID: 15259271.

62. Schlter, A., H. Heuer, R. Szczepanowski, L.J. Forney, C.M. Thomas, A. Phler and E.M. Top. (2003). The 64,508 bp IncP-1 antibiotic multiresistance plasmid pB10 isolated from a wastewater treatment plant provides evidence for recombination between members of different branches of the IncP-1 group. Microbiology 149(11):3139-3153. PMID: 14600226.

63. Bent S.J., C.L. Gucker, Y. Oda, and L.J. Forney. (2003). Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale. Appl Environ Microbiol., 69(9):5192-5197. PMID: 12957901.

64. Oda, Y., B. Star, L.A. Huisman, J.C. Gottschal, and L.J. Forney. (2003). Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. Appl. Environ.

Microbiol. 69(9): 5186-5191. PMID: 12957900.

65. Morillas M., C.E. McVey, J.A. Brannigan, A.G. Ladurner, L.J. Forney, and R. Virden.

(2003). Mutations of penicillin acylase residue B71 extend substrate specificity by decreasing steric constraints for substrate binding. Biochem. J. 371(1):143-150.

PMID: 12511194.

66. Oda, Y., W. Wanders, L.A. Huisman, W.G. Huisman, W.G. Meijer, J.C. Meijer, J.C.

Gottschal, and L.J. Forney. (2002). Genotypic and phenotypic diversity within species of purple nonsulfur bacteria isolated from aquatic sediments. Appl Environ Microbiol., 68(7):3467-3477. PMID: 12089030.

67. Tauch A., S. Schneiker, W. Selbitschka, A. Phler, L. S. van Overbeek, K. Smalla, C.

M. Thomas, M. J. Bailey, L. J. Forney, A. Weightman, P. Ceglowski, T. Pembroke, E.

Tietze, G. Schrder, E. Lanka, and J. D. van Elsas. (2002). The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere. Microbiology 148(6):1637-1653. PMID: 12055285.

68. Aloisi, G., I. Bouloubassi, S.K. Heijs, R.D. Pancost, C. Pierre, J.S. Sinninghe Damst, J.C. Gottschal, L.J. Forney, and J. Rouche. (2002). CH4 consuming microorganisms and the formation of carbonate crusts at cold seeps. Earth and Planetary Science Letters 203(1):195-203.

69. Oda, Y., Y.P. de Vries, L.J. Forney, and J.C. Gottschal. (2001). Acquisition of the ability for Rhodopseudomonas palustris to degrade chlorinated benzoic acids as the sole carbon source. FEMS Microbiol. Ecol. 38(3-2):133-139.

70. Boczar B.A., L.J. Forney, W.M. Begley, R.J. Larson, and T.W. Federle. (2001).

Characterization and distribution of esterase activity in activated sludge. Water Res.

35(17):4208-4216. PMID: 11791851.

71. Noordkamp, D. J. B., W. W. C. Gieskes, J. C. Gottschal, L.J. Forney, and M. van Rijssel M. (2000) Acrylate in Phaeocystis colonies does not affect the surrounding bacteria. J. Sea Research 43(3):287-296.

72. Riley, M.S., V.S. Cooper, R.E. Lenski, L.J. Forney, and T.L. Marsh. (2000). Rapid phenotypic radiation of a soil bacterium during experimental evolution for 1000 generations. Microbiology 147(4):995-1006. PMID: 11283295.

73. Liu, W.-T., K.D. Linning, K. Nakamura, T. Mino, T. Matsuo, and L.J. Forney. (2000).

The use of chemotaxonomic and 16S rDNA-based methods to characterize the microbial diversity of biological phosphorus removal systems. Microbiology 145:1099Krooneman J., Sliekers A.O., Pedro Gomes T.M., Forney L.J., and Gottschal J.C.

(2000). Characterization of 3-chlorobenzoate degrading aerobic bacteria isolated

under various environmental conditions. FEMS Microbiol Ecol., 32(1):53-59. PMID:

10779619.

75. Oda, Y., S.-J. Slagman, W.G. Meijer, L.J. Forney, and J.C. Gottschal. (2000).

Influence of growth rate and starvation on fluorescent in situ hybridization of

Rhodopseudomonas palustris. FEMS Microbiol Ecology, 32(3):205-213. PMID:

10858579.

76. Liu, W.-T., K.D. Linning, K. Nakamura, T, Matsuo, and L.J. Forney. (2000). Microbial community changes in biological phosphate-removal systems on altering sludge phosphorus content. Microbiology 146(5):1099-1107. PMID: 10832637.

77. Hyndman, D. W., M. J. Dybas, L.J. Forney, R. Heine, T. Mayotte, M. S. Phanikumar, G. Tatara, J. Tiedje, T. Voice, R. Wallace, D. Wiggert, X. Zhao, C. S. Criddle. (2000).

Hydraulic characterization and design of a full-scale biocurtain. Ground Water, 38(3):

462-474.

78. Noordkamp, D. J. B., W. W. C. Gieskes, J. C. Gottschal, L.J. Forney, and M. van Rijssel M. (2000). Acrylate in Phaeocystis colonies does not affect the surrounding bacteria. J. Sea Research 43(3):287-296.

79. van der Maarel MJ, W. Sprenger, R. Haanstra, and L.J. Forney. (1999). Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species. FEMS Microbiol Lett. 173(1):189-194. PMID: 10220894.

80. Forney, L.J., W-T Liu, M. Nasu, J. B. Guckert, T. Nishihara, E. Namkung, and R.J.

Larson. (1999). Structure of microbial communities in activated sludge: potential implications for assessing biodegradability of chemicals. Ecotoxicol Environ Saf.

49(1):40-53. PMID: 11386714.

81. Dybas, M. J., M. Barcelona, S. Bezborodnikov, S. Davies, L.J. Forney, H. Heuer, O.

Kawka, T. Mayotte, L. Sepulveda-Torres, K. Smalla, M. Sneathen, J. Tiedje, T. Voice, D.C. Wiggert, M.E. Witt, and C.S. Criddle, (1998). Pilot-scale evaluation of bioaugmentation for in situ remediation of a carbon tetrachloride-contaminated aquifer. Environ. Sci. Technol. 32(22):3598-3611.

82. Krooneman, J., S. van der Akker, T.M.P. Gomes, L.J. Forney, and J.C. Gottschal.

(1999). Degradation of 3-chlorobenzoate under low-oxygen conditions in pure and mixed cultures of the anoxygenic photoheterotroph Rhodopseudomonas palustris DCP3 and an aerobic Alcaligenes species. Appl Environ Microbiol., 65(1):131-137.

PMID: 9872770.

83. Skubal, K.L., S.K. Haack, L.J. Forney, and P. Adriaens. (1999). Effects of dynamic redox zonation on the potential for natural attenuation of trichloroethylene at a firetraining-impacted aquifer. Physics and Chemistry of the Earth 24(6):517-527.

84. Krooneman, J., E.R.B. Moore, J.C.L. van Velzen, R.A. Prins, L.J. Forney, and J.C.

Gottschal. (1998). Competition for oxygen and 3-chlorobenzoate between two aerobic bacteria using different degradation pathways. FEMS Microbial Ecol.

26(3):171-179.

85. Noordkamp, D.J.B., M. Schotten, W.W.C. Gieskes, L.J. Forney, J.C. Gottschal, M.

van Rijssel. (1998). High acrylate concentrations in the mucus of Phaeocystis globosa colonies. Aquat Microb Ecol., 16(1):45-52.

86. van der Maarel, R.R.E. Artz, R. Haanstra, and L.J. Forney. (1998). Association of marine archaea with the digestive tracts of two marine fish species. Appl Environ Microbiol. 64(8):2894-2898. PMID: 9687447.

87. Smalla, K., U. Wachtendorf, H. Heuer, W.-T. Liu, and L.J. Forney. (1998). Analysis of BIOLOG GN Substrate Utilization Patterns by Microbial Communities. Appl Environ Microbiol. 64(4):1220-1225. PMID: 16349535.

88. Nakatsu, C.H., R. Korona, R.E. Lenski, F.J. de Bruijn, T.L. Marsh and L.J. Forney.

(1998). Genomic rearrangements observed in Ralstonia sp. during experimental evolution. J. Bacteriol, 180(17):4325-4331. PMID: 9721265.

89. Marsh, T. L., W-T. Liu, and L. J. Forney, (1998). Beginning a molecular analysis of the eucaryal community in activated sludge. Water Sci Tech. 37(4-5):455-460.

90. Liu, W-T., T. L. Marsh, and L. J. Forney, (1998). Determination of the microbial diversity of anaerobic-aerobic activated sludge by a novel molecular biological technique. Water Sci Tech. 37(4-5):417-422.

91. Liu, W-T., T.L. Marsh, L.J. Forney. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rDNA. Appl Environ Microbiol. 63(11):4516-4522. PMID: 9361437.

92. Top, E., P. van Daele and L.J. Forney. (1997). Enhancement of 2,4dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic

plasmids. Antonie van Leeuwenhoek Inter. J. Gen. Mol. Microbiol. 73(1):87-94. PMID:

9602282.

93. Ovreas, L., L.J. Forney, V. Torsvik. (1997). Distribution of bacterioplancton in a

meromictic lake as evaluated by denaturing gradient gel electrophoresis of PCRamplified 16S rDNA fragments. Appl Environ Microbiol. 63(9):3367-3373. PMID:

9292986.

94. Matheson, V. G., J. Munakata-Marr, G. D. Hopkins, P. L. McCarty, J. M. Tiedje and L.

J. Forney. (1997). A novel means to develop strain-specific DNA probes for detecting

bacteria in the environment. Appl Environ Microbiol. 63(7):2863-2869. PMID:

9212434.

95. Dunbar J., S. White and L. J. Forney. (1997). Genetic diversity through the looking

glass: Effect of enrichment bias. Appl Environ Microbiol. 63(4):1326-1331. PMID:

16535569.

96. Kamagata, Y., R. R. Fulthorpe, K. Tamura, H. Takami, L. J. Forney and J. M. Tiedje.

(1997). Pristine environments harbor a new group of oligotrophic 2,4dichlorophenoxyacetic acid-degrading bacteria. Appl Environ Microbiol. 63(6):2266PMID: 9172346.

97. Fries, M. R., L. J. Forney and J. M. Tiedje. (1997). Phenol- and toluene-degrading microbial populations from an aquifer in which successful trichloroethene cometabolism occurred. Appl Environ Microbiol. 63(4):1523-1530. PMID: 16535577.

98. Fries, M. R., G.D. Hopkins, P. L. McCarty, L. J. Forney and J. M. Tiedje. (1997).

Microbial succession during a field evaluation of phenol and toluene as the primary substrates for trichloroethene cometabolism. Appl Environ Microbiol. 63(4):1515PMID: 16535576.

99. Munakata-Marr, J., V.G. Matheson, L.J. Forney, J.M. Tiedje and P.L. McCarty. (1997).

Long-term biodegradation of trichloroethylene influenced by bioaugmentation and dissolved oxygen in aquifer microcosms. Environ Sci Technol. 31(3):786-791.

100. Michel Jr., F.C., C.A. Reddy and L.J. Forney. (1997). Fate of 14C-Diazinon during the composting of yard trimmings. J Environ Quality. 26:200-205.

101. Suwa, Y., A.D. Wright, F. Fukumori, R. Hausinger, Y. Kamagata, W.E. Holben and L.J. Forney. (1996). Characterization of a chromosomally encoded 2,4dichlorophenoxyacetate acid/-ketoglutarate dioxygenase from Burkholderia sp.

strain RASC. Appl Environ Microbiol. 62(7):2464-2469. PMID: 8779585.

102. Top, E.M., O. Maltseva and L.J. Forney. (1996). Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid:-ketoglutaric acid dioxygenase (TfdA)

by genetic complementation. Appl Environ Microbiol. 62(7):2470-2476. PMID:

8779586.

103. Matheson, V.G., L.J. Forney, Y. Suwa, C.H. Nakatsu, A.J. Sexstone and W.E.

Holben. (1996). Evidence for acquisition in nature of a chromosomal 2,4dichlorophenoxyacetic acid/-ketoglutarate dioxygenase gene by different Burkholderia sp. Appl Environ Microbiol. 62(7):2457-2463. PMID: 16535356.

104. Zlatkin, I.V., G.M. Schneider, F.J. de Bruijn and L.J. Forney. (1996). Diversity among bacteria isolated from the deep subsurface. J Industrial Microbiol. 17(3-4):219-227.

105. Dunbar, J.M., A. Rhodes, D.C.L. Wong, M. Yarus and L.J. Forney. (1996).

Autoradiographic method for isolation of diverse microbial species with unique catabolic traits. Appl Env Microbiol. 62(11):4180-4185. PMID: 16535444.

106. Michel Jr., F.C., D. Graeber, L.J. Forney, C.A. Reddy. (1996). The fate of lawncare pesticides during composting. BioCycle 37:64-66.

107. Top, E.M., W.E. Holben and L.J. Forney. (1995). Characterization of diverse 2,4dichlorophenoxyacetic acid catabolic plasmids isolated from soil by complementation.

Appl Environ Microbiol. 61(5):1691-1698. PMID: 7646006.

108. Haack, S.K., H. Garchow, D.A. Odelson, M.J. Klug, L.J. Forney. (1995). Analysis of factors affecting the interpretation of whole community substrate utilization profiles

from model bacterial communities. Appl Environ Microbiol. 61(4):1458-1468. PMID:

16534996.

109. Michel Jr., F.C., S. Drew, C.A. Reddy, L.J. Forney, E. Trondle. (1995).

Characterization and composting of source-separated supermarket organics.

BioCycle 36:68-70.

110. Michel Jr., F.C., C.A. Reddy, L.J. Forney. (1995). Microbial degradation and humification of the lawn care pesticide 2,4-dichlorophenoxyacetic acid during the

composting of yard trimmings. Appl. Environ. Microbiol. 61(7): 2566-2571. PMID:

7618868.

111. Korona, R., C.H. Nakatsu, L.J. Forney, R.E. Lenski. (1994). Evidence for multiple fitness peaks from evolving populations of bacteria. Proc Natl Acad Sci. USA 91(19):9037-9041. PMID: 8090765.

112. Top, E.M. and L.J. Forney. 1994. The significance of degradative plasmids in soil bioremediation. Med. Fac. Landbouww. Univ. Gent. 59(4):1847-1855.

113. Haack, S.K., H. Garchow, D.A. Odelson, L.J. Forney, M.J. Klug. (1994). Microbial community analysis: accuracy, reproducibility and interpretation of fatty acid methyl ester profiles from model bacterial communities. Appl Environ Microbiol. 60(7):2483PMID: 16349327.

114. Watson, W.J., J.R. Gilsdorf, M.A. Tucci, K.W. McCrea, L.J. Forney, C.F. Marrs.

(1993). Identification of a gene essential for piliation in Haemophilus influenzae type b with homology to the pilus assembly platforms of Gram-negative bacteria. Infect Immun. 62(2):468-475. PMID: 7905461.

115. Michel Jr., F.C., C.A. Reddy, L.J. Forney. (1993). Yard waste composting:

Physiological studies using different mixes of leaves and grass in a laboratory scale system. Compost Science and Utilization 1(3):85-96.

116. Gilsdorf, J.R., M.A. Tucci, L.J. Forney, W. Watson, C.F. Marrs and E. Hansen. (1993).

Paradoxical effect of pilus expression on binding of antibodies to Haemophilus influenzae. Infect Immun. 61(8):3375-3381. PMID: 7687585.

117. Forney, L.J., J.R. Gilsdorf, C.F. Marrs, K.W. McCrea and S. Bektish. (1992).

Comparison of the alpha-pilins of Haemophilus influenzae type b strains Eagan (p+) M43 (p+), and 770235 f+. J Infect Dis. 165(1):S106-107. PMID: 1350298.

118. Gilsdorf, J.R., L.J. Forney, K.W. McCrea. (1992). Reactivity of antibodies against conserved regions of pilins of Haemophilus influenzae b. J Infect Dis. 167(4):962-965.

PMID: 7680701.

119. Bakaletz, L.O., M.A. Ahmed, P.E. Kolattukudy, D.J. Lim and L.J. Forney. (1992).

Cloning and sequence analysis of a pilin-like gene from an otitis media isolate of nontypeable Haemophilus influenzae. J Infect Dis. 165(1):S201-203. PMID: 1588166.

120. Forney, L.J., D.C.L. Wong and J.R. Gilsdorf. (1992). Effect of pili-specific antibodies on the adherence of Haemophilus influenzae type b to human buccal epithelial cells. J Infect Dis. 165(3): 464-470. PMID: 1347055.

121. Weber, A., K. Harris, S. Lohrke, L.J. Forney, A. Smith. (1991). Mutations in hifA impair the ability of Haemophilus influenzae to colonize the monkey nasopharynx. Infect Immun 59:4724-4728.

122. Forney, L.J., C.F. Marrs, S.L. Bektesh and J.R. Gilsdorf. (1991). Comparison and analysis of the nucleotide sequences of pilin genes from Haemophilus influenzae type b. Infect Immun. 59(6):1991-1996. PMID: 2037360.

123. Gilsdorf, J.R., C.F. Marrs, K.W. McCrea, L.J. Forney. (1990). Cloning, expression, and sequence analysis of the Haemophilus influenzae type b strain M43p+ pilin gene.

Infect Immun. 58(4):1065-1072. PMID: 1969389.

124. Gilsdorf, J.R., K.W. McCrea, L.J. Forney. (1990). Conserved and nonconserved epitopes among Haemophilus influenzae type b pili. Infect Immun. 58(7):2252-2257.

PMID: 1694821.

125. Armes, L.G. and L.J. Forney. 1990. The complete primary structure of pilin from

Haemophilus influenzae type b strain Eagan. J Protein Chem. 9(1):45-52. PMID:

1971175.

126. Gilsdorf, J.R., L.J. Forney, J.J. LiPuma. (1989). Reactivity of Haemophilus influenzae type b anti-pili antibodies. Microbiol Pathog. 7(4):311-316. PMID: 2576090.

127. Forney, L.J., D.C.L. Wong and D.M. Ferber. (1989). Selection of amidases with novel substrate specificity from penicillin amidase of Escherichia coli. Appl Environ Microbiol.

55(10):2550-2555. PMID: 2690733.

128. Forney, L.J. and D.C.L. Wong. (1989). Alteration of the catalytic efficiency of penicillin

amidase from Escherichia coli. Appl Environ Microbiol. 55(10):2556-2560. PMID:

1690734.

129. Forney, L.J., C.A. Reddy, M. Tien and S.D. Aust. (1982). The involvement of hydroxyl radical derived from hydrogen peroxide in lignin degradation by the white-rot fungus Phanerchaete chrysosporium. J Biol Chem. 257(19):11455-11462. PMID: 6288685.

130. Forney, L.J., C.A. Reddy and H.S. Pankratz. (1982). Ultrastructural localization of hydrogen peroxide production in ligninolytic Phanerchaete chrysosporium cells. Appl Environ Microbiol. 44(3):732-736. PMID: 16346099.

Book

Chapters:

131. Nakatsu, C.H. and L.J. Forney. 2004. Parameters of nucleic acid hybridization experiments. In G.A. Kowalchuk, F.J. de Bruijn, I.M. Head, A.D.L. Akkermans & J.

Dirk van Elsas, (eds.) Molecular Microbial Ecology Manual. Kluyver Academic Publishers, Netherlands, 1774 p.

132. Larson, RL., C.P.L. Grady, S. Masunaga, L. Wolfe, W. Peijnenburg, and L.J. Forney.

2000. Quantification of Persistence in Water, Soil, and Sediments, In: G.M. Klecka et al. (eds.) Criteria for Persistence and Long-Range Transport of Chemicals in the Environment, Society of Environmental Toxicology and Chemistry (SETAC), Pensacola, FL, USA, 400 p.

133. Punch. B., A. Patton, K. Wight, B. Larson, P. Masscheleyn, L.J. Forney. 1997. A biodegradability evaluation and simulation system (BESS) based on knowledge of biodegradation pathways. In: Biodegradability Prediction, Peijnenberg and Damborsky, eds., NATO ASI Series 23:65-84.

134. Matheson, V.G., J. Munakata-Marr, P.L. McCarty, J.M. Tiedje, and L. J. Forney.

1996. Use of strain-specific nucleic acid probes to assess remediation of an aquifer contaminated with trichloroethylene by bioaugmentation with Burkholderia cepacia G4. Mededelingen Faculteit Landbouwkundige en Toegepaste Biologische Wetenschappen 61:1823-1830. (Proceedings of the Tenth Forum of Applied Biotechnology 96).

135. Brannigan, J., A. Ladurner, C. McVey, L.J. Forney. 1995. Altered specificity mutants of penicillin acylase. In: M. Geisow and R. Epton (eds.), Perspectives on Protein Engineering, Mayflower Worldwide, UK.

136. Michel Jr., F.C., C.A. Reddy, L.J. Forney. 1995. Characterization of yard waste compost produced from mixtures of leaves and grass. In: A. Bousher, M. Chandra, R.

Edyvean, (eds.), Biodeterior. Biodeg. 9, Institution of Chemical Engineers, Rugby, UK, pp. 380-385.

137. Michel Jr., F.C., C.A. Reddy, L.J. Forney. 1995. Fate of the lawn care herbicide 2,4dichlorophenoxyacetic acid (2,4-D) during yard waste composting. In: A. Bousher, M.

Chandra, R. Edyvean, (eds.), Biodeterior. Biodeg. 9, Institution of Chemical Engineers, Rugby, UK, pp. 391-394.

138. Nakatsu, C.H. and L.J. Forney. 1995. Parameters of nucleic acid hybridization experiments. In: A.D.L. Akkermans, J.D. van Elsas and F.J. de Bruijn (eds.) Molecular Microbial Ecology Manual. Kluyver Academic Publishers, Netherlands.

139. Michel Jr., F.C., C.A. Reddy, L.J. Forney. 1994. Fate of the lawn care pesticides 2,4D and Diazinon during yard waste composting. In: Proc. 87th Annual Meeting, Air and Waste Management Association

140. Michel Jr., F.C., C.A. Reddy and L.J. Forney. 1994. Fate of the lawn care herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) during yard waste composting. In:

Proceedings of the International Symposium on Biodeterioration and Biodegradation.

141. Michel Jr., F.C., C.A. Reddy and L.J. Forney. 1994. Characteristics of yard waste compost produced from mixtures of leaves and grass. In: Proceedings of the International Symposium on Biodeterioration and Biodegradation, Leeds, UK, Sept. 9, 1993.

142. Forney, L.J. and J.M. Tiedje. 1993. The fundamentals of microbial ecology in situ bioremediation. Proceedings of the CoBioRem Conference, Lansing, MI, March 1993.

143. Michel Jr., F.C., C.A. Reddy, L.J. Forney. 1993. Fate of certain lawn care pesticides during yard waste composting. In: Proceedings of the The Composting Council's Fourth National Conference, Research Symposium, pp. 5-7, Composting Council, Arlington, VA.

144. Forney, L.J. 1993. Molecular mechanisms governing the regulation of bacterial virulence. In: Proceedings of the Fifth International Symposium on Recent Advances on Otitis Media, B.C. Decker, Inc., pp. 361-367.

145. Reddy, C.A., L.J. Forney, R.L. Kelley. 1983. Involvement of hydrogen peroxidederived hydroxyl radical in lignin degradation by the white-rot fungus Phanerchaete chrysosporium. In: Recent Adv. Lignin Biodegrad. Res., pp. 153-163.

146. Forney, L.J. and C.A. Reddy. 1979. Bacterial degradation of kraft lignin. In: Dev. Ind.

Microbiol. 20: 163-175.

147. Forney, L.J. and C.A. Reddy. 1978. Lignin chemistry and structure: a brief review. In:

Dev. Ind. Microbiol. 19: 27-34.

148. Forney, L.J. and C.A. Reddy. 1977. Fermentative conversion of potato processing wastes into a crude protein feed supplement by lactobacilli. In: Dev. Ind. Microbiol.

18: 135-143.




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