Patents

1. Gerbi SA, Lange TS and Borovjagin AV (2000). Title: Methods to screen for antibiotic agents and their use in treatment of opportunistic infections. Patent issue # PCT/OS01/20520.

2(a). Provisional patent – Gerbi, SA, Doris SD, Beamesderfer JN, Smith DR and Raphael B (2013). Conserved nucleotide elements in ribosomal RNA. U.S. Patent Application No.: 61/798,468.

2(b). Full patent – Gerbi, SA, Doris SM, Smith DR, Beamesderfer JN and Raphael B (2014). Conserved nucleotide elements in ribosomal RNA. U.S. Patent Application No.: 14/204,223.

Publications

1. M.L. Pardue, S.A. Gerbi, R.A. Eckhardt, and J.G. Gall (1970) Cytological localization of DNA complementary to ribosomal RNA in polytene chromosomes of Diptera.  Chromosoma 29:  268-290.

2. S.A. Gerbi (1971) Localization and characterization of rRNA cistrons in Sciara coprophila.  J Mol Biol 58:  499-511.

3. S.L. Mowbray, S.A. Gerbi, and A. Landy (1975)  Interdigitated repeated sequences in bovine satellite DNA.  Nature 253:  367-370.

4. S.A. Gerbi and H.V. Crouse (1976) Further studies on the ribosomal RNA cistrons of Sciara coprophila (Diptera).  Genetics 83:  81-90.

5. S.A. Gerbi (1976) Fine structure of ribosomal RNA. I. Conservation of homologous regions within ribosomal RNA of eukaryotes.  J Mol Biol 106:  791-811.

6. S.A. Gerbi (1976) Fine structure of ribosomal RNA.  Appendix.  DNA elution during thermal melting of RNA-DNA hybrids on nitrocellulose filters.  J Mol Biol 106:  812-816.

7. S.A. Gerbi (1977) Analysis of RNA-DNA competition hybridization using the Scatchard plot.  Exp Cell Res 106:  454-457.

8. H.V. Crouse, S.A. Gerbi, C.M. Liang, L. Magnus, and I.M. Mercer (1977) Localization of ribosomal DNA within the proximal heterochromatin of Sciara coprophila (Diptera, Sciaridae).  Chromosoma 64:  305-318.

9. R. Renkawitz, S.A. Gerbi, K.-H. Glätzer (1979) Ribosomal DNA of the fly Sciara coprophila has a very small and homogenous repeat unit.  Mol Gen Genetics 173:  1-13.

10. R.C. Brand and S.A. Gerbi (1979) Fine structure of ribosomal RNA.  II.  Distribution of methylated sequences within Xenopus laevis rRNA.  Nucleic Acids Res 7:  1497-1511.

11. R.L. Gourse and S.A. Gerbi (1980) Fine structure of ribosomal RNA.  III. Location of evolutionarily conserved regions within ribosomal DNA.  J Mol Biol 140:  321-339.

12. R.L. Gourse and S.A. Gerbi (1980) Fine structure of ribosomal RNA.  IV.  Extraordinary evolutionary conservation in sequences that flank introns.  Nucleic Acids Res 8:  3623-3637.

13. R.L. Gourse, D.L. Thurlow, S.A. Gerbi, and R.A. Zimmermann (1981) Specific binding of a prokaryotic ribosomal protein to a eukaryotic ribosomal RNA: implications for evolution and autoregulation.  Proc Nat Acad Sci 78:  2722-2726.

14. A.G. Abbott, J. Hess, and S.A. Gerbi (1981) Spermatogenesis in Sciara coprophila.  I. Chromosome orientation on the monopolar spindle of meiosis I.  Chromosoma 83:  1-18.

15. A.G. Abbott and S.A. Gerbi (1981) Spermatogenesis in Sciara coprophila.  II. Precocious chromosome orientation in meiosis II.  Chromosoma 83:  19-27.

16. R. Renkawitz-Pohl, L. Matsumoto and S.A. Gerbi (1981) Two distinct intervening sequences in different rDNA repeat units of Sciara coprophila.  Nucleic Acids Res 9:  3747-3764.

17. S.A. Gerbi, R.L. Gourse and C.G. Clark (1981) Conserved regions within ribosomal DNA;  locations and some possible functions.  In The Cell Nucleus, ed:  H. Busch and L. Rothblum (New York:  Academic Press), Vol. 10, pp. 351-386.

18. C.G. Clark and S.A. Gerbi (1982) Ribosomal RNA evolution by fragmentation of the 23S progenitor:  maturation pathway parallels evolutionary emergence.  J Molec Evolution 18:  329-336.

19. L.M. Matsumoto and S.A. Gerbi (1982) Bovine satellite DNA I initiates its replication early in S phase.  Exp Cell Res 140:  47-54.

20. E.J. Taparowsky and S.A. Gerbi (1982) Sequence analysis of bovine satellite I DNA (1.715 gm/cm3).  Nucleic Acids Res 10:  1271-1281.

21. E.J. Taparowsky and S.A. Gerbi (1982) Structure of 1.711b gm/cm3 bovine satellite DNA:  evolutionary relationship to satellite I. Nucleic Acids Res 10:  5503-5515.

22. H. Bäumlein, U. Wobus, S. Gerbi, and F.C. Kafatos (1982) Characterization of a 249 bp tandemly repetitive satellite-like repeat in the translated portion of Balbiani Ring C of Chironomus thummi.  EMBO J 1:  641‑647.

23. H. Bäumlein, U. Wobus, S.A. Gerbi, and F.C. Kafatos (1982) The basic repeat unit of a Chironomus Balbiani Ring gene.  Nucleic Acids Res earch 10:  3893-3904.

24. S. DeLucchini and S.A. Gerbi (1982) DNA ribosomale extrachromosomico in nuclei politenici di Sciara coprophila (Ditteri):  analisi biochimica.  Atti Della Societa Toscana di Scienze Naturali Memorie Vol. LXXXIX Ser. B:  pp. 13-27.

25. V.C. Ware, B.W. Tague, C.G. Clark, R.L. Gourse, R.C. Brand, and S.A. Gerbi (1983) Sequence analysis of 28S ribosomal RNA from the amphibian Xenopus laevis.  Nucleic Acids Res 11:  7795-7817.

26. C.G. Clark, B.W. Tague, V.C. Ware and S.A. Gerbi (1984) Xenopus laevis 28S ribosomal RNA:  a secondary structure model and its evolutionary and functional implications.  Nucleic Acids Res earch 12:  6197‑6220.

27. B.W. Tague and S.A. Gerbi (1984) Processing of the large rRNA precursor:  two proposed categories of RNA-RNA interactions in eukaryotes.  J Molec Evolution 20:  362-367.

28. V.C. Ware, R. Renkawitz, and S.A. Gerbi (1985) rRNA processing:  removal of only nineteen bases at the gap between 28Sa and 28b rRNAs in Sciara coprophila.  Nucleic Acids Res 13:  3581-3597.

29. S.A. Gerbi (1985) Evolution of ribosomal DNA.  In Molecular Evolutionary Genetics, ed:  Ross McIntyre (Plenum Press).  pp. 419‑517.

30. S.A. Gerbi (1986) Unusual chromosome movements in Sciarid flies.  In Results and Problems in Cell Differentiation, ed:  W. Hennig (Springer-Verlag) Vol. 13 Germ Line – Soma Differentiation, pp. 71-104.

31. S.A. Gerbi (1986) The evolution of eukaryotic ribosomal DNA.  Biosystems 19:  247-258.

32. L.J. Rothschild, M.A. Ragan, A.W. Coleman, P. Heywood, and S.A. Gerbi (1986) Are rRNA sequence comparisons the Rosetta Stone of phylogenetics?  Cell 47:  640.

33. S.A. Gerbi (1987) (second edition in 1993) From genes to proteins.  Carolina Biology Reader #158.  ed: J.J. Head, pp. 1-16.

34. S.A. Gerbi, C. Jeppesen, B. Stebbins-Boaz, and M. Ares (1987) Evolution of eukaryotic ribosomal RNA.  Cold Spring Harbor Symp Quant Biol 52:  709-719.

35. C. Jeppesen, B. Stebbins-Boaz, and S.A. Gerbi (1988) Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA.  Nucleic Acids Res 16:  2127-2148.

36. A.W. Kerrebrock, R.Srivastava and S.A. Gerbi (1989) Isolation and characterization of ribosomal DNA variants from Sciara coprophila.  J Mol Biol 210:  1-13.

37. S.M. DiBartolomeis and S.A. Gerbi (1989) Molecular characterization of DNA puff II/9A genes in Sciara coprophila.  J Mol Biol 210:  531-540.

38. S.A. Gerbi, R. Savino, B. Stebbins-Boaz, C. Jeppesen and R. Rivera-Leon (1990) A role for U3 in the nucleolus?  In The Ribosome:  Structure, Function and Evolution, eds. W.E. Hill, A. Dahlberg, R.A. Garrett, P.B. Moore, D. Schlessinger and J.R. Warner.  American Society for Microbiology, Washington, DC, pp. 452-469.

39. R. Savino and S.A. Gerbi (1990) In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing.  EMBO J 9:  2289-2308.

40. B. Stebbins-Boaz and S.A. Gerbi (1991) Structural analysis of the peptidyl transferase region in ribosomal RNA of the eukaryote Xenopus laevis.  J Mol Biol 217:  93-112.

41. M. Andreazzoli and S.A. Gerbi (1991) Changes in 7SL RNA conformation during the signal recognition particle cycle.  EMBO J 10:  767-777.

42. B. Bienz-Tadmor, H.S. Smith and S.A. Gerbi (1991) (and cover photo for this issue of the journal) The promoter of DNA puff gene II/9-1 of Sciara coprophila is inducible by ecdysone in late prepupal salivary glands of Drosophila melanogaster.  Cell Regulation (Mol Biol Cell) 2:  875-888.

43. R. Savino and S.A. Gerbi (1991) Preribosomal RNA processing in Xenopus oocytes does not include cleavage within the external transcribed spacer as an early step.  Biochimie (Wittmann memorial issue) 73: 805-812 (1991); (erratum) 78: 295.

44. B. Bienz-Tadmor, P. Tolias, B. Stebbins-Boaz, B. Mariani, S.A. Gerbi and F.C. Kafatos (1992) Chorion gene cis-regulatory DNA restricts tissue specificity of reporter gene expression in transformed Drosophila.  Chromosoma 101:  538-548.

45. R. Savino, Y. Hitti and S.A. Gerbi (1992) Genes for Xenopus laevis U3 small nuclear RNA.  Nucleic Acids Res 20:  5435-5442.

46. C. Liang, J.D. Spitzer, H.S. Smith, and S.A. Gerbi (1993) Replication initiates at a confined region during DNA amplification in Sciara DNA puff II/9A. Genes Dev 7: 1072-1084.

47. N. Wu, C. Liang, S.M. DiBartolomeis, H.S. Smith and S.A. Gerbi (1993) Developmental progression of DNA puffs in Sciara coprophila: amplification and transcription. Dev Biol 160: 73-84.

48. S.A. Gerbi, C. Liang, N. Wu, F.D. Urnov, H.S. Smith and J.D. Spitzer (1993) Ecdysone regulation of DNA amplification and transcription in DNA puff II/9A of Sciara coprophila. Cold Spring Harbor Symp Quant Biol 58: 487-494.

49. C. Liang and S.A. Gerbi (1994) Analysis of an origin of DNA amplification in Sciara coprophila using a novel three-dimensional gel method. Mol Cell Biol 14: 1520-1529.

50. S.A. Gerbi (1995) Small nucleolar RNA. Biochimie et Biologie Cellulaire 73: 845-858.

51. S.A. Gerbi (1996) Expansion segments: regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. In Ribosomal RNA: Structure, Evolution, Processing and Function in Protein Synthesis, eds: R.A. Zimmermann and A.E. Dahlberg. Telford – CRC Press, Boca Raton, FL. pp. 71-87.

52. S.A. Gerbi and F.D. Urnov (1996) Differential DNA replication in insect chromosomes.  In DNA Replication in Eukaryotic Cells, ed: M. DePamphilis.  Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 947-969.

53. S.A. Gerbi (1997) The nucleolus: then and now.  Chromosoma 105 (Hadjiolov memorial issue): 385-387.

54. S.A. Gerbi and A. Borovjagin (1997) U3 snoRNA may recycle through different compartments of the nucleolus.  Chromosoma 105 (Hadjiolov memorial issue): 401-406.

55. R. Rivera-León and S.A. Gerbi (1997) Delocalization of some small nucleolar RNPs after actinomycin D treatment to deplete early pre-rRNAs. Chromosoma 105 (Hadjiolov memorial issue): 506-514.

56. S.A. Gerbi and A.-K. Bielinsky (1997) Replication initiation point mapping.  METHODS: A companion to Methods in Enzymology 13: 271-280.

57. A.-K. Bielinsky and S.A. Gerbi (1998) Discrete start sites for DNA synthesis in the yeast ARSI origin. Science 279: 95-98.

58. T.S. Lange, A., Borovjagin, E.S. Maxwell and S.A. Gerbi (1998) Conserved Boxes C and D are essential           nucleolar localization elements of U8 and U14 snoRNAs. EMBO J 17: 3176-3187.

59. T.S. Lange, A. V. Borovjagin and S.A. Gerbi (1998) Nucleolar localization elements in U8 snoRNA differ from sequences required for rRNA processing.  RNA 4: 789-800.

60. T.S. Lange, M. Ezrokhi, A. V. Borovjagin, R. Rivera-León, M.T. North and S.A. Gerbi (1998) (including journal cover) Nucleolar localization elements of Xenopus laevis U3 small nucleolar RNA.  Mol Biol Cell 9:2973-2985.

61. A.V. Borovjagin and S.A. Gerbi (1999) U3 small nucleolar RNA is essential for cleavage at sites 1, 2 and 3 in pre-rRNA and determines which rRNA processing pathway is taken in Xenopus oocytes. J Mol Biol 286: 1347-1363.

62. S.A. Gerbi, A.-K. Bielinsky, C. Liang, V.V. Lunyak, and F.D. Urnov  (1999) Methods to map origins of replication in eukaryotes. In Eukaryotic DNA Replication: a Practical Approach (ed., S. Cotterill), Oxford University Press, pp. 1-42.

63. A.-K. Bielinsky and S.A. Gerbi. (1999) Chromosomal ARSI has a single leading strand start site. Mol Cell 3: 477-486.

64. T.S. Lange, M. Ezrokhi, F. Amaldi and S.A. Gerbi (1999)  Box H and Box ACA are nucleolar localization elements of U17 snoRNA.  Mol Biol Cell 10: 3877-3890.

65. A.V. Borovjagin and S.A. Gerbi (2000)  The spacing between functional cis-elements of U3 snoRNA is critical for rRNA processing.  J Mol Biol 300: 57-74.

66. T.S. Lange and S.A. Gerbi (2000)  Transient localization of U6 small nucleolar RNA in Xenopus laevis oocytes.  Mol Biol Cell 11: 2419-2428.

67. A.-K. Bielinsky and S.A. Gerbi (2000)  Where it all starts: eukaryotic origins of DNA replication.  J Cell Science 114:643-651.

68. E.H. Mok, H.S. Smith, S.M. DiBartolomeis, A.W. Kerrebrock, L.J. Rothschild, T.S. Lange and S.A. Gerbi (2000) Maintenance of the DNA puff expanded state is independent of active replication and transcription. Chromosoma (W. Beerman Memorial Issue) 110: 186-196.

69. A.V. Borovjagin and S.A. Gerbi (2001) Xenopus U3 snoRNA GAC-Box A’ and Box A sequences play distinct functional roles in rRNA processing. Mol Cell Biol 21: 6210-6221.

70. S.A. Gerbi, A.V. Borovjagin, M. Ezrokhi and T.S. Lange (2001) Ribosome biogenesis: role of small nucleolar RNA in maturation of eukaryotic rRNA. Cold Spring Harbor Symp. Quant. Biol.  LXVI: 575-590.

71. A.-K. Bielinsky, H. Blitzblau, E.L. Beall, M. Ezrokhi, H.S. Smith, M.R. Botchan and S.A. Gerbi (2001) Origin recognition complex binding to a metazoan replication origin. Current Biol 11: 1427-1431.

72. S.A. Gerbi and A.-K. Bielinsky (2002) DNA replication and chromatin. Current Opinion Genetics and Devel  12: 243-248.

73. F.D. Urnov, C. Liang, H.G. Blitzblau, H.S. Smith and S.A. Gerbi (2002) A DNase I hypersensitive site flanks an origin of replication and amplification in Sciara. Chromosoma 111: 291-303 (A. Wolffe Memorial Issue).

74. V.V. Lunyak, M. Ezrokhi, H.S. Smith and S.A. Gerbi (2002) Developmental changes in the Sciara II/9A initiation zone for DNA replication.  Mol Cell Biol 22: 8426-8437.

75. S.A. Gerbi and T.S. Lange (2002) All snRNAs of the (U4/U6.U5) tri-snRNP localize to nucleoli; identification of the NoLE of U6 snRNA. Mol Biol Cell 13: 3123-3137.

76. S.A. Gerbi, Z. Strezoska and J.M. Waggener (2002) Initiation of DNA replication in multicellular eukaryotes. J Struct Biol 140: 17-30.

77. S.A. Gerbi, A.V. Borovjagin, F.E. Odreman and T.S. Lange (2003) U4 snRNA nucleolar localization requires the NHPX/15.5 KD protein binding site but not Sm protein or U6 snRNA association. J Cell Biol 162: 821-832.

78. S.A. Gerbi, A.V. Borovjagin and T.S. Lange (2003) The nucleolus – a site of ribonucleoprotein maturation. Current Opinion Cell Biol 15: 318-325.

79. S.A. Gerbi and A.V. Borovjagin (2004) Pre-ribosomal RNA processing in multicellular organisms. In The Nucleolus (ed.: M.O.J. Olson), Landes Bioscience Publishing; Kluwer Academic/Plenum Publishers, pp. 170-198.

80. A.V. Borovjagin and S.A. Gerbi (2004) Xenopus U3 snoRNA docks on pre-rRNA through a novel base-pairing interaction. RNA 10: 942-953.

81. S.A. Gerbi (2005) Mapping origins of DNA replication in eukaryotes. In Methods in Molecular Biology -Protocols in Cell Cycle Control (eds: G. Brooks and T. Humphrey), Humana Press, Totowa, N.J.; vol. 296: pp.167-180.

82. A.V. Borovjagin and S.A. Gerbi (2005) An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA. Nucleic Acids Res 33: 4995-5005.

83. M.S. Foulk, C. Liang, N. Wu, H.G. Blitzblau, H. Smith, D. Alam, M. Batra, and S.A. Gerbi, S.A. (2006) Ecdysone induces transcription and amplification in Sciara coprophila DNA puff II/9A. Dev Biol 299: 151-163.

84. M.S. Foulk, J.M. Waggener, J.M. Johnson, Y. Yamamoto, G.M. Liew, F.D. Urnov, Y. Young, G. Lee, H.S. Smith and S.A. Gerbi (2013) Isolation and characterization of the ecdysone receptor and its heterodimeric partner ultraspiracle through development in Sciara coprophila. Chromosoma 122: 103-119.

85. G.M. Liew, M.S. Foulk and S.A. Gerbi (2013) The ecdysone receptor (ScEcR-A) binds DNA puffs at the start of DNA amplification in Sciara coprophila. Chromosome Res 21: 345-360.

86. M.S. Foulk, J.M. Urban, C. Casella and S.A. Gerbi (2015) Characterizing and controlling intrinsic biases of Lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res 25: 725-735.

87. J.M. Urban, M.S. Foulk, C. Casella and S.A. Gerbi (2015) The hunt for origins of DNA replication in multicellular eukaryotes. F1000: 7:30 (ePub).

88. S.M. Doris, D.R. Smith, J.N. Beamesderfer, B.J. Raphael, J.A. Nathanson and S.A. Gerbi (2015) Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics. RNA 21: 1719-1730.

89. S.A. Gerbi (2015) Beginning at the end: DNA replication within the telomere. J Cell Biol 210: 177-179.

90. Y. Yamamoto, J. Bliss and S.A. Gerbi (2015) Whole organism genome editing: Targeted large DNA insertion via ObLiGaRe nonhomologous end-joining in vivo capture.  G3: Genes/Genomes/Genetics 5: 1843-1847.

91. J.M. Urban, J. Bliss, C.E. Lawrence and S.A. Gerbi (2015) Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION. BioRxiv doi: http://dx.doi.org/10.1101/019281