Jay Gralla - Publications

Affiliations: 
University of California, Los Angeles, Los Angeles, CA 
Area:
regulation and expression of genes
Website:
http://faculty.chemistry.ucla.edu/institution/personnel?personnel_id=45416

105 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2014 Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y, Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE. DNA recognition by a σ(54) transcriptional activator from Aquifex aeolicus. Journal of Molecular Biology. 426: 3553-68. PMID 25158097 DOI: 10.1016/j.jmb.2014.08.009  1
2010 Tran K, Gralla JD. The TFIIB tip domain couples transcription initiation to events involved in RNA processing. The Journal of Biological Chemistry. 285: 39580-7. PMID 20880846 DOI: 10.1074/jbc.M110.171850  1
2009 Altendorf K, Booth IR, Gralla J, Greie JC, Rosenthal AZ, Wood JM. Osmotic Stress. Ecosal Plus. 3. PMID 26443764 DOI: 10.1128/ecosalplus.5.4.5  0.6
2008 Gralla JD, Huo YX. Remodeling and activation of Escherichia coli RNA polymerase by osmolytes. Biochemistry. 47: 13189-96. PMID 19053283 DOI: 10.1021/bi801075x  1
2008 Huo YX, Rosenthal AZ, Gralla JD. General stress response signalling: unwrapping transcription complexes by DNA relaxation via the sigma38 C-terminal domain. Molecular Microbiology. 70: 369-78. PMID 18761624 DOI: 10.1111/j.1365-2958.2008.06412.x  1
2008 Tran K, Gralla JD. Control of the timing of promoter escape and RNA catalysis by the transcription factor IIb fingertip. The Journal of Biological Chemistry. 283: 15665-71. PMID 18411280 DOI: 10.1074/jbc.M801439200  1
2008 Rosenthal AZ, Kim Y, Gralla JD. Regulation of transcription by acetate in Escherichia coli: in vivo and in vitro comparisons. Molecular Microbiology. 68: 907-17. PMID 18331469 DOI: 10.1111/j.1365-2958.2008.06186.x  1
2008 Rosenthal AZ, Kim Y, Gralla JD. Poising of Escherichia coli RNA polymerase and its release from the sigma 38 C-terminal tail for osmY transcription. Journal of Molecular Biology. 376: 938-49. PMID 18201723 DOI: 10.1016/j.jmb.2007.12.037  1
2006 Kim Y, Lew CM, Gralla JD. Escherichia coli pfs transcription: regulation and proposed roles in autoinducer-2 synthesis and purine excretion. Journal of Bacteriology. 188: 7457-63. PMID 16950920 DOI: 10.1128/JB.00868-06  1
2006 Gralla JD, Vargas DR. Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation. The Embo Journal. 25: 1515-21. PMID 16541105 DOI: 10.1038/sj.emboj.7601041  1
2006 Rosenthal AZ, Hu M, Gralla JD. Osmolyte-induced transcription: -35 region elements and recognition by sigma38 (rpoS). Molecular Microbiology. 59: 1052-61. PMID 16420371 DOI: 10.1111/j.1365-2958.2005.04999.x  1
2005 Lin YC, Choi WS, Gralla JD. TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape. Nature Structural & Molecular Biology. 12: 603-7. PMID 15937491 DOI: 10.1038/nsmb949  1
2005 Lin YC, Gralla JD. Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE. Nucleic Acids Research. 33: 3072-81. PMID 15917439 DOI: 10.1093/nar/gki623  1
2005 Gralla JD. Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Molecular Microbiology. 55: 973-7. PMID 15686546 DOI: 10.1111/j.1365-2958.2004.04455.x  1
2004 Lew CM, Gralla JD. Nucleotide-dependent isomerization of Escherichia coli RNA polymerase. Biochemistry. 43: 12660-6. PMID 15449955 DOI: 10.1021/bi0492814  1
2004 Choi WS, Lin YC, Gralla JD. The Schizosaccharomyces pombe open promoter bubble: mammalian-like arrangement and properties. Journal of Molecular Biology. 340: 981-9. PMID 15236961 DOI: 10.1016/j.jmb.2004.04.075  1
2004 Lee SJ, Gralla JD. Osmo-regulation of bacterial transcription via poised RNA polymerase. Molecular Cell. 14: 153-62. PMID 15099515 DOI: 10.1016/S1097-2765(04)00202-3  1
2004 Lew CM, Gralla JD. Mechanism of stimulation of ribosomal promoters by binding of the +1 and +2 nucleotides. The Journal of Biological Chemistry. 279: 19481-5. PMID 15010465 DOI: 10.1074/jbc.M401285200  1
2003 Fenton MS, Gralla JD. Roles for inhibitory interactions in the use of the -10 promoter element by sigma 70 holoenzyme. The Journal of Biological Chemistry. 278: 39669-74. PMID 12902332 DOI: 10.1074/jbc.M307412200  1
2003 Lee SJ, Gralla JD. Open complex formation in vitro by sigma38 (rpoS) RNA polymerase: roles for region 2 amino acids. Journal of Molecular Biology. 329: 941-8. PMID 12798684 DOI: 10.1016/S0022-2836(03)00369-3  1
2003 Fenton MS, Gralla JD. Effect of DNA bases and backbone on sigma70 holoenzyme binding and isomerization using fork junction probes. Nucleic Acids Research. 31: 2745-50. PMID 12771200 DOI: 10.1093/nar/gkg400  1
2002 Lee SJ, Gralla JD. Promoter use by sigma 38 (rpoS) RNA polymerase. Amino acid clusters for DNA binding and isomerization. The Journal of Biological Chemistry. 277: 47420-7. PMID 12351645 DOI: 10.1074/jbc.M208363200  1
2002 Lew CM, Gralla JD. New roles for conserved regions within a sigma 54-dependent enhancer-binding protein. The Journal of Biological Chemistry. 277: 41517-24. PMID 12186874 DOI: 10.1074/jbc.M206912200  1
2002 Choi WS, Yan M, Nusinow D, Gralla JD. In vitro transcription and start site selection in Schizosaccharomyces pombe. Journal of Molecular Biology. 319: 1005-13. PMID 12079343 DOI: 10.1016/S0022-2836(02)00329-7  1
2001 Fenton MS, Gralla JD. Function of the bacterial TATAAT -10 element as single-stranded DNA during RNA polymerase isomerization. Proceedings of the National Academy of Sciences of the United States of America. 98: 9020-5. PMID 11470900 DOI: 10.1073/pnas.161085798  1
2001 Lee SJ, Gralla JD. Sigma38 (rpoS) RNA polymerase promoter engagement via -10 region nucleotides. The Journal of Biological Chemistry. 276: 30064-71. PMID 11375988 DOI: 10.1074/jbc.M102886200  1
2001 Wang L, Gralla JD. Roles for the C-terminal Region of Sigma 54 in Transcriptional Silencing and DNA Binding Journal of Biological Chemistry. 276: 8979-8986. PMID 11124262 DOI: 10.1074/jbc.M009587200  1
2001 Wolner BS, Gralla JD. TATA-flanking sequences influence the rate and stability of TATA-binding protein and TFIIB binding. The Journal of Biological Chemistry. 276: 6260-6. PMID 11096089 DOI: 10.1074/jbc.M008273200  1
2000 Guo Y, Lew CM, Gralla JD. Promoter opening by sigma(54) and sigma(70) RNA polymerases: sigma factor-directed alterations in the mechanism and tightness of control. Genes & Development. 14: 2242-55. PMID 10970887 DOI: 10.1101/gad.794800  1
2000 Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD. The bacterial enhancer-dependent σ54 (σ(N)) transcription factor Journal of Bacteriology. 182: 4129-4136. PMID 10894718 DOI: 10.1128/JB.182.15.4129-4136.2000  1
2000 Gralla JD. Signaling through sigma Nature Structural Biology. 7: 530-532. PMID 10876232 DOI: 10.1038/76732  1
2000 Wolner BS, Gralla JD. Roles for non-TATA core promoter sequences in transcription and factor binding. Molecular and Cellular Biology. 20: 3608-15. PMID 10779350 DOI: 10.1128/MCB.20.10.3608-3615.2000  1
2000 Fenton MS, Lee SJ, Gralla JD. Escherichia coli promoter opening and -10 recognition: mutational analysis of sigma70. The Embo Journal. 19: 1130-7. PMID 10698953 DOI: 10.1093/emboj/19.5.1130  1
1999 Wang L, Guo Y, Gralla JD. Regulation of sigma 54-dependent transcription by core promoter sequences: Role of -12 region nucleotides Journal of Bacteriology. 181: 7558-7565. PMID 10601214  1
1999 Yan M, Gralla JD. The use of ATP and initiating nucleotides during postrecruitment steps at the activated adenovirus E4 promoter Journal of Biological Chemistry. 274: 34819-34824. PMID 10574953 DOI: 10.1074/jbc.274.49.34819  1
1999 Guo Y, Wang L, Gralla JD. A fork junction DNA-protein switch that controls promoter melting by the bacterial enhancer-dependent sigma factor Embo Journal. 18: 3736-3745. PMID 10393188 DOI: 10.1093/emboj/18.13.3736  1
1999 Yean D, Gralla JD. Transcription reinitiation rate: A potential role for TATA box stabilization of the TFIID:TFIIA:DNA complex Nucleic Acids Research. 27: 831-838. PMID 9889280 DOI: 10.1093/nar/27.3.831  1
1998 Wang L, Gralla JD. Multiple in vivo roles for the -12-region elements of sigma 54 promoters Journal of Bacteriology. 180: 5626-5631. PMID 9791111  1
1998 Syed A, Gralla JD. Identification of an N-terminal region of sigma 54 required for enhancer responsiveness Journal of Bacteriology. 180: 5619-5625. PMID 9791110  1
1998 Guo Y, Gralla JD. Promoter opening via a DNA fork junction binding activity Proceedings of the National Academy of Sciences of the United States of America. 95: 11655-11660. PMID 9751721 DOI: 10.1073/pnas.95.20.11655  1
1998 Pérez-Rueda E, Gralla JD, Collado-Vides J. Genomic position analyses and the transcription machinery Journal of Molecular Biology. 275: 165-170. PMID 9466899 DOI: 10.1006/jmbi.1997.1465  1
1997 Wolner BS, Gralla JD. Promoter activation via a cyclic AMP response element in vitro. The Journal of Biological Chemistry. 272: 32301-7. PMID 9405436 DOI: 10.1074/jbc.272.51.32301  1
1997 Yan M, Gralla JD. Multiple ATP-dependent steps in RNA polymerase II promoter melting and initiation Embo Journal. 16: 7457-7467. PMID 9405374 DOI: 10.1093/emboj/16.24.7457  1
1997 Wang JT, Syed A, Gralla JD. Multiple pathways to bypass the enhancer requirement of sigma 54 RNA polymerase: Roles for DNA and protein determinants Proceedings of the National Academy of Sciences of the United States of America. 94: 9538-9543. PMID 9275158 DOI: 10.1073/pnas.94.18.9538  1
1997 Yean D, Gralla J. Transcription reinitiation rate: A special role for the TATA box Molecular and Cellular Biology. 17: 3809-3816. PMID 9199314  1
1997 Syed A, Gralla JD. Isolation and properties of enhancer-bypass mutants of sigma 54 Molecular Microbiology. 23: 987-995. PMID 9076735  1
1997 Guo Y, Gralla JD. DNA-binding determinants of sigma 54 as deduced from libraries of mutations Journal of Bacteriology. 179: 1239-1245. PMID 9023207  1
1996 Wang JT, Gralla JD. The transcription initiation pathway of sigma 54 mutants that bypass the enhancer protein requirement: Implications for the mechanism of activation Journal of Biological Chemistry. 271: 32707-32713. PMID 8955103  1
1996 Gralla JD. Activation and repression of E. coli promoters Current Opinion in Genetics and Development. 6: 526-530. PMID 8939721 DOI: 10.1016/S0959-437X(96)80079-7  1
1996 Gralla JD. Global steps during initiation by RNA polymerase II Methods in Enzymology. 273: 99-109. PMID 8791602  1
1996 Yean D, Gralla J. Transcription activation by GC-boxes: Evaluation of kinetic and equilibrium contributions Nucleic Acids Research. 24: 2723-2729. PMID 8759003 DOI: 10.1093/nar/24.14.2723  1
1996 Jiang Y, Yan M, Gralla JD. A three-step pathway of transcription initiation leading to promoter clearance at an activated RNA polymerase II promoter Molecular and Cellular Biology. 16: 1614-1621. PMID 8657136  1
1995 Jiang Y, Gralla JD. Nucleotide requirements for activated RNA polymerase II open complex formation in vitro Journal of Biological Chemistry. 270: 1277-1281. PMID 7836391 DOI: 10.1074/jbc.270.3.1277  1
1995 Jiang Y, Yan M, Gralla JD. Abortive initiation and first bond formation at an activated adenovirus E4 promoter Journal of Biological Chemistry. 270: 27332-27338. PMID 7592996 DOI: 10.1074/jbc.270.45.27332  1
1995 Tintut Y, Wang JT, Gralla JD. Abortive cycling and the release of polymerase for elongation at the σ54- dependent glnAp2 promoter Journal of Biological Chemistry. 270: 24392-24398. PMID 7592652 DOI: 10.1074/jbc.270.41.24392  1
1995 Tintut Y, Gralla JD. PCR mutagenesis identifies a polymerase-binding sequence of sigma 54 that includes a sigma 70 homology region Journal of Bacteriology. 177: 5818-5825. PMID 7592329  1
1995 Tintut Y, Wang JT, Gralla JD. A novel bacterial transcription cycle involving σ54 Genes and Development. 9: 2305-2313. PMID 7557383  1
1994 Hsieh M, Tintut Y, Gralla JD. Functional roles for the glutamines within the glutamine-rich region of the transcription factor σ54 Journal of Biological Chemistry. 269: 373-378. PMID 8276822  1
1994 Hsieh M, Gralla JD. Analysis of the N-terminal leucine heptad and hexad repeats of sigma 54 Journal of Molecular Biology. 239: 15-24. PMID 8196043 DOI: 10.1006/jmbi.1994.1347  1
1994 Tintut Y, Wong C, Jiang Y, Hsieh M, Gralla JD. RNA polymerase binding using a strongly acidic hydrophobic-repeat region of σ54 Proceedings of the National Academy of Sciences of the United States of America. 91: 2120-2124. PMID 8134358  1
1994 Jiang Y, Triezenberg SJ, Gralla JD. Defective transcriptional activation by diverse VP16 mutants associated with a common inability to form open promoter complexes Journal of Biological Chemistry. 269: 5505-5508. PMID 8119881  1
1994 Wong C, Tintut Y, Gralla JD. The domain structure of sigma 54 as determined by analysis of a set of deletion mutants Journal of Molecular Biology. 236: 81-90. PMID 8107127 DOI: 10.1006/jmbi.1994.1120  1
1994 Chang C, Gralla JD. A critical role for chromatin in mounting a synergistic transcriptional response to GAL4-VP16 Molecular and Cellular Biology. 14: 5175-5181. PMID 8035798  1
1994 Ellinger T, Behnke D, Knaus R, Bujard H, Gralla JD. Context-dependent effects of upstream A-tracts: Stimulation or inhibition of Escherichia coli promoter function Journal of Molecular Biology. 239: 466-475. PMID 8006962  1
1994 Ellinger T, Behnke D, Bujard H, Gralla JD. Stalling of Escherichia coli RNA polymerase in the +6 to +12 region in vivo is associated with tight binding to consensus promoter elements Journal of Molecular Biology. 239: 455-465. PMID 8006961 DOI: 10.1006/jmbi.1994.1388  1
1994 Jiang Y, Gralla JD. RNA polymerase II phosphorylation: Uncoupling from GAL4-VP16 directed open complex formation and transcription in a reconstituted system Nucleic Acids Research. 22: 4958-4962. PMID 7800486 DOI: 10.1093/nar/22.23.4958  1
1993 Jiang Y, Smale ST, Gralla JD. A common ATP requirement for open complex formation and transcription at promoters containing initiator or TATA elements. The Journal of Biological Chemistry. 268: 6535-40. PMID 8454623  1
1993 Jiang Y, Gralla JD. Uncoupling of Initiation and Reinitiation Rates during HeLa RNA Polymerase II Transcription in Vitro Molecular and Cellular Biology. 13: 4572-4577. PMID 8336702  1
1993 Gralla JD. Opening promoters for m-RNA transcription Cellular and Molecular Biology Research. 39: 319-322. PMID 8312966  1
1993 Chang C, Gralla JD. Properties of initiator-associated transcription mediated by GAL4-VP16 Molecular and Cellular Biology. 13: 7469-7475. PMID 8246964  1
1992 Evans GL, Gralla JD. Differential effects of cisplatin on the expression of chimeric marker genes in CV-1 cells Biochemical Pharmacology. 44: 107-119. PMID 1632825 DOI: 10.1016/0006-2952(92)90044-J  1
1992 Evans GL, Gralla JD. Cisplatin-induced imbalances in the pattern of chimeric marker gene expression in HeLa cells Biochemical and Biophysical Research Communications. 184: 1-8. PMID 1567415 DOI: 10.1016/0006-291X(92)91149-K  1
1992 Wang W, Gralla JD, Carey M. The acidic activator GAL4-AH can stimulate polymerase II transcription by promoting assembly of a closed complex requiring TFIID and TFIIA Genes and Development. 6: 1716-1727. PMID 1516830  1
1992 Wong C, Gralla JD. A role for the acidic trimer repeat region of transcription factor σ54 in setting the rate and temperature dependence of promoter melting in vivo Journal of Biological Chemistry. 267: 24762-24768. PMID 1447214  1
1992 Ohlsen KL, Gralla JD. Interrelated effects of DNA supercoiling, ppGpp, and low salt on melting within the Escherichia coli ribosomal RNA rrnB P1 promoter Molecular Microbiology. 6: 2243-2251. PMID 1406265  1
1992 Ohlsen KL, Gralla JD. DNA melting within stable closed complexes at the Escherichia coli rrnB P1 promoter Journal of Biological Chemistry. 267: 19813-19818. PMID 1400295  1
1992 Ohlsen KL, Gralla JD. Melting during steady-state transcription of the rrnB P1 promoter in vivo and in vitro Journal of Bacteriology. 174: 6071-6075. PMID 1400157  1
1992 Hoang AT, Wang W, Gralla JD. The replication activation potential of selected RNA polymerase II promoter elements at the simian virus 40 origin Molecular and Cellular Biology. 12: 3087-3093. PMID 1320196  1
1992 Wang W, Carey M, Gralla JD. Polymerase II promoter activation: Closed complex formation and ATP-driven start site opening Science. 255: 450-453. PMID 1310361  1
1991 Collado-Vides J, Magasanik B, Gralla JD. Control site location and transcriptional regulation in Escherichia coli. Microbiological Reviews. 55: 371-94. PMID 1943993  1
1991 Wang W, Gralla JD. Differential ability of proximal and remote element pairs to cooperate in activating RNA polymerase II transcription Molecular and Cellular Biology. 11: 4561-4571. PMID 1875939  1
1991 Gralla JD. Transcriptional control - Lessons from an E. coli promoter data base Cell. 66: 415-418. PMID 1868543  1
1991 Sasse-Dwight S, Gralla JD. Footprinting protein-DNA complexes in vivo Methods in Enzymology. 208: 146-168. PMID 1779834  1
1990 Gralla JD. Promoter recognition and mRNA initiation by Escherichia coli Eσ70 Methods in Enzymology. 185: 37-54. PMID 2199788 DOI: 10.1016/0076-6879(90)85006-A  1
1990 Buchanan RL, Gralla JD. Cisplatin resistance and mechanism in a viral test system: SV40 isolates that resist inhibition by the antitumor drug have lost regulatory DNA Biochemistry. 29: 3436-3442. PMID 2162191  1
1990 Zhang L, Gralla JD. In situ nucleoprotein structure involving origin-proximal SV40 DNA control elements Nucleic Acids Research. 18: 1797-1803. PMID 2159622  1
1990 Buchanan RL, Gralla JD. Programmed factor binding to simian virus 40 GC-box replication and transcription control sequences Journal of Virology. 64: 347-353. PMID 2152821  1
1989 Sasse-Dwight S, Gralla JD. KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo Journal of Biological Chemistry. 264: 8074-8081. PMID 2722774  1
1989 Zhang L, Gralla JD. Micrococcal nuclease as a probe for bound and distorted DNA in lac transcription and repression complexes Nucleic Acids Research. 17: 5017-5028. PMID 2668875  1
1989 Zhang L, Gralla JD. In situ nucleoprotein structure at the SV40 major late promoter: melted and wrapped DNA flank the start site Genes & Development. 3: 1814-1822. PMID 2558048  1
1989 Meiklejohn AL, Gralla JD. Activation of the lac promoter and its variants. Synergistic effects of catabolite activator protein and supercoiling in vitro Journal of Molecular Biology. 207: 661-673. PMID 2547970 DOI: 10.1016/0022-2836(89)90236-2  1
1989 Gralla JD. Bacterial gene regulation from distant DNA sites Cell. 57: 193-195. PMID 2522819 DOI: 10.1016/0092-8674(89)90955-0  1
1988 Sasse-Dwight S, Gralla JD. Probing co-operative DNA-binding in vivo. The lac O1: O3 interaction Journal of Molecular Biology. 202: 107-119. PMID 3050119 DOI: 10.1016/0022-2836(88)90523-2  1
1988 Flashner Y, Gralla JD. DNA dynamic flexibility and protein recognition: Differential stimulation by bacterial histone-like protein HU Cell. 54: 713-721. PMID 3044609 DOI: 10.1016/S0092-8674(88)80016-3  1
1988 Sasse-Dwight S, Gralla JD. Probing the Escherichia coli glnALG upstream activation mechanism in vivo Proceedings of the National Academy of Sciences of the United States of America. 85: 8934-8938. PMID 2904147  1
1987 Borowiec JA, Zhang L, Sasse-Dwight S, Gralla JD. DNA supercoiling promotes formation of a bent repression loop in lac DNA Journal of Molecular Biology. 196: 101-111. PMID 3656441 DOI: 10.1016/0022-2836(87)90513-4  1
1987 Borowiec JA, Gralla JD. All three elements of the lac pS promoter mediate its transcriptional response to DNA supercoiling Journal of Molecular Biology. 195: 89-97. PMID 3309333 DOI: 10.1016/0022-2836(87)90329-9  1
1987 Balke VL, Gralla JD. Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli Journal of Bacteriology. 169: 4499-4506. PMID 3308843  1
1987 Poljak LG, Gralla JD. The SV40 termination region exhibits an altered helical DNA conformation Nucleic Acids Research. 15: 5433-5442. PMID 3037492 DOI: 10.1093/nar/15.13.5433  1
1987 Poljak LG, Gralla JD. Competition for formation of nucleosomes on fragmented SV40 DNA: A hyperstable nucleosome forms on the termination region Biochemistry. 26: 295-303. PMID 3030401  1
1987 Watson JB, Gralla JD. Simian virus 40 associates with nuclear superstructures at early times of infection. Journal of Virology. 61: 748-54. PMID 3027402  1
1974 Ravetch J, Gralla J, Crothers DM. Thermodynamic and kinetic properties of short RNA helices: the oligomer sequence AnGCUn. Nucleic Acids Research. 1: 109-27. PMID 10793665  1
1974 Gralla J, Steitz JA, Crothers DM. Direct physical evidence for secondary structure in an isolated fragment of R17 bacteriophage mRNA. Nature. 248: 204-8. PMID 4819414  1
1973 Gralla J, Crothers DM. Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches. Journal of Molecular Biology. 78: 301-19. PMID 4747633  1
1973 Gralla J, Crothers DM. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. Journal of Molecular Biology. 73: 497-511. PMID 4715014  1
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