-
1
-
-
0036899934
-
Extremely low levels of genetic polymorphism in endosymbionts (Buchnera) of aphids (Pemphigus)
-
Abbot, P. & Moran, N. A. (2002). Extremely low levels of genetic polymorphism in endosymbionts (Buchnera) of aphids (Pemphigus). Mol Ecol 11, 2649-2660.
-
(2002)
Mol. Ecol.
, vol.11
, pp. 2649-2660
-
-
Abbot, P.1
Moran, N.A.2
-
2
-
-
0028220048
-
Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
-
Akashi, H. (1994). Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136, 927-935.
-
(1994)
Genetics
, vol.136
, pp. 927-935
-
-
Akashi, H.1
-
3
-
-
0031593202
-
Codon bias evolution in Drosophila. Population genetics of mutation-selection drift
-
Akashi, H. (1997). Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene 205, 269-278.
-
(1997)
Gene
, vol.205
, pp. 269-278
-
-
Akashi, H.1
-
4
-
-
0037133671
-
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
-
Akashi, H. & Gojobori, T. (2002). Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A 99, 3695-3700.
-
(2002)
Proc. Natl. Acad. Sci. U S A
, vol.99
, pp. 3695-3700
-
-
Akashi, H.1
Gojobori, T.2
-
5
-
-
0036842986
-
Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia
-
Akman, L., Yamashita, A., Watanabe, H., Oshima, K., Shiba, T., Hattori, M. & Aksoy, S. (2002). Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet 32, 402-407.
-
(2002)
Nat. Genet.
, vol.32
, pp. 402-407
-
-
Akman, L.1
Yamashita, A.2
Watanabe, H.3
Oshima, K.4
Shiba, T.5
Hattori, M.6
Aksoy, S.7
-
6
-
-
0029240197
-
Molecular analysis of the endosymbionts of tsetse flies: 16S rDNA locus and over-expression of a chaperonin
-
Aksoy, S. (1995). Molecular analysis of the endosymbionts of tsetse flies: 16S rDNA locus and over-expression of a chaperonin. Insect Mol Biol 4, 23-29.
-
(1995)
Insect Mol. Biol.
, vol.4
, pp. 23-29
-
-
Aksoy, S.1
-
7
-
-
0025297285
-
Codon preferences in free-living microorganisms
-
Andersson, S. G. & Kurland, C. G. (1990). Codon preferences in free-living microorganisms. Microbiol Rev 54, 198-210.
-
(1990)
Microbiol. Rev.
, vol.54
, pp. 198-210
-
-
Andersson, S.G.1
Kurland, C.G.2
-
8
-
-
0029938306
-
Codon usage and base composition in Rickettsia prowazekii
-
Andersson, S. G. & Sharp, P. M. (1996). Codon usage and base composition in Rickettsia prowazekii. J Mol Evol 42, 525-536.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 525-536
-
-
Andersson, S.G.1
Sharp, P.M.2
-
9
-
-
0029990946
-
Levels of Buchnera aphidicola chaperonin groEL during growth of the aphid Schizaphis graminum
-
Baumann, L., Baumann, P. & Clark, M. A. (1996). Levels of Buchnera aphidicola chaperonin groEL during growth of the aphid Schizaphis graminum. Curr Microbiol 32, 279-285.
-
(1996)
Curr. Microbiol.
, vol.32
, pp. 279-285
-
-
Baumann, L.1
Baumann, P.2
Clark, M.A.3
-
10
-
-
0032900069
-
Genetic characterization of plasmids containing genes encoding enzymes of leucine biosynthesis in endosymbionts (Buchnera) of aphids
-
Baumann, L., Baumann, P., Moran, N. A., Sandstrom, J. & Thao, M. L. (1999). Genetic characterization of plasmids containing genes encoding enzymes of leucine biosynthesis in endosymbionts (Buchnera) of aphids. J Mol Evol 48, 77-85.
-
(1999)
J. Mol. Evol.
, vol.48
, pp. 77-85
-
-
Baumann, L.1
Baumann, P.2
Moran, N.A.3
Sandstrom, J.4
Thao, M.L.5
-
11
-
-
0022292284
-
Codon usage and genome composition
-
Bernardi, G. (1985). Codon usage and genome composition. J Mol Evol 22, 363-365.
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 363-365
-
-
Bernardi, G.1
-
12
-
-
0035986891
-
Integrating genomics, bioinformatics, anti classical genetics to study the effects of recombination on genome evolution
-
Birdsell, J. A. (2002). Integrating genomics, bioinformatics, anti classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol 19, 1181-1197.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1181-1197
-
-
Birdsell, J.A.1
-
13
-
-
15444350252
-
The complete genome sequence of Escherichia coli K12
-
& 14 other authors
-
Blattner, F. R., Plunkett, G. I., Bloch, C. A. & 14 other authors (1997). The complete genome sequence of Escherichia coli K12. Science 277, 1453-1474.
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett, G.I.2
Bloch, C.A.3
-
14
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
Bulmer, M. (1991). The selection-mutation-drift theory of synonymous codon usage. Genetics 129, 897-907.
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.1
-
15
-
-
0034996704
-
A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, inferred from phylogenetic analysis based on a heterogeneous model of DNA evolution
-
Charles, H., Heddi, A. & Rahbe, Y. (2001). A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, inferred from phylogenetic analysis based on a heterogeneous model of DNA evolution. C R Acad Sci III 324, 489-494.
-
(2001)
C. R. Acad. Sci. III
, vol.324
, pp. 489-494
-
-
Charles, H.1
Heddi, A.2
Rahbe, Y.3
-
16
-
-
0031935160
-
Sequence analysis of a 34-7-kb DNA segment from the genome of Buchnera aphidicola (endosymbiont of aphids) containing groEL, dnaA, the atp operon, gidA, and rho
-
Clark, M. A., Baumann, L. & Baumann, P. (1998). Sequence analysis of a 34-7-kb DNA segment from the genome of Buchnera aphidicola (endosymbiont of aphids) containing groEL, dnaA, the atp operon, gidA, and rho. Curr Microbiol 36, 158-163.
-
(1998)
Curr. Microbiol.
, vol.36
, pp. 158-163
-
-
Clark, M.A.1
Baumann, L.2
Baumann, P.3
-
17
-
-
0032731436
-
Sequence evolution in bacterial endosymbionts having extreme base compositions
-
Clark, M. A., Moran, N. A. & Baumann, P. (1999). Sequence evolution in bacterial endosymbionts having extreme base compositions. Mol Biol Evol 16, 1586-1598.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1586-1598
-
-
Clark, M.A.1
Moran, N.A.2
Baumann, P.3
-
18
-
-
0035095118
-
Degenerative minimalism in the genome of a psyllid endosymbiont
-
Clark, M. A., Baumann, L., Thao, M. L., Moran, N. A. & Baumann, P. (2001). Degenerative minimalism in the genome of a psyllid endosymbiont. J Bacteriol 183, 1853-1861.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 1853-1861
-
-
Clark, M.A.1
Baumann, L.2
Thao, M.L.3
Moran, N.A.4
Baumann, P.5
-
19
-
-
0033921447
-
Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae
-
de Miranda, A. B., Alvarez-Valin, F., Jabbari, K., Degrave, W. M. & Bernardi, G. (2000). Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae. J Mol Evol 50, 45-55.
-
(2000)
J. Mol. Evol.
, vol.50
, pp. 45-55
-
-
de Miranda, A.B.1
Alvarez-Valin, F.2
Jabbari, K.3
Degrave, W.M.4
Bernardi, G.5
-
20
-
-
0025775913
-
Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins
-
D'Onofrio, G., Mouchiroud, D., Aissani, B., Gautier, C. & Bernardi, G. (1991). Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J Mol Evol 32, 504-510.
-
(1991)
J. Mol. Evol.
, vol.32
, pp. 504-510
-
-
D'Onofrio, G.1
Mouchiroud, D.2
Aissani, B.3
Gautier, C.4
Bernardi, G.5
-
21
-
-
0031020582
-
Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria
-
Foster, P. G., Jermiin, L. S. & Hickey, D. A. (1997). Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44, 282-288.
-
(1997)
J. Mol. Evol.
, vol.44
, pp. 282-288
-
-
Foster, P.G.1
Jermiin, L.S.2
Hickey, D.A.3
-
22
-
-
0032805876
-
A comparative genomics approach to DNA asymmetry
-
Francino, M. P. & Ochman, H. (1999). A comparative genomics approach to DNA asymmetry. Ann N Y Acad Sci 870, 428-431.
-
(1999)
Ann. N. Y. Acad. Sci.
, vol.870
, pp. 428-431
-
-
Francino, M.P.1
Ochman, H.2
-
23
-
-
0035107978
-
Intraspecific variation in symbiont genomes: Bottlenecks and the aphid-Buchnera association
-
Funk, D. J., Wernegreen, J. J. & Moran, N. A. (2001). Intraspecific variation in symbiont genomes: bottlenecks and the aphid-Buchnera association. Genetics 157, 477-489.
-
(2001)
Genetics
, vol.157
, pp. 477-489
-
-
Funk, D.J.1
Wernegreen, J.J.2
Moran, N.A.3
-
25
-
-
0031801256
-
Molecular characterization of the principal symbiotic bacteria of the weevil Sitophilus oryzae: A peculiar G + C content of an endocytobiotic DNA
-
Heddi, A., Charles, H., Khatchadourian, C., Bonnot, G. & Nardon, P. (1998). Molecular characterization of the principal symbiotic bacteria of the weevil Sitophilus oryzae: a peculiar G + C content of an endocytobiotic DNA. J Mol Evol 47, 52-61.
-
(1998)
J. Mol. Evol.
, vol.47
, pp. 52-61
-
-
Heddi, A.1
Charles, H.2
Khatchadourian, C.3
Bonnot, G.4
Nardon, P.5
-
26
-
-
0141812670
-
The Population and Evolutionary Genetics of Codon Bias
-
Cambridge: Cambridge University Press
-
Kreitman, M. & Antezana, M. (1999). The Population and Evolutionary Genetics of Codon Bias. Cambridge: Cambridge University Press.
-
(1999)
-
-
Kreitman, M.1
Antezana, M.2
-
27
-
-
0034086295
-
Absence of translationally selected synonymous codon usage bias in Helicobacter pylori
-
Lafay, B., Atherton, J. C. & Sharp, P. M. (2000). Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiology 146, 851-860.
-
(2000)
Microbiology
, vol.146
, pp. 851-860
-
-
Lafay, B.1
Atherton, J.C.2
Sharp, P.M.3
-
28
-
-
0028217395
-
Amplification of trpEG: Adaptation of Buchnera aphidicola to an endosymbiotic association with aphids
-
Lai, C. Y., Baumann, L. & Baumann, P. (1994). Amplification of trpEG: adaptation of Buchnera aphidicola to an endosymbiotic association with aphids. Proc Natl Acad Sci U S A 91, 3819-3823.
-
(1994)
Proc. Natl. Acad. Sci. U S A
, vol.91
, pp. 3819-3823
-
-
Lai, C.Y.1
Baumann, L.2
Baumann, P.3
-
29
-
-
0000957556
-
Secretory discharge and microflora of milk gland in tsetse flies
-
Ma, W.-C. & Denlinger, D. L. (1974). Secretory discharge and microflora of milk gland in tsetse flies. Nature 247, 301-303.
-
(1974)
Nature
, vol.247
, pp. 301-303
-
-
Ma, W.-C.1
Denlinger, D.L.2
-
30
-
-
0003766436
-
MacClade: Analysis of Phylogeny and Character Evolution
-
Sunderland, MA: Sinauer Associates
-
Maddison, D. & Maddison, W. (2002). MacClade: Analysis of Phylogeny and Character Evolution. Sunderland, MA: Sinauer Associates.
-
(2002)
-
-
Maddison, D.1
Maddison, W.2
-
31
-
-
0032169578
-
Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
-
McInerney, J. O. (1998a). Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci U S A 95, 10698-10703.
-
(1998)
Proc. Natl. Acad. Sci. U S A
, vol.95
, pp. 10698-10703
-
-
McInerney, J.O.1
-
32
-
-
0031851853
-
GCUA (General Codon Usage Analysis)
-
McInerney, J. O. (1998b). GCUA (General Codon Usage Analysis). Bionformatics 14, 372-373.
-
(1998)
Bionformatics
, vol.14
, pp. 372-373
-
-
McInerney, J.O.1
-
33
-
-
0036690426
-
Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria
-
Mira, A. & Moran, N. A. (2002). Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria. Microb Ecol 44, 137-143.
-
(2002)
Microb. Ecol.
, vol.44
, pp. 137-143
-
-
Mira, A.1
Moran, N.A.2
-
34
-
-
0034255952
-
Lifestyle evolution in symbiotic bacteria: Insights from genomics
-
Moran, N. A. & Wernegreen, J. J. (2000). Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol Evol 15, 321-326.
-
(2000)
Trends Ecol. Evol.
, vol.15
, pp. 321-326
-
-
Moran, N.A.1
Wernegreen, J.J.2
-
35
-
-
0027254254
-
A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts
-
Moran, N. A., Munson, M. A., Baumann, P. & Ishikawa, H. (1993). A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc R Soc Lond B Biol Sci 253, 167-171.
-
(1993)
Proc. R. Soc. Lond. B Biol. Sci.
, vol.253
, pp. 167-171
-
-
Moran, N.A.1
Munson, M.A.2
Baumann, P.3
Ishikawa, H.4
-
36
-
-
0000060475
-
Significance of symbionts for the maintenance of an optional nutritional state for successful reproduction in hematophagous arthropods
-
Nogge, G. (1981). Significance of symbionts for the maintenance of an optional nutritional state for successful reproduction in hematophagous arthropods. Parasitology 82, 101-104.
-
(1981)
Parasitology
, vol.82
, pp. 101-104
-
-
Nogge, G.1
-
37
-
-
0023514080
-
Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes
-
Ochman, H. & Wilson, A. C. (1987). Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26, 74-86.
-
(1987)
J. Mol. Evol.
, vol.26
, pp. 74-86
-
-
Ochman, H.1
Wilson, A.C.2
-
38
-
-
0025283965
-
The role of GC-biased mutation pressure on synonymous codon choice in Mycoplasma luteus, a bacterium with a high genomic GC-content
-
Ohama, T., Muto, A. & Osawa, S. (1990). The role of GC-biased mutation pressure on synonymous codon choice in Mycoplasma luteus, a bacterium with a high genomic GC-content. Nucleic Acids Res 18, 1565-1569.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 1565-1569
-
-
Ohama, T.1
Muto, A.2
Osawa, S.3
-
39
-
-
0036730186
-
A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high expression genes
-
Palacios, C. & Wernegreen, J. J. (2002). A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high expression genes. Mol Biol Evol 19, 1575-1584.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1575-1584
-
-
Palacios, C.1
Wernegreen, J.J.2
-
41
-
-
0034888796
-
Ongoing evolution of strand composition in bacterial genomes
-
Rocha, E. P. & Danchin, A. (2001). Ongoing evolution of strand composition in bacterial genomes. Mol Biol Evol 18, 1789-1799.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1789-1799
-
-
Rocha, E.P.1
Danchin, A.2
-
42
-
-
0032873222
-
How nutritionally imbalanced is phloem sap for aphids?
-
Sandström, J. & Moran, N. (1999). How nutritionally imbalanced is phloem sap for aphids? Entomol Exp Appl 91, 203-210.
-
(1999)
Entomol. Exp. Appl.
, vol.91
, pp. 203-210
-
-
Sandström, J.1
Moran, N.2
-
43
-
-
0026002819
-
Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: Codon usage, map position, and concerted evolution
-
Sharp, P. M. (1991). Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol 33, 23-33.
-
(1991)
J. Mol. Evol.
, vol.33
, pp. 23-33
-
-
Sharp, P.M.1
-
44
-
-
0023650543
-
The Codon Adaptation Index - A measure of directional synonymous codon usage bias, and its potential applications
-
Sharp, P. M. & Li, W. H. (1987). The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15, 1281-1295.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
45
-
-
0034618559
-
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
-
Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y. & Ishikawa, H. (2000). Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407, 81-86.
-
(2000)
Nature
, vol.407
, pp. 81-86
-
-
Shigenobu, S.1
Watanabe, H.2
Hattori, M.3
Sakaki, Y.4
Ishikawa, H.5
-
46
-
-
0033745103
-
Nucleotide bias causes a genomewide bias in the amino acid composition of proteins
-
Singer, G. A. & Hickey, D. A. (2000). Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 17, 1581-1588.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 1581-1588
-
-
Singer, G.A.1
Hickey, D.A.2
-
48
-
-
0025153770
-
Mechanism and regulation of bacterial ribosomal RNA processing
-
Srivastava, A. K. & Schlessinger, D. (1990). Mechanism and regulation of bacterial ribosomal RNA processing. Annu Rev Microbiol 44, 105-129.
-
(1990)
Annu Rev. Microbiol.
, vol.44
, pp. 105-129
-
-
Srivastava, A.K.1
Schlessinger, D.2
-
49
-
-
73049156042
-
Compositional correlation between deoxyribonucleic acid and protein
-
Sueoka, N. (1961). Compositional correlation between deoxyribonucleic acid and protein. Cold Spring Harb Symp Quant Biol 26, 35-43.
-
(1961)
Cold Spring Harb. Symp. Quant. Biol.
, vol.26
, pp. 35-43
-
-
Sueoka, N.1
-
50
-
-
0004248459
-
PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods)
-
Sunderland, MA: Sinauer Associates
-
Swofford, D. L. (2002). PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, MA: Sinauer Associates.
-
(2002)
-
-
Swofford, D.L.1
-
51
-
-
0037457901
-
Reductive genome evolution in Buchnera aphidicola
-
& 13 other authors
-
van Ham, R. C., Kamerbeek, J., Palacios, C. & 13 other authors (2003). Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A 100, 581-586.
-
(2003)
Proc. Natl. Acad. Sci. U S A
, vol.100
, pp. 581-586
-
-
van Ham, R.C.1
Kamerbeek, J.2
Palacios, C.3
-
52
-
-
0032948901
-
Evidence for genetic drift in endosymbionts (Buchnera): Analyses of protein-coding genes
-
Wernegreen, J. J. & Moran, N. A. (1999). Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol Biol Evol 16, 83-97.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 83-97
-
-
Wernegreen, J.J.1
Moran, N.A.2
-
53
-
-
0035162072
-
Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera)
-
Wernegreen, J. J. & Moran, N. A. (2001). Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera). J Bacteriol 183, 785-790.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 785-790
-
-
Wernegreen, J.J.1
Moran, N.A.2
-
54
-
-
0034044069
-
Decoupling of genome size and sequence divergence in a symbiotic bacterium
-
Wernegreen, J. J., Ochman, H., Jones, I. B. & Moran, N. A. (2000). Decoupling of genome size and sequence divergence in a symbiotic bacterium. J Bacteriol 182, 3867-3869.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 3867-3869
-
-
Wernegreen, J.J.1
Ochman, H.2
Jones, I.B.3
Moran, N.A.4
-
55
-
-
0037396914
-
Genome evolution in an insect cell: Distinct features of an ant-bacterial partnership
-
Wernegreen, J., Degnan, P., Lazarus, A., Palacios, C. & Bordenstein, S. (2003). Genome evolution in an insect cell: distinct features of an ant-bacterial partnership. Biol Bull 204, 221-231.
-
(2003)
Biol. Bull.
, vol.204
, pp. 221-231
-
-
Wernegreen, J.1
Degnan, P.2
Lazarus, A.3
Palacios, C.4
Bordenstein, S.5
-
56
-
-
0025318864
-
The 'effective number of codons' used in a gene
-
Wright, F. (1990). The 'effective number of codons' used in a gene. Gene 87, 23-29.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
57
-
-
0004139886
-
Phylogenetic Analysis by Maximum Likelihood (PAML)
-
version 3.12. London: University College London
-
Yang, Z. (2002). Phylogenetic Analysis by Maximum Likelihood (PAML), version 3.12. London: University College London.
-
(2002)
-
-
Yang, Z.1
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