메뉴 건너뛰기




Volumn 2, Issue 9, 2013, Pages 497-505

Probing cell-free gene expression noise in femtoliter volumes

Author keywords

cell free expression; confinement; noise; stochastic

Indexed keywords

DIMETICONE; LIPOSOME;

EID: 84884612696     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb400028c     Document Type: Article
Times cited : (36)

References (62)
  • 2
    • 55749115817 scopus 로고    scopus 로고
    • Cohesin subunit SMC1 associates with mitotic microtubules at the spindle pole
    • Wong, R. W. and Blobel, G. (2008) Cohesin subunit SMC1 associates with mitotic microtubules at the spindle pole Proc. Natl. Acad. Sci. U.S.A. 105, 15441-15445
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 15441-15445
    • Wong, R.W.1    Blobel, G.2
  • 4
    • 0028034493 scopus 로고
    • Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae
    • Iizuka, N., Najita, L., Franzusoff, A., and Sarnow, P. (1994) Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae Mol. Cell. Biol. 14, 7322-7330
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 7322-7330
    • Iizuka, N.1    Najita, L.2    Franzusoff, A.3    Sarnow, P.4
  • 6
    • 62449123034 scopus 로고    scopus 로고
    • A chance at survival: Gene expression noise and phenotypic diversification strategies
    • Fraser, D. and Kaern, M. (2009) A chance at survival: gene expression noise and phenotypic diversification strategies Mol. Microbiol. 71, 1333-1340
    • (2009) Mol. Microbiol. , vol.71 , pp. 1333-1340
    • Fraser, D.1    Kaern, M.2
  • 7
    • 77955830290 scopus 로고    scopus 로고
    • Biological role of noise encoded in a genetic network motif
    • Kittisopikul, M. and Suel, G. M. (2010) Biological role of noise encoded in a genetic network motif Proc. Natl. Acad. Sci. U.S.A. 107, 13300-13305
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 13300-13305
    • Kittisopikul, M.1    Suel, G.M.2
  • 8
    • 41349095731 scopus 로고    scopus 로고
    • Transient-mediated fate determination in a transcriptional circuit of HIV
    • Weinberger, L. S., Dar, R. D., and Simpson, M. L. (2008) Transient-mediated fate determination in a transcriptional circuit of HIV Nat. Genet. 40, 466-470
    • (2008) Nat. Genet. , vol.40 , pp. 466-470
    • Weinberger, L.S.1    Dar, R.D.2    Simpson, M.L.3
  • 9
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz, M. B., Levine, A. J., Siggia, E. D., and Swain, P. S. (2002) Stochastic gene expression in a single cell Science 297, 1183-1186
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 10
    • 79952638264 scopus 로고    scopus 로고
    • Cellular decision making and biological noise: From microbes to mammals
    • Balázsi, G., van Oudenaarden, A., and Collins, J. J. (2011) Cellular decision making and biological noise: From microbes to mammals Cell 144, 910-925
    • (2011) Cell , vol.144 , pp. 910-925
    • Balázsi, G.1    Van Oudenaarden, A.2    Collins, J.J.3
  • 12
    • 0037447260 scopus 로고    scopus 로고
    • Frequency domain analysis of noise in autoregulated gene circuits
    • Simpson, M. L., Cox, C. D., and Sayler, G. S. (2003) Frequency domain analysis of noise in autoregulated gene circuits Proc. Natl. Acad. Sci. U.S.A. 100, 4551-4556
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 4551-4556
    • Simpson, M.L.1    Cox, C.D.2    Sayler, G.S.3
  • 13
    • 22744441386 scopus 로고    scopus 로고
    • Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity
    • Weinberger, L. S., Burnett, J. C., Toettcher, J. E., Arkin, A. P., and Schaffer, D. V. (2005) Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity Cell 122, 169-182
    • (2005) Cell , vol.122 , pp. 169-182
    • Weinberger, L.S.1    Burnett, J.C.2    Toettcher, J.E.3    Arkin, A.P.4    Schaffer, D.V.5
  • 14
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
    • Arkin, A., Ross, J., and McAdams, H. H. (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells Genetics 149, 1633-1648
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 21
    • 77952492425 scopus 로고    scopus 로고
    • Tuning and controlling gene expression noise in synthetic gene networks
    • Murphy, K. F., Adams, R. M., Wang, X., Balázsi, G., and Collins, J. J. (2010) Tuning and controlling gene expression noise in synthetic gene networks Nucleic Acids Res. 38, 2712-2726
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2712-2726
    • Murphy, K.F.1    Adams, R.M.2    Wang, X.3    Balázsi, G.4    Collins, J.J.5
  • 24
    • 0033609146 scopus 로고    scopus 로고
    • The cell surface-associated intercellular C-signal induces behavioral changes in individual Myxococcus xanthus cells during fruiting body morphogenesis
    • Jelsbak, L. and Søgaard-Andersen, L. (1999) The cell surface-associated intercellular C-signal induces behavioral changes in individual Myxococcus xanthus cells during fruiting body morphogenesis Proc. Natl. Acad. Sci. U.S.A. 96, 5031-5036
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 5031-5036
    • Jelsbak, L.1    Søgaard-Andersen, L.2
  • 26
    • 13944272143 scopus 로고    scopus 로고
    • Aging and death in an organism that reproduces by morphologically symmetric division
    • Stewart, E. J., Madden, R., Paul, G., and Taddei, F. (2005) Aging and death in an organism that reproduces by morphologically symmetric division PLoS Biol. 3, e45
    • (2005) PLoS Biol. , vol.3 , pp. 45
    • Stewart, E.J.1    Madden, R.2    Paul, G.3    Taddei, F.4
  • 27
    • 79961051673 scopus 로고    scopus 로고
    • Separating intrinsic from extrinsic fluctuations in dynamic biological systems
    • Hilfinger, A. and Paulsson, J. (2011) Separating intrinsic from extrinsic fluctuations in dynamic biological systems Proc. Natl. Acad. Sci. U.S.A. 108, 12167-12172
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 12167-12172
    • Hilfinger, A.1    Paulsson, J.2
  • 28
    • 4344670572 scopus 로고    scopus 로고
    • Substrate replenishment extends protein synthesis with an in vitro translation system designed to mimic the cytoplasm
    • Jewett, M. C. and Swartz, J. R. (2004) Substrate replenishment extends protein synthesis with an in vitro translation system designed to mimic the cytoplasm Biotechnol. Bioeng. 87, 465-471
    • (2004) Biotechnol. Bioeng. , vol.87 , pp. 465-471
    • Jewett, M.C.1    Swartz, J.R.2
  • 29
    • 84872237058 scopus 로고    scopus 로고
    • Condensation of an additive-free cell extract to mimic the conditions of live cells
    • Fujiwara, K. and Shin-ichiro, M. N. (2013) Condensation of an additive-free cell extract to mimic the conditions of live cells PloS One 8, e54155
    • (2013) PloS One , vol.8 , pp. 54155
    • Fujiwara, K.1    Shin-Ichiro, M.N.2
  • 31
    • 77956069180 scopus 로고    scopus 로고
    • Protein subcellular localization in bacteria
    • a000307 10.1101/cshperspect.a000307
    • Rudner, D. Z. and Losick, R. (2010) Protein subcellular localization in bacteria Cold Spring Harbor Perspect. Biol. 2 a000307 10.1101/cshperspect. a000307
    • (2010) Cold Spring Harbor Perspect. Biol. , vol.2
    • Rudner, D.Z.1    Losick, R.2
  • 33
    • 84876584820 scopus 로고    scopus 로고
    • Linking genotype and phenotype in protein synthesizing liposomes with external supply of resources
    • Nourian, Z. and Danelon, C. (2013) Linking genotype and phenotype in protein synthesizing liposomes with external supply of resources ACS Synth. Biol. 2, 186-193
    • (2013) ACS Synth. Biol. , vol.2 , pp. 186-193
    • Nourian, Z.1    Danelon, C.2
  • 34
    • 65549091378 scopus 로고    scopus 로고
    • The minimal size of liposome-based model cells brings about a remarkably enhanced entrapment and protein synthesis
    • Pereira de Souza, T., Stano, P., and Luisi, P. L. (2009) The minimal size of liposome-based model cells brings about a remarkably enhanced entrapment and protein synthesis ChemBioChem 10, 1056-1063
    • (2009) ChemBioChem , vol.10 , pp. 1056-1063
    • Pereira De Souza, T.1    Stano, P.2    Luisi, P.L.3
  • 35
    • 84863705728 scopus 로고    scopus 로고
    • Cell-free protein synthesis from a single copy of DNA in a glass microchamber
    • Okano, T., Matsuura, T., Kazuta, Y., Suzuki, H., and Yomo, T. (2012) Cell-free protein synthesis from a single copy of DNA in a glass microchamber Lab Chip 12, 2704-2711
    • (2012) Lab Chip , vol.12 , pp. 2704-2711
    • Okano, T.1    Matsuura, T.2    Kazuta, Y.3    Suzuki, H.4    Yomo, T.5
  • 36
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: Stochastic gene expression and its consequences
    • Raj, A. and van Oudenaarden, A. (2008) Nature, nurture, or chance: Stochastic gene expression and its consequences Cell 135, 216-226
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    Van Oudenaarden, A.2
  • 37
    • 0022888115 scopus 로고
    • Determination of bacterial cell volume with the Coulter Counter
    • Kubitschek, H. E. and Friske, J. A. (1986) Determination of bacterial cell volume with the Coulter Counter J. Bacteriol. 168, 1466-1467
    • (1986) J. Bacteriol. , vol.168 , pp. 1466-1467
    • Kubitschek, H.E.1    Friske, J.A.2
  • 39
    • 44249122424 scopus 로고    scopus 로고
    • Fast mixing and reaction initiation control of single-enzyme kinetics in confined volumes
    • Jung, S.-Y., Liu, Y., and Collier, C. P. (2008) Fast mixing and reaction initiation control of single-enzyme kinetics in confined volumes Langmuir 24, 4439-4442
    • (2008) Langmuir , vol.24 , pp. 4439-4442
    • Jung, S.-Y.1    Liu, Y.2    Collier, C.P.3
  • 41
    • 77957197223 scopus 로고    scopus 로고
    • Spontaneous protein crowding in liposomes: A new vista for the origin of cellular metabolism
    • Luisi, P. L., Allegretti, M., Pereira de Souza, T., Steiniger, F., Fahr, A., and Stano, P. (2010) Spontaneous protein crowding in liposomes: A new vista for the origin of cellular metabolism ChemBioChem 11, 1989-1992
    • (2010) ChemBioChem , vol.11 , pp. 1989-1992
    • Luisi, P.L.1    Allegretti, M.2    Pereira De Souza, T.3    Steiniger, F.4    Fahr, A.5    Stano, P.6
  • 43
    • 11144220854 scopus 로고    scopus 로고
    • A vesicle bioreactor as a step toward an artificial cell assembly
    • Noireaux, V. and Libchaber, A. (2004) A vesicle bioreactor as a step toward an artificial cell assembly Proc. Natl. Acad. Sci. U.S.A. 101, 17669-17674
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 17669-17674
    • Noireaux, V.1    Libchaber, A.2
  • 44
    • 84855967334 scopus 로고    scopus 로고
    • Continuous protein production in nanoporous, picolitre volume containers
    • Siuti, P., Retterer, S. T., and Doktycz, M. J. (2011) Continuous protein production in nanoporous, picolitre volume containers Lab Chip 11, 3523-3529
    • (2011) Lab Chip , vol.11 , pp. 3523-3529
    • Siuti, P.1    Retterer, S.T.2    Doktycz, M.J.3
  • 45
    • 79251603722 scopus 로고    scopus 로고
    • Non-genetic heterogeneity from stochastic partitioning at cell division
    • Huh, D. and Paulsson, J. (2010) Non-genetic heterogeneity from stochastic partitioning at cell division Nat. Genet. 43, 95-100
    • (2010) Nat. Genet. , vol.43 , pp. 95-100
    • Huh, D.1    Paulsson, J.2
  • 46
    • 80052565008 scopus 로고    scopus 로고
    • Random partitioning of molecules at cell division
    • Huh, D. and Paulsson, J. (2011) Random partitioning of molecules at cell division Proc. Natl. Acad. Sci. U.S.A. 108, 15004-15009
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 15004-15009
    • Huh, D.1    Paulsson, J.2
  • 48
    • 79251480753 scopus 로고    scopus 로고
    • Coarse-grained dynamics of protein synthesis in a cell-free system
    • Karzbrun, E., Shin, J., Bar-Ziv, R. H., and Noireaux, V. (2011) Coarse-grained dynamics of protein synthesis in a cell-free system Phys. Rev. Lett. 106, 048104
    • (2011) Phys. Rev. Lett. , vol.106 , pp. 048104
    • Karzbrun, E.1    Shin, J.2    Bar-Ziv, R.H.3    Noireaux, V.4
  • 49
  • 50
    • 78649429731 scopus 로고    scopus 로고
    • Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisae
    • 037106 10.1063/1.3486800
    • Dar, R. D., Karig, D. K., Cooke, J. F., Cox, C. D., and Simpson, M. L. (2010) Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisae Chaos 20 037106 10.1063/1.3486800
    • (2010) Chaos , vol.20
    • Dar, R.D.1    Karig, D.K.2    Cooke, J.F.3    Cox, C.D.4    Simpson, M.L.5
  • 51
    • 3042601065 scopus 로고    scopus 로고
    • Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation
    • Simpson, M. L., Cox, C. D., and Sayler, G. S. (2004) Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation J. Theor. Biol. 229, 383-394
    • (2004) J. Theor. Biol. , vol.229 , pp. 383-394
    • Simpson, M.L.1    Cox, C.D.2    Sayler, G.S.3
  • 52
    • 79957608918 scopus 로고    scopus 로고
    • General properties of transcriptional time series in Escherichia coli
    • So, L.-h., Ghosh, A., Zong, C., Sepulveda, L. A., Segev, R., and Golding, I. (2011) General properties of transcriptional time series in Escherichia coli Nat. Genet. 43, 554-560
    • (2011) Nat. Genet. , vol.43 , pp. 554-560
    • So, L.-H.1    Ghosh, A.2    Zong, C.3    Sepulveda, L.A.4    Segev, R.5    Golding, I.6
  • 53
    • 77955102352 scopus 로고    scopus 로고
    • Quantifying E. Coli proteome and transcriptome with single-molecule sensitivity in single cells
    • Taniguchi, Y., Choi, P. J., Li, G.-W., Chen, H., Babu, M., Hearn, J., Emili, A., and Xie, X. S. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 329, 533-538
    • (2010) Science , vol.329 , pp. 533-538
    • Taniguchi, Y.1    Choi, P.J.2    Li, G.-W.3    Chen, H.4    Babu, M.5    Hearn, J.6    Emili, A.7    Xie, X.S.8
  • 55
    • 84860375823 scopus 로고    scopus 로고
    • Expression optimization and synthetic gene networks in cell-free systems
    • Karig, D. K., Iyer, S., Simpson, M. L., and Doktycz, M. J. (2012) Expression optimization and synthetic gene networks in cell-free systems Nucleic Acids Res. 40, 3763-3774
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3763-3774
    • Karig, D.K.1    Iyer, S.2    Simpson, M.L.3    Doktycz, M.J.4
  • 56
    • 0037162469 scopus 로고    scopus 로고
    • Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    • Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S., and Cohen, S. N. (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays Proc. Natl. Acad. Sci. U.S.A. 99, 9697-9702
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 9697-9702
    • Bernstein, J.A.1    Khodursky, A.B.2    Lin, P.H.3    Lin-Chao, S.4    Cohen, S.N.5
  • 57
    • 23244446620 scopus 로고    scopus 로고
    • Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis
    • Underwood, K. A., Swartz, J. R., and Puglisi, J. D. (2005) Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis Biotechnol. Bioeng. 91, 425-435
    • (2005) Biotechnol. Bioeng. , vol.91 , pp. 425-435
    • Underwood, K.A.1    Swartz, J.R.2    Puglisi, J.D.3
  • 58
    • 41349119880 scopus 로고    scopus 로고
    • Stochastic switching as a survival strategy in fluctuating environments
    • Acar, M., Mettetal, J. T., and van Oudenaarden, A. (2008) Stochastic switching as a survival strategy in fluctuating environments Nat. Genet. 40, 471-475
    • (2008) Nat. Genet. , vol.40 , pp. 471-475
    • Acar, M.1    Mettetal, J.T.2    Van Oudenaarden, A.3
  • 59
    • 70350336588 scopus 로고    scopus 로고
    • Architecture-dependent noise discriminates functionally analogous differentiation circuits
    • Çaǧatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J., and Süel, G. M. (2009) Architecture-dependent noise discriminates functionally analogous differentiation circuits Cell 139, 512-522
    • (2009) Cell , vol.139 , pp. 512-522
    • Çaǧatay, T.1    Turcotte, M.2    Elowitz, M.B.3    Garcia-Ojalvo, J.4    Süel, G.M.5
  • 61
    • 77950810816 scopus 로고    scopus 로고
    • Development and fabrication of nanoporous silicon-based bioreactors within a microfluidic chip
    • Retterer, S. T., Siuti, P., Choi, C.-K., Thomas, D. K., and Doktycz, M. J. (2010) Development and fabrication of nanoporous silicon-based bioreactors within a microfluidic chip Lab Chip 10, 1174-1181
    • (2010) Lab Chip , vol.10 , pp. 1174-1181
    • Retterer, S.T.1    Siuti, P.2    Choi, C.-K.3    Thomas, D.K.4    Doktycz, M.J.5
  • 62
    • 84863205849 scopus 로고    scopus 로고
    • NIH Image to ImageJ: 25 years of image analysis
    • Schneider, C. A., Rasband, W. S., and Eliceiri, K. W. (2012) NIH Image to ImageJ: 25 years of image analysis Nat. Methods 9, 671-675
    • (2012) Nat. Methods , vol.9 , pp. 671-675
    • Schneider, C.A.1    Rasband, W.S.2    Eliceiri, K.W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.