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Volumn 54, Issue , 2018, Pages 33-40

Advances in analytical tools for high throughput strain engineering

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; CHEMICAL ANALYSIS; DATA INTEGRATION; GENES; PIPELINES; STRAIN;

EID: 85041833041     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2018.01.027     Document Type: Review
Times cited : (30)

References (61)
  • 1
    • 84960941501 scopus 로고    scopus 로고
    • Estimating the biotech sector's contribution to the US economy
    • Carlson, R., Estimating the biotech sector's contribution to the US economy. Nat Biotechnol 34 (2016), 247–255.
    • (2016) Nat Biotechnol , vol.34 , pp. 247-255
    • Carlson, R.1
  • 2
    • 84982179570 scopus 로고    scopus 로고
    • Living factories of the future
    • Eisenstein, M., Living factories of the future. Nature 531 (2016), 401–403.
    • (2016) Nature , vol.531 , pp. 401-403
    • Eisenstein, M.1
  • 3
    • 85018521893 scopus 로고    scopus 로고
    • Fully automated one-step synthesis of single-transcript TALEN pairs using a biological foundry
    • Chao, R., Liang, J., Tasan, I., Si, T., Ju, L., Zhao, H., Fully automated one-step synthesis of single-transcript TALEN pairs using a biological foundry. ACS Synth Biol 6 (2017), 678–685.
    • (2017) ACS Synth Biol , vol.6 , pp. 678-685
    • Chao, R.1    Liang, J.2    Tasan, I.3    Si, T.4    Ju, L.5    Zhao, H.6
  • 4
    • 85020710659 scopus 로고    scopus 로고
    • Engineering biological systems using automated biofoundries
    • This review summarizes the enabling technologies for biofoundries as well as their early successes and remaining challenges.
    • Chao, R., Mishra, S., Si, T., Zhao, H.M., Engineering biological systems using automated biofoundries. Metab Eng 42 (2017), 98–108 This review summarizes the enabling technologies for biofoundries as well as their early successes and remaining challenges.
    • (2017) Metab Eng , vol.42 , pp. 98-108
    • Chao, R.1    Mishra, S.2    Si, T.3    Zhao, H.M.4
  • 5
    • 85020737000 scopus 로고    scopus 로고
    • Automated multiplex genome-scale engineering in yeast
    • Using an automated platform for engineering in Saccharomyces cerevisiae, the authors describe a platform tool for overexpression and knockdown mutations of 490% of the yeast genes in a single step from a cDNA library. Using robotic automation CRISPR-Cas, parts are iteratively integrated for isobutanol production, glycerol utilization and acetic acid tolerance.
    • Si, T., Chao, R., Min, Y., Wu, Y., Ren, W., Zhao, H., Automated multiplex genome-scale engineering in yeast. Nat Commun, 8, 2017, 15187 Using an automated platform for engineering in Saccharomyces cerevisiae, the authors describe a platform tool for overexpression and knockdown mutations of 490% of the yeast genes in a single step from a cDNA library. Using robotic automation CRISPR-Cas, parts are iteratively integrated for isobutanol production, glycerol utilization and acetic acid tolerance.
    • (2017) Nat Commun , vol.8 , pp. 15187
    • Si, T.1    Chao, R.2    Min, Y.3    Wu, Y.4    Ren, W.5    Zhao, H.6
  • 6
    • 85030751430 scopus 로고    scopus 로고
    • Chemistry challenges to enable a sustainable bioeconomy
    • Fitzgerald, N.D., Chemistry challenges to enable a sustainable bioeconomy. Nat Rev Chem, 1, 2017.
    • (2017) Nat Rev Chem , vol.1
    • Fitzgerald, N.D.1
  • 8
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard, A.P., Pharkya, P., Maranas, C.D., Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84 (2003), 647–657.
    • (2003) Biotechnol Bioeng , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 9
    • 84898548508 scopus 로고    scopus 로고
    • A hybrid of bees algorithm and flux balance analysis with OptKnock as a platform for in silico optimization of microbial strains
    • Choon, Y.W., Mohamad, M.S., Deris, S., Illias, R.M., Chong, C.K., Chai, L.E., A hybrid of bees algorithm and flux balance analysis with OptKnock as a platform for in silico optimization of microbial strains. Bioprocess Biosyst Eng 37 (2014), 521–532.
    • (2014) Bioprocess Biosyst Eng , vol.37 , pp. 521-532
    • Choon, Y.W.1    Mohamad, M.S.2    Deris, S.3    Illias, R.M.4    Chong, C.K.5    Chai, L.E.6
  • 12
    • 77953578214 scopus 로고    scopus 로고
    • Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
    • Henry, C.S., Broadbelt, L.J., Hatzimanikatis, V., Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol Bioeng 106 (2010), 462–473.
    • (2010) Biotechnol Bioeng , vol.106 , pp. 462-473
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 15
    • 85009128777 scopus 로고    scopus 로고
    • Double dutch: a tool for designing combinatorial libraries of biological systems
    • Roehner, N., Young, E.M., Voigt, C.A., Gordon, D.B., Densmore, D., Double dutch: a tool for designing combinatorial libraries of biological systems. ACS Synth Biol 5 (2016), 507–517.
    • (2016) ACS Synth Biol , vol.5 , pp. 507-517
    • Roehner, N.1    Young, E.M.2    Voigt, C.A.3    Gordon, D.B.4    Densmore, D.5
  • 17
    • 84901846633 scopus 로고    scopus 로고
    • Interactive assembly algorithms for molecular cloning
    • Appleton, E., Tao, J., Haddock, T., Densmore, D., Interactive assembly algorithms for molecular cloning. Nat Methods 11 (2014), 657–662.
    • (2014) Nat Methods , vol.11 , pp. 657-662
    • Appleton, E.1    Tao, J.2    Haddock, T.3    Densmore, D.4
  • 18
    • 84963568291 scopus 로고    scopus 로고
    • Genetic circuit design automation
    • The authors use electronic design automation to design computational circuits for living cells. They use plasmids expressed in E. coli to regulate cellular functions in response to multiple environmental signals, achieving 92% of the 412 output to function as predicted.
    • Nielsen, A.A.K., Der, B.S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E.A., Ross, D., Densmore, D., Voigt, C.A., Genetic circuit design automation. Science, 352, 2016 The authors use electronic design automation to design computational circuits for living cells. They use plasmids expressed in E. coli to regulate cellular functions in response to multiple environmental signals, achieving 92% of the 412 output to function as predicted.
    • (2016) Science , vol.352
    • Nielsen, A.A.K.1    Der, B.S.2    Shin, J.3    Vaidyanathan, P.4    Paralanov, V.5    Strychalski, E.A.6    Ross, D.7    Densmore, D.8    Voigt, C.A.9
  • 22
    • 84859633048 scopus 로고    scopus 로고
    • Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
    • Zhang, F., Carothers, J.M., Keasling, J.D., Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30 (2012), 354–359.
    • (2012) Nat Biotechnol , vol.30 , pp. 354-359
    • Zhang, F.1    Carothers, J.M.2    Keasling, J.D.3
  • 24
    • 84910631853 scopus 로고    scopus 로고
    • Core-shell particles lead the way to renewing high-performance liquid chromatography
    • Gonzalez-Ruiz, V., Olives, A.I., Martin, M.A., Core-shell particles lead the way to renewing high-performance liquid chromatography. Trends Anal Chem 64 (2015), 17–28.
    • (2015) Trends Anal Chem , vol.64 , pp. 17-28
    • Gonzalez-Ruiz, V.1    Olives, A.I.2    Martin, M.A.3
  • 25
    • 84947763523 scopus 로고    scopus 로고
    • High-throughput platforms for metabolomics
    • The authors present a critical review on high-throughput MS-based platforms and their potential application in metabolomics. The authors review how MS platforms can now achieve very high throughputs and highlight that separation methods remain the bottle neck. The trade-off between sample throughput and metabolite coverage is reviewed in detail.
    • de Raad, M., Fischer, C.R., Northen, T.R., High-throughput platforms for metabolomics. Curr Opin Chem Biol 30 (2016), 7–13 The authors present a critical review on high-throughput MS-based platforms and their potential application in metabolomics. The authors review how MS platforms can now achieve very high throughputs and highlight that separation methods remain the bottle neck. The trade-off between sample throughput and metabolite coverage is reviewed in detail.
    • (2016) Curr Opin Chem Biol , vol.30 , pp. 7-13
    • de Raad, M.1    Fischer, C.R.2    Northen, T.R.3
  • 26
    • 84946400095 scopus 로고    scopus 로고
    • Comparison of the most recent chromatographic approaches applied for fast and high resolution separations: theory and practice
    • Fekete, S., Veuthey, J.L., Guillarme, D., Comparison of the most recent chromatographic approaches applied for fast and high resolution separations: theory and practice. J Chromatogr A 1408 (2015), 1–14.
    • (2015) J Chromatogr A , vol.1408 , pp. 1-14
    • Fekete, S.1    Veuthey, J.L.2    Guillarme, D.3
  • 27
    • 77953476888 scopus 로고    scopus 로고
    • New trends in fast and high-resolution liquid chromatography: a critical comparison of existing approaches
    • Guillarme, D., Ruta, J., Rudaz, S., Veuthey, J.L., New trends in fast and high-resolution liquid chromatography: a critical comparison of existing approaches. Anal Bioanal Chem 397 (2010), 1069–1082.
    • (2010) Anal Bioanal Chem , vol.397 , pp. 1069-1082
    • Guillarme, D.1    Ruta, J.2    Rudaz, S.3    Veuthey, J.L.4
  • 28
    • 85008391609 scopus 로고    scopus 로고
    • Frontiers of high-throughput metabolomics
    • Researchers from the Sauer group describe progress in high-throughput metabolomics for profiling large cohorts and dynamic systems with high temporal resolution and automated sampling for functional genomics, drug discovery, and personalized medicine. They discuss progress in single cell analyses where high-throughput analytics can resolve metabolic heterogeneity in populations and compartmentalization of metabolites.
    • Zampieri, M., Sekar, K., Zamboni, N., Sauer, U., Frontiers of high-throughput metabolomics. Curr Opin Chem Biol 36 (2017), 15–23 Researchers from the Sauer group describe progress in high-throughput metabolomics for profiling large cohorts and dynamic systems with high temporal resolution and automated sampling for functional genomics, drug discovery, and personalized medicine. They discuss progress in single cell analyses where high-throughput analytics can resolve metabolic heterogeneity in populations and compartmentalization of metabolites.
    • (2017) Curr Opin Chem Biol , vol.36 , pp. 15-23
    • Zampieri, M.1    Sekar, K.2    Zamboni, N.3    Sauer, U.4
  • 29
    • 77955981385 scopus 로고    scopus 로고
    • Fully automated screening of veterinary drugs in milk by turbulent flow chromatography and tandem mass spectrometry
    • Stolker, A.A., Peters, R.J., Zuiderent, R., DiBussolo, J.M., Martins, C.P., Fully automated screening of veterinary drugs in milk by turbulent flow chromatography and tandem mass spectrometry. Anal Bioanal Chem 397 (2010), 2841–2849.
    • (2010) Anal Bioanal Chem , vol.397 , pp. 2841-2849
    • Stolker, A.A.1    Peters, R.J.2    Zuiderent, R.3    DiBussolo, J.M.4    Martins, C.P.5
  • 30
    • 84884920570 scopus 로고    scopus 로고
    • Label-free high-throughput assays to screen and characterize novel lactate dehydrogenase inhibitors
    • VanderPorten, E., Frick, L., Turincio, R., Thana, P., LaMarr, W., Liu, Y.C., Label-free high-throughput assays to screen and characterize novel lactate dehydrogenase inhibitors. Anal Biochem 441 (2013), 115–122.
    • (2013) Anal Biochem , vol.441 , pp. 115-122
    • VanderPorten, E.1    Frick, L.2    Turincio, R.3    Thana, P.4    LaMarr, W.5    Liu, Y.C.6
  • 31
    • 84950126258 scopus 로고    scopus 로고
    • Globally optimized targeted mass spectrometry: reliable metabolomics analysis with broad coverage
    • Gu, H., Zhang, P., Zhu, J., Raftery, D., Globally optimized targeted mass spectrometry: reliable metabolomics analysis with broad coverage. Anal Chem 87 (2015), 12355–12362.
    • (2015) Anal Chem , vol.87 , pp. 12355-12362
    • Gu, H.1    Zhang, P.2    Zhu, J.3    Raftery, D.4
  • 34
    • 85030212556 scopus 로고    scopus 로고
    • Advances in stem cell proteomics
    • Abazova, N., Krijgsveld, J., Advances in stem cell proteomics. Curr Opin Genet Dev 46 (2017), 149–155.
    • (2017) Curr Opin Genet Dev , vol.46 , pp. 149-155
    • Abazova, N.1    Krijgsveld, J.2
  • 35
    • 84988336041 scopus 로고    scopus 로고
    • Proteome complexity and the forces that drive proteome imbalance
    • Harper, J.W., Bennett, E.J., Proteome complexity and the forces that drive proteome imbalance. Nature 537 (2016), 328–338.
    • (2016) Nature , vol.537 , pp. 328-338
    • Harper, J.W.1    Bennett, E.J.2
  • 41
    • 84899742652 scopus 로고    scopus 로고
    • Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome
    • Licona-Cassani, C., Lim, S., Marcellin, E., Nielsen, L.K., Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome. Mol Cell Proteomics 13 (2014), 1219–1230.
    • (2014) Mol Cell Proteomics , vol.13 , pp. 1219-1230
    • Licona-Cassani, C.1    Lim, S.2    Marcellin, E.3    Nielsen, L.K.4
  • 43
    • 84861860481 scopus 로고    scopus 로고
    • Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis
    • Gillet, L.C., Navarro, P., Tate, S., Rost, H., Selevsek, N., Reiter, L., Bonner, R., Aebersold, R., Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteom, 11, 2012.
    • (2012) Mol Cell Proteom , vol.11
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Rost, H.4    Selevsek, N.5    Reiter, L.6    Bonner, R.7    Aebersold, R.8
  • 45
    • 85038848913 scopus 로고    scopus 로고
    • Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results
    • Bruderer, R., Bernhardt, O.M., Gandhi, T., Xuan, Y., Sondermann, J., Schmidt, M., Gomez-Varela, D., Reiter, L., Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results. Mol Cell Proteom 16 (2017), 2296–2309.
    • (2017) Mol Cell Proteom , vol.16 , pp. 2296-2309
    • Bruderer, R.1    Bernhardt, O.M.2    Gandhi, T.3    Xuan, Y.4    Sondermann, J.5    Schmidt, M.6    Gomez-Varela, D.7    Reiter, L.8
  • 48
    • 84908323876 scopus 로고    scopus 로고
    • Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models
    • Benedict, M.N., Mundy, M.B., Henry, C.S., Chia, N., Price, N.D., Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models. PLoS Comput Biol, 10, 2014.
    • (2014) PLoS Comput Biol , vol.10
    • Benedict, M.N.1    Mundy, M.B.2    Henry, C.S.3    Chia, N.4    Price, N.D.5
  • 49
  • 50
    • 85004191344 scopus 로고    scopus 로고
    • Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli
    • Sevin, D.C., Fuhrer, T., Zamboni, N., Sauer, U., Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat Methods 14 (2017), 187–194.
    • (2017) Nat Methods , vol.14 , pp. 187-194
    • Sevin, D.C.1    Fuhrer, T.2    Zamboni, N.3    Sauer, U.4
  • 51
    • 85026662178 scopus 로고    scopus 로고
    • redGEM: systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
    • Ataman, M., Hernandez Gardiol, D.F., Fengos, G., Hatzimanikatis, V., redGEM: systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PLoS Comput Biol, 13, 2017, e1005444.
    • (2017) PLoS Comput Biol , vol.13 , pp. e1005444
    • Ataman, M.1    Hernandez Gardiol, D.F.2    Fengos, G.3    Hatzimanikatis, V.4
  • 53
    • 78649832864 scopus 로고    scopus 로고
    • Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast
    • Fendt, S.M., Oliveira, A.P., Christen, S., Picotti, P., Dechant, R.C., Sauer, U., Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol Syst Biol, 6, 2010.
    • (2010) Mol Syst Biol , vol.6
    • Fendt, S.M.1    Oliveira, A.P.2    Christen, S.3    Picotti, P.4    Dechant, R.C.5    Sauer, U.6
  • 55
    • 84903164690 scopus 로고    scopus 로고
    • A novel platform for automated high-throughput fluxome profiling of metabolic variants
    • 13C-labelling and sampling with NMR-based isotopic fingerprinting and data interpretation profiling is presented. The workflow presented compares Escherichia coli mutants with gradual expression of the glucose-6-phosphate dehydrogenase. The platform clearly discriminated pathways that support metabolic flexibility towards modulation of a single enzyme.
    • 13C-labelling and sampling with NMR-based isotopic fingerprinting and data interpretation profiling is presented. The workflow presented compares Escherichia coli mutants with gradual expression of the glucose-6-phosphate dehydrogenase. The platform clearly discriminated pathways that support metabolic flexibility towards modulation of a single enzyme.
    • (2014) Metab Eng , vol.25 , pp. 8-19
    • Heux, S.1    Poinot, J.2    Massou, S.3    Sokol, S.4    Portais, J.C.5
  • 56
    • 84956858710 scopus 로고    scopus 로고
    • Trans-omics: how to reconstruct biochemical networks across multiple ‘omic’ layers
    • Yugi, K., Kubota, H., Hatano, A., Kuroda, S., Trans-omics: how to reconstruct biochemical networks across multiple ‘omic’ layers. Trends Biotechnol 34 (2016), 276–290.
    • (2016) Trends Biotechnol , vol.34 , pp. 276-290
    • Yugi, K.1    Kubota, H.2    Hatano, A.3    Kuroda, S.4
  • 61
    • 85029661882 scopus 로고    scopus 로고
    • Formulation, construction and analysis of kinetic models of metabolism: a review of modelling frameworks
    • As kinetic models can accurately capture the complexity of metabolic systems, the authors present a comprehensive revision of kinetic modelling, reviewing kinetic formalisms, construction and analysis methods.
    • Saa, P.A., Nielsen, L.K., Formulation, construction and analysis of kinetic models of metabolism: a review of modelling frameworks. Biotechnol Adv 35 (2017), 981–1003 As kinetic models can accurately capture the complexity of metabolic systems, the authors present a comprehensive revision of kinetic modelling, reviewing kinetic formalisms, construction and analysis methods.
    • (2017) Biotechnol Adv , vol.35 , pp. 981-1003
    • Saa, P.A.1    Nielsen, L.K.2


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