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Artykuły w czasopismach na temat "Synthetic gene circuits"
Santos-Moreno, Javier, i Yolanda Schaerli. "CRISPR-based gene expression control for synthetic gene circuits". Biochemical Society Transactions 48, nr 5 (23.09.2020): 1979–93. http://dx.doi.org/10.1042/bst20200020.
Pełny tekst źródłaRay, L. Bryan. "Stabilizing synthetic gene circuits". Science 365, nr 6457 (5.09.2019): 995.15–997. http://dx.doi.org/10.1126/science.365.6457.995-o.
Pełny tekst źródłaZhang, Yongpeng, Yuhua Feng, Yuan Liang, Jing Yang i Cheng Zhang. "Development of Synthetic DNA Circuit and Networks for Molecular Information Processing". Nanomaterials 11, nr 11 (4.11.2021): 2955. http://dx.doi.org/10.3390/nano11112955.
Pełny tekst źródłaNandagopal, Nagarajan, i Michael B. Elowitz. "Synthetic Biology: Integrated Gene Circuits". Science 333, nr 6047 (1.09.2011): 1244–48. http://dx.doi.org/10.1126/science.1207084.
Pełny tekst źródłaAlamos, Simon, i Patrick M. Shih. "Synthetic gene circuits take root". Science 377, nr 6607 (12.08.2022): 711–12. http://dx.doi.org/10.1126/science.add6805.
Pełny tekst źródłaChalancon, Guilhem, i M. Madan Babu. "Scaling up synthetic gene circuits". Nature Nanotechnology 5, nr 9 (wrzesień 2010): 631–33. http://dx.doi.org/10.1038/nnano.2010.178.
Pełny tekst źródłaRay, L. Bryan. "Cooperativity in synthetic gene circuits". Science 364, nr 6440 (9.05.2019): 542.10–544. http://dx.doi.org/10.1126/science.364.6440.542-j.
Pełny tekst źródłaCloney, Ross. "Cooperating on synthetic gene circuits". Nature Biotechnology 37, nr 7 (lipiec 2019): 729. http://dx.doi.org/10.1038/s41587-019-0182-3.
Pełny tekst źródłaGardner, Laura, i Alexander Deiters. "Light-controlled synthetic gene circuits". Current Opinion in Chemical Biology 16, nr 3-4 (sierpień 2012): 292–99. http://dx.doi.org/10.1016/j.cbpa.2012.04.010.
Pełny tekst źródłaBashor, Caleb J., Nikit Patel, Sandeep Choubey, Ali Beyzavi, Jané Kondev, James J. Collins i Ahmad S. Khalil. "Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies". Science 364, nr 6440 (18.04.2019): 593–97. http://dx.doi.org/10.1126/science.aau8287.
Pełny tekst źródłaRozprawy doktorskie na temat "Synthetic gene circuits"
Checkley, Stephen. "Engineering tuneable gene circuits in yeast". Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/engineering-tuneable-gene-circuits-in-yeast(71dda344-8802-4862-9b29-1a671f4c96ab).html.
Pełny tekst źródłaBoada, Acosta Yadira Fernanda. "A systems engineering approach to model, tune and test synthetic gene circuits". Doctoral thesis, Universitat Politècnica de València, 2018. http://hdl.handle.net/10251/112725.
Pełny tekst źródłaLa biologia sintètica es defineix com l'enginyeria de la biologia: el (re) disseny i construcció de noves parts, dispositius i sistemes biològics per a realitzar noves funcions útils que es basen a principis elucidats de la biologia i l'enginyeria. Per facilitar la construcció ràpida, reproduïble i predictible de aquests sistemes biològics a partir de conjunts de components és necessari desenvolupar nous mètodes i eines. La tesi planteja la optimització multiobjectiu com el marc adequat per a tractar els problemes comuns que apareixen en el disseny racional i l' ajust òptim dels circuits genètics sintètics. Utilitzant un enfocament clàssic d'enginyeria de sistemes, la tesi es centra principalment en: i) el modelatge de circuits genètics sintètics basat en primers principis, ii) l' estimació de paràmetres de models a partir de dades experimentals i iii) l' ajust basat en models per aconseguir el rendiment desitjat dels circuits. S'han utilitzat dos circuits genètics sintètics de diferent naturalesa i amb diferents objectius i problemes: un circuit de prealimentació de tipus 1 incoherent (I1-FFL) que exhibeix la important propietat biològica d'adaptació, i un circuit de quorum sensing i realimentació (QS/Fb) que comprèn dos bucles de realimentació entrellaçats -un intracel·lular i un basat en la comunicació de cèl·lula a cèl·lula- dis-senyat per regular el nivell mitjà d'expressió normal d'una proteïna d'interès mentre es minimitza la seua variació al llarg de la població de cèl·lules. Els dos circuits han estat analitzats in silico i implementats in vivo. En tots dos casos, s'han desenvolupat models basats en primers principis d'aquests circuits. Després es presta especial atenció a delinear com obtenir models d'ordre reduït susceptibles de estimació de paràmetres, però mantenint el significat biològic. L' estimació dels paràmetres del model a partir de les dades experimentals es considera en diferents escenaris, tant utilitzant models determinístics com estocàstics. Per al circuit I1-FFL es consideren models determinístics. La tesi planteja la utilització de models locals utilitzant la optimització multiobjectiu per realitzar l'estimació de parametres del model sota escenaris amb estructura de model incompleta (dinàmica no modelada). Per al circuit de QS/Fb, una estructura controlada per realimentació, el problema tractat és la manca d'excitabilitat dels senyals. La tesi proposa una metodologia de estimació en dues etapes utilitzant models estocàstics. La metodologia permet utilitzar dades de curs temporal promediats de la població i mesures de distribució en estat estacionari d'una sola una cèl·lula. L' ajust de circuits basat en models per aconseguir el rendiment desitjat dels circuits també s' aborda mitjançant la optimització multiobjectiu. Per al circuit QS/Fb, es fa un anàlisi estocàstic complet. La tesi aborda com tenir en compte correctament tant el soroll intrínsec com l' extrínsec, les dues principals fonts de soroll en els circuits genètics sintètics. S' analitza l'equilibri entre dues fonts de soroll i el paper que exerceixen en el bucle de realimentació intracel·lular, les i en la realimentació extracel·lular de tota la població. La principal conclusió es que la complexa interacció entre els dos canals de realimentació fa necessari l' ús de la optimització multiobjectiu per al adequat ajust del circuit. En aquesta tesi, a més de l'ús adequat d'eines d'optimització multiobjectiu, la principal preocupació és com derivar directives per al ajust in silico de paràmetres de circuits que puguin aplicar-se de forma realista en viu en un laboratori estàndard. Així, com a alternativa a l'anàlisi de sensibilitat de paràmetres clàssic, la tesi proposa l'ús de l' tècniques de l'agrupació al llarg dels fronts de Pareto, relacionant el compromís de dessempeny amb les regions en l'espai d'paràmetres.
Synthetic biology is defined as the engineering of biology: the deliberate (re)design and construction of novel biological and biologically based parts, devices and systems to perform new functions for useful purposes, that draws on principles elucidated from biology and engineering. Methods and tools are needed to facilitate fast, reproducible and predictable construction of biological systems from sets of biological components. This thesis raises multi-objective optimization as the proper framework to deal with common problems arising in rational design and optimal tuning of synthetic gene circuits. Using a classical systems engineering approach, the thesis mainly addresses: i) synthetic gene circuit modeling based on first principles, ii) model parameters estimation from experimental data and iii) model-based tuning to achieve desired circuit performance. Two gene synthetic circuits of different nature and with different goals and inherent problems have been used throughout the thesis: an Incoherent type 1 feedforward circuit (I1-FFL) that exhibits the important biological property of adaptation, and a Quorum sensing/Feedback circuit (QS/Fb) comprising two intertwined feedback loops -an intracellular one and a cell-to-cell communication-based one-- designed to regulate the mean expression level of a protein of interest while minimizing its variance across the population of cells. Both circuits have been analyzed in silico and implemented in vivo. In both cases, circuit modeling based on first principles has been carried out. Then, special attention is paid to illustrate how to obtain reduced order models amenable for parameters estimation yet keeping biological significance. Model parameters estimation from experimental data is considered in different scenarios, both using deterministic and stochastic models. For the I1-FFL circuit, deterministic models are considered. In this case, the thesis raises ensemble modeling using multi-objective optimization to perform model parameters estimation under scenarios with incomplete model structure (unmodeled dynamics). For the QS/Fb gene circuit, a feedback controlled structure, the lack of excitability of the signals is the problem addressed. The thesis proposes a two-stage estimation methodology using stochastic models. The methodology allows using population averaged time-course data and steady state distribution measurements at the single-cell level. Model-based circuit tuning to achieve desired circuit performance is also addressed using multi-objective optimization. First, for the QS/Fb feedback control circuit, a complete stochastic analysis is performed. Here, the thesis addresses how to correctly take into account both intrinsic and extrinsic noise, the two main sources of noise in gene synthetic circuits. The trade-off between both sources of noise, and the role played by in the intracellular single-cell feedback loop and the extracellular population-wide feedback is analyzed. The main conclusion being that the complex interplay between both feedback channels compel the use of multi-objective optimization for proper tuning of the circuit to achieve desired performance. Thus, the thesis wraps up all the previous results and uses them to address circuit tuning for desired performance. Here, besides the proper use of multi-objective optimization tools, the main concern is how to derive guidelines for circuit parameters tuning in silico that can realistically be applied in vivo in a standard laboratory. Thus, as an alternative to classical parameters sensitivity analysis, the thesis proposes the use of clustering techniques along the optimal Pareto fronts relating the performance trade-offs with regions in the circuits parameters space.
This work has been partially supported by the Spanish Government (CICYT DPI2014- 55276-C5-1) and the European Union (FEDER). The author was recipient of the grant Formación de Personal Investigador by the Universitat Politècnica de València, subprogram 1 (FPI/2013-3242). She was also recipient of the competitive grants for pre-doctoral stays Erasmus Student Placement-European Programme 2015, and FPI Mobility program 2016 of the Universitat Politècnica de València. She also received the competitive grant for a pre-doctoral stay Becas de movilidad para Jóvenes Profesores e Investigadores 2016, Programa de Becas Iberoamérica of the Santander Bank.
Boada Acosta, YF. (2018). A systems engineering approach to model, tune and test synthetic gene circuits [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/112725
TESIS
Zhao, Jia. "Engineering serine integrase-based synthetic gene circuits for cellular memory and counting". Thesis, University of Glasgow, 2015. http://theses.gla.ac.uk/6911/.
Pełny tekst źródłaTroisi, Lucie. "Development of a new class of synthetic gene circuits based on protein-protein interactions". Electronic Thesis or Diss., Sorbonne université, 2023. http://www.theses.fr/2023SORUS728.
Pełny tekst źródłaSynthetic biology, by its engineering approach, promise to revolutionize the way scientists manipulate and analyze living systems. In this project, we propose to develop a new class of synthetic gene circuits whose fine tuning rely on the affinity competition between active and inactive forms of a transcription factor. Modelling, together with an in silico evolutionary approach, will be used to determine molecular parameters and network topologies required for a given functionality. Circuits will be assembled accordingly and their expression in mammalian cells measured to confirm the expected response or correct our model. Using this methodology, we plan to build multi-inputs circuits with tunable response function, as well as new bistable and oscillatory circuits. The new investigated class of circuits will also be extended to multi-cellular networks exhibiting symmetry breaking or oscillating patterns. This fundamental project bridging modelling and experimental validation will promote the development of advanced targeting circuits with promising applications in diagnosis, gene therapy and complex tissue engineering
Bandiera, Lucia <1988>. "Effects of Transcriptional and Post-Transcriptional Control Mechanisms on Biological Noise in Synthetic Gene Circuits". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amsdottorato.unibo.it/7403/1/Bandiera_Lucia_Tesi.pdf.
Pełny tekst źródłaFerry, Quentin R. V. "RNA-based engineering of inducible CRISPR-Cas9 transcription factors for de novo assembly of eukaryotic gene circuits". Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:b89c1b17-ea75-4049-a5d0-7cd1b5d0bd8e.
Pełny tekst źródłaHarris, Andreas William Kisling. "The design of gene regulatory networks with feedback and small non-coding RNA". Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:e3a323b1-9067-415d-8728-6c70c1b6cf23.
Pełny tekst źródłaAo, Xue. "Study of fluctuations in gene regulation circuits with memory". HKBU Institutional Repository, 2012. https://repository.hkbu.edu.hk/etd_ra/1428.
Pełny tekst źródłaMatsuura, Satoshi. "Synthetic RNA-based logic computation in mammalian cells". Kyoto University, 2019. http://hdl.handle.net/2433/242426.
Pełny tekst źródłaJunetha, Syed Jabarulla. "Chemical Biology Approaches for Regulating Eukaryotic Gene Expression". 京都大学 (Kyoto University), 2015. http://hdl.handle.net/2433/202664.
Pełny tekst źródłaKsiążki na temat "Synthetic gene circuits"
Menolascina, Filippo, red. Synthetic Gene Circuits. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1032-9.
Pełny tekst źródłaMenolascina, Filippo. Synthetic Gene Circuits: Methods and Protocols. Humana Press, 2020.
Znajdź pełny tekst źródłaMenolascina, Filippo. Synthetic Gene Circuits: Methods and Protocols. Springer, 2022.
Znajdź pełny tekst źródłaCzęści książek na temat "Synthetic gene circuits"
Charlebois, Daniel A., Junchen Diao, Dmitry Nevozhay i Gábor Balázsi. "Negative Regulation Gene Circuits for Efflux Pump Control". W Synthetic Biology, 25–43. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7795-6_2.
Pełny tekst źródłaLiss, Michael, i Ralf Wagner. "Gene Synthesis – Enabling Technologies for Synthetic Biology". W Design and Analysis of Biomolecular Circuits, 317–35. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6766-4_15.
Pełny tekst źródłaLiao, James C. "Design of Synthetic Gene-Metabolic Circuits". W Biologically Inspired Approaches to Advanced Information Technology, 1. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11613022_1.
Pełny tekst źródłaTurpin, Baptiste, Eline Y. Bijman, Hans-Michael Kaltenbach i Jörg Stelling. "Population Design for Synthetic Gene Circuits". W Computational Methods in Systems Biology, 181–97. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-85633-5_11.
Pełny tekst źródłaYing, Bei-Wen, Yuya Akeno i Tetsuya Yomo. "Construction of Synthetic Gene Circuits in the Escherichia coli Genome". W Synthetic Biology, 157–68. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-625-2_13.
Pełny tekst źródłaMarchisio, Mario Andrea, i Jörg Stelling. "Simplified Computational Design of Digital Synthetic Gene Circuits". W A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems, 257–71. Dordrecht: Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-017-9047-5_11.
Pełny tekst źródłaYu, Lifang, i Mario Andrea Marchisio. "dCas12a:Pre-crRNA: A New Tool to Induce mRNA Degradation in Saccharomyces cerevisiae Synthetic Gene Circuits". W Synthetic Biology, 95–114. New York, NY: Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-3658-9_6.
Pełny tekst źródłaMarshall, Ryan, i Vincent Noireaux. "Synthetic Biology with an All E. coli TXTL System: Quantitative Characterization of Regulatory Elements and Gene Circuits". W Synthetic Biology, 61–93. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7795-6_4.
Pełny tekst źródłaArgibay, Nina G., Eric M. Vazquez, Cortney E. Wilson, Travis J. A. Craddock i Robert P. Smith. "Synthetic Biology: From Gene Circuits to Novel Biological Tools". W Nanotechnology in Biology and Medicine, 371–88. Taylor & Francis Group, 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742: CRC Press, 2017. http://dx.doi.org/10.1201/9781315374581-18.
Pełny tekst źródłaArgibay, Nina G., Eric M. Vazquez, Cortney E. Wilson, Travis J. A. Craddock i Robert P. Smith. "Synthetic Biology: From Gene Circuits to Novel Biological Tools". W Nanotechnology in Biology and Medicine, 371–88. Second edition. | Boca Raton : Taylor & Francis, 2017.: CRC Press, 2017. http://dx.doi.org/10.4324/9781315374581-17.
Pełny tekst źródłaStreszczenia konferencji na temat "Synthetic gene circuits"
Marchisio, Mario Andrea, i Jorg Stelling. "Synthetic gene network computational design". W 2009 IEEE International Symposium on Circuits and Systems - ISCAS 2009. IEEE, 2009. http://dx.doi.org/10.1109/iscas.2009.5117747.
Pełny tekst źródłaPolynikis, A., G. Cuccato, S. Criscuolo, S. J. Hogan, M. di Bernardo i D. di Bernardo. "Analysis and design of a versatile synthetic network for inducible gene expression in mammalian systems". W 2010 IEEE Biomedical Circuits and Systems Conference (BioCAS). IEEE, 2010. http://dx.doi.org/10.1109/biocas.2010.5709601.
Pełny tekst źródłaByrom, Daniel P., i Alexander P. S. Darlington. "On the Implications of Controller Resource Consumption for the Long-Term Performance of Synthetic Gene Circuits". W 2023 62nd IEEE Conference on Decision and Control (CDC). IEEE, 2023. http://dx.doi.org/10.1109/cdc49753.2023.10383537.
Pełny tekst źródłaFowlkes, P. M., P. K. Lund, M. Blake i J. Snouwaert. "THE REGULATION OF FIBRINOGEN PRODUCTION INVOLVES AT LEAST ONE OTHER HEPATOCYTE GENE". W XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644317.
Pełny tekst źródłaOyarzun, D. A., i G.-B. Stan. "Design tradeoffs in a synthetic gene control circuit for metabolic networks". W 2012 American Control Conference - ACC 2012. IEEE, 2012. http://dx.doi.org/10.1109/acc.2012.6314705.
Pełny tekst źródłaLiu, Feng, Feiyue Zhuo, Shujiang Sun, Zhi-Hong Guan i Hua O. Wang. "Bifurcation control and circuit simulation of a fractional-order synthetic gene networks". W 2022 41st Chinese Control Conference (CCC). IEEE, 2022. http://dx.doi.org/10.23919/ccc55666.2022.9901982.
Pełny tekst źródłaGan, Zhaohui, Tao Shang, Gang Shi i Chao Chen. "Automatic Synthesis of Combinational Logic Circuit with Gene Expression-Based Clonal Selection Algorithm". W 2008 Fourth International Conference on Natural Computation. IEEE, 2008. http://dx.doi.org/10.1109/icnc.2008.338.
Pełny tekst źródłaAmin, Farooq, Shuai Zhou, Long Huang, Christopher Latorre, Folu Popoola i Parrish Ralston. "Gen1 Active Tunable SiGe Integrated Parallel Synthesis Filters (PSF) without Q-Enhancement". W 2023 IEEE BiCMOS and Compound Semiconductor Integrated Circuits and Technology Symposium (BCICTS). IEEE, 2023. http://dx.doi.org/10.1109/bcicts54660.2023.10311033.
Pełny tekst źródłaBaptista, Millena Amélia Fontes, Maria Fernanda Ribeiro Farias, Luma Lainny Pereira de Oliveira, Wynni Gabrielly Pereira de Oliveira i Rafaella Dias Galvão. "Molecular and cellular mechanisms involved in learning and memory". W XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.615.
Pełny tekst źródłaLiu, Qiang, Yubing Cao, Man Zhang, Shuguang Peng, Yiqi Liu, Huiya Huang i Bin Chen. "Abstract 1148: SynOV1.1: A synthetic gene circuit controlled oncolytic adenovirus demonstrating high tumor specificity, potent antitumor efficacy and high synergy with an anti-PD-L1 monoclonal antibody in preclinical hepatocellular carcinoma models". W Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-1148.
Pełny tekst źródłaRaporty organizacyjne na temat "Synthetic gene circuits"
Maddie Perdoncin, Maddie Perdoncin. Hot Metal Switch: Synthetic In Vitro Gene Circuit for the Detection of Metal Ions. Experiment, lipiec 2016. http://dx.doi.org/10.18258/7452.
Pełny tekst źródłaRon, Eliora, i Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, marzec 2009. http://dx.doi.org/10.32747/2009.7695860.bard.
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