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Relevant bibliographies by topics / Systems Biology, Synthetic Biology, Metabolic Engineering

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Academic literature on the topic 'Systems Biology, Synthetic Biology, Metabolic Engineering'

Author: Grafiati

Published: 6 September 2023

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Journal articles on the topic "Systems Biology, Synthetic Biology, Metabolic Engineering"

1

Nielsen, Jens, and Jack T. Pronk. "Metabolic engineering, synthetic biology and systems biology." FEMS Yeast Research 12, no. 2 (2012): 103. http://dx.doi.org/10.1111/j.1567-1364.2011.00783.x.

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He, Fei, Ettore Murabito, and Hans V. Westerhoff. "Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering." Journal of The Royal Society Interface 13, no. 117 (2016): 20151046. http://dx.doi.org/10.1098/rsif.2015.1046.

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Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo , not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and inve

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Choi, Kyeong Rok, Woo Dae Jang, Dongsoo Yang, Jae Sung Cho, Dahyeon Park, and Sang Yup Lee. "Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering." Trends in Biotechnology 37, no. 8 (2019): 817–37. http://dx.doi.org/10.1016/j.tibtech.2019.01.003.

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Lee, Hyang-Mi, Phuong Vo, and Dokyun Na. "Advancement of Metabolic Engineering Assisted by Synthetic Biology." Catalysts 8, no. 12 (2018): 619. http://dx.doi.org/10.3390/catal8120619.

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Synthetic biology has undergone dramatic advancements for over a decade, during which it has expanded our understanding on the systems of life and opened new avenues for microbial engineering. Many biotechnological and computational methods have been developed for the construction of synthetic systems. Achievements in synthetic biology have been widely adopted in metabolic engineering, a field aimed at engineering micro-organisms to produce substances of interest. However, the engineering of metabolic systems requires dynamic redistribution of cellular resources, the creation of novel metaboli

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Fong, Stephen S. "Computational approaches to metabolic engineering utilizing systems biology and synthetic biology." Computational and Structural Biotechnology Journal 11, no. 18 (2014): 28–34. http://dx.doi.org/10.1016/j.csbj.2014.08.005.

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King, Jason R., Steven Edgar, Kangjian Qiao, and Gregory Stephanopoulos. "Accessing Nature’s diversity through metabolic engineering and synthetic biology." F1000Research 5 (March 24, 2016): 397. http://dx.doi.org/10.12688/f1000research.7311.1.

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In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and

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Chen, Bor-Sen, and Chia-Chou Wu. "Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering." Cells 2, no. 4 (2013): 635–88. http://dx.doi.org/10.3390/cells2040635.

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McArthur, George H., and Stephen S. Fong. "Toward Engineering Synthetic Microbial Metabolism." Journal of Biomedicine and Biotechnology 2010 (2010): 1–10. http://dx.doi.org/10.1155/2010/459760.

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The generation of well-characterized parts and the formulation of biological design principles in synthetic biology are laying the foundation for more complex and advanced microbial metabolic engineering. Improvements inde novoDNA synthesis and codon-optimization alone are already contributing to the manufacturing of pathway enzymes with improved or novel function. Further development of analytical and computer-aided design tools should accelerate the forward engineering of precisely regulated synthetic pathways by providing a standard framework for the predictable design of biological systems

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Ma, Jingbo, Yang Gu, Monireh Marsafari, and Peng Xu. "Synthetic biology, systems biology, and metabolic engineering of Yarrowia lipolytica toward a sustainable biorefinery platform." Journal of Industrial Microbiology & Biotechnology 47, no. 9-10 (2020): 845–62. http://dx.doi.org/10.1007/s10295-020-02290-8.

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Jeong, Yujin, Sang-Hyeok Cho, Hookeun Lee, et al. "Current Status and Future Strategies to Increase Secondary Metabolite Production from Cyanobacteria." Microorganisms 8, no. 12 (2020): 1849. http://dx.doi.org/10.3390/microorganisms8121849.

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Cyanobacteria, given their ability to produce various secondary metabolites utilizing solar energy and carbon dioxide, are a potential platform for sustainable production of biochemicals. Until now, conventional metabolic engineering approaches have been applied to various cyanobacterial species for enhanced production of industrially valued compounds, including secondary metabolites and non-natural biochemicals. However, the shortage of understanding of cyanobacterial metabolic and regulatory networks for atmospheric carbon fixation to biochemical production and the lack of available engineer

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Dissertations / Theses on the topic "Systems Biology, Synthetic Biology, Metabolic Engineering"

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Boyle, Patrick M. "Network-Scale Engineering: Systems Approaches to Synthetic Biology." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10298.

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The field of Synthetic Biology seeks to develop engineering principles for biological systems. Modular biological parts are repurposed and recombined to develop new synthetic biological devices with novel functions. The proper functioning of these devices is dependent on the cellular context provided by the host organism, and the interaction of these devices with host systems. The field of Systems Biology seeks to measure and model the properties of biological phenomena at the network scale. We present the application of systems biology approaches to synthetic biology, with particular emphasis

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Libis, Vincent. "New inputs for synthetic biological systems." Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCC127/document.

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Les chercheurs en biologie de synthèse programment l’ADN pour construire des systèmes biologiques capables de répondre à certaines conditions de manière prédéfinie. Cette capacité pourrait avoir un impact sur plusieurs domaines, de la médecine à la fermentation industrielle. Le traitement de signal par des circuits biologiques synthétiques est en train d’être démontré à large échelle, mais hélas la variété des signaux d’entrée capables de contrôler ces circuits est pour l’instant limitée. Ce manque de diversité est un obstacle majeur au développement de nouvelles applications car en général ch

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Triana, Dopico Julián. "Model-based analysis and metabolic design of a cyanobacterium for bio-products synthesis." Doctoral thesis, Universitat Politècnica de València, 2014. http://hdl.handle.net/10251/39351.

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The current investigation is aimed at the reconstruction and analysis of genome-scale metabolic models. Specifically, it is focused on the use of mathematical-computational simulations to predict the cellular metabolism behavior towards bio-products production. The photosynthetic cyanobacterium Synechococcus elongatus PCC7942 was studied as biological system. This prokaryotic has been used in several studies as a biological platform for the synthesis of several substances for industrial interest. These studies are based on the advantage of autotrophic systems, which basically requires light a

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Merrick, Christine. "A synthetic biology approach to metabolic pathway engineering." Thesis, University of Glasgow, 2015. http://theses.gla.ac.uk/6383/.

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Microbial biosynthesis of commodity compounds offers a cheaper, greener and more reliable method of production than does chemical synthesis. However, engineering metabolic pathways within a microbe for biosynthesis of a target compound is a complicated process: levels of gene expression, protein stability, enzyme activity, and metabolic flux must be balanced for high productivity without compromising host cell viability. A major rate-limiting step in engineering microbes for optimum biosynthesis of a target compound is DNA assembly, as current methods can be cumbersome and costly. This study a

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Torella, Joseph Peter. "Synthetic biology approaches to bio-based chemical production." Thesis, Harvard University, 2014. http://nrs.harvard.edu/urn-3:HUL.InstRepos:13088835.

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Inexpensive petroleum is the cornerstone of the modern global economy despite its huge environmental costs and its nature as a non-renewable resource. While ninety percent of petroleum is ultimately used as fuel and can in principle be replaced by sources of renewable electricity, ten percent is used as a feedstock to produce societally important chemicals that cannot currently be made at a reasonable cost through alternative processes. In this dissertation, I will discuss my efforts, together with several colleagues, to apply synthetic biology approaches to the challenge of producing renewabl

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Pedersen, Michael. "Modular languages for systems and synthetic biology." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4602.

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Systems biology is a rapidly growing field which seeks a refined quantitative understanding of organisms, particularly studying how molecular species such as metabolites, proteins and genes interact in cells to form the complex emerging behaviour exhibited by living systems. Synthetic biology is a related and emerging field which seeks to engineer new organisms for practical purposes. Both fields can benefit from formal languages for modelling, simulation and analysis. In systems biology there is however a trade-off in the landscape of existing formal languages: some are modular but may be dif

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Martínez-Klimova, Elena. "Synthetic biology approaches to the metabolic engineering of Geobacillus thermoglucosidans for isobutanol production." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/45409.

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Renewable green alternatives to fossil fuels need to be sought in order to address the challenges of environmental and energy crises. Up until now, ethanol has been the major biofuel. Geobacillus thermoglucosidans is a thermophilic bacterium that is capable of producing bioethanol in an industrial setting at high temperatures and is capable of metabolizing pentoses and hexoses commonly found in lignocellulosic biomass. Due to these attractive properties, the aim of this work has been to construct a toolbox of genetic components to develop G. thermoglucosidans as as the leading thermophile chas

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Campodonico, Alt Miguel Ángel. "Systems biology and chemoinformatics methods for biomining and systems metabolic engineering applications." Tesis, Universidad de Chile, 2014. http://repositorio.uchile.cl/handle/2250/132047.

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Doctor en Ciencias de la Ingeniería, Mención Química<br>In the first chapter, this thesis aims to demonstrate the great potential of Constraint-Based Reconstruction and Analysis (COBRA) methods for studying and predicting specific phenotypes in the bacterium Acidithiobacillus ferrooxidans. A genome-scale metabolic reconstruction of Acidithiobacillus ferrooxidans ATCC 23270 (iMC507) is presented and characterized. iMC507 is validated for aerobic chemolithoautotrophic conditions by fixating carbon dioxide and using three different electron donors: ferrous ion, tetrathionate and thiosulfate. Furt

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McArthur, George Howard IV. "Orthogonal Expression of Metabolic Pathways." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3087.

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Microbial metabolism can be tailored to meet human specifications, but the degree to which these living systems can be repurposed is still unknown. Artificial biological control strategies are being developed with the goal of enabling the predictable implementation of novel biological functions (e.g., engineered metabolism). This dissertation project contributes genetic tools useful for modulating gene expression levels (extending promoters with UP elements) and isolating transcription and translation of engineered DNA from the endogenous cellular network (expression by orthogonal cellular mac

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Huttanus, Herbert M. "Screening and Engineering Phenotypes using Big Data Systems Biology." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/102706.

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Biological systems display remarkable complexity that is not properly accounted for in small, reductionistic models. Increasingly, big data approaches using genomics, proteomics, metabolomics etc. are being applied to predicting and modifying the emergent phenotypes produced by complex biological systems. In this research, several novel tools were developed to assist in the acquisition and analysis of biological big data for a variety of applications. In total, two entirely new tools were created and a third, relatively new method, was evaluated by applying it to questions of clinical importan

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Books on the topic "Systems Biology, Synthetic Biology, Metabolic Engineering"

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Zhao, Huimin, and An-Ping Zeng, eds. Synthetic Biology – Metabolic Engineering. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-55318-4.

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Pengcheng, Fu, and Panke Sven, eds. Systems biology and synthetic biology. John Wiley & Sons, 2009.

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Selvarajoo, Kumar, ed. Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2617-7.

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Wittmann, Christoph. Systems Metabolic Engineering. Springer Netherlands, 2012.

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Alper, Hal S. Systems metabolic engineering: Methods and protocols. Humana Press, 2013.

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Clay, Sylvia M. Developing Biofuel Bioprocesses Using Systems and Synthetic Biology. Springer New York, 2013.

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Pray, Leslie A. The science and applications of synthetic and systems biology: Workshop summary. National Academies Press, 2011.

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Metabolic flux analysis: Methods and protocols. Humana Press, 2014.

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Chen, Bor-Sen, and Chia-Chou Wu. Systems Biology: An Integrated Platform for Bioinformatics, Systems Synthetic Biology and Systems Metabolic Engineering. Nova Science Publishers, Incorporated, 2014.

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Zeng, An-Ping, and Huimin Zhao. Synthetic Biology – Metabolic Engineering. Springer, 2018.

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Book chapters on the topic "Systems Biology, Synthetic Biology, Metabolic Engineering"

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Yan, Qiang, and Stephen S. Fong. "Biosensors for Metabolic Engineering." In Systems Biology Application in Synthetic Biology. Springer India, 2016. http://dx.doi.org/10.1007/978-81-322-2809-7_5.

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Becker, Judith, Gideon Gießelmann, Sarah Lisa Hoffmann, and Christoph Wittmann. "Corynebacterium glutamicum for Sustainable Bioproduction: From Metabolic Physiology to Systems Metabolic Engineering." In Synthetic Biology – Metabolic Engineering. Springer International Publishing, 2016. http://dx.doi.org/10.1007/10_2016_21.

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Singh, Vijai, Indra Mani, and Dharmendra Kumar Chaudhary. "Metabolic Engineering of Microorganisms for Biosynthesis of Antibiotics." In Systems and Synthetic Biology. Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-017-9514-2_18.

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Roldão, António, Il-Kwon Kim, and Jens Nielsen. "Bridging Omics Technologies with Synthetic Biology in Yeast Industrial Biotechnology." In Systems Metabolic Engineering. Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4534-6_9.

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Pei, Lei, and Markus Schmidt. "Sustainable Assessment on Using Bacterial Platform to Produce High-Added-Value Products from Berries through Metabolic Engineering." In Systems Biology Application in Synthetic Biology. Springer India, 2016. http://dx.doi.org/10.1007/978-81-322-2809-7_6.

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Nikel, Pablo I. "Systems and Synthetic Biology Approaches for Metabolic Engineering of Pseudomonas putida." In Microbial Models: From Environmental to Industrial Sustainability. Springer Singapore, 2016. http://dx.doi.org/10.1007/978-981-10-2555-6_1.

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Papoutsakis, Eleftherios T., and Keith V. Alsaker. "Towards a Synthetic Biology of the Stress-Response and the Tolerance Phenotype: Systems Understanding and Engineering of the Clostridium acetobutylicum Stress-Response and Tolerance to Toxic Metabolites." In Systems Metabolic Engineering. Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4534-6_7.

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Zhu, Qinlong, and Yao-Guang Liu. "TransGene Stacking II Vector System for Plant Metabolic Engineering and Synthetic Biology." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1068-8_2.

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Marx, Hans, Stefan Pflügl, Diethard Mattanovich, and Michael Sauer. "Synthetic Biology Assisting Metabolic Pathway Engineering." In Synthetic Biology. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-22708-5_7.

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Guo, Weihua, Jiayuan Sheng, and Xueyang Feng. "Synergizing 13C Metabolic Flux Analysis and Metabolic Engineering for Biochemical Production." In Synthetic Biology – Metabolic Engineering. Springer International Publishing, 2017. http://dx.doi.org/10.1007/10_2017_2.

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Conference papers on the topic "Systems Biology, Synthetic Biology, Metabolic Engineering"

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Malcata, F. Xavier. "Engineering of microalgae toward biodiesel: Facts and prospects." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/jeul5047.

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Excessive release to the atmosphere of greenhouse-effect gases—arising from combustion of fossil fuels, has urged a worldwide search for alternative sources of environment-friendly fuels; microalgae constitute an interesting possibility, owing to their widespread presence in most habitats and unique ability to synthesize oil. Microalgae require indeed only sunlight and water to grow—both freely available; together with CO2 as source of carbon—which concomitantly conveys a path for its direct sequestering from the atmosphere; and low-cost inorganic sources of phosphorus and nitrogen. However, t

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"Metabolic engineering of corynebacteria to create a producer of L-valine." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-317.

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Jensen, P. A., and J. A. Papin. "A scalable systems analysis approach for regulated metabolic networks." In 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2009. http://dx.doi.org/10.1109/iembs.2009.5334060.

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Egan, Paul F., Jonathan Cagan, Christian Schunn, and Philip R. LeDuc. "Utilizing Emergent Levels to Facilitate Complex Systems Design: Demonstrated in a Synthetic Biology Domain." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-12072.

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Designing complex systems often requires consideration of many components interacting across vast scales of space and time, thus producing highly challenging design spaces to search. In particular, nano-based technologies may require considerations of how nanoscale (10−9) embodiments affect macroscale (∼100) systems and typically have multiple layers of emergent behavior. It is frequently cited that counter-intuitive properties of emergence complicates design tasks; however, we investigate whether some multiscale emergent systems have organizational levels that may inform more effective design

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Bay, Brian, and Mike Bailey. "Pre-Programmed Failure Behavior Using Biology-Inspired Structures." In ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-34685.

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Core (filler) materials are key components of the sandwich panel and box-beams that are used in the design of lightweight structures. They perform a variety of elastic-range functions such as transferring and supporting working stresses and energy and collapse management. There is an increasing demand, however, for post-yield performance characteristics such as buckling control, impact toughness, and maintenance of component strength after damage. Low density is also an important consideration, as overall component mass is critical in most applications. These cellular solids need to perform we

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Reports on the topic "Systems Biology, Synthetic Biology, Metabolic Engineering"

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Gupta, Shweta. Synthetic Biology: The Gateway to Future Biotechnological Industry. Science Repository OÜ, 2021. http://dx.doi.org/10.31487/sr.blog.34.

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Synthetic biology has come up as a new interdisciplinary area involving the application of engineering principles in the field of biology aiming at fabricating and redesigning biological systems and components that are not naturally found in the world.

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Jung, Carina, Karl Indest, Matthew Carr, Richard Lance, Lyndsay Carrigee, and Kayla Clark. Properties and detectability of rogue synthetic biology (SynBio) products in complex matrices. Engineer Research and Development Center (U.S.), 2022. http://dx.doi.org/10.21079/11681/45345.

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Synthetic biology (SynBio) aims to rationally engineer or modify traits of an organism or integrate the behaviors of multiple organisms into a singular functional organism through advanced genetic engineering techniques. One objective of this research was to determine the environmental persistence of engineered DNA in the environment. To accomplish this goal, the environmental persistence of legacy engineered DNA building blocks were targeted that laid the foundation for SynBio product development and application giving rise to “post-use products.” These building blocks include genetic constru

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