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Lecturer(s)
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Plíhal Ondřej, RNDr. Ph.D.
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Course content
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1. Definition of the field, systems biology vs synthetic biology, history, methodological approaches. Model organisms, anchoring in microbiology and definition of biological components and circuits. 2. Biomolecules, the basic organization of the cell due to the synthesis of biomolecules. Information flow in the cell. Genetic and metabolic engineering, high-throughput methods and functional genomics. Use of CRISPR-Cas technology in synthetic biology. 3. Synthetic genomes, methods of preparation, purification and examples of their use in biotechnology. Synthetic transcription factors, biosensors, riboswitches and ribozymes and construction of a biological computer. 4. Mathematical modeling of genetic regulatory circuits. Microbial killer circuits (essentializer and cryodeath circuits). Self-regulatory mechanisms based on negative and positive feedback. 5. Database and tools for reconstruction of metabolic networks. Interactive in silico model building. In silico model-based metabolic engineering for controlled production of bioproducts. 6. De novo construction of genes. Replication of DNA, RNA and proteins and compartmentalization of these processes. Biological oscillators, molecular machines and automata. 7. Microbial robotics based on communication in multicellular systems. Quorum sensing, cell consortia and mechanisms of cell density detection. Use of robotic systems in fungi (possibility of using cytokinins and their receptors for intercellular communication, etc.). Yeast as a model organism. 8. Artificial genetic networks and their building blocks. Characterization of simple and complex networks, partially natural systems. The effect of "noise". 9. Possibilities of using tissue engineering in biomedicine. Biological resistance theory for system stability. Chemoprevention and other uses in cancer therapy, possible strategies and evaluation of effectiveness; use in toxicology. Possibilities of optogenetics in clinical research. 10. "Synthetic life" project. Synthetic genomics and preparation of Mycoplasma laboratory, creation of new biological entities. "Alien" DNA and protein coding possibilities through synthetic bases. 11. Use of controlled processes in bioenergy. Lignocellulose degradation and fermentation technology for biofuel production. Higher order cellular communication - synthetic ecosystems. Metabolic engineering for the production of marine natural bioproducts. 12. Normative ethics in synthetic biology. Benefits and risks associated with the use of artificial organisms. Forecasts of future development. Legislation and legal framework. ?
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Learning activities and teaching methods
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Lecture, Dialogic Lecture (Discussion, Dialog, Brainstorming), Group work
- Attendace
- 26 hours per semester
- Preparation for the Exam
- 55 hours per semester
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Learning outcomes
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The aim of the course is to familiarize students with the concept of artificial life, the organization of genomes and the creation of artificial genomes, biological circuits and the possibilities of using artificially prepared organisms.
Ability to define the concept of minimal life, design and use biological circuits and apply them in practice.
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Prerequisites
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Basic orientation in the field of molecular biology, structure of DNA and RNA, organization of genes and chromosomes.
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Assessment methods and criteria
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Dialog, Systematic Observation of Student, Final project
Students will present one of the topics of their choice - specialist literature on this topic will be recommended. The presentation is followed by oral questions on the chosen topic.
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Recommended literature
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Davies, J. A. (2020). Mammalian Synthetic Biology. Oxford University Press.
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Lesk, A. M. (2017). Introduction to genomics, 3rd edition.
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Pengcheng Fu, Sven Panke. (2009). Systems Biology and Synthetic Biology.
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Smolke, C. (editor). (2018). Synthetic Biology: Parts, Devices and Applications. Wiley.
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