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Vyučující
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Obsah předmětu
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LLecture 1. Introduction to Systems Biology (SB) and Basic Definitions - 26.09.2024 Lecture 2. Structures, Complexity and Chaos - 3.10.2024 Lecture 3. Living Systems and Information - 10.10.2024 Lecture 4. Living Systems and Energy - 17.10.2024 Lecture 5. Living Systems and Adaptation - 24.10.2024 Lecture 6. Living Systems and Evolution - 31.10.2024 Lecture 7. Systems Biology in Plant Science - 7.11.2024 Lecture 8. Systems Biology in Medicine - 14.11.2024 Lecture 9. Systems Biology in Drug Development and Material Science - 21.11.2024 Lecture 10. Patterns in Nature - 28.11.2024 Lecture 11. Artificial Intelligence in Systems Biology - 5.12.2024 Lecture 12. Emerging Topics in Systems Biology - 12.12.2024 Topics: order; complexity; non-equilibrium systems; homeostasis; metabolism; self-sustenance and self-regulation; holism; reductionism; top-down; bottom-up; "omics"; emergence; nested hierarchy; biological robustness; systems theory; mathematical modelling; networks (graphs) theory; chaos theory; the butterfly effect; synergy; Markov chains; signals and messages; inter-and intracellular communication; 3D-bioprinting; enthalpy; entropy; Gibbs free energy; bioenergetics; phototrophy; chemotrophy; autotrophy; heterotrophy; detrivory; saprotrophy; mixotrophy; mycoheterotrophy; parasitism; endergonic vs. exergonic reactions; compartmentalization; bioluminescence; adaptations; homeostasis; allostasis; allostatic load; stress; eustress; distress; general adaptation syndrome; "fight-or-flight-or-freeze";"fight-flight"; microbiome; successions; Bergman's rule; Allen's rule; Gloger's rule; Foster's rule; latitudinal gradient; dormancy mechanisms; extremophiles; evolution theory; micro- and macroevolution; gene pool; gene flow; gene drift; bottleneck effect; founder effect; lateral (horizontal) gene transfer; conjugation; transformation; transduction; vesiduction; mutations; endosymbiosis; organellogenesis; "junk DNA"; speciation; phylogeny; taxonomy; cladistics;smart farming; plant phenotyping; drones; plant microbiome; hub microorganisms; keystone species; biofilm; quorum sensing; P4 medicine; personalized healthcare; stratified medicine; precision medicine; systems medicine; disease maps; biomarkers; exposome; translational biomedicine; cojoint analysis; orphan drugs; drug delivery systems; drug repurposing/repositioning; biomimetics; biomimicry; bionics; robotics; bio-inspired technologies; biomimetic products; aircraft; taq-polymerase; Velcro; biomimetic architecture; self-healing materials; biomimetic synthesis; artificial enzymes; nanozymes; symmetry and antisymmetry in living systems; plant axes; trees and branching patterns (ramifications); spirals (logarithmic spiral, phyllotaxis, parastichy, Fibonacci ratios, Fermat's spiral); phyllotaxis; tessellations in nature; fractals; fractal-like patterns; Mandelbrot set; geomorphology; aeolian landforms; Voronoi diagrams in developmental biology; neural networks (NN); Neocortical column; Markram's model; artificial intelligence; machine learning; deep learning; supervised and unsupervised machine learning; astrobiology (exobiology); RNA world hypothesis; space farming; seed films; Veggie; astrobotany; simulated microgravity; clinostat rotation; synthetic biology; aptamers; gene circuits; bioreporters; biosensors; Xna-xeno-DNA; Mycoplasma laboratorium or Synthia; protocells; artificial life (A-life); synthetic minimal cells; DNA nanostructures for drug delivery; DNA origami.
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Studijní aktivity a metody výuky
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Monologická (výklad, přednáška, instruktáž), Dialogická (diskuze, rozhovor, brainstorming)
- Semestrální práce
- 20 hodin za semestr
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Výstupy z učení
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The main purpose of the Systems Biology course is to explore multidisciplinarity in modern biological research. The structure of the discipline includes the integration of knowledge from the different levels of living organisms organization, the introduction of basic definitions (holism/reductionism, emergence principle, graph, chaos, information theories, multi-"omics" approach, etc.), and their implementation in various fields of biology, biomedicine and related fields (plant biology, medicine, drug design, and material science). Special attention is dedicated to emerging topics in systems biology and biology in general (e.g., synthetic biology, cell-free systems, XNA, Astro- (exo-)biology, and others) as well as to neural networks, artificial intelligence, machine, and deep learning.
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Předpoklady
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Lecture 1. Introduction to Systems Biology (SB) and Basic Definitions - 26.09.2024 Lecture 2. Structures, Complexity and Chaos - 3.10.2024 Lecture 3. Living Systems and Information - 10.10.2024 Lecture 4. Living Systems and Energy - 17.10.2024 Lecture 5. Living Systems and Adaptation - 24.10.2024 Lecture 6. Living Systems and Evolution - 31.10.2024 Lecture 7. Systems Biology in Plant Science - 7.11.2024 Lecture 8. Systems Biology in Medicine - 14.11.2024 Lecture 9. Systems Biology in Drug Development and Material Science - 21.11.2024 Lecture 10. Patterns in Nature - 28.11.2024 Lecture 11. Artificial Intelligence in Systems Biology - 5.12.2024 Lecture 12. Emerging Topics in Systems Biology - 12.12.2024 Topics: order; complexity; non-equilibrium systems; homeostasis; metabolism; self-sustenance and self-regulation; holism; reductionism; top-down; bottom-up; "omics"; emergence; nested hierarchy; biological robustness; systems theory; mathematical modelling; networks (graphs) theory; chaos theory; the butterfly effect; synergy; Markov chains; signals and messages; inter-and intracellular communication; 3D-bioprinting; enthalpy; entropy; Gibbs free energy; bioenergetics; phototrophy; chemotrophy; autotrophy; heterotrophy; detrivory; saprotrophy; mixotrophy; mycoheterotrophy; parasitism; endergonic vs. exergonic reactions; compartmentalization; bioluminescence; adaptations; homeostasis; allostasis; allostatic load; stress; eustress; distress; general adaptation syndrome; "fight-or-flight-or-freeze";"fight-flight"; microbiome; successions; Bergman's rule; Allen's rule; Gloger's rule; Foster's rule; latitudinal gradient; dormancy mechanisms; extremophiles; evolution theory; micro- and macroevolution; gene pool; gene flow; gene drift; bottleneck effect; founder effect; lateral (horizontal) gene transfer; conjugation; transformation; transduction; vesiduction; mutations; endosymbiosis; organellogenesis; "junk DNA"; speciation; phylogeny; taxonomy; cladistics;smart farming; plant phenotyping; drones; plant microbiome; hub microorganisms; keystone species; biofilm; quorum sensing; P4 medicine; personalized healthcare; stratified medicine; precision medicine; systems medicine; disease maps; biomarkers; exposome; translational biomedicine; cojoint analysis; orphan drugs; drug delivery systems; drug repurposing/repositioning; biomimetics; biomimicry; bionics; robotics; bio-inspired technologies; biomimetic products; aircraft; taq-polymerase; Velcro; biomimetic architecture; self-healing materials; biomimetic synthesis; artificial enzymes; nanozymes; symmetry and antisymmetry in living systems; plant axes; trees and branching patterns (ramifications); spirals (logarithmic spiral, phyllotaxis, parastichy, Fibonacci ratios, Fermat's spiral); phyllotaxis; tessellations in nature; fractals; fractal-like patterns; Mandelbrot set; geomorphology; aeolian landforms; Voronoi diagrams in developmental biology; neural networks (NN); Neocortical column; Markram's model; artificial intelligence; machine learning; deep learning; supervised and unsupervised machine learning; astrobiology (exobiology); RNA world hypothesis; space farming; seed films; Veggie; astrobotany; simulated microgravity; clinostat rotation; synthetic biology; aptamers; gene circuits; bioreporters; biosensors; Xna-xeno-DNA; Mycoplasma laboratorium or Synthia; protocells; artificial life (A-life); synthetic minimal cells; DNA nanostructures for drug delivery; DNA origami.
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Hodnoticí metody a kritéria
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Známkou, Didaktický test
Successful completion of Final Test.
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Doporučená literatura
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& Choi, S. (2007). Introduction to systems biology. Totowa, NJ: Humana Press.
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Coruzzi GM, Gutierrez RA, Eds. Plant Systems Biology. Annual Plant Reviews vol. 35. Blackwell Publishing.
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Davidson EA, Windram OP, Bayer TS. (2012). Building synthetic systems to learn nature's design principles. Adv Exp Med Biol. 751:411-29.
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Dubitzky W, Southgate J, Fuß H, Edis. Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biolog. Springer.
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Goldbeter A, Gérard C, Gonze D, Leloup JC, Dupont G. (2012). Systems biology of cellular rhythms. FEBS Lett. 586(18):2955-65.
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Kholodenko BN. (2006). Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol. 7(3):165-76.
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Kirschner MW. (2005). The meaning of systems biology. Cell. 20;121(4):503-4.
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Krawetz S, Ed. Bioinformatics for Systems Biology. Springer, Heidelberg.
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Mu?oz-García J, Kholodenko BN. (2010). Signalling over a distance: gradient patterns and phosphorylation waves within single cells. Biochem Soc Trans. 38(5):1235-41.
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