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Lecturer(s)
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Krasylenko Yuliya, Ph.D.
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Krasylenko Yuliya, Ph.D.
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Course content
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ecture 1. Principles of the Course ad Introduction to Systems Biology (SB) Lecture 2. Structures, Complexity and Chaos Lecture 3. Living Systems and Information Lecture 4. Living Systems and Energy Lecture 5. Living Systems and Adaptation Lecture 6. Living Systems and Evolution Lecture 7. Systems Biology in Plant Science Lecture 8. Systems Biology in Medicine Lecture 9. Systems Biology in Drug Development and Material Science Lecture 10. Patterns in Nature Lecture 11. Artificial Intelligence in Systems Biology Lecture 12. Emerging Topics in Systems Biology Key words and main definitions: 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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Learning activities and teaching methods
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Lecture, Monologic Lecture(Interpretation, Training), Dialogic Lecture (Discussion, Dialog, Brainstorming)
- Semestral Work
- 20 hours per semester
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Learning outcomes
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The main purpose of the Systems Biology course is to explore multidisciplinarity in modern biological research. The course introduces the integration of knowledge across different levels of biological organization, along with key foundational concepts such as holism and reductionism, the principle of emergence, graph theory, chaos theory, information theory, and multi-omics approaches. It also emphasizes their application across diverse fields of biology, biomedicine, and related disciplines, including plant biology, medicine, drug design, and materials science. Special attention is given to emerging topics in systems biology and biology more broadly, such as synthetic biology, cell-free systems, XNA, astro- and exobiology, and others, as well as to neural networks, artificial intelligence, machine and deep learning.
Systems medicine implications in novel drug research and development. Translational biomedicine. Comparison between traditional and systems approaches to drug development. Systems pharmacology: when multi-targeting is advantageous. Phases of drug discovery and development: discovery and development; preclinical research; clinical development; review and approval. The topology-based target identification process. Conjoint analysis. The hit-effect association and prediction process. Network-based technologies for early drug discovery. Drug approval: U.S. Food and Drug Administration, European Medicines Agency, Pharmaceuticals, and Medical Devices Agency. Orphan drugs. Drug delivery systems. Hierarchy of targeted drug delivery: primary, secondary, tertiary. Drug Central and Drugmap Central. Drug repurposing/repositioning. Biomimetics, biomimicry, bionics, robotics, bio-inspired technologies. Biomimetic products and technologies: aircraft, taq-polymerase, Velcro, biomimetic architecture, self-healing materials, etc. Biomimetic synthesis. History of natural patterns study Plato, Pythagoras of Samos, Empedocles, Joseph Plateau, Ernst Haeckel, Sir D'Arcy Thompson, Alan Turing, Aristid Lindenmayer, Benoit Mandelbrot, and others. Geometrical figures and nature forms. Symmetry in living systems (bilateral/mirror; radial/rotational; fivefold; spherical) and in non-living ones (crystal habits). The different planes of bilateral symmetry: sagittal, transverse, posterior, anterior, dorsal, ventral. the order of rotational symmetry. plant axes: mediolateral; adaxial-abaxial; distal-proximal axis; descending and ascending. Trees and branching patterns (ramifications). Spirals (logarithmic spiral, phyllotaxis, parastichy, Fibonacci ratios, Fermat's spiral). Phyllotaxis as the relative positioning of new leaves: distichous, spiral (parastichous), decussate, and whorled. Asymmetry in nature and its importance. Different types of asymmetry: fluctuating asymmetry, directional asymmetry, and antisymmetry. Tessellations in nature. Fractals, fractal-like patterns, and Mandelbrot set. Voronoi diagram and tesselations. Geomorphology: aeolian landforms. Neural networks (NN): biological and artificial NN. Blue Brain Project. Neocortical column. Markram's model. Six layers of the neocortex. A theory of how columns in the neocortex enable learning the structure of the world. Artificial neural networks (ANN): definition, examples, applications, training. Artificial intelligence, machine learning, and deep learning. Supervised and unsupervised machine learning. Astrobiology (exobiology): a new horizon. Extreme environments and extremotolerant organisms. Extremophilic models for astrobiology. RNA world hypothesis. Growing plants in space (space farming), missions VEG-03I and VEG-03J, seed films, Veggie. Astrobotany: simulated microgravity and clinostat rotation. Synthetic biology: definitions and key features. The second decade of synthetic biology: 2010-2020. Top-down and bottom-up approaches in synthetic biology. Cell-free synthetic biology: engineering beyond the cell. Advantages and applications of cell-free synthetic biology. DNA nanostructures for drug delivery: "DNA-brick self-assembly" and DNA origami. CADNANO software for designing three-dimensional DNA origami nanostructures. Aptamers. Gene circuits and gene circuit engineering. Synthetic minimal cells. Protocells and artificial life (A-life). Xna-Xeno-DNA nucleic acid analogs. Bioreporters. RNA-based biosensors and synthetic biology platforms for in vitro diagnostics. Synthetic biology devices for in vivo diagnostics. Biosafety and bioethics concerns.
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Prerequisites
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Basic knowledge of cell and molecular biology, genetics, biochemistry, and organismal physiology. Ability to work with scientific literature in English. Basic familiarity with mathematics, statistics, and bioinformatics is an advantage but is not required.
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Assessment methods and criteria
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Mark, Didactic Test
Successful completion of Final Test.
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Recommended literature
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& Choi, S. (2007). Introduction to systems biology. Totowa, NJ.
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Alon, U. An introduction to systems biology: design principles of biological circuits. 2019.
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Coruzzi GM, Gutierrez RA, Eds. Plant Systems Biology. Annual Plant Reviews vol. 35.
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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.
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Dubitzky W, Southgate J, Fuß H, Edis. Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biolog.
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Goldbeter A, Gérard C, Gonze D, Leloup JC, Dupont G. (2012). Systems biology of cellular rhythms. FEBS Lett. 586(18).
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Katsoulakis, E., Wang, Q., Wu, H., Shahriyari, L., Fletcher, R., Liu, J.. & Deng, J. Digital twins for health: a scoping review. .
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Kholodenko BN. (2006). Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol. 7(3).
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Kirschner MW. (2005). The meaning of systems biology. Cell. 20;121(4).
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Klipp, E., Liebermeister, W., Wierling, C., & Kowald, A. Systems biology: a textbook. 2016.
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Koutrouli , M., Karatzas , E., Paez Espino , D., & Pavlopoulos , G. A. (. A guide to conquer the biological network era using graph theory. 2020.
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Krawetz S, Ed. Bioinformatics for Systems Biology. Heidelberg.
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Libault, M., Pingault, L., Zogli, P., & Schiefelbein, J. Plant systems biology at the single-cell level. 2017.
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Milano, M., Agapito, G., & Cannataro, M. Challenges and limitations of biological network analysis. 2022.
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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).
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Raza, A. Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants. 2022.
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Sophien Kamoun. Can a biologist fix a smartphone??Just hack it!. 2017.
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Voit, Eberhard O. (2017). A first course in systems biology.
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Yuri Lazebnik. Can a biologist fix a radio?-Or, what I learned while studying apoptosis. 2002.
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