Postgraduate Course: Information Processing in Biological Cells (INFR11056)
|School||School of Informatics
||College||College of Science and Engineering
|Credit level (Normal year taken)||SCQF Level 11 (Postgraduate)
||Availability||Not available to visiting students
|Summary||All biological cells process information. They integrate signals from their environment, respond and adapt to internal changes and store information in a variety of means from transient to persistent. In this course we will look at the various strategies used by cells to process and store information.
* General survey of the flow of information and matter in the cell: anatomy of eukaryotic and prokaryotic cells, building blocks and structural elements, cell as a self-reproducing distributed chemical computer. Main flows of information.
* Proteins as elementary units of cellular computation: modular structure, evolution, allosteric regulation, multistability, post-translational modifications that regulate protein conformation. Operation of proteins within functional complexes, cooperative effects. Protein design.
* Transport processes and propagation of cellular information. Diffusion, its laws and fundamental constraints on the information propagation with diffusion. Molecular crowding, failure of propagation, superdiffusion and subdiffusion.
* Non-diffusive intracellular propagation. Molecular motors, principles of motor-mediated transport and the information flows.
* Acquisition of external information. Sensing of extracellular chemical signals, light, pH, temperature, etc. Principles of mechanosensation and mechanotransduction.
* Principles of signal transduction: protein modifications as signals. Encoding and decoding of spatial and temporal information.
* Abstraction of molecular interactions within a cell. Molecular networks, graphical notations, symbolic representations of interactions. Problems, pitfalls and standards. SBGN and SBML.
* Methods of quantitative description and modeling of biochemical and signal transduction networks. Chemical kinetics, mass-action rate law, particle conservation, reaction fluxes.
* Further abstraction of molecular networks. Graph representation. Stability and instability of networks. Positive and negative feedback as the basis for instability. Closed cycles within reaction networks.
* Dynamical elements of intracellular computer. Memory elements through multiple bistable elements. Oscillations. Response time of biological networks to external stimuli and 'futile cycles'.
* Organizational hierarchy of the cellular hard drive. Storage of genetic information on the DNA, its duplication, maintenance (error protection), extraction and transformations.
* Principles of operation of the nuclear computer. Cis-regulatory elements: 'Junk' DNA, regulatory motifs and signals. Trans-regulatory elements: Transcription factors and their regulation. Combinatorial computer in the nucleus.
* Systemic operation of cellular computer. Examples of bacterial networks of signal transduction and gene regulation: principles of logical design, integration of multiple information sources, decision making.
* Advanced topics of cellular information networks. Stoichiometric networks and matrixes, metabolic control analysis, elementary modes and extreme pathways.
Relevant QAA Computing Curriculum Sections: Data Structures and Algorithms, Developing Technologies
Entry Requirements (not applicable to Visiting Students)
||Co-requisites|| Students MUST also take:
Bioinformatics 1 (INFR11016)
||Other requirements|| None
Course Delivery Information
|Not being delivered|
| 1 - Be able to describe a range of examples of information processing in biological cells.
2 - Compare and contrast biological methods for storing information across different time scales.
3 - Discuss the computational limits of the simplest biological organisms.
4 - Explain with reference to examples how cells integrate information from multiple modalities.
5 - Critically evaluate research literature in the field.
|See course web page for reading list.|
|Course organiser||Dr Michael Rovatsos
Tel: (0131 6)51 3263
|Course secretary||Miss Gillian Bell
Tel: (0131 6)50 2692