Modeling and simulation of stimulation of motility in Synechocystis PCC 6803
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(2) Molecular Biotechnology Programme Uppsala University School of Engineering Date of issue 2005-02. UPTEC X 05 010 Author. Hanna Härdin Title (English). Modeling and simulation of stimulation of motility in Synechocystis PCC 6803 Abstract When the cyanobacterium Synechocystis PCC 6803 is exposed to blue light, it responds by moving away from the light source. There are also indications that, when exposed to glucose, the bacterium responds by decreasing its motility. These processes are controlled by a large and complex network of genes, a so-called genetic regulatory network. Because of the lack of information about the components of the network underlying these processes in Synechocystis PCC 6803, several alternative networks can be imagined. These possible networks have been modeled and simulated. Since almost no quantitative data on the system is available, a qualitative simulation method that can handle these constraints has been used. By analyzing the simulation results, it has been possible to select experiments that would discriminate effectively between possible networks. Keywords Qualitative modeling and simulation, genetic regulatory networks, chemotaxis, phototaxis, motility, Synechocystis PCC 6803, piecewise-linear differential equations Supervisors. Hidde de Jong Helix bionformatics, INRIA Rhône-Alpes, Grenoble Scientific reviewer. Måns Ehrenberg Department of Cell & Molecular Biology, Uppsala University Project name. Sponsors. Language. Security. English Classification. ISSN 1401-2138 Supplementary bibliographical information. Pages. 49 Biology Education Centre. Biomedical Center. Husargatan 3 Uppsala. Box 592 S-75124 Uppsala. Tel +46 (0)18 4710000. Fax +46 (0)18 555217.
(3) Modellering och simulering av stimulans av motilitet i Synechocystis PCC 6803 Hanna Härdin Sammanfattning Vissa bakterier kan röra sig mot, alternativt ifrån, en ljuskälla. Det finns också bakterier vars rörelseförmåga påverkas av vissa typer av kemikalier. I bakterier med sådana egenskaper finns molekyler som har förmåga att registrera ljus eller kemikalier. Dessa molekyler för vidare informationen inuti bakterien genom att reagera med andra molekyler. Signalerna resulterar i att bakterien bygger upp, eller bryter ner, det molekylära maskineri som får bakterien att röra sig. De signalerande molekylerna som för vidare informationen genom bakterien utgör ett stort och komplext så kallat genetiskt regulatoriskt nätverk. Bakterien Synechocystis PCC 6803 rör sig bort från blått ljus. Man har också visat att sockermolekylen glukos tycks minska bakteriens rörlighet. Eftersom man inte har fullständig information om det genetiska regulatoriska nätverk som ligger bakom dessa beteenden finns flera tänkbara alternativa nätverk. I detta arbete har dessa tänkbara nätverk modellerats och simulerats. Genom att analysera simuleringsresultat har det varit möjligt att föreslå experiment vars resultat kan hjälpa till att urskilja bland de möjliga nätverken. Urskiljningen bland de möjliga nätverken kan göras genom att de nätverk vars simuleringsresultat ej överensstämmer med resultat från de föreslagna experimenten förkastas. Genom att med hjälp av modellering och simulering föreslå informativa experiment effektiviseras det experimentella arbetet.. Examensarbete 20 p i Molekylär bioteknikprogrammet Uppsala universitet, februari 2005.
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