Dinamički model odaziva središnjeg metabolizma Escherichia coli na impuls glukoze

master's thesis

• Title (english): Dynamic model of Escherichia coli central metabolism response upon glucose impulse
• Author: Sonja Čerić
• Mentor: Želimir Kurtanjek (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Process Engineering); (Laboratory for Measurement, Regulation and Automatisation); Zagreb
• Defense date and country: 2005-07-06, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Ovaj rad se temelji na eksperimentalnim podacima iz literature (Degenring, 2004) dobivenim metodom brzog uzorkovanja sa E. coli izloženom impulsu glukoze. Napravljena je simulacija modela centralnog metabolizma E. coli pomoću programskog sustava W.R. Mathematica upotrebom krute integracijske metode NDSolve. Početni kinetički model preuzet je iz literature (Degenring et. al., 2004). Rezultati simulacije početnog modela pokazali su značajno odstupanje od eksperimentalnih podataka za pojedine metabolite. Kako bi se predvidjele moguće problematične reakcije u početnom modelu provedena je dinamička analiza metaboličkih tokova. Zatim je na osnovi rezultata dinamičke analize metaboličkih tokova početni model korigiran. Unesene izmjene uključuju dvije nove reakcije (fosfoenol-piruvat karboksikinaza i konverzija piruvata u biomasu), izmjenu kinetičkih izraza za tri reakcije (PTS, fosfoglukoza-izomerazu i aldolazu) i prilagodbu kinetičkih parametara nizom simulacijskih pokusa. Rezultati simulacije novog modela pokazuju značajno bolje slaganje sa eksperimentalnim podatcima.

Abstract (english)

This work is based on experimental data published by D. Degenring (2004) from rapid sampling experiment with E. coli exposed to glucose pulse. In this work a model of central metabolism of E. coli was simulated with programming system W.R. Mathematica by use of the stiff integration method NDSolve. The original kinetic model used is taken from literature (Degenring et. al., 2004). The results from simulations of the original model showed significant difference from experimental data for some metabolites. In order to predict possible problematic reactions in original model dynamic metabolic flux analysis (DMFA) was preformed. Based on the results of DMFA the original model was altered. The changes introduced include insertion of two novel reactions (PEP carboxykinase and conversion of Pyr into biomass), alteration of three kinetic rate equations (PTS, phosphoglucose-isomerase and aldolase), and adjustment of kinetic parameters through series of simulation experiments. The results of a new model are much more consistent with experimental data.

• Keywords: analiza metaboličkih tokova; brzo uzorkovanje; E. coli; kinetički model
• Keywords (english): E. coli; kinetic model; metabolic flux analysis; rapid sampling
• Language: croatian
• URN:NBN: urn:nbn:hr:159:453272
• Study programme: Title: Biotechnology; specializations in: Biochemical Engineering; Course: Biochemical Engineering; Study programme type: university; Study level: graduate; Academic / professional title: diplomirani inženjer biotehnologije; smjer biokemijsko inženjerstvo (diplomirani inženjer biotehnologije; smjer biokemijsko inženjerstvo)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-09-13 12:52:04