Summary – Principles of systems
biology
Made by: Abduallah Lemdjad Date: 18-02-2024 Course: Principles of systems
, biology
Table of Contents
LECTURE 1 -DYNAMIC MODELS.........................................................................................................3
1.1 EXAMPLE 1: MODELLING OF CELLULAR GLUCOSE UPTAKE AND CONSUMPTION IN MOUSE C2C12 MYOBLASTS.....3
1.2 EXAMPLE 2: MODELLING PYRUVATE AND ATP PRODUCTION IN MOUSE MUSCLE MITOCHONDRIA......................4
LECTURE 2- TRANSCRIPTOMICS, PROTEOMICS, METABOLOMICS, AND FLUXOMICS..........................5
LECTURE 3- MS-BASED METABOLITE ANALYSIS: METABOLOMICS AND FLUXOMICS..........................9
LECTURE 4- SYSTEMS MICROSCOPY................................................................................................10
4.1 MICROSCOPY AUTOMATION RAISES THROUGHPUT...............................................................................10
4.2 MARKER MULTIPLEXING BOOSTS CONTENT.........................................................................................10
4.3 QUANTITATIVE IMAGE ANALYSIS AND DATA MINING ALLOW CELL PROFILING...............................................11
4.4 NEW CELLULAR MODELS DEMAND TAILORED SOLUTIONS........................................................................11
LECTURE 5 – RANDOM-WALK ANALYSIS OF PROTEIN DIFFUSION....................................................12
5.1 MITOCHONDRIA AS DYNAMIC MODELS..............................................................................................12
5.2 QUANTIFICATION OF PROTEIN DIFFUSION IN CELLS...............................................................................13
LECTURE 6 – SYSTEMS MEDICINE....................................................................................................15
LECTURE 7 – METHODS FOR THE DETERMINATION OF PROTEIN CONCENTRATIONS.......................17
7.1 DIFFERENT TECHNIQUES TO QUANTIFY PROTEIN CONCENTRATIONS...........................................................17
7.1.1 COOMASSIE BRILLIANT BLUE STAINING.................................................................................................17
7.1.2 ELISA (ENZYME-LINKED IMMUNOSORBENT ASSAY) OR WESTERN BLOT......................................................18
7.1.3 MASS SPECTROMETRY -BASED TECHNIQUES..........................................................................................18
7.2 QUANTIFICATION BY WESTERN BLOT................................................................................................19
7.3 QUANTIFICATION BY MASS SPECTROMETRY........................................................................................20
LECTURE 8 – MATHEMATICAL MODELLING OF MACROMOLECULAR DRUG DELIVERY.....................21
, Lecture 1 -Dynamic models
A dynamic model focusses on how system components influence rates of change of each
component concentration in the model.
Cellular energy metabolism consists of multiple subsystems that have the same goal,
generate energy. The subsystems are:
- Glycolysis
- Pentose phosphate pathway
- Tricarboxylic acid cycle (TCA)
- Oxidative phosphorylation
- An ATP consuming system: calcium homeostasis
1.1 Example 1: Modelling of cellular glucose uptake and
consumption in mouse C2C12 myoblasts
Important to know how the mitochondrial OXPHOS system works.
1) NADH is converted to NAD+ and H+ (by CI)
2) The first reaction provide energy for the conversion of succinate to fumarate (by CII)
3) CIII allows for the efflux of 4 hydrogen atoms
4) Followed by the conversion of O2 into H2O (by CIV)
5) The proton motive force generates energy so ADP+Pi is converted into ATP (by CV)
Step 1-4 belong to the electron transport chain
Step 1-5 belong to the oxidative phosphorylation system
CI inhibitor – PA
CIII inhibitor – AA
After a certain concentration of AA and/or PA, no O2 is consumed anymore meaning no
activation of the OXPHOS system.
Example 1. A simple model for glucose dynamics in living mouse myoblasts.
[GLC]ext (glucose outside of the cell) travels through the plasma membrane via glucose
transporter (GLUT) to the inside of the cell [GLC]c. Flux form outside the cell the cell is called
“v1”. K is a constant, does not change in time.
Initial intracellular glucose concentration can be calculated via: [GLC]c (t) = v1 – v2
Finally, the v2 can be calculated via:
biology
Made by: Abduallah Lemdjad Date: 18-02-2024 Course: Principles of systems
, biology
Table of Contents
LECTURE 1 -DYNAMIC MODELS.........................................................................................................3
1.1 EXAMPLE 1: MODELLING OF CELLULAR GLUCOSE UPTAKE AND CONSUMPTION IN MOUSE C2C12 MYOBLASTS.....3
1.2 EXAMPLE 2: MODELLING PYRUVATE AND ATP PRODUCTION IN MOUSE MUSCLE MITOCHONDRIA......................4
LECTURE 2- TRANSCRIPTOMICS, PROTEOMICS, METABOLOMICS, AND FLUXOMICS..........................5
LECTURE 3- MS-BASED METABOLITE ANALYSIS: METABOLOMICS AND FLUXOMICS..........................9
LECTURE 4- SYSTEMS MICROSCOPY................................................................................................10
4.1 MICROSCOPY AUTOMATION RAISES THROUGHPUT...............................................................................10
4.2 MARKER MULTIPLEXING BOOSTS CONTENT.........................................................................................10
4.3 QUANTITATIVE IMAGE ANALYSIS AND DATA MINING ALLOW CELL PROFILING...............................................11
4.4 NEW CELLULAR MODELS DEMAND TAILORED SOLUTIONS........................................................................11
LECTURE 5 – RANDOM-WALK ANALYSIS OF PROTEIN DIFFUSION....................................................12
5.1 MITOCHONDRIA AS DYNAMIC MODELS..............................................................................................12
5.2 QUANTIFICATION OF PROTEIN DIFFUSION IN CELLS...............................................................................13
LECTURE 6 – SYSTEMS MEDICINE....................................................................................................15
LECTURE 7 – METHODS FOR THE DETERMINATION OF PROTEIN CONCENTRATIONS.......................17
7.1 DIFFERENT TECHNIQUES TO QUANTIFY PROTEIN CONCENTRATIONS...........................................................17
7.1.1 COOMASSIE BRILLIANT BLUE STAINING.................................................................................................17
7.1.2 ELISA (ENZYME-LINKED IMMUNOSORBENT ASSAY) OR WESTERN BLOT......................................................18
7.1.3 MASS SPECTROMETRY -BASED TECHNIQUES..........................................................................................18
7.2 QUANTIFICATION BY WESTERN BLOT................................................................................................19
7.3 QUANTIFICATION BY MASS SPECTROMETRY........................................................................................20
LECTURE 8 – MATHEMATICAL MODELLING OF MACROMOLECULAR DRUG DELIVERY.....................21
, Lecture 1 -Dynamic models
A dynamic model focusses on how system components influence rates of change of each
component concentration in the model.
Cellular energy metabolism consists of multiple subsystems that have the same goal,
generate energy. The subsystems are:
- Glycolysis
- Pentose phosphate pathway
- Tricarboxylic acid cycle (TCA)
- Oxidative phosphorylation
- An ATP consuming system: calcium homeostasis
1.1 Example 1: Modelling of cellular glucose uptake and
consumption in mouse C2C12 myoblasts
Important to know how the mitochondrial OXPHOS system works.
1) NADH is converted to NAD+ and H+ (by CI)
2) The first reaction provide energy for the conversion of succinate to fumarate (by CII)
3) CIII allows for the efflux of 4 hydrogen atoms
4) Followed by the conversion of O2 into H2O (by CIV)
5) The proton motive force generates energy so ADP+Pi is converted into ATP (by CV)
Step 1-4 belong to the electron transport chain
Step 1-5 belong to the oxidative phosphorylation system
CI inhibitor – PA
CIII inhibitor – AA
After a certain concentration of AA and/or PA, no O2 is consumed anymore meaning no
activation of the OXPHOS system.
Example 1. A simple model for glucose dynamics in living mouse myoblasts.
[GLC]ext (glucose outside of the cell) travels through the plasma membrane via glucose
transporter (GLUT) to the inside of the cell [GLC]c. Flux form outside the cell the cell is called
“v1”. K is a constant, does not change in time.
Initial intracellular glucose concentration can be calculated via: [GLC]c (t) = v1 – v2
Finally, the v2 can be calculated via:
