Related Experiment Video
Updated: Jun 21, 2026
08:27
Use of a Caspase Multiplexing Assay to Determine Apoptosis in a Hypothalamic Cell Model
Published on: April 16, 2014
Analysis of an apoptotic core model focused on experimental design using artificial data.
R Schlatter1, H Conzelmann, E D Gilles
1University of Stuttgart, Institute for System Dynamics, Stuttgart, Germany. rebekka.schlatter@isys.uni-stuttgart.de
IET Systems Biology
|July 31, 2009
Summary
Mathematical modeling of caspase activation in apoptosis aids experimental design. Measuring activated caspase 8 provides the most information, optimizing future research and avoiding redundant experiments.
Area of Science:
- Systems Biology
- Computational Biology
- Molecular Biology
Background:
- Caspase activation is crucial for apoptosis.
- Mathematical modeling, particularly using ordinary differential equations (ODEs), is a powerful tool for understanding complex biological processes like apoptosis.
- A significant challenge in building kinetic models is the lack of measurement data, which limits parameter identifiability.
Purpose of the Study:
- To design future experimental setups that maximize information gain for a mathematical model of caspase activation during apoptosis.
- To identify which measurements would most effectively improve parameter estimates in the model.
- To determine the information content of potential experiments, including those involving inhibitor of apoptosis protein (IAP) knockout cells.
Main Methods:
- Utilized an existing mathematical model of caspase activation.
- Generated artificial measurement data in silico to simulate potential experiments.
- Fitted the model to the simulated data.
- Performed analyses using observability gramian and sensitivity analyses.
- Compared different analysis methods.
Main Results:
- Identified that several kinetic parameters in the caspase activation model are poorly identifiable.
- Determined that measurements of activated caspase 8 would maximally improve parameter estimates.
- Showed that many experiments with IAP knockout cells provide redundant information and are not necessary.
Conclusions:
- The in silico artificial data approach is effective for analyzing system properties and parameter identifiability.
- Improved experimental design can be achieved by focusing on measurements that yield the most information.
- Future research should prioritize measuring activated caspase 8 and can likely omit many IAP knockout cell assays to optimize resource allocation and data acquisition.
Related Concept Videos
01:30Apoptosis
Apoptosis is a combination of two Greek words, 'apo' and 'ptosis,' meaning separation and falling off, respectively. Hippocrates used this word to describe gangrene, which was caused due to bandaging of fractured bones. Apoptosis was distinguished from necrosis in 1970 when John Kerr reported observations of morphological changes occurring during apoptosis. During one experiment, he observed that the disruption of blood supply to the liver tissue resulted in a size reduction of the tissue.
01:31The Intrinsic Apoptotic Pathway
Internal cellular stress, such as cellular injury or hypoxia, triggers intrinsic apoptosis. The B-cell lymphoma 2 (Bcl-2) family of proteins are the primary regulators of the intrinsic apoptotic pathway. For example, during DNA damage, checkpoint proteins, such as Ataxia Telangiectasia Mutated (ATM protein) and Checkpoints Factor-2 (Chk2) proteins, are activated. These proteins phosphorylate p53 which further activates pro-apoptotic proteins, such as Bax, Bak, PUMA, and Noxa, and inhibits...
01:17The Extrinsic Apoptotic Pathway
The extrinsic apoptotic pathway is initiated when extracellular death-inducing signals, such as specific cytokines, activate the death receptors expressed on the cell surface. The immune cells involved in this pathway are natural killer cells (NK cells) and cytotoxic T-lymphocytes. NK cells are critical in innate immune response, while cytotoxic T-lymphocytes are associated with adaptive immune response. These cells recognize specific receptors expressed on the altered cells and activate...
01:16Experimental Designs
An experimental design is a systematic process that allows researchers to evaluate the relationship between dependent and independent variables. There are three widely used types of experimental design - pre-experimental design, true experimental design, and quasi-experimental design. In pre-experimental design, the researcher compares the data before and after some interventions or treatments. The true-experimental design has more than one purposefully created group, a commonly measured...
01:30Overview of Cell Death
Cell death is an essential process where the body gets rid of old or damaged cells. Cell proliferation and death need to be balanced, as an imbalance between the two may lead to cancer or autoimmune diseases.
Cell death was observed in the early 19th century, but there was no experimental evidence to prove it. In 1842, Carl Vogt first discovered cell death in a metamorphic toad; however, it was not termed ‘cell death.’ Scientists discovered different cell death pathways only in the 20th century...
Cell death was observed in the early 19th century, but there was no experimental evidence to prove it. In 1842, Carl Vogt first discovered cell death in a metamorphic toad; however, it was not termed ‘cell death.’ Scientists discovered different cell death pathways only in the 20th century...
01:22Cellular Injury V: Apoptosis and Autophagy
Cells respond to damage and stress through highly coordinated processes that decide whether they survive or undergo controlled self-destruction. Two major pathways involved in this regulation are apoptosis, a type of programmed cell death, and autophagy, a survival mechanism that helps cells adapt to adverse conditions.ApoptosisApoptosis removes aged or injured cells to maintain tissue balance. During this process, the cell shrinks, chromatin condenses and fragments, and membrane-bound...