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PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli.

Esmaeili A, Davison T, Wu A, Alcantara J, Jacob C - BMC Bioinformatics (2015)

Bottom Line: Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes.Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Faculty of Science, University of Calgary, 2500 University Drive NW, Calgary, T2N 1N4, Canada. afshin@invistaware.com.

ABSTRACT

Background: We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes. Our illustrative model focuses on the gene regulatory processes that control the expression of genes involved in the lactose operon. Prokaryo, our agent-based cell simulator, incorporates cellular structures, such as plasma membranes and cytoplasm, as well as elements of the molecular machinery, including RNA polymerase, messenger RNA, lactose permease, and ribosomes.

Results: The dynamics of cellular 'agents' are defined by their rules of interaction, implemented as finite state machines. The agents are embedded within a 3-dimensional virtual environment with simulated physical and electrochemical properties. The hybrid model is driven by a combination of (1) mathematical equations (DEQs) to capture higher-scale phenomena and (2) agent-based rules to implement localized interactions among a small number of molecular elements. Consequently, our model is able to capture phenomena across multiple spatial scales, from changing concentration gradients to one-on-one molecular interactions. We use the classic gene regulatory mechanism of the lactose operon to demonstrate our model's resolution, visual presentation, and real-time interactivity. Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.

Conclusion: We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes. Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

No MeSH data available.


Related in: MedlinePlus

Schematic of the lac operon regulatory pathways
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Fig2: Schematic of the lac operon regulatory pathways

Mentions: Surprisingly though, exact details of how a biological cell works—to a large extent—still remain a mystery. This is even the case for comparatively simple bacterial (prokaryotic) cells. Eukaryotic cells are even more complex, and consequently even harder to model [7]. A good starting point for understanding the molecular dynamics inside a bacterium is to investigate how its small building blocks (molecules) interact with other building blocks and structural elements (cytoplasm, periplasm) within the cell. For instance, proteins acting as repressors regulate gene expressions, which further trigger a cascade of events. Understanding the regulation processes is crucial for identifying cellular responses to internal and external signals. As a cell reacts to signals by switching different genes on and off, different proteins are manufactured in response [8]. Given the prominent role of gene regulation in a cell’s life cycle, we have chosen a classical, well-studied gene regulation mechanism inside E. coli to be modeled and simulated as part of this work: the lactose operon switch (Fig. 2).Fig. 2


PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli.

Esmaeili A, Davison T, Wu A, Alcantara J, Jacob C - BMC Bioinformatics (2015)

Schematic of the lac operon regulatory pathways
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4587781&req=5

Fig2: Schematic of the lac operon regulatory pathways
Mentions: Surprisingly though, exact details of how a biological cell works—to a large extent—still remain a mystery. This is even the case for comparatively simple bacterial (prokaryotic) cells. Eukaryotic cells are even more complex, and consequently even harder to model [7]. A good starting point for understanding the molecular dynamics inside a bacterium is to investigate how its small building blocks (molecules) interact with other building blocks and structural elements (cytoplasm, periplasm) within the cell. For instance, proteins acting as repressors regulate gene expressions, which further trigger a cascade of events. Understanding the regulation processes is crucial for identifying cellular responses to internal and external signals. As a cell reacts to signals by switching different genes on and off, different proteins are manufactured in response [8]. Given the prominent role of gene regulation in a cell’s life cycle, we have chosen a classical, well-studied gene regulation mechanism inside E. coli to be modeled and simulated as part of this work: the lactose operon switch (Fig. 2).Fig. 2

Bottom Line: Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes.Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Faculty of Science, University of Calgary, 2500 University Drive NW, Calgary, T2N 1N4, Canada. afshin@invistaware.com.

ABSTRACT

Background: We are creating software for agent-based simulation and visualization of bio-molecular processes in bacterial and eukaryotic cells. As a first example, we have built a 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes. Our illustrative model focuses on the gene regulatory processes that control the expression of genes involved in the lactose operon. Prokaryo, our agent-based cell simulator, incorporates cellular structures, such as plasma membranes and cytoplasm, as well as elements of the molecular machinery, including RNA polymerase, messenger RNA, lactose permease, and ribosomes.

Results: The dynamics of cellular 'agents' are defined by their rules of interaction, implemented as finite state machines. The agents are embedded within a 3-dimensional virtual environment with simulated physical and electrochemical properties. The hybrid model is driven by a combination of (1) mathematical equations (DEQs) to capture higher-scale phenomena and (2) agent-based rules to implement localized interactions among a small number of molecular elements. Consequently, our model is able to capture phenomena across multiple spatial scales, from changing concentration gradients to one-on-one molecular interactions. We use the classic gene regulatory mechanism of the lactose operon to demonstrate our model's resolution, visual presentation, and real-time interactivity. Our agent-based model expands on a sophisticated mathematical E. coli metabolism model, through which we highlight our model's scientific validity.

Conclusion: We believe that through illustration and interactive exploratory learning a model system like Prokaryo can enhance the general understanding and perception of biomolecular processes. Our agent-DEQ hybrid modeling approach can also be of value to conceptualize, illustrate, and--eventually--validate cell experiments in the wet lab.

No MeSH data available.


Related in: MedlinePlus