Computer Model Of A Cell

 

All of life is made up of cells.  Some cells are plant cells while others are animal but up to this point in time, no one has made a complete model of a cell.  Recently, a team at the University of Illinois at Urbana-Champaign created the most complete three dimensional computer simulation. I chose it for today's column because it is digitally based. 

This group created a computational model of a very complex system.  They've used the simulation to make some very interesting discoveries about both the psychology  and reproduction of the cell.  In addition, it provides people with an opportunity to generate more ideas for experimentation. This simulation looks at the metabolic functions of the whole cell rather than the biochemical reactions for an artificial system.  They are getting results as if it is a real cell.  

In the past, others have tried to model cells but have not been successful because most cells are quite complex.  This simulation differs in that it uses a much simpler cell with fewer genes so it is much easier to figure out how the system works.    Researchers can monitor the simulation for waste, use of nutrients, gene products and other biochemical processes in a three dimensional environment.  This model allows scientists to understand how the simplest cells work and what the minimal requirements are for life.

The results of this simulation lead the way to creating more complex models so eventually they will be able to create simulations of specific cells such as the common intestinal E.Coli. 

Researchers started with a version developed by J. Craig Venter Institute back in 2016 and was based on the simple bacterium cell  Mycoplasmas mycoides.  They stripped any parts out of the cell that didn't have anything to do with survival so it only had 493 genes which is about half of what the original had.  The 493 is about one eighth of the number of genes in the E. coli.

Scientists are not sure what 94 of the 493 genes do but they are aware that when the cell dies, these 94 genes are not present. It is suggested that these genes help with life but we just haven't figure out what they do.  It is hoped that this simulation will help them figure out what these 94 genes do. 

The group who created the simulation combined all the data available for cells and how they function before using flash frozen thin sliced images of the minimal cell developed by the J. Craig people to position its organic machinery precisely. They then sprinkled all the necessary proteins throughout the cell using a protein analysis before relying on a detailed chemical composition of analysis of the cell membrane from the Dresden University to correctly place molecules around outside of the cell. They also used a map of biochemical interactions to determine the appropriate interactions.

They observed the digital cell as it grew and divided, all the while monitoring thousands of biochemical interactions so they could see how the cell acts over time as it grows.  In addition to seeing the results from the original cell, they noticed some new, previously unobserved such as how the cell distributes energy and how fast messenger RNA degrades.

One of the most surprising results had to do with the speed of growth and division of the cells.  Normally, the cell needs the enzyme - transaldolase - but there does not appear any is present so either the cell is able to do it without the enzyme or it exists in a different form. Although this simulation does have some problems, it is one of the best available right now and will lead to better models as more is learned.  Let me know what you think, I'd love to hear.  Have a great day.