Almaas

Question 1

Describe the three primary fundamental concepts in constraint-based
reconstruction and analysis methods

Answer 1

There are three primary fundamental concepts in constraint-based reconstruction and analysis methods;

• network constraints, physiological constraints that limit computable phenotypes. Limitations include substrate and enzyme availability, mass and charge conversion, and thermodynamics.
• identification and mathematical description of evolutionary selective pressures. A metabilic reconstruction is converted into an in silico model by mathematically describing the reactions and adding network inpirts and -outputs (like uptake and secretion of a given compound).
• a genome-scale persoective of cell metabolism that accounts for all metabolic gene products in a cell.

Question 2

Reason why optimization of biomass production is a reasonable objective when modeling microbes

Answer 2

The biomass function and other objective functions can be used with optimization algorithms (like linear programming) to predict metabolic pathway usage and cellular phenotypes. As these mathematically state cellular aims and can predict phenotypes, they capture the pressures guiding evolution and therefore represent agents of causation in biology.
Also, by knowing how the metabolic network is put together, and simulating what will happen by affecting different parts of it, one could use the algorithm to possibly optimize the production of a desired biomass in an organism.

Question 3

Briefly discuss reasons for why the “simplistic” FBA method works so well in predicting cellular phenotypes

Answer 3

the FBA inputs include a list of metabolic reactions, reactions stoichiometry, mass balance and steady state, and the optimized goal functions. The outputs include fluctuations and transients, enzyme efficiencies, metabolite concentrations/toxicity, regulatory effects and cellular location.

This can be used to target processes in the cell by adjusting different aspects of the environment/conditions, and see whether it improves the production of the desired molecule or not. It can also predict metabolic vurnerabilities for design of antimicrobials, effects of gene deletions and changes in nutrient availability, and understanding the dynamic interplat of the metabolism.

Question 4

Is it possible to model genetic pertubations using COBRA methods? Why?

Answer 4

Since whole-genome metabolic networks can analyze and capture the activities of hundreds of enzymes, mutated genes/gene products can be assayed through in silico gene perturbation and simulation. Multiple simulations can be made, in which different genes/enzymes are knocked out, and the predicted results might be in line with the real-life results. It can be used to predict the metabolic side effects of off-target protein-drug interactions and prediction of novel antimicrobial targets.

Question 5

Briefly describe three limitations for current implementations of constrant-based modeling

Answer 5

One of the fundamental concepts of constraint-based modeling is network constraints that limit computable phenotypes. This is limited by multiple factors, including the avalibility of substrates and enzymes, the conversion of mass and charge, and thermodynamics (constrains the direction of the reactions).