Whole-cell modeling

A. R. Joyce and B. 0. Palsson. Toward whole cell modeling and simulation comprehensive functional genomics through the constraint-based approach. Prog. Drug Res., 64 266-309, 2007. 

In the whole cell model, a gigaseal is formed as the pipette is attached to the cell, and then a more dynamic suction is applied, which causes the interior of the cell to be sucked into the pipette tip (Fig. 3a). This action allows current and conductance of the entire cell to be measured. Therefore, the whole cell model measures changes caused by many ion channels on the entire cell membrane. Additionally, the liquid content of the cell will mix and equilibrate with the solution in the pipette, which allows pharmacological agents to be administered into the cell. Of the patch clamp techniques, the whole cell method is the most common and can be used to determine how pharmacological agents affect the total conductance of neurons. 

In the outside-out model, the pipette is attached to the entire cell as in the whole cell model, followed by a sharp pull that causes the cell membrane to break and reseal with the pipette tip (Fig. 3b). With the extracellular region exposed, channel activity as a response to different external stimuli can be probed. This configuration is less common than the inside-out method. Using an outside-out method, single-channel opening activity has been recorded while various neurotransmitters were released. For example, this patch clamp method was used as a detector for capillary electrophoresis separations of GABA, glutamate, and NMDA (7). 

Traditionally, to identify the function of a protein the first step was to obtain a mutant and study its properties. This same procedure can also be applied to whole-cell models. A detailed understanding of the metabolic network is possible by understanding the behavior of the system without a key component. The FBA has been used to predict the whole-cell metabolic flux distribution for a number of mutants under different conditions. The results of the computational gene deletion analysis indicate that the model accurately predicts the qualitative growth behavior in over 85% of the cases. Genome enabled studies, such as the analysis of large sets of mutants in parallel and whole-cell transcript profiling, can be further aided by the interpretation of the data from a metabolic model. ... 

There are at least two clear levels of simulation required in many cases, well illustrated by simulations of the heart. The cellular level includes whole cell modeling in approximate detail and, in finer detail, studies of proteins that as enzymes catalyze biochemical reactions, as transporters or gates that carry ions... 

INTEGRATING GENOME AND METABOLOME TOWARD WHOLE CELL MODELING WITH THE E-CELL SYSTEM... 

Integrating Genome and Metabolome Toward Whole Cell Modeling with the... 

Bioinformatics The use of infonnatics to upgrade biological information, e.g., to identify genes in sequenced genomes, to predict protein structures, and to construct whole cell models. 

Although simple models are essential for a fundamental understanding, in the future more realistic models are required, in particular in view of possible applications in cell and tissue engineering. Here we have used cable networks as a first step towards more realistic models for both cell and the matrix. Anisotropic force contraction dipoles are only the first order approximation for the complex mechanical activity of cells and might be extended to more general tensors for mechanical activity and susceptibility. A more sophisticated model would be to replace the force dipoles by whole cell models incorporating the focal adhesion dynamics and stress fibers evolution. 

Castro, C.E., Yokoyama, W.H., Belser, N.O., 1988. Biohalogenation reactivities of microbial and mammalian cytochrome P450 compared with heme and whole-cell models. J. Agric. Food Chem. 36, 915-919. 

Previously, we have shown that functional secretion of OPH molecules into the periplasmic space induced about 2.8-fold higher specific whole cell OPH activity [10]. From the detail reaction kinetic studies in this work, we showed that this periplasmic space-secretion strategy provided much improved bioconversion capability and efficiency ( 1.8-fold) for Paraoxon as a model organophosphate compound. From these results, we confirmed that Tat-driven periplasmic secretion of OPH can be successfully employed to develop a whole cell biocatalysis system with notable enhanced bioconversion efficiency and capability for environmental toxic organophosphates. 

Cardiac models are amongst the most advanced in silico tools for bio-med-icine, and the above scenario is bound to become reality rather sooner than later. Both cellular and whole organ models have aheady matured to a level where they have started to possess predictive power. We will now address some aspects of single cell model development (the cars ), and then look at how virtual cells interact to simulate the spreading wave of electrical excitation in anatomically representative, virtual hearts (the traffic ). 

These may be produced by grouping together multiple cell models to form virtual tissue segments, or even the whole organ. The validity of such multi-cellular constructs crucially depends on whether or not they take into account the heart s fine architecture, as cardiac structure and function are tightly interrelated. 

The complexity of prostate cell cross talk that may be partially assessed by prostate cell cocultures should add to our understanding of how lycopene or its oxidation products participate. However, of utmost importance is the characterization of lycopene or lycopene oxidation product binding to particular proteins that shift their function and therefore the pathways in which they act. Such characterization is foundational to understanding the mechanism of action of lycopenoids. Simpler model systems where even the whole cell is too complex may be useful in working out these mechanisms of action. 

Screening assays were used to study the effects on cell proliferation and cytotoxicity of whole leachate and relative organic and hydrophilic extracts on cell model after 24-72 h of exposure. 

Phytochemicals have been the subject of many studies evaluating their effects in relation to common chronic human illnesses such as cancer and cardiovascular diseases. These studies encounter difficulties in using this information to influence the dietary patterns of consumers because in the past they have used models or experiments with animals. However, in the last decade, researchers have moved away from animal studies in favour of human cell models or human intervention studies. Scientists still need to determine the likely incidence of illness from exposure to known amounts of a given natural compound in the diet and specifically in relation to the complex matrices of whole foods. Therefore, it is inevitable that some animal studies have to be continued for toxicological studies. 

Stimulation for 24 hours with LPS leads to the release of interleukin-1 [3, IL-6, IL-8, TNF-a and by prolonging the incubation period from 48 to 72 hours, the whole blood model can detect the release of other lymphokines [45], including IL-2, IL-4, IL-13 and IFN-y. Skewing of the T-helper cell response to antigens can likewise be detected by evaluating the pattern of cytokine release, corresponding to a predominance of Th 1 or Th2 cytokine production. The predictive value of these approaches is currently under investigation. 

The recommended profile is based on the model prediction for the average k-factor of the whole cell, but it is modified according to operating experience, which indicates which areas of the cell are subject to the quickest build-up of thick mercury. In the field the operators used hand-held k-factor probes to set the cell up according to the results from the model. 

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