The regulatory modes and their combinations can explain all kinds of regulatory systems at any level in a biological system. These include, but are not limited to, physiological regulation, gene expression regulation, regulation of signaling pathways, metabolism, ecosystem food webs and ecosystem self-organization. In the following, some widely studied regulatory systems are described with the PLTR model.
Regulation mechanisms can be simple or complex. Control of one process can affect many other processes as systems form networks. Similarly, one system may be regulated by several other processes which again can be regulated by several systems. Factor X can be a regulator of another system and it can be regulated by other systems. Many types of network motifs are known . Non-lagom extent of heterogeneity of an entity can affect the lagom and regulation at connected levels.
lac operon in Escherichia coli is a textbook example of a regulatory system. In the absence of lactose, the lac repressor inhibits the expression of the lactose utilization genes from an operon by binding to operator region in front of the coding genes. Binding of RNA polymerase to the promoter is aided by the cAMP-bound catabolite activator protein (CAP). The repressor is constitutively expressed, unless a co-inducer binds to it. The repressor inhibits transcription by blocking binding of RNA polymerase to the operator of the operon. It can only be removed when allolactose binds and inactivates the repressor. As another step of lactose regulation, when glucose, the major carbon source, is available, CAP, which is essential for the lactose utilization gene expression, prevents lactose transport into the cell.
PLTR model explains the lac operon regulation as follows. In the absence of lactose, the system is at a lagom maintenance mode and stays there as far as no lactose is available. The binding of allolactose and inactivation of the repressor is a reguland regulation step where the repressor conformation is changed. The system enters to new state where genes are expressed from the operon. The new lagom is maintained by the lagom maintenance mode. The removal of allolactose reactivates the repressor in another reguland regulation step. CAP regulation is explained by the model as follows. When glucose is available, CAP is inactivated in a lagom maintenance mode and thus preventing lactose permease expression and consequent transport of lactose. The two regulatory mechanisms together regulate lac operon, the first one controlling lactose utilization gene expression and the other transport of lactose and allolactose into cells.
At lagom state a status quo persists in a system and there is no need for regulation. The system is relaxed and active, energy consuming actions do not occur. Lagom emerges from combined outcome of TCMs and the complexity of the systems. When X1 is smaller or higher than lagom, intrinsic TCM mechanisms restrict the change and can return the system back to lagom extent of heterogeneity. Attenuation mechanisms are the major TCMs involved in this mode of regulation. Robustness, which originates from the complex organization of the system, buffers and makes systems slow to change their state (systemic inertia) and thereby effectively attenuates small/medium changes and perturbations.
Many enzymes display saturation kinetics - their hyperbolic Michaelis-Menten curves show a long asymptotic tail. Even extensive reduction of the activity may not have a major effect on the flux through the process  since even the reduced activity is of lagom extent. In some diseases patients have a severe phenotype only when majority, even 95%, of the normal activity is lost . As many enzyme activities in cells are close to saturation , even a substantially reduced activity is still at lagom extent and does not have a major impact or phenotype. In systems formed of enzymes, such as the pentose phosphate pathway, the flux can be reduced to 15% and in the tricarboxylic cycle to 19% of normal activity without significant effect on optimal growth of Escherichia coli . These systems are very robust and the lagom state is maintained in a very wide activity range.
Once the perturbation cannot be controlled by the intrinsic TCMs, adaptive tolerance, repair and/or resistance mechanisms are activated. This type of regulation consumes energy. Depending on the extent of regulation and perturbation, the system returns to the original lagom extent or enters to new lagom. When at the new lagom state, attenuation mechanisms keep that extent.
Chaperones are ever-present in cells, but their expression can also be induced by perturbations. They act as folding chaperones and assist proteins to fold correctly. Repair mechanisms actively correct effects of perturbations. Many types of suppression mechanisms are activated by genetic or protein variants . Rewiring of pathways is relatively common and provides robustness for cells and organisms .
Regulator can be external or intrinsic within the system. It either increases or decreases the activity of the factor and can be called in different names depending on the system and function, including regulator, activator, enhancer, inducer, inhibitor, insulator, repressor, silencer, and allosteric regulator. In addition to the natural regulators, there can be external factors, such as toxins, addiction-causing substances, drugs and environmental, population and ecosystem changes. Regulator-mediated control is active and consumes energy, however the consumption is small as one regulator can regulate many regulands. TCM mechanisms are active also in this form of regulation, in fact they cannot be switched off.
Emergent processes are common in biology, although often ignored. Whenever the system outcome cannot be derived from the output of independent factors, it is likely that the system has emergent properties. In the case of regulation, robustness is an example of an emergent property [9, 10]. It originates from the joint contribution of regulatory processes, molecules, networks and lagom states. System resilience effectively restricts changes to the state of a system and defines the lagom state.
Maintenance of lagom and perturbation control have a range of responses, whereas regulator control is largely binary. Activation or inactivation can be permanent or reversible. Proteolytic activation of many proteases is an example of irreversible form of control, it lasts until the activated protein is degraded, since there is no mechanism to attach inactivating propeptide back to the protein. Certain functions, such as cellular signalling, demand for fast switching on or off. Protein phosphorylation and dephosphorylation are examples of reversible post translational modifications in signalling molecules with immediate effect on system activity.
Physiological regulation is complex, and the regulatory systems are composed of several regulated processes. Processes like glucose level regulation require the concerted action of many factors. Several hundreds of genes have been implicated in diabetes type 2 , although the actual function and role is known just for a few. The regulatory factors can be regulated by other regulators and TCMs forming a large and complicated network. However, the action and regulation of the components can be described by the lagom maintenance and reguland regulation modes in the PLTR model. This has important implications for modelling of biological processes.