Optical monitoring system

Instrument can measure optical transmission, reflectance, and scattering. This information can be used to identify changes in optical properties or deviations from required optical standards. Device consists of monochromatic source, photo detector, transfer mirror, and hemiellipsoid. System might be used to measure optical properties of thin film

Mathematical models of microbial growth and metabolism: A whole-organism perspective

This is the author accepted manuscript. The final version is available from Science Reviews 2000 via the DOI in this record.We review the principles underpinning the development of mathematical models of the metabolic activities of micro-organisms. Such models are important to understand and chart the substantial contributions made by micro-organisms to geochemical cycles, and also to optimise the performance of bioreactors that exploit the biochemical capabilities of these organisms. We advocate an approach based on the principle of dynamic allocation. We survey the biological background that motivates this approach, including nutrient assimilation, the regulation of gene expression, and the principles of microbial growth. In addition, we discuss the classic models of microbial growth as well as contemporary approaches. The dynamic allocation theory generalises these classic models in a natural manner and is readily amenable to the additional information provided by transcriptomics and proteomics approaches. Finally, we touch upon these organising principles in the context of the transition from the free-living unicellular mode of life to multicellularity.Olga Nev was funded through EU Research Framework programme 7 Marie Curie Actions, grant 316630 Centre for Analytical Science – Innovative Doctoral Programme (CAS-IDP)

Variable-Internal-Stores models of microbial growth and metabolism with dynamic allocation of cellular resources.

This is the final version of the article. Available from Springer via the DOI in this record.An erratum to this article is available at http://dx.doi.org/10.1007/s00285-016-1044-y and in ORE at http://hdl.handle.net/10871/31444Variable-Internal-Stores models of microbial metabolism and growth have proven to be invaluable in accounting for changes in cellular composition as microbial cells adapt to varying conditions of nutrient availability. Here, such a model is extended with explicit allocation of molecular building blocks among various types of catalytic machinery. Such an extension allows a reconstruction of the regulatory rules employed by the cell as it adapts its physiology to changing environmental conditions. Moreover, the extension proposed here creates a link between classic models of microbial growth and analyses based on detailed transcriptomics and proteomics data sets. We ascertain the compatibility between the extended Variable-Internal-Stores model and the classic models, demonstrate its behaviour by means of simulations, and provide a detailed treatment of the uniqueness and the stability of its equilibrium point as a function of the availabilities of the various nutrients.OAN was funded through EU Research Framework programme 7 Marie Curie Actions, grant 316630 Centre for Analytical Science – Innovative Doctoral Programme (CAS-IDP)

Holling Type I versus Holling Type II functional responses in Gram-negative bacteria

We consider how the double-membrane structure of the cell envelope of Gram-negative bacteria affects its functional response, which is the mathematical relationship that expresses how the nutrient uptake flux depends on environmental conditions. We show that, under suitable conditions, the Holling Type I functional response is a plausible model, as opposed to the Holling Type II (rectangular hyperbolic, ‘Michaelis–Menten’) response that is the default model in much of the literature. We investigate both diffusion-limited and capacity-limited regimes. Furthermore, we reconcile our findings with the preponderance in the established literature of hyperbolic models for the growth response, which are generally assumed to be valid, for both Gram-negative and Gram-positive bacteria. Finally, we consider the phenomenon of dynamic adjustment of investment of molecular building blocks in cellular components, and show how this will affect the functional response as observed by the experimenter

Optimal management of nutrient reserves in microorganisms under time-varying environmental conditions

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Intracellular reserves are a conspicuous feature of many bacteria; such internal stores are often present in the form of inclusions in which polymeric storage compounds are accumulated. Such reserves tend to increase in times of plenty and be used up in times of scarcity. Mathematical models that describe the dynamical nature of reserve build-up and use are known as “cell quota,” “dynamic energy/nutrient budget,” or “variable-internal-stores” models. Here we present a stoichiometrically consistent macro-chemical model that accounts for variable stores as well as adaptive allocation of building blocks to various types of catalytic machinery. The model posits feedback loops linking expression of assimilatory machinery to reserve density. The precise form of the “regulatory law” at the heart of such a loop expresses how the cell manages internal stores. We demonstrate how this “regulatory law” can be recovered from experimental data using several empirical data sets. We find that stores should be expected to be negligibly small in stable growth-sustaining environments, but prominent in environments characterised by marked fluctuations on time scales commensurate with the inherent dynamic time scale of the organismal system.OAN was funded through EU Research Framework programme 7 Marie Curie Actions, grant 316630 Centre for Analytical Science – Innovative Doctoral Programme (CAS-IDP)