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)

Erratum to: 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. The online version of the original article can be found under doi: 10.1007/s00285-016-1030-4In the original publication of the article the symbol Phi ‘φ’ should be changed to symbol Psi ‘φ’in Table 1 under the section “Unscaled stoichiometric coefficients”,line 2, column 1.The original article has been updated to reflect the above change

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)

Real-time enzyme dynamics illustrated with fluorescence spectroscopy of p-Hydroxybenzoate Hydroxylase.

We have used the flavoenzyme p-hydroxybenzoate hydroxylase (PHBH) to illustrate that a strongly fluorescent donor label can communicate with the flavin via single-pair Forster resonance energy transfer (spFRET). The accessible Cys-116 of PHBH was labeled with two different fluorescent maleimides with full preservation of enzymatic activity. One of these labels shows overlap between its fluorescence spectrum and the absorption spectrum of the FAD prosthetic group in the oxidized state, while the other fluorescent probe does not have this spectral overlap. The spectral overlap strongly diminished when the flavin becomes reduced during catalysis. The donor fluorescence properties can then be used as a sensitive antenna for the flavin redox state. Time-resolved fluorescence experiments on ensembles of labeled PHBH molecules were carried out in the absence and presence of enzymatic turnover. Distinct changes in fluorescence decays of spFRET-active PHBH can be observed when the enzyme is performing catalysis using both substrates p-hydroxybenzoate and NADPH. Single-molecule fluorescence correlation spectroscopy on spFRET-active PHBH showed the presence of a relaxation process (relaxation time of 23 mus) that is related to catalysis. In addition, in both labeled PHBH preparations the number of enzyme molecules reversibly increased during enzymatic turnover indicating that the dimer-monomer equilibrium is affected

Simplivariate Models: Ideas and First Examples

One of the new expanding areas in functional genomics is metabolomics: measuring the metabolome of an organism. Data being generated in metabolomics studies are very diverse in nature depending on the design underlying the experiment. Traditionally, variation in measurements is conceptually broken down in systematic variation and noise where the latter contains, e.g. technical variation. There is increasing evidence that this distinction does not hold (or is too simple) for metabolomics data. A more useful distinction is in terms of informative and non-informative variation where informative relates to the problem being studied. In most common methods for analyzing metabolomics (or any other high-dimensional x-omics) data this distinction is ignored thereby severely hampering the results of the analysis. This leads to poorly interpretable models and may even obscure the relevant biological information. We developed a framework from first data analysis principles by explicitly formulating the problem of analyzing metabolomics data in terms of informative and non-informative parts. This framework allows for flexible interactions with the biologists involved in formulating prior knowledge of underlying structures. The basic idea is that the informative parts of the complex metabolomics data are approximated by simple components with a biological meaning, e.g. in terms of metabolic pathways or their regulation. Hence, we termed the framework ‘simplivariate models’ which constitutes a new way of looking at metabolomics data. The framework is given in its full generality and exemplified with two methods, IDR analysis and plaid modeling, that fit into the framework. Using this strategy of ‘divide and conquer’, we show that meaningful simplivariate models can be obtained using a real-life microbial metabolomics data set. For instance, one of the simple components contained all the measured intermediates of the Krebs cycle of E. coli. Moreover, these simplivariate models were able to uncover regulatory mechanisms present in the phenylalanine biosynthesis route of E. coli

Depletion of homeostatic antibodies against malondialdehyde-modified low-density lipoprotein correlates with adverse events in major vascular surgery

We aimed to investigate if major vascular surgery induces LDL oxidation, and whether circulating antibodies against malondialdehyde-modified LDL (MDA-LDL) alter dynamically in this setting. We also questioned relationships between these biomarkers and post-operative cardiovascular events. Major surgery can induce an oxidative stress response. However, the role of the humoral immune system in clearance of oxidized LDL following such an insult is unknown. Plasma samples were obtained from a prospective cohort of 131 patients undergoing major non-cardiac vascular surgery, with samples obtained preoperatively and at 24- and 72 h postoperatively. Enzyme-linked immunoassays were developed to assess MDA-LDL-related antibodies and complexes. Adverse events were myocardial infarction (primary outcome), and a composite of unstable angina, stroke and all-cause mortality (secondary outcome). MDA-LDL significantly increased at 24 h post-operatively (p < 0.0001). Conversely, levels of IgG and IgM anti-MDA-LDL, as well as IgG/IgM-MDA-LDL complexes and total IgG/IgM, were significantly lower at 24 h (each p < 0.0001). A smaller decrease in IgG anti-MDA-LDL related to combined clinical adverse events in a post hoc analysis, withstanding adjustment for age, sex, and total IgG (OR 0.13, 95% CI [0.03–0.5], p < 0.001; p value for trend <0.001). Major vascular surgery resulted in an increase in plasma MDA-LDL, in parallel with a decrease in antibody/complex levels, likely due to antibody binding and subsequent removal from the circulation. Our study provides novel insight into the role of the immune system during the oxidative stress of major surgery, and suggests a homeostatic clearance role for IgG antibodies, with greater reduction relating to downstream adverse events

Magnetism in reduced dimensions

We propose a short overview of a few selected issues of magnetism in reduced dimensions, which are the most relevant to set the background for more specialized contributions to the present Special Issue. Magnetic anisotropy in reduced dimensions is discussed, on a theoretical basis, then with experimental reports and views from surface to single-atom anisotropy. Then conventional magnetization states are reviewed, including macrospins, single domains, multidomains, and domain walls in stripes. Dipolar coupling is examined for lateral interactions in arrays, and for interlayer interactions in films and dots. Finally thermally-assisted magnetization reversal and superparamagnetism are presented. For each topic we sought a balance between well established knowledge and recent developments.Comment: 13 pages. Part of a Special Issue of the C. R. Physique devoted to spinelectronics (2005

Electrical control over single hole spins in nanowire quantum dots

Single electron spins in semiconductor quantum dots (QDs) are a versatile platform for quantum information processing, however controlling decoherence remains a considerable challenge. Recently, hole spins have emerged as a promising alternative. Holes in III-V semiconductors have unique properties, such as strong spin-orbit interaction and weak coupling to nuclear spins, and therefore have potential for enhanced spin control and longer coherence times. Weaker hyperfine interaction has already been reported in self-assembled quantum dots using quantum optics techniques. However, challenging fabrication has so far kept the promise of hole-spin-based electronic devices out of reach in conventional III-V heterostructures. Here, we report gate-tuneable hole quantum dots formed in InSb nanowires. Using these devices we demonstrate Pauli spin blockade and electrical control of single hole spins. The devices are fully tuneable between hole and electron QDs, enabling direct comparison between the hyperfine interaction strengths, g-factors and spin blockade anisotropies in the two regimes