Hybrid Prediction-Driven High-Throughput Sustainability Screening for Advancing Waste-to-Dimethyl Ether Valorization.

Assessing the prospective climate preservation potential of novel, innovative, but immature chemical production techniques is limited by the high number of process synthesis options and the lack of reliable, high-throughput quantitative sustainability pre-screening methods. This study presents the sequential use of data-driven hybrid prediction (ANN-RSM-DOM) to streamline waste-to-dimethyl ether (DME) upcycling using a set of sustainability criteria. Artificial neural networks (ANNs) are developed to generate in silico waste valorization experimental results and ex-ante model the operating space of biorefineries applying the organic fraction of municipal solid waste (OFMSW) and sewage sludge (SS). Aspen Plus process flowsheeting and ANN simulations are postprocessed using the response surface methodology (RSM) and desirability optimization method (DOM) to improve the in-depth mechanistic understanding of environmental systems and identify the most benign configurations. The hybrid prediction highlights the importance of targeted waste selection based on elemental composition and the need to design waste-specific DME synthesis to improve techno-economic and environmental performances. The developed framework reveals plant configurations with concurrent climate benefits (-1.241 and -2.128 kg CO2-eq (kg DME)-1) and low DME production costs (0.382 and 0.492 € (kg DME)-1) using OFMSW and SS feedstocks. Overall, the multi-scale explorative hybrid prediction facilitates early stage process synthesis, assists in the design of block units with nonlinear characteristics, resolves the simultaneous analysis of qualitative and quantitative variables, and enables the high-throughput sustainability screening of low technological readiness level processes.

Transition metal-free approach for late-stage benzylic C(sp3)-H etherifications and esterifications.

We report a transition metal-free approach for the regioselective functionalization of benzylic C(sp3)-H bonds using alcohols and carboxylic acids as the nucleophiles. This straightforward and general route has provided various benzylic ethers and esters, including twelve pharmaceutically relevant compounds.

Bioproduction of the Recombinant Sweet Protein Thaumatin: Current State of the Art and Perspectives.

There is currently a worldwide trend to reduce sugar consumption. This trend is mostly met by the use of artificial non-nutritive sweeteners. However, these sweeteners have also been proven to have adverse health effects such as dizziness, headaches, gastrointestinal issues, and mood changes for aspartame. One of the solutions lies in the commercialization of sweet proteins, which are not associated with adverse health effects. Of these proteins, thaumatin is one of the most studied and most promising alternatives for sugars and artificial sweeteners. Since the natural production of these proteins is often too expensive, biochemical production methods are currently under investigation. With these methods, recombinant DNA technology is used for the production of sweet proteins in a host organism. The most promising host known today is the methylotrophic yeast, Pichia pastoris. This yeast has a tightly regulated methanol-induced promotor, allowing a good control over the recombinant protein production. Great efforts have been undertaken for improving the yields and purities of thaumatin productions, but a further optimization is still desired. This review focuses on (i) the motivation for using and producing sweet proteins, (ii) the properties and history of thaumatin, (iii) the production of recombinant sweet proteins, and (iv) future possibilities for process optimization based on a systems biology approach.

Comparing design of experiments and optimal experimental design techniques for modelling the microbial growth rate under static environmental conditions.

Building secondary models that describe the growth rate as a function of multiple environmental conditions is often very labour intensive and costly. As such, the current research aims to assist in decreasing the required experimental effort by studying the efficacy of both design of experiments (DOE) and optimal experimental designs (OED) techniques. This is the first research in predictive microbiology (i) to make a comparison of these techniques based on the (relative) model prediction uncertainty of the obtained models and (ii) to compare OED criteria for the design of experiments with static (instead of dynamic) environmental conditions. A comparison of the DOE techniques demonstrated that the inscribed central composite design and full factorial design were most suitable. Five conventional and two tailor made OED criteria were tested. The commonly used D-criterion performed best out of the conventional designs and almost equally well as the best of the dedicated criteria. Moreover, the modelling results of the D-criterion were less dependent on the experimental variability and differences in the microbial response than the two selected DOE techniques. Finally, it was proven that solving the optimisation of the D-criterion can be made more efficient by considering the sensitivities of the growth rate relative to its value as Jacobian matrix instead of the sensitivities of the cell density measurements.

A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli.

Over the last decades, predictive microbiology has made significant advances in the mathematical description of microbial spoiler and pathogen dynamics in or on food products. Recently, the focus of predictive microbiology has shifted from a (semi-)empirical population-level approach towards mechanistic models including information about the intracellular metabolism in order to increase model accuracy and genericness. However, incorporation of this subpopulation-level information increases model complexity and, consequently, the required run time to simulate microbial cell and population dynamics. In this paper, results of metabolic flux balance analyses (FBA) with a genome-scale model are used to calibrate a low-complexity linear model describing the microbial growth and metabolite secretion rates of Escherichia coli as a function of the nutrient and oxygen uptake rate. Hence, the required information about the cellular metabolism (i.e., biomass growth and secretion of cell products) is selected and included in the linear model without incorporating the complete intracellular reaction network. However, the applied FBAs are only representative for microbial dynamics under specific extracellular conditions, viz., a neutral medium without weak acids at a temperature of 37℃. Deviations from these reference conditions lead to metabolic shifts and adjustments of the cellular nutrient uptake or maintenance requirements. This metabolic dependency on extracellular conditions has been taken into account in our low-complex metabolic model. In this way, a novel approach is developed to take the synergistic effects of temperature, pH, and undissociated acids on the cell metabolism into account. Consequently, the developed model is deployable as a tool to describe, predict and control E. coli dynamics in and on food products under various combinations of environmental conditions. To emphasize this point,three specific scenarios are elaborated: (i) aerobic respiration without production of weak acid extracellular metabolites, (ii) anaerobic fermentation with secretion of mixed acid fermentation products into the food environment, and (iii) respiro-fermentative metabolic regimes in between the behaviors at aerobic and anaerobic conditions.

A tutorial on uncertainty propagation techniques for predictive microbiology models: A critical analysis of state-of-the-art techniques.

Building mathematical models in predictive microbiology is a data driven science. As such, the experimental data (and its uncertainty) has an influence on the final predictions and even on the calculation of the model prediction uncertainty. Therefore, the current research studies the influence of both the parameter estimation and uncertainty propagation method on the calculation of the model prediction uncertainty. The study is intended as well as a tutorial to uncertainty propagation techniques for researchers in (predictive) microbiology. To this end, an in silico case study was applied in which the effect of temperature on the microbial growth rate was modelled and used to make simulations for a temperature profile that is characterised by variability. The comparison of the parameter estimation methods demonstrated that the one-step method yields more accurate and precise calculations of the model prediction uncertainty than the two-step method. Four uncertainty propagation methods were assessed. The current work assesses the applicability of these techniques by considering the effect of experimental uncertainty and model input uncertainty. The linear approximation was demonstrated not always to provide reliable results. The Monte Carlo method was computationally very intensive, compared to its competitors. Polynomial chaos expansion was computationally efficient and accurate but is relatively complex to implement. Finally, the sigma point method was preferred as it is (i) computationally efficient, (ii) robust with respect to experimental uncertainty and (iii) easily implemented.

Effect of chyme viscosity and nutrient feedback mechanism on gastric emptying.

A comprehensive mathematical model of the digestive processes in humans could allow for better design of functional foods which may play a role in stemming the prevalence of food related diseases around the world. This work presents a mathematical model for a nutrient based feedback mechanism controlling gastric emptying, which has been identified in vivo by numerous researchers. The model also takes into account the viscosity of nutrient meals upon gastric secretions and emptying. The results show that modelling the nutrient feedback mechanism as an on/off system, with an initial emptying rate dependent upon the secretion rate (which is a function of the gastric chyme viscosity) provides a good fit to the trends of emptying rate for liquid meals of low and high nutrient content with varying viscosity.

Identifiability of large-scale non-linear dynamic network models applied to the ADM1-case study.

In this work, both the structural and practical identifiability of the Anaerobic Digestion Model no. 1 (ADM1) is investigated, which serves as a relevant case study of large non-linear dynamic network models. The structural identifiability is investigated using the probabilistic algorithm, adapted to deal with the specifics of the case study (i.e., a large-scale non-linear dynamic system of differential and algebraic equations). The practical identifiability is analyzed using a Monte Carlo parameter estimation procedure for a 'non-informative' and 'informative' experiment, which are heuristically designed. The model structure of ADM1 has been modified by replacing parameters by parameter combinations, to provide a generally locally structurally identifiable version of ADM1. This means that in an idealized theoretical situation, the parameters can be estimated accurately. Furthermore, the generally positive structural identifiability results can be explained from the large number of interconnections between the states in the network structure. This interconnectivity, however, is also observed in the parameter estimates, making uncorrelated parameter estimations in practice difficult.

Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information.

Clustered microbial communities are omnipresent in the food industry, e.g., as colonies of microbial pathogens in/on food media or as biofilms on food processing surfaces. These clustered communities are often characterized by metabolic differentiation among their constituting cells as a result of heterogeneous environmental conditions in the cellular surroundings. This paper focuses on the role of metabolic differentiation due to oxygen gradients in the development of Escherichia coli cell communities, whereby low local oxygen concentrations lead to cellular secretion of weak acid products. For this reason, a metabolic model has been developed for the facultative anaerobe E. coli covering the range of aerobic, microaerobic, and anaerobic environmental conditions. This metabolic model is expressed as a multiparametric programming problem, in which the influence of low extracellular pH values and the presence of undissociated acid cell products in the environment has been taken into account. Furthermore, the developed metabolic model is incorporated in MICRODIMS, an in-house developed individual-based modeling framework to simulate microbial colony and biofilm dynamics. Two case studies have been elaborated using the MICRODIMS simulator: (i) biofilm growth on a substratum surface and (ii) submerged colony growth in a semi-solid mixed food product. In the first case study, the acidification of the biofilm environment and the emergence of typical biofilm morphologies have been observed, such as the mushroom-shaped structure of mature biofilms and the formation of cellular chains at the exterior surface of the biofilm. The simulations show that these morphological phenomena are respectively dependent on the initial affinity of pioneer cells for the substratum surface and the cell detachment process at the outer surface of the biofilm. In the second case study, a no-growth zone emerges in the colony center due to a local decline of the environmental pH. As a result, cellular growth in the submerged colony is limited to the colony periphery, implying a linear increase of the colony radius over time. MICRODIMS has been successfully used to reproduce complex dynamics of clustered microbial communities.

Dynamic optimization of biological networks under parametric uncertainty.

BACKGROUND: Micro-organisms play an important role in various industrial sectors (including biochemical, food and pharmaceutical industries). A profound insight in the biochemical reactions inside micro-organisms enables an improved biochemical process control. Biological networks are an important tool in systems biology for incorporating microscopic level knowledge. Biochemical processes are typically dynamic and the cells have often more than one objective which are typically conflicting, e.g., minimizing the energy consumption while maximizing the production of a specific metabolite. Therefore multi-objective optimization is needed to compute trade-offs between those conflicting objectives. In model-based optimization, one of the inherent problems is the presence of uncertainty. In biological processes, this uncertainty can be present due to, e.g., inherent biological variability. Not taking this uncertainty into account, possibly leads to the violation of constraints and erroneous estimates of the actual objective function(s). To account for the variance in model predictions and compute a prediction interval, this uncertainty should be taken into account during process optimization. This leads to a challenging optimization problem under uncertainty, which requires a robustified solution. RESULTS: Three techniques for uncertainty propagation: linearization, sigma points and polynomial chaos expansion, are compared for the dynamic optimization of biological networks under parametric uncertainty. These approaches are compared in two case studies: (i) a three-step linear pathway model in which the accumulation of intermediate metabolites has to be minimized and (ii) a glycolysis inspired network model in which a multi-objective optimization problem is considered, being the minimization of the enzymatic cost and the minimization of the end time before reaching a minimum extracellular metabolite concentration. A Monte Carlo simulation procedure has been applied for the assessment of the constraint violations. For the multi-objective case study one Pareto point has been considered for the assessment of the constraint violations. However, this analysis can be performed for any Pareto point. CONCLUSIONS: The different uncertainty propagation strategies each offer a robustified solution under parametric uncertainty. When making the trade-off between computation time and the robustness of the obtained profiles, the sigma points and polynomial chaos expansion strategies score better in reducing the percentage of constraint violations. This has been investigated for a normal and a uniform parametric uncertainty distribution. The polynomial chaos expansion approach allows to directly take prior knowledge of the parametric uncertainty distribution into account.