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Despite our continuous improvement in understanding antibiotic resistance, the interplay between natural selection of resistance mutations and the environment remains unclear. To investigate the role of bacterial metabolism in constraining the evolution of antibiotic resistance, we evolved Escherichia coli growing on glycolytic or gluconeogenic carbon sources to the selective pressure of three different antibiotics. Profiling more than 500 intracellular and extracellular putative metabolites in 190 evolved populations revealed that carbon and energy metabolism strongly constrained the evolutionary trajectories, both in terms of speed and mode of resistance acquisition. To interpret and explore the space of metabolome changes, we developed a novel constraint‐based modeling approach using the concept of shadow prices. This analysis, together with genome resequencing of resistant populations, identified condition‐dependent compensatory mechanisms of antibiotic resistance, such as the shift from respiratory to fermentative metabolism of glucose upon overexpression of efflux pumps. Moreover, metabolome‐based predictions revealed emerging weaknesses in resistant strains, such as the hypersensitivity to fosfomycin of ampicillin‐resistant strains. Overall, resolving metabolic adaptation throughout antibiotic‐driven evolutionary trajectories opens new perspectives in the fight against emerging antibiotic resistance. Synopsis Bacterial metabolism constrains the evolution of antibiotic resistance. A modeling approach is developed to interpret the functionality of metabolic rewiring in resistance‐evolving E. coli growing on glycolytic or gluconeogenic carbon sources from metabolomics data. Large‐scale untargeted metabolome profiling reveals metabolic adaptations in 190 evolved antibiotic‐resistant E. coli populations, in part as compensation for consequences of the primary resistance mechanisms. Carbon and energy metabolism strongly constrain the evolutionary trajectories, both in terms of speed and mode of resistance acquisition. A novel constraint‐based modeling approach, together with genome re‐sequencing of resistant populations, identifies condition‐dependent compensatory mechanisms. Graphical Abstract Bacterial metabolism constrains the evolution of antibiotic resistance. A modeling approach is developed to interpret the functionality of metabolic rewiring in resistance‐evolving E. coli growing on glycolytic or gluconeogenic carbon sources from metabolomics data.

A novel trajectory tracking control problem based on constraint modeling and analysis is addressed by the way of constraint-following control for the unmanned tracked vehicle in this paper. The unmanned tracked vehicle system contains time-varying uncertainty which is possibly swift but bounded, and the bound is possibly unknown. First, the coupled dynamics model of unmanned tracked vehicle is established. By taking into account the kinematic characteristics, it makes the motion control of unmanned tracked vehicles more precise. Meanwhile, a 3D virtual prototype model is established for the unmanned tracked vehicle. Second, for the control objective of trajectory tracking, the related problem is converted into a constraint-following problem, and an adaptive robust controller is therefore proposed based on this for the controlled unmanned tracked vehicle system to satisfy the trajectory tracking constraint. Finally, it is proved that the controlled unmanned tracked vehicle system can achieve accurate trajectory tracking with the proposed adaptive robust control, even under the interference of complex time-varying uncertainties. Modeling accurate dynamics and trajectory tracking constraints for unmanned tracked vehicles while designing an adaptive robust controller to realize accurate motion control for unmanned tracked vehicles even under strong external disturbances are the main contributions of this paper.

Production of biofuels and bioenergy precursors by phototrophic microorganisms, such as microalgae and cyanobacteria, is a promising alternative to conventional fuels obtained from non-renewable resources. Several species of microalgae have been investigated as potential candidates for the production of biofuels, for the most part due to their exceptional metabolic capability to accumulate large quantities of lipids. Constraint-based modeling, a systems biology approach that accurately predicts the metabolic phenotype of phototrophs, has been deployed to identify suitable culture conditions as well as to explore genetic enhancement strategies for bioproduction. Core metabolic models were employed to gain insight into the central carbon metabolism in photosynthetic microorganisms. More recently, comprehensive genome-scale models, including organelle-specific information at high resolution, have been developed to gain new insight into the metabolism of phototrophic cell factories. Here, we review the current state of the art of constraint-based modeling and computational method development and discuss how advanced models led to increased prediction accuracy and thus improved lipid production in microalgae.

Background The growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical compounds and even eliminate it in the evaluation of cosmetics, highlights the need for adequate computational methodologies. Data from omics technologies allow the exploration of a wide range of biological processes, therefore providing a better understanding of mechanisms of action (MoA) related to chemical exposure in biological systems. However, the analysis of these large datasets remains difficult due to the complexity of modulations spanning multiple biological processes. Results To address this, we propose a strategy to reduce information overload by computing, based on transcriptomics data, a comprehensive metabolic sub-network reflecting the metabolic impact of a chemical. The proposed strategy integrates transcriptomic data to a genome scale metabolic network through enumeration of condition-specific metabolic models hence translating transcriptomics data into reaction activity probabilities. Based on these results, a graph algorithm is applied to retrieve user readable sub-networks reflecting the possible metabolic MoA (mMoA) of chemicals. This strategy has been implemented as a three-step workflow. The first step consists in building cell condition-specific models reflecting the metabolic impact of each exposure condition while taking into account the diversity of possible optimal solutions with a partial enumeration algorithm. In a second step, we address the challenge of analyzing thousands of enumerated condition-specific networks by computing differentially activated reactions (DARs) between the two sets of enumerated possible condition-specific models. Finally, in the third step, DARs are grouped into clusters of functionally interconnected metabolic reactions, representing possible mMoA, using the distance-based clustering and subnetwork extraction method. The first part of the workflow was exemplified on eight molecules selected for their known human hepatotoxic outcomes associated with specific MoAs well described in the literature and for which we retrieved primary human hepatocytes transcriptomic data in Open TG-GATEs. Then, we further applied this strategy to more precisely model and visualize associated mMoA for two of these eight molecules (amiodarone and valproic acid). The approach proved to go beyond gene-based analysis by identifying mMoA when few genes are significantly differentially expressed (2 differentially expressed genes (DEGs) for amiodarone), bringing additional information from the network topology, or when very large number of genes were differentially expressed (5709 DEGs for valproic acid). In both cases, the results of our strategy well fitted evidence from the literature regarding known MoA. Beyond these confirmations, the workflow highlighted potential other unexplored mMoA. Conclusion The proposed strategy allows toxicology experts to decipher which part of cellular metabolism is expected to be affected by the exposition to a given chemical. The approach originality resides in the combination of different metabolic modelling approaches (constraint based and graph modelling). The application to two model molecules shows the strong potential of the approach for interpretation and visual mining of complex omics in vitro data. The presented strategy is freely available as a python module ( https://pypi.org/project/manamodeller/ ) and jupyter notebooks ( https://github.com/LouisonF/MANA ).

Constraints, although ubiquitous in production and distribution planning, scheduling and control, often lead to inconsistencies in the decision-making process. The constraint-based modeling helps circumvent many organization-impacting issues. To address this, we developed a multi-level approach to the modeling and solving of combinatorial optimization problems. It is versatile and effective owing to the use of multi-level presolving and multiple paradigms, such as constraint programming, logic programming, mathematical programming and fuzzy logic, for their complementary strengths. The capability of this framework and its advantage over mathematical programming alone or over hybrid frameworks is shown in the illustrative example, in which combinatorial optimization is used as a benchmark to prove the effectiveness of the proposed approach. Knowledge of the problem is stored in the form of facts.

ObjectiveChinese hamster ovary (CHO) cells are the leading cell factories for producing recombinant proteins in the biopharmaceutical industry. In this regard, constraint-based metabolic models are useful platforms to perform computational analysis of cell metabolism. These models need to be regularly updated in order to include the latest biochemical data of the cells, and to increase their predictive power. Here, we provide an update to iCHO1766, the metabolic model of CHO cells.ResultsWe expanded the existing model of Chinese hamster metabolism with the help of four gap-filling approaches, leading to the addition of 773 new reactions and 335 new genes. We incorporated these into an updated genome-scale metabolic network model of CHO cells, named iCHO2101. In this updated model, the number of reactions and pathways capable of carrying flux is substantially increased.ConclusionsThe present CHO model is an important step towards more complete metabolic models of CHO cells.

Anthocyanin biosynthesis is regulated by environmental factors (such as light, temperature, and water availability) and nutrient status (such as carbon, nitrogen, and phosphate nutrition). Previous reports show that low nitrogen availability strongly enhances anthocyanin accumulation in non carbon-limited plant organs or cell suspensions. It has been hypothesized that high carbon-to-nitrogen ratio would lead to an energy excess in plant cells, and that an increase in flavonoid pathway metabolic fluxes would act as an \"energy escape valve,\" helping plant cells to cope with energy and carbon excess. However, this hypothesis has never been tested directly. To this end, we used the grapevine L. cultivar Gamay Teinturier (syn. Gamay Freaux or Freaux Tintorier, VIVC #4382) cell suspension line as a model system to study the regulation of anthocyanin accumulation in response to nitrogen supply. The cells were sub-cultured in the presence of either control (25 mM) or low (5 mM) nitrate concentration. Targeted metabolomics and enzyme activity determinations were used to parametrize a constraint-based model describing both the central carbon and nitrogen metabolisms and the flavonoid (phenylpropanoid) pathway connected by the energy (ATP) and reducing power equivalents (NADPH and NADH) cofactors. The flux analysis (2 flux maps generated, for control and low nitrogen in culture medium) clearly showed that in low nitrogen-fed cells all the metabolic fluxes of central metabolism were decreased, whereas fluxes that consume energy and reducing power, were either increased (upper part of glycolysis, shikimate, and flavonoid pathway) or maintained (pentose phosphate pathway). Also, fluxes of flavanone 3β-hydroxylase, flavonol synthase, and anthocyanidin synthase were strongly increased, advocating for a regulation of the flavonoid pathway by alpha-ketoglutarate levels. These results strongly support the hypothesis of anthocyanin biosynthesis acting as an energy escape valve in plant cells, and they open new possibilities to manipulate flavonoid production in plant cells. They do not, however, support a role of anthocyanins as an effective mechanism for coping with carbon excess in high carbon to nitrogen ratio situations in grape cells. Instead, constraint-based modeling output and biomass analysis indicate that carbon excess is dealt with by vacuolar storage of soluble sugars.

Hospital internships are the most essential and important component of any medical training to acquire and develop different clinical skills. The main management issue related to this point is the allocation of internship students to different services undergoing several logistical and pedagogical constraints during the hospital university calendar. In this paper, we show how we can use Constraint Programming design to model and solve this problem through the Constraint Satisfaction Problems ( CSP ). Then, we propose an extended model (Constraint Optimization model) to cover the limitations of the CSP model and find the optimal scheduling taking in account students’ preferences. Finally, we show that using several What-If scenarios can help to suggest and recommend to decision makers some adjustments to the problem inner rules to get the optimal solution.

In the medium- and long-term electricity market, uncertain power output, and power load will lead to the deviation between the actual generation and the signed medium- and long-term contract electricity. In order to reduce the system deviation balance cost and ensure the balance of power supply and demand, it is necessary to find a suitable dispatch method. First, a monthly electricity decomposition model of thermal power units is proposed in this paper. After that, we propose a power dispatching model under the constraint of deviated electricity quantity to minimize the cost of electricity deviation. The simulation results of numerical examples show that the proposed dispatching model and method can effectively reduce the monthly contract power deviation and the balance cost.

The standard model of particle physics 1 – 4 describes the known fundamental particles and forces that make up our Universe, with the exception of gravity. One of the central features of the standard model is a field that permeates all of space and interacts with fundamental particles 5 – 9 . The quantum excitation of this field, known as the Higgs field, manifests itself as the Higgs boson, the only fundamental particle with no spin. In 2012, a particle with properties consistent with the Higgs boson of the standard model was observed by the ATLAS and CMS experiments at the Large Hadron Collider at CERN 10 , 11 . Since then, more than 30 times as many Higgs bosons have been recorded by the ATLAS experiment, enabling much more precise measurements and new tests of the theory. Here, on the basis of this larger dataset, we combine an unprecedented number of production and decay processes of the Higgs boson to scrutinize its interactions with elementary particles. Interactions with gluons, photons, and W and Z bosons—the carriers of the strong, electromagnetic and weak forces—are studied in detail. Interactions with three third-generation matter particles (bottom ( b ) and top ( t ) quarks, and tau leptons ( τ )) are well measured and indications of interactions with a second-generation particle (muons, μ ) are emerging. These tests reveal that the Higgs boson discovered ten years ago is remarkably consistent with the predictions of the theory and provide stringent constraints on many models of new phenomena beyond the standard model. Ten years after the discovery of the Higgs boson, the ATLAS  experiment at CERN probes its kinematic properties with a significantly larger dataset from 2015–2018 and provides further insights on its interaction with other known particles.