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The discipline of Synthetic Biology has recently emerged at the interface of biology and engineering. The definition of Synthetic Biology has been dynamic over time ever since, which exemplifies that the field is rapidly moving and comprises a broad range of research areas. In the frame of this Research Topic, we focus on Synthetic Biology approaches that aim at rearranging biological parts/ entities in order to generate novel biochemical functions with inherent metabolic activity. This Research Topic encompasses Pathway Engineering in living systems as well as the in vitro assembly of biomolecules into nano- and microscale bioreactors. Both, the engineering of metabolic pathways in vivo, as well as the conceptualization of bioreactors in vitro, require rational design of assembled synthetic pathways and depend on careful selection of individual biological functions and their optimization. Mathematical modelling has proven to be a powerful tool in predicting metabolic flux in living and artificial systems, although modelling approaches have to cope with a limitation in experimentally verified, reliable input variables. This Research Topic puts special emphasis on the vital role of modelling approaches for Synthetic Biology, i.e. the predictive power of mathematical simulations for (i) the manipulation of existing pathways and (ii) the establishment of novel pathways in vivo as well as (iii) the translation of model predictions into the design of synthetic assemblies.

Metabolic Engineering --- reconstitution --- molecular dynamics simulations --- Membrane Transport Proteins --- Protein Engineering --- Protein scaffolds --- metabolite profiling --- Interaction domains --- Metabolic Modelling --- Starch biosynthesis

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The discipline of Synthetic Biology has recently emerged at the interface of biology and engineering. The definition of Synthetic Biology has been dynamic over time ever since, which exemplifies that the field is rapidly moving and comprises a broad range of research areas. In the frame of this Research Topic, we focus on Synthetic Biology approaches that aim at rearranging biological parts/ entities in order to generate novel biochemical functions with inherent metabolic activity. This Research Topic encompasses Pathway Engineering in living systems as well as the in vitro assembly of biomolecules into nano- and microscale bioreactors. Both, the engineering of metabolic pathways in vivo, as well as the conceptualization of bioreactors in vitro, require rational design of assembled synthetic pathways and depend on careful selection of individual biological functions and their optimization. Mathematical modelling has proven to be a powerful tool in predicting metabolic flux in living and artificial systems, although modelling approaches have to cope with a limitation in experimentally verified, reliable input variables. This Research Topic puts special emphasis on the vital role of modelling approaches for Synthetic Biology, i.e. the predictive power of mathematical simulations for (i) the manipulation of existing pathways and (ii) the establishment of novel pathways in vivo as well as (iii) the translation of model predictions into the design of synthetic assemblies.

Metabolic Engineering --- reconstitution --- molecular dynamics simulations --- Membrane Transport Proteins --- Protein Engineering --- Protein scaffolds --- metabolite profiling --- Interaction domains --- Metabolic Modelling --- Starch biosynthesis --- Metabolic Engineering --- reconstitution --- molecular dynamics simulations --- Membrane Transport Proteins --- Protein Engineering --- Protein scaffolds --- metabolite profiling --- Interaction domains --- Metabolic Modelling --- Starch biosynthesis

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Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections:•Reviews of Computational Methods•Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels•The Interface of Biotic and Abiotic Processes•Processing of Large Data Sets for Enhanced Analysis•Parameter Optimization and Measurement

n/a --- inosine --- immune checkpoint inhibitor --- geometric singular perturbation theory --- simulation --- BioModels Database --- ADAR --- calcium current --- bifurcation analysis --- bacterial biofilms --- nonlinear dynamics --- explanatory model --- turning point bifurcation --- oscillator --- workflow --- bioreactor integrated modeling --- modeling methods --- elementary flux modes visualization --- multiscale systems biology --- evolutionary algorithm --- metabolic model --- differential evolution --- reduced-order model --- computational model --- gut microbiota dysbiosis --- canard-induced EADs --- computational biology --- metabolic modelling --- methods --- SREBP-2 --- mechanistic model --- systems modeling --- biological networks --- macromolecular composition --- provenance --- flux balance analysis --- immunotherapy --- compartmental modeling --- immuno-oncology --- metabolic network visualization --- mechanism --- bistable switch --- Clostridium difficile infection --- bioreactor operation optimization --- microRNA targeting --- CFD simulation --- biomass reaction --- RNA editing --- ordinary differential equation --- metabolic modeling --- mass-action networks --- hybrid model --- multiple time scales --- quantitative systems pharmacology (QSP) --- mathematical modeling --- microRNA --- cancer --- parameter optimization --- Hopf bifurcation --- breast

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This book is a printed edition of the Special Issue Wine Fermentation that was published in Fermentation

peculiar yeasts --- red wine --- wine color --- non-targeted analysis --- volatile sulfur compounds --- phenolic content --- reductive off-odors --- Saccharomyces --- Saccharomyces bayanus --- partially dehydrated grapes --- elemental sulfur --- yield manipulation --- fermented drinks --- appassimento --- metabolomics --- yeast mixtures --- oenological enzymes --- metabolite profiling --- sulfur compounds --- cluster thinning --- winemaking --- yeast hybrids --- anthocyanins --- microwave-assisted extraction --- extraction --- color intensity --- spontaneous fermentation --- yeast --- extraction methods --- stuck and sluggish fermentation --- phenoloxidase --- process control --- non-Saccharomyces yeasts --- pioneering winemaking techniques --- reappearance --- Ontario --- wine --- Central Coast of California --- CFD --- classical chemical analysis --- color --- metabolic modelling --- temperature control --- wine clarification --- vine balance --- vineyard management --- protease --- crop load --- sensor placement --- Lachancea --- end-user software --- yeast physiology and metabolism --- microwave --- polymeric pigments --- polythionates as precursors --- grape maturity --- volatile acidity --- ultrasound --- glycosidase --- Pinot noir --- pectinase --- sensory --- climate change adaptation --- tannins --- aroma --- Merlot