Rising demands for biopharmaceuticals and the need to reduce manufacturing costs increase the pressure to develop productive and efficient bioprocesses. Among others, a major hurdle during process development and optimization studies is the huge experimental effort in conventional design of experiments (DoE) methods. As being an explorative approach, DoE requires extensive expert knowledge about the investigated factors and their boundary values and often leads to multiple rounds of time-consuming and costly experiments. The combination of DoE with a virtual representation of the bioprocess, called digital twin, in model-assisted DoE (mDoE) can be used as an alternative to decrease the number of experiments significantly. mDoE enables a knowledge-driven bioprocess development including the definition of a mathematical process model in the early development stages. In this chapter, digital twins and their role in mDoE are discussed. First, statistical DoE methods are introduced as the basis of mDoE. Second, the combination of a mathematical process model and DoE into mDoE is examined. This includes mathematical model structures and a selection scheme for the choice of DoE designs. Finally, the application of mDoE is discussed in a case study for the medium optimization in an antibody-producing Chinese hamster ovary cell culture process.

Living organisms have been exploited as production hosts for a large variety of compounds. To improve the efficiency of bioproduction, metabolic pathways in an organism are usually manipulated by various genetic modifications. However, bottlenecks during the conversion of substrate to a desired product may result from cellular regulations at different levels. Dynamic regulation of metabolic pathways according to the need of cultivation process is therefore essential for developing effective bioprocesses, but represents a major challenge in metabolic engineering and synthetic biology. To this end, switchable biomolecules which can sense the intracellular concentrations of metabolites with different response types and dynamic ranges are of great interest. This chapter summarizes recent progress in the development of biomolecular switches and their applications for improvement of bioproduction via dynamic control of metabolic fluxes. Further studies of bioswitches and their applications in industrial strain development are also discussed.

This chapter summarizes in the beginning our current understanding of extracellular electron transport processes in organisms belonging to the genera Shewanella and Geobacter. Organisms belonging to these genera developed strategies to transport respiratory electrons to the cell surface that are defined by modules of which some seem to be rather unique for one or the other genus while others are similar. We use this overview regarding our current knowledge of extracellular electron transfer to explain the physiological interaction of microorganisms in direct interspecies electron transfer, a process in which one organism basically comprises the electron acceptor for another microbe and that depends also on extended electron transport chains. This analysis of mechanisms for the transport of respiratory electrons to insoluble electron acceptors ends with an overview of questions that remain so far unanswered. Moreover, we use the description of the biochemistry of extracellular electron transport to explain the fundamentals of biosensors based on this process and give an overview regarding their status of development and applicability.

Diols are compounds with two hydroxyl groups and have a wide range of appealing applications as chemicals and fuels. In particular, five low molecular diol compounds, namely 1,3-propanediol (1,3-PDO), 1,2-propanediol (1,2-PDO), 2,3-butanediol (2,3-BDO), 1,3-butanediol (1,3-BDO), and 1,4-butanediol (1,4-BDO), can be biotechnologically produced by direct microbial bioconversion of renewable materials. In this review, we summarize recent developments in the microbial production of diols, especially regarding the engineering of typical microbial strains as cell factory and the development of corresponding bioconversion processes.

In recent years, protein and peptide-based hydrogels have received great attention for applications in biomedicine. Compared to hydrogels based on synthetic materials, they have the decisive advantages of being biological origin, providing cells with a more in vivo-like microenvironment and possessing potential biological activity. Empowered by the steadily deepened understanding of the sequence-structure-function relationship of natural proteins and the rapid development of molecular-biological tools for accurate protein sequence editing, researchers have developed a series of recombinant proteins as building blocks and responsive blocks to design novel functional hydrogels. The use of multi-block design further expands the customizability of protein hydrogels. With the improvement of standardization of preparation and testing methods, protein hydrogels are expected to be widely used in medical treatment, skin care, artificial organs and wearable electronic devices. More recently, the emergence of catalytically active protein hydrogel brings new opportunities for applications of protein hydrogels. It is believed that through integrated approaches of engineering biology and materials sciences novel and hereto unthinkable protein hydrogels and properties may be generated for applications in areas beyond medicine and health, including biotechnology, food and agriculture, and even energy.