Stefan Hennig

Artificial cell-cell communication as an emerging tool in synthetic biology applications

Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication modes offer the possibility to control the behavior of an entire community by modifying the performance of individual cells in specific ways. Synthetic biology, i.e., the implementation of artificial functions within biological systems, is a promising approach towards the engineering of sophisticated, autonomous devices based on specifically functionalized cells. With the growing complexity of the functions performed by such systems, both the risk of circuit crosstalk and the metabolic burden resulting from the expression of numerous foreign genes are increasing. Therefore, systems based on a single type of cells are no longer feasible. Synthetic biology approaches with multiple subpopulations of specifically functionalized cells, wired by artificial cell-cell communication systems, provide an attractive and powerful alternative. Here we review recent applications of synthetic cell-cell communication systems with a specific focus on recent advances with fungal hosts.

Evaluation of OPC UA secure communication in web browser applications

OPC UA XML Web services mapping offers a Web service interface to access process data. Web services use XML technology for data exchange. Present-day Web browsers include XML functionality already as a standard feature, they are therefore very promising candidates for the implementation of monitoring and operating functions for industrial processes. However, the acceptance of Web services in industrial automation depends on adequate security realizations. For this purpose, the Web services security stack provides several specifications to meet the requirements for secure message exchange. The OPC UA XML Web services mapping refers to these specifications. The application of Web browsers for monitoring and operating of technical processes using OPC UA Web services demand the computation of cryptographic algorithms within the scripting engine of the Web browser. However, available scripting languages are not designed to compute complex mathematical, i.e., cryptographic, algorithms. Therefore, at the Institute of Automation of the Technische Universitat Dresden the suitability of a native Web browser for monitoring and operating of industrial processes with OPC UA based secure communication was analyzed. The paper shows representative measured computing times of cryptographic algorithms in JavaScript. The security specification XML signature - which is mandatory for OPC UA Web services mapping - requires about 700 ms to create a signature. Finally, the paper discusses methods to improve the performance.

Towards context adaptive HMIs in process industries

This paper presents the combination of two distinct model driven HMI engineering approaches. Together they setup a complete toolchain that lays the basis for the model driven (semi)automatic generation of flexible, multi-platform HMIs for process industries. The two approaches are autoHMI which derives a concrete UI design from Computer Aided Engineering Data, and XVCML which allows to generate final UIs for different web implementation paradigms like XHTML or Java on top of OPC UA. This tool integration provides a complete model driven software engineering architecture that cuts down the manual efforts in HMI engineering close to zero. This is a prerequisite to handle the complexity of context adaptive interfaces.

A yeast pheromone-based inter-species communication system

We report on a pheromone-based inter-species communication system, allowing for a controlled cell-cell communication between the two species Saccharomyces cerevisiae and Schizosaccharomyces pombe as a proof of principle. It exploits the mating response pathways of the two yeast species employing the pheromones, α- or P-factor, as signaling molecules. The authentic and chimeric pheromone-encoding genes were engineered to code for the P-factor in S. cerevisiae and the α-factor in S. pombe. Upon transformation of the respective constructs, cells were enabled to express the mating pheromone of the opposite species. The supernatant of cultures of S. pombe cells expressing α-factor were able to induce a G1 arrest in the cell cycle, a change in morphology to the typical shmoo effect and expression driven by the pheromone-responsive FIG1 promoter in S. cerevisiae. The supernatant of cultures of S. cerevisiae cells expressing P-factor similarly induced cell cycle arrest in G1, an alteration in morphology typical for mating as well as the activation of the pheromone-responsive promoters of the rep1 and sxa2 genes in a pheromone-hypersensitive reporter strain of S. pombe. Apparently, both heterologous pheromones were correctly processed and secreted in an active form by the cells of the other species. Our data clearly show that the species-specific pheromone systems of yeast species can be exploited for a controlled inter-species communication.

Sustainable visualization solutions in industrial automation with Movisa — A case study

Current visualization systems in industrial automation mostly rely on dedicated runtime environments making the migration of visualization solutions from one platform to another almost impossible. On the other hand, an increasing number of different platforms has to be used also in industrial automation, to monitor or to operate the technical process. We propose with Movisa a model-driven approach to the development of sustainable visualization solutions in industrial automation. Movisa is a Domain Specific Language designed to capture only functional contents of visualization solutions. This paper presents Movisa by introducing its main concepts in a case study. It will also point out the potential of model-driven approaches concerning the sustainability of visualization solution in industrial automation.

Hydrophobin-Based Surface Engineering for Sensitive and Robust Quantification of Yeast Pheromones

Detection and quantification of small peptides, such as yeast pheromones, are often challenging. We developed a highly sensitive and robust affinity-assay for the quantification of the α-factor pheromone of Saccharomyces cerevisiae based on recombinant hydrophobins. These small, amphipathic proteins self-assemble into highly stable monolayers at hydrophilic-hydrophobic interfaces. Upon functionalization of solid supports with a combination of hydrophobins either lacking or exposing the α-factor, pheromone-specific antibodies were bound to the surface. Increasing concentrations of the pheromone competitively detached the antibodies, thus allowing for quantification of the pheromone. By adjusting the percentage of pheromone-exposing hydrophobins, the sensitivity of the assay could be precisely predefined. The assay proved to be highly robust against changes in sample matrix composition. Due to the high stability of hydrophobin layers, the functionalized surfaces could be repeatedly used without affecting the sensitivity. Furthermore, by using an inverse setup, the sensitivity was increased by three orders of magnitude, yielding a novel kind of biosensor for the yeast pheromone with the lowest limit of detection reported so far. This assay was applied to study the pheromone secretion of diverse yeast strains including a whole-cell biosensor strain of Schizosaccharomyces pombe modulating α-factor secretion in response to an environmental signal.

User driven evolution of user interface models - The FLEPR approach

In model-based user interface development, models at different levels of abstraction are used. While ideas may initially only be expressed in more abstract models, modifications and improvements according to users feedback will likely be made at the concrete level, which may lead to model inconsistencies that need to be fixed in every iteration. Transformations form the bridge between these models. Because one-to-one mappings between models cannot always be defined, these transformations are completely manual or they require manual post-treatment. We propose interactive but automatic transformations to address the mapping problem while still allowing designers creativity. To manage consistency and semantic correctness within and between models and therefore to foster iterative development processes, we are combining these with techniques to track decisions and modifications and techniques of intra- and inter-model validation. Our approach has been implemented for abstract and concrete user interface models using Eclipse-based frameworks for model-driven engineering. Our approach and tool support is illustrated by a case study.

Using Executable UML to model algorithmic aspects of visualization systems

The XML based modeling language of graphical user interfaces for visualization systems in automation, XVCML, has been developed to ensure the consistency of visualization solutions in the fast-moving field of consumer technology. Until now, it only provides modeling elements for visualization of real time process data and the necessary communication relationships with data servers. In order to be accepted in practice, XVCML also needs modeling components for additional, user defined algorithms. This paper presents an approach to enhance XVCML with generic, algorithmic components to perform e.g. simple algebraic operations. For this purpose, Executable UML has been used and proven to be suitable. Therefore, Executable UML will be introduced and first experiences will be shown by an early prototype which realizes a typical scenario of industrial automation.

Towards a model driven approach for development of visualization applications in industrial automation

The eXtensible Visualization Components Markup Language (XVCML) was developed in order to ensure the sustainability of visualization solutions. Therefore, XVCML follows the Model-Driven Software Development (MDSD) approach: It enables technology independent modeling of visualization solutions whereas those models are compliant to a formal metamodel. XVCML was enhanced by a mean to express arbitrary routines using Executable UML. Since we realized the latter aspect only as a first proof of concept, this part of XVCML lacks a formal metamodel—a requirement for MDSD. This paper seizes on this topic so much that a Domain Specific Language, which enables the creation of Executable UML models, will be worked out in the context of MDSD. Therefore, this paper explains the required foundations for the subject matter at hand before it presents the way of proceeding towards a model-driven approach with XVCML.

Modelltransformationen in nutzer-zentrierten Entwurfsprozessen der Automation

Zusammenfassung Die Zusammenführung modellbasierter und nutzerzentrierter Entwurfsprozesse bei der Entwicklung von Benutzungsschnittstellen kann die Gebrauchstauglichkeit der resultierenden Benutzungsschnittstellen verbessern. Aus der Kombination der Entwurfsprozesse erwachsen Anforderungen an die notwendigen Modelltransformationen. Als zentrale Herausforderung wird in diesem Beitrag die Überwindung der Abstraktionslücke zwischen abstrakten und konkreten Modellen betrachtet. Anhand einer Transformation innerhalb des nutzerzentrierten Entwicklungsprozesses der Useware zur Integration einer domänenspezifischen Sprache der Automatisierungstechnik, werden die Herausforderungen der Modelltransformationen analysiert und mit den Mitteln der modellgetriebenen Software-Entwicklung gelöst. Weiterhin wird die Unterstützung von iterativem Vorgehen in modellbasierten Entwicklungsprozessen untersucht und als Lösung das Persistant Transformation Mapping vorgeschlagen. Abstract Joining model-based and user-centered design processes for the development of user interfaces can improve the usability of the resulting user interfaces. Due to the combination of the design processes challenges arise for the necessary model transformations. Bridging the abstraction gap between abstract and concrete models is the key challenge that is addressed by this paper. By example of a transformation within the user-centered development process to integrate a domainspecific language of the automation challenges are analyzed and solved by means of the model-driven software development. Furthermore, the support of iterative procedures in model-based development processes is examined and as a solution the Persistent Transformation Mapping is proposed.