A modular and extensible RNA-based gene-regulatory platform for engineering cellular function

Engineered biological systems hold promise in addressing pressing human needs in chemical processing, energy production, materials construction, and maintenance and enhancement of human health and the environment. However, significant advancements in our ability to engineer biological systems have been limited by the foundational tools available for reporting on, responding to, and controlling intracellular components in living systems. Portable and scalable platforms are needed for the reliable construction of such communication and control systems across diverse organisms. We report an extensible RNA-based framework for engineering ligand-controlled gene-regulatory systems, called ribozyme switches, that exhibits tunable regulation, design modularity, and target specificity. These switch platforms contain a sensor domain, comprised of an aptamer sequence, and an actuator domain, comprised of a hammerhead ribozyme sequence. We examined two modes of standardized information transmission between these domains and demonstrate a mechanism that allows for the reliable and modular assembly of functioning synthetic RNA switches and regulation of ribozyme activity in response to various effectors. In addition to demonstrating examples of small molecule-responsive, in vivo functional, allosteric hammerhead ribozymes, this work describes a general approach for the construction of portable and scalable gene-regulatory systems. We demonstrate the versatility of the platform in implementing application-specific control systems for small molecule-mediated regulation of cell growth and noninvasive in vivo sensing of metabolite production

A framework for developing engineering design ontologies within the aerospace industry

This paper presents a framework for developing engineering design ontologies within the aerospace industry. The aim of this approach is to strengthen the modularity and reuse of engineering design ontologies to support knowledge management initiatives within the aerospace industry. Successful development and effective utilisation of engineering ontologies strongly depends on the method/framework used to develop them. Ensuring modularity in ontology design is essential for engineering design activities due to the complexity of knowledge that is required to be brought together to support the product design decision-making process. The proposed approach adopts best practices from previous ontology development methods, but focuses on encouraging modular architectural ontology design. The framework is comprised of three phases namely: (1) Ontology design and development; (2) Ontology validation and (3) Implementation of ontology structure. A qualitative research methodology is employed which is composed of four phases. The first phase defines the capture of knowledge required for the framework development, followed by the ontology framework development, iterative refinement of engineering ontologies and ontology validation through case studies and experts’ opinion. The ontology-based framework is applied in the combustor and casing aerospace engineering domain. The modular ontologies developed as a result of applying the framework and are used in a case study to restructure and improve the accessibility of information on a product design information-sharing platform. Additionally, domain experts within the aerospace industry validated the strengths, benefits and limitations of the framework. Due to the modular nature of the developed ontologies, they were also employed to support other project initiatives within the case study company such as role-based computing (RBC), IT modernisation activity and knowledge management implementation across the sponsoring organisation. The major benefit of this approach is in the reduction of man-hours required for maintaining engineering design ontologies. Furthermore, this approach strengthens reuse of ontology knowledge and encourages modularity in the design and development of engineering ontologies

Automated robotic liquid handling assembly of modular DNA devices

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available "design space" represented by "devices" created as combinations of individual genetic components. However, manual assembly of such large numbers of devices is time-intensive, error-prone, and costly. The increasing sophistication and scale of synthetic biology research necessitates an efficient, reproducible way to accommodate large-scale, complex, and high throughput device construction. Here, a DNA assembly protocol using the Type-IIS restriction endonuclease based Modular Cloning (MoClo) technique is automated on two liquid-handling robotic platforms. Automated liquid-handling robots require careful, often times tedious optimization of pipetting parameters for liquids of different viscosities (e.g. enzymes, DNA, water, buffers), as well as explicit programming to ensure correct aspiration and dispensing of DNA parts and reagents. This makes manual script writing for complex assemblies just as problematic as manual DNA assembly, and necessitates a software tool that can automate script generation. To this end, we have developed a web-based software tool, http://mocloassembly.com, for generating combinatorial DNA device libraries from basic DNA parts uploaded as Genbank files. We provide access to the tool, and an export file from our liquid handler software which includes optimized liquid classes, labware parameters, and deck layout. All DNA parts used are available through Addgene, and their digital maps can be accessed via the Boston University BDC ICE Registry. Together, these elements provide a foundation for other organizations to automate modular cloning experiments and similar protocols. The automated DNA assembly workflow presented here enables the repeatable, automated, high-throughput production of DNA devices, and reduces the risk of human error arising from repetitive manual pipetting. Sequencing data show the automated DNA assembly reactions generated from this workflow are ~95% correct and require as little as 4% as much hands-on time, compared to manual reaction preparation

Improving cross-functional communication about product architecture

Product architecture decisions, such as product modularity, component commonality, and design reuse, are important for balancing costs, responsiveness, quality, and other important business objectives. Firms are challenged with complex tradeoffs between competing design priorities, face the need to facilitate communication between functional silos, and to learn from past experiences. In this paper we present a qualitative approach for systematically evaluating the product architecture of an existing product or product family, linking the original architecture objectives and actual experiences. The intended contribution of our research is to present a framework that brings together a diverse set of product architecture-related decisions that are relevant from a business point of view (and not from a technical point of view) and a set of business performance elements. This framework can be used in workshop that improves cross-functional communication about the product architecture of an existing product family, and this results in practical improvement actions for future architecture design projects. Initial experiences with this approach have been obtained in pilots with Philips domestic appliances & personal care, and Philips consumer electronics

Wearable flexible lightweight modular RFID tag with integrated energy harvester

A novel wearable radio frequency identification (RFID) tag with sensing, processing, and decision-taking capability is presented for operation in the 2.45-GHz RFID superhigh frequency (SHF) band. The tag is powered by an integrated light harvester, with a flexible battery serving as an energy buffer. The proposed active tag features excellent wearability, very high read range, enhanced functionality, flexible interfacing with diverse low-power sensors, and extended system autonomy through an innovative holistic microwave system design paradigm that takes antenna design into consideration from the very early stages. Specifically, a dedicated textile shorted circular patch antenna with monopolar radiation pattern is designed and optimized for highly efficient and stable operation within the frequency band of operation. In this process, the textile antenna's functionality is augmented by reusing its surface as an integration platform for light-energy-harvesting, sensing, processing, and transceiver hardware, without sacrificing antenna performance or the wearer's comfort. The RFID tag is validated by measuring its stand-alone and on-body characteristics in free-space conditions. Moreover, measurements in a real-world scenario demonstrate an indoor read range up to 23 m in nonline-of-sight indoor propagation conditions, enabling interrogation by a reader situated in another room. In addition, the RFID platform only consumes 168.3 mu W, when sensing and processing are performed every 60 s

Strategic perspectives on modularity

In this paper we argue that the debate on modularity has come to a point where a consensus is slowly emerging. However, we also contend that this consensus is clearly technology driven. In particular, no room is left for firm strategies. Typically, technology is considered as an exogenous variable to which firms have no choices but to adapt. Taking a slightly different perspective, our main objective is to offer a conceptual framework enabling to shed light on the role of corporate strategies in the process of modularization. From interviews with academic design engineers, we show that firms often consider product architecture as a critical variable to fit their strategic requirements. Based on design sciences, we build an original approach to product modularity. This approach, which leaves an important space for firms' strategic choices, proves also to seize a large part of the industrial reality of modularity. Our framework, which is a first step towards the consideration of strategies within the framework of modularity, gives an account for the diversity of industrial logics related to product modularization.product modularity ; corporate strategy ; technological determinism