Computational protein design-the next generation tool to expand synthetic biology applications.

Science.gov (United States)

Gainza-Cirauqui, Pablo; Correia, Bruno Emanuel

2018-05-02

One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells. Copyright © 2018. Published by Elsevier Ltd.

From bricolage to BioBricks™: Synthetic biology and rational design.

Science.gov (United States)

Lewens, Tim

2013-12-01

Synthetic biology is often described as a project that applies rational design methods to the organic world. Although humans have influenced organic lineages in many ways, it is nonetheless reasonable to place synthetic biology towards one end of a continuum between purely 'blind' processes of organic modification at one extreme, and wholly rational, design-led processes at the other. An example from evolutionary electronics illustrates some of the constraints imposed by the rational design methodology itself. These constraints reinforce the limitations of the synthetic biology ideal, limitations that are often freely acknowledged by synthetic biology's own practitioners. The synthetic biology methodology reflects a series of constraints imposed on finite human designers who wish, as far as is practicable, to communicate with each other and to intervene in nature in reasonably targeted and well-understood ways. This is better understood as indicative of an underlying awareness of human limitations, rather than as expressive of an objectionable impulse to mastery over nature. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research. PMID:20150964

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Directory of Open Access Journals (Sweden)

Eric Young

2010-01-01

Full Text Available The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1 the process units and associated streams of the central dogma, (2 the intrinsic regulatory mechanisms, and (3 the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Synthetic biology: tools to design, build, and optimize cellular processes.

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Design and construction of synthetic microbial consortia in China

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Ming-Zhu Ding

2016-12-01

Full Text Available The rapid development of synthetic biology enables the design, construction and optimization of synthetic microbial consortia to achieve specific functions. In China, the “973” project-“Design and Construction of Microbial Consortia” was funded by the National Basic Research Program of China in January 2014. It was proposed to address the fundamental challenges in engineering natural microbial consortia and reconstructing microbial consortia to meet industrial demands. In this review, we will introduce this “973” project, including the significance of microbial consortia, the fundamental scientific issues, the recent research progresses, and some case studies about synthetic microbial consortia in the past two and a half years.

Designing synthetic RNA for delivery by nanoparticles

International Nuclear Information System (INIS)

Jedrzejczyk, Dominika; Pawlowska, Roza; Chworos, Arkadiusz; Gendaszewska-Darmach, Edyta

2017-01-01

The rapid development of synthetic biology and nanobiotechnology has led to the construction of various synthetic RNA nanoparticles of different functionalities and potential applications. As they occur naturally, nucleic acids are an attractive construction material for biocompatible nanoscaffold and nanomachine design. In this review, we provide an overview of the types of RNA and nucleic acid’s nanoparticle design, with the focus on relevant nanostructures utilized for gene-expression regulation in cellular models. Structural analysis and modeling is addressed along with the tools available for RNA structural prediction. The functionalization of RNA-based nanoparticles leading to prospective applications of such constructs in potential therapies is shown. The route from the nanoparticle design and modeling through synthesis and functionalization to cellular application is also described. For a better understanding of the fate of targeted RNA after delivery, an overview of RNA processing inside the cell is also provided. (topical review)

Automatic design of digital synthetic gene circuits.

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Mario A Marchisio

2011-02-01

Full Text Available De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input-output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions.

Techniques for Modeling Human Performance in Synthetic Environments: A Supplementary Review

National Research Council Canada - National Science Library

Ritter, Frank E; Shadbolt, Nigel R; Elliman, David; Young, Richard M; Gobet, Fernand; Baxter, Gordon D

2003-01-01

Selected recent developments and promising directions for improving the quality of models of human performance in synthetic environments are summarized, beginning with the potential uses and goals for behavioral models...

Techniques for Modeling Human Performance in Synthetic Environments: A Supplementary Review

National Research Council Canada - National Science Library

Ritter, Frank E; Shadbolt, Nigel R; Elliman, David; Young, Richard M; Gobet, Fernand; Baxter, Gordon D

2003-01-01

... architectures including hybrid architectures, and agent and Belief, Desires and Intentions (BDI) architectures. A list of projects with high payoff for modeling human performance in synthetic environments is provided as a conclusion.

Synthetic Biology and Personalized Medicine

Science.gov (United States)

Jain, K.K.

2013-01-01

Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task. PMID:22907209

Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality.

Science.gov (United States)

Otero-Muras, Irene; Banga, Julio R

2017-07-21

In this work we consider Pareto optimality for automated design in synthetic biology. We present a generalized framework based on a mixed-integer dynamic optimization formulation that, given design specifications, allows the computation of Pareto optimal sets of designs, that is, the set of best trade-offs for the metrics of interest. We show how this framework can be used for (i) forward design, that is, finding the Pareto optimal set of synthetic designs for implementation, and (ii) reverse design, that is, analyzing and inferring motifs and/or design principles of gene regulatory networks from the Pareto set of optimal circuits. Finally, we illustrate the capabilities and performance of this framework considering four case studies. In the first problem we consider the forward design of an oscillator. In the remaining problems, we illustrate how to apply the reverse design approach to find motifs for stripe formation, rapid adaption, and fold-change detection, respectively.

Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

Science.gov (United States)

Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

2012-01-01

Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits. PMID:22536398

Micro/nanofabricated environments for synthetic biology.

Science.gov (United States)

Collier, C Patrick; Simpson, Michael L

2011-08-01

A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy.

Directory of Open Access Journals (Sweden)

Michael Volpers

Full Text Available The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms that can effectively and efficiently fix carbon dioxide by using sustainable energy sources. This challenge involves the integration of carbon fixation and energy uptake systems. A variety of carbon fixation pathways and several types of photosystems and other energy uptake systems can be chosen and, potentially, modularly combined to design synthetic autotrophic metabolism. Prior to implementation, these designs can be evaluated by the combination of several computational pathway analysis techniques. Here we present a systematic, integrated in silico analysis of photo-electro-autotrophic pathway designs, consisting of natural and synthetic carbon fixation pathways, a proton-pumping rhodopsin photosystem for ATP regeneration and an electron uptake pathway. We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force. The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the proton pumping rhodopsin photosystems and the high ATP maintenance of E. coli. If these factors can be tackled, our analysis indicates the highest growth potential for the natural reductive tricarboxylic acid cycle and the synthetic pyruvate synthase-pyruvate carboxylate -glyoxylate bicycle. Both carbon fixation cycles are very ATP efficient, while maintaining fast kinetics, which also results in relatively low estimated protein costs for these pathways. Furthermore, the synthetic bicycles are highly

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

Science.gov (United States)

Tien, Shin-Ming; Hsu, Chih-Yuan; Chen, Bor-Sen

2016-01-01

Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

Directory of Open Access Journals (Sweden)

Shin-Ming Tien

Full Text Available Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

Designing synthetic networks in silico: a generalised evolutionary algorithm approach.

Science.gov (United States)

Smith, Robert W; van Sluijs, Bob; Fleck, Christian

2017-12-02

Evolution has led to the development of biological networks that are shaped by environmental signals. Elucidating, understanding and then reconstructing important network motifs is one of the principal aims of Systems & Synthetic Biology. Consequently, previous research has focused on finding optimal network structures and reaction rates that respond to pulses or produce stable oscillations. In this work we present a generalised in silico evolutionary algorithm that simultaneously finds network structures and reaction rates (genotypes) that can satisfy multiple defined objectives (phenotypes). The key step to our approach is to translate a schema/binary-based description of biological networks into systems of ordinary differential equations (ODEs). The ODEs can then be solved numerically to provide dynamic information about an evolved networks functionality. Initially we benchmark algorithm performance by finding optimal networks that can recapitulate concentration time-series data and perform parameter optimisation on oscillatory dynamics of the Repressilator. We go on to show the utility of our algorithm by finding new designs for robust synthetic oscillators, and by performing multi-objective optimisation to find a set of oscillators and feed-forward loops that are optimal at balancing different system properties. In sum, our results not only confirm and build on previous observations but we also provide new designs of synthetic oscillators for experimental construction. In this work we have presented and tested an evolutionary algorithm that can design a biological network to produce desired output. Given that previous designs of synthetic networks have been limited to subregions of network- and parameter-space, the use of our evolutionary optimisation algorithm will enable Synthetic Biologists to construct new systems with the potential to display a wider range of complex responses.

A synthetic computational environment: To control the spread of respiratory infections in a virtual university

Science.gov (United States)

Ge, Yuanzheng; Chen, Bin; liu, Liang; Qiu, Xiaogang; Song, Hongbin; Wang, Yong

2018-02-01

Individual-based computational environment provides an effective solution to study complex social events by reconstructing scenarios. Challenges remain in reconstructing the virtual scenarios and reproducing the complex evolution. In this paper, we propose a framework to reconstruct a synthetic computational environment, reproduce the epidemic outbreak, and evaluate management interventions in a virtual university. The reconstructed computational environment includes 4 fundamental components: the synthetic population, behavior algorithms, multiple social networks, and geographic campus environment. In the virtual university, influenza H1N1 transmission experiments are conducted, and gradually enhanced interventions are evaluated and compared quantitatively. The experiment results indicate that the reconstructed virtual environment provides a solution to reproduce complex emergencies and evaluate policies to be executed in the real world.

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

Science.gov (United States)

McLaughlin, James Alastair; Pocock, Matthew; Mısırlı, Göksel; Madsen, Curtis; Wipat, Anil

2016-08-19

VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.

History, Progress and New Results in Synthetic Passive Element Design Employing CFTAs

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Jaroslav Koton

2015-03-01

Full Text Available After the presentation of the Current Follower Transconductance Amplifier (CFTA active element, it has found a numerous application possibilities while designing linear and non-linear analog function blocks. This paper gives a short review of the CFTA and mainly focuses on the synthetic floating and grounded passive element design, which can also be electronically controllable. Except the design of synthetic inductors, also possible realizations of floating and grounded capacitors and resistors are described, where the value of these passive elements can be adjusted by means of active elements’ parameters. For the design of the corresponding circuit realizations, the Mason-Coates signal flow graph approach is used. The performance of some discussed synthetic elements is verified and  evaluated by Spice simulations on simple analog frequency filters.

Predicting Translation Initiation Rates for Designing Synthetic Biology

International Nuclear Information System (INIS)

Reeve, Benjamin; Hargest, Thomas; Gilbert, Charlie; Ellis, Tom

2014-01-01

In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process, models of prokaryotic protein production have been described. Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5′-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels. In this review, three currently available translation rate calculators developed for synthetic biology are considered, with limitations and possible future progress discussed.

Data Integration and Mining for Synthetic Biology Design.

Science.gov (United States)

Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

2016-10-21

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Energy Technology Data Exchange (ETDEWEB)

Gould, Nathan [Department of Computer Science, The College of New Jersey, Ewing, NJ (United States); Hendy, Oliver [Department of Biology, The College of New Jersey, Ewing, NJ (United States); Papamichail, Dimitris, E-mail: papamicd@tcnj.edu [Department of Computer Science, The College of New Jersey, Ewing, NJ (United States)

2014-10-06

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

International Nuclear Information System (INIS)

Gould, Nathan; Hendy, Oliver; Papamichail, Dimitris

2014-01-01

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Advantageous application of Synthetic Environments in product design

NARCIS (Netherlands)

Miedema, J.; van der Voort, Mascha C.; van Houten, Frederikus J.A.M.

2009-01-01

Despite the abundance of supporting tools and methods engineers have at their disposal nowadays, the early stages of design processes are still not extensively supported. Strikingly, the whole of design aids is characterized by mono-disciplinarity, scattered availability and the fact that the

Visualization Design Environment

Energy Technology Data Exchange (ETDEWEB)

Pomplun, A.R.; Templet, G.J.; Jortner, J.N.; Friesen, J.A.; Schwegel, J.; Hughes, K.R.

1999-02-01

Improvements in the performance and capabilities of computer software and hardware system, combined with advances in Internet technologies, have spurred innovative developments in the area of modeling, simulation and visualization. These developments combine to make it possible to create an environment where engineers can design, prototype, analyze, and visualize components in virtual space, saving the time and expenses incurred during numerous design and prototyping iterations. The Visualization Design Centers located at Sandia National Laboratories are facilities built specifically to promote the ''design by team'' concept. This report focuses on designing, developing and deploying this environment by detailing the design of the facility, software infrastructure and hardware systems that comprise this new visualization design environment and describes case studies that document successful application of this environment.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Directory of Open Access Journals (Sweden)

Nathan eGould

2014-10-01

Full Text Available Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de-novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Reprint of Design of synthetic microbial communities for biotechnological production processes.

Science.gov (United States)

Jagmann, Nina; Philipp, Bodo

2014-12-20

In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes. Copyright © 2014 Elsevier B.V. All rights reserved.

Stereoscopy in cinematographic synthetic imagery

Science.gov (United States)

Eisenmann, Jonathan; Parent, Rick

2009-02-01

In this paper we present experiments and results pertaining to the perception of depth in stereoscopic viewing of synthetic imagery. In computer animation, typical synthetic imagery is highly textured and uses stylized illumination of abstracted material models by abstracted light source models. While there have been numerous studies concerning stereoscopic capabilities, conventions for staging and cinematography in stereoscopic movies have not yet been well-established. Our long-term goal is to measure the effectiveness of various cinematography techniques on the human visual system in a theatrical viewing environment. We would like to identify the elements of stereoscopic cinema that are important in terms of enhancing the viewer's understanding of a scene as well as providing guidelines for the cinematographer relating to storytelling. In these experiments we isolated stereoscopic effects by eliminating as many other visual cues as is reasonable. In particular, we aim to empirically determine what types of movement in synthetic imagery affect the perceptual depth sensing capabilities of our viewers. Using synthetic imagery, we created several viewing scenarios in which the viewer is asked to locate a target object's depth in a simple environment. The scenarios were specifically designed to compare the effectiveness of stereo viewing, camera movement, and object motion in aiding depth perception. Data were collected showing the error between the choice of the user and the actual depth value, and patterns were identified that relate the test variables to the viewer's perceptual depth accuracy in our theatrical viewing environment.

Towards the Development of Synthetic Antibiotics: Designs Inspired by Natural Antimicrobial Peptides.

Science.gov (United States)

Azmi, Fazren; Skwarczynski, Mariusz; Toth, Istvan

2016-01-01

Virtually every living organism produces gene-encoded antimicrobial peptides (AMPs) that provide an immediate defence against pathogen invasion. Many AMPs have been isolated and used as antibiotics that are effective against multidrug-resistant bacteria. Although encouraging, AMPs have such poor drug-like properties that their application for clinical use is restricted. In turn, this has diverted research to the development of synthetic molecules that retain the therapeutic efficacy of AMPs but are endowed with greater biological stability and safety profiles. Most of the synthetic molecules, either based on a peptidic or non-peptidic scaffold, have been designed to mimic the amphiphilic properties of native AMPs, which are widely believed to be the key determinant of their antibacterial activity. In this review, the structural, chemical and biophysical features that govern the biological activities of various synthetic designs are discussed extensively. Recent innovative approaches from the literature that exhibit novel concepts towards the development of new synthetic antibacterial agents, including the engineered delivery platform incorporated with AMP mimetics, are also emphasised.

Synthetic Self-Assembled Materials in Biological Environments

NARCIS (Netherlands)

Versluis, F.; van Esch, J.H.; Eelkema, R.

2016-01-01

Synthetic self-assembly has long been recognized as an excellent approach for the formation of ordered structures on the nanoscale. Although the development of synthetic self-assembling materials has often been inspired by principles observed in nature (e.g., the assembly of lipids, DNA,

Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

Science.gov (United States)

Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

2017-11-13

A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

Plant synthetic biology.

Science.gov (United States)

Liu, Wusheng; Stewart, C Neal

2015-05-01

Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthetic design and the art of virtual reality in theatre and film ...

African Journals Online (AJOL)

This new found space is known as Virtual Reality. This article delves into the field of Virtual Reality (VR), a current trend in audiovisual design for the entertainment industry and is therefore designed to examine the synergetic relationships between synthetic design and the art of Virtual Reality and how they influence modern ...

Pareto Optimal Design for Synthetic Biology.

Science.gov (United States)

Patanè, Andrea; Santoro, Andrea; Costanza, Jole; Carapezza, Giovanni; Nicosia, Giuseppe

2015-08-01

Recent advances in synthetic biology call for robust, flexible and efficient in silico optimization methodologies. We present a Pareto design approach for the bi-level optimization problem associated to the overproduction of specific metabolites in Escherichia coli. Our method efficiently explores the high dimensional genetic manipulation space, finding a number of trade-offs between synthetic and biological objectives, hence furnishing a deeper biological insight to the addressed problem and important results for industrial purposes. We demonstrate the computational capabilities of our Pareto-oriented approach comparing it with state-of-the-art heuristics in the overproduction problems of i) 1,4-butanediol, ii) myristoyl-CoA, i ii) malonyl-CoA , iv) acetate and v) succinate. We show that our algorithms are able to gracefully adapt and scale to more complex models and more biologically-relevant simulations of the genetic manipulations allowed. The Results obtained for 1,4-butanediol overproduction significantly outperform results previously obtained, in terms of 1,4-butanediol to biomass formation ratio and knock-out costs. In particular overproduction percentage is of +662.7%, from 1.425 mmolh⁻¹gDW⁻¹ (wild type) to 10.869 mmolh⁻¹gDW⁻¹, with a knockout cost of 6. Whereas, Pareto-optimal designs we have found in fatty acid optimizations strictly dominate the ones obtained by the other methodologies, e.g., biomass and myristoyl-CoA exportation improvement of +21.43% (0.17 h⁻¹) and +5.19% (1.62 mmolh⁻¹gDW⁻¹), respectively. Furthermore CPU time required by our heuristic approach is more than halved. Finally we implement pathway oriented sensitivity analysis, epsilon-dominance analysis and robustness analysis to enhance our biological understanding of the problem and to improve the optimization algorithm capabilities.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

Science.gov (United States)

Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Pocock, Matthew; Flanagan, Keith; Hallinan, Jennifer; Wipat, Anil

2016-06-17

Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.

Unveiling Collaborative Group Identities in Social Synthetic Environments from Interaction Data

DEFF Research Database (Denmark)

Grappiolo, Corrado

used to simulate aspects of real-life, yet by maintaining a customisable level of control of the phenomena under investigation. Examples of social synthetic environments are theoretical games and cooperative computer games. The proposed framework is composed of two pipelined modules. The first one....... This dissertation successfully leverages on the hypothesis that it is possible to infer the existence of group structures by solely focusing on the ongoing interactions. The limitations of the approach and possible strategies to overcome them are also proposed....

Synthetic circuit designs for earth terraformation.

Science.gov (United States)

Solé, Ricard V; Montañez, Raúl; Duran-Nebreda, Salva

2015-07-18

Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries. We hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls. Testing this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics). Our hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success.

Computational approaches in the design of synthetic receptors - A review.

Science.gov (United States)

Cowen, Todd; Karim, Kal; Piletsky, Sergey

2016-09-14

The rational design of molecularly imprinted polymers (MIPs) has been a major contributor to their reputation as "plastic antibodies" - high affinity robust synthetic receptors which can be optimally designed, and produced for a much reduced cost than their biological equivalents. Computational design has become a routine procedure in the production of MIPs, and has led to major advances in functional monomer screening, selection of cross-linker and solvent, optimisation of monomer(s)-template ratio and selectivity analysis. In this review the various computational methods will be discussed with reference to all the published relevant literature since the end of 2013, with each article described by the target molecule, the computational approach applied (whether molecular mechanics/molecular dynamics, semi-empirical quantum mechanics, ab initio quantum mechanics (Hartree-Fock, Møller-Plesset, etc.) or DFT) and the purpose for which they were used. Detailed analysis is given to novel techniques including analysis of polymer binding sites, the use of novel screening programs and simulations of MIP polymerisation reaction. The further advances in molecular modelling and computational design of synthetic receptors in particular will have serious impact on the future of nanotechnology and biotechnology, permitting the further translation of MIPs into the realms of analytics and medical technology. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthetic Cathinone and Cannabinoid Designer Drugs Pose a Major Risk for Public Health

Directory of Open Access Journals (Sweden)

Aviv M. Weinstein

2017-08-01

Full Text Available As part of an increasing worldwide use of designer drugs, recent use of compounds containing cathinones and synthetic cannabinoids is especially prevalent. Here, we reviewed current literature on the prevalence, epidemiology, bio-behavioral effects, and detection of these compounds. Gender differences and clinical effects will also be examined. Chronic use of synthetic cathinone compounds can have major effects on the central nervous system and can induce acute psychosis, hypomania, paranoid ideation, and delusions, similar to the effects of other better-known amphetamine-type stimulants. Synthetic cannabinoid products have effects that are somewhat similar to those of natural cannabis but more potent and long-lasting than THC. Some of these compounds are potent and dangerous, having been linked to psychosis, mania, and suicidal ideation. Novel compounds are developed rapidly and new screening techniques are needed to detect them as well as a rigorous regulation and legislation reinforcement to prevent their distribution and use. Given the rapid increase in the use of synthetic cathinones and cannabinoid designer drugs, their potential for dependence and abuse, and harmful medical and psychiatric effects, there is a need for research and education in the areas of prevention and treatment.

Proceedings of Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2015

Energy Technology Data Exchange (ETDEWEB)

Silver, Pamela [Harvard Univ., Cambridge, MA (United States); SEED 2015 Conference Chair; Flach, Evan [American Institute of Chemical Engineers; SEED 2015 Conference Organizer

2016-10-27

Synthetic Biology is an emerging discipline that seeks to accelerate the process of engineering biology. As such, the tools are broadly applicable to application areas, including chemicals and biofuels, materials, medicine and agriculture. A characteristic of the field is to look holistically at cellular design, from sensing and genetic circuitry to the manipulation of cellular processes and actuators, to controlling metabolism, to programming multicellular behaviors. Further, the types of cells that are manipulated are broad, from in vitro systems to microbes and fungi to mammalian and plant cells and living animals. Many of the projects in synthetic biology seek to move biochemical functions across organisms. The field is highly interdisciplinary with faculty and students spread across departments that focus on engineering (biological, chemical, electrical, mechanical, civil, computer science) and basic science (biology and systems biology, chemistry, physics). While there have been many one-off workshops and meeting on synthetic biology, the 2014 Synthetic Biology: Engineering, Evolution and Design (SEED) was the first of an annual conference series that serves as a reliable place to pull together the involved disciplines in order to organize and exchange advances in the science and technology in the field. Further, the SEED conferences have a strong focus on industry, with many companies represented and actively participating. A number of these companies have started major efforts in synthetic biology including large companies (e.g., Pfizer, Novartis, Dow, Dupont, BP, Total), smaller companies have recently gone public (e.g., Amyris, Gevo, Intrexon), and many start-ups (e.g., Teslagen, Refactored Materials, Pivot, Genomatica). There are a number of loosely affiliated Synthetic Biology Centers, including ones at MIT, Boston University, UCSD, UCSF, UC-Berkeley, Imperial College, Oxford, and ETH. SEED 2015 will serve as the primary meeting at which international

Modular design of synthetic gene circuits with biological parts and pools.

Science.gov (United States)

Marchisio, Mario Andrea

2015-01-01

Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

Synthetic biology, inspired by synthetic chemistry.

Science.gov (United States)

Malinova, V; Nallani, M; Meier, W P; Sinner, E K

2012-07-16

The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Design parameters to control synthetic gene expression in Escherichia coli.

Directory of Open Access Journals (Sweden)

Mark Welch

Full Text Available BACKGROUND: Production of proteins as therapeutic agents, research reagents and molecular tools frequently depends on expression in heterologous hosts. Synthetic genes are increasingly used for protein production because sequence information is easier to obtain than the corresponding physical DNA. Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles. PRINCIPAL FINDINGS: To identify sequence features that affect protein expression we synthesized and expressed in E. coli two sets of 40 genes encoding two commercially valuable proteins, a DNA polymerase and a single chain antibody. Genes differing only in synonymous codon usage expressed protein at levels ranging from undetectable to 30% of cellular protein. Using partial least squares regression we tested the correlation of protein production levels with parameters that have been reported to affect expression. We found that the amount of protein produced in E. coli was strongly dependent on the codons used to encode a subset of amino acids. Favorable codons were predominantly those read by tRNAs that are most highly charged during amino acid starvation, not codons that are most abundant in highly expressed E. coli proteins. Finally we confirmed the validity of our models by designing, synthesizing and testing new genes using codon biases predicted to perform well. CONCLUSION: The systematic analysis of gene design parameters shown in this study has allowed us to identify codon usage within a gene as a critical determinant of achievable protein expression levels in E. coli. We propose a biochemical basis for this, as well as design algorithms to ensure high protein production from synthetic genes. Replication of this methodology should allow similar design algorithms to be empirically derived for any expression system.

Computational approaches in the design of synthetic receptors – A review

Energy Technology Data Exchange (ETDEWEB)

Cowen, Todd, E-mail: tc203@le.ac.uk; Karim, Kal; Piletsky, Sergey

2016-09-14

The rational design of molecularly imprinted polymers (MIPs) has been a major contributor to their reputation as “plastic antibodies” – high affinity robust synthetic receptors which can be optimally designed, and produced for a much reduced cost than their biological equivalents. Computational design has become a routine procedure in the production of MIPs, and has led to major advances in functional monomer screening, selection of cross-linker and solvent, optimisation of monomer(s)-template ratio and selectivity analysis. In this review the various computational methods will be discussed with reference to all the published relevant literature since the end of 2013, with each article described by the target molecule, the computational approach applied (whether molecular mechanics/molecular dynamics, semi-empirical quantum mechanics, ab initio quantum mechanics (Hartree-Fock, Møller–Plesset, etc.) or DFT) and the purpose for which they were used. Detailed analysis is given to novel techniques including analysis of polymer binding sites, the use of novel screening programs and simulations of MIP polymerisation reaction. The further advances in molecular modelling and computational design of synthetic receptors in particular will have serious impact on the future of nanotechnology and biotechnology, permitting the further translation of MIPs into the realms of analytics and medical technology. - Highlights: • A review of computational modelling in the design of molecularly imprinted polymers. • Target analytes and method of analysis for the vast majority of recent articles. • Explanations are given of all the popular and emerging techniques used in design. • Highlighted examples of sophisticated analysis of imprinted polymer systems.

Computational approaches in the design of synthetic receptors – A review

International Nuclear Information System (INIS)

Cowen, Todd; Karim, Kal; Piletsky, Sergey

2016-01-01

The rational design of molecularly imprinted polymers (MIPs) has been a major contributor to their reputation as “plastic antibodies” – high affinity robust synthetic receptors which can be optimally designed, and produced for a much reduced cost than their biological equivalents. Computational design has become a routine procedure in the production of MIPs, and has led to major advances in functional monomer screening, selection of cross-linker and solvent, optimisation of monomer(s)-template ratio and selectivity analysis. In this review the various computational methods will be discussed with reference to all the published relevant literature since the end of 2013, with each article described by the target molecule, the computational approach applied (whether molecular mechanics/molecular dynamics, semi-empirical quantum mechanics, ab initio quantum mechanics (Hartree-Fock, Møller–Plesset, etc.) or DFT) and the purpose for which they were used. Detailed analysis is given to novel techniques including analysis of polymer binding sites, the use of novel screening programs and simulations of MIP polymerisation reaction. The further advances in molecular modelling and computational design of synthetic receptors in particular will have serious impact on the future of nanotechnology and biotechnology, permitting the further translation of MIPs into the realms of analytics and medical technology. - Highlights: • A review of computational modelling in the design of molecularly imprinted polymers. • Target analytes and method of analysis for the vast majority of recent articles. • Explanations are given of all the popular and emerging techniques used in design. • Highlighted examples of sophisticated analysis of imprinted polymer systems.

Designing Creative Learning Environments

Directory of Open Access Journals (Sweden)

Thomas Cochrane

2015-05-01

Full Text Available Designing creative learning environments involves not only facilitating student creativity, but also modeling creative pedagogical practice. In this paper we explore the implementation of a framework for designing creative learning environments using mobile social media as a catalyst for redefining both lecturer pedagogical practice, as well as redesigning the curriculum around student generated m-portfolios.

Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation.

Science.gov (United States)

Tomazou, Marios; Barahona, Mauricio; Polizzi, Karen M; Stan, Guy-Bart

2018-04-25

To perform well in biotechnology applications, synthetic genetic oscillators must be engineered to allow independent modulation of amplitude and period. This need is currently unmet. Here, we demonstrate computationally how two classic genetic oscillators, the dual-feedback oscillator and the repressilator, can be re-designed to provide independent control of amplitude and period and improve tunability-that is, a broad dynamic range of periods and amplitudes accessible through the input "dials." Our approach decouples frequency and amplitude modulation by incorporating an orthogonal "sink module" where the key molecular species are channeled for enzymatic degradation. This sink module maintains fast oscillation cycles while alleviating the translational coupling between the oscillator's transcription factors and output. We characterize the behavior of our re-designed oscillators over a broad range of physiologically reasonable parameters, explain why this facilitates broader function and control, and provide general design principles for building synthetic genetic oscillators that are more precisely controllable. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Natural and Synthetic Biohydrogels Design, Characterization, Network Structure Imaging and Modeling

Science.gov (United States)

Marmorat, Clement

Biocompatible hydrogels can be derived from materials that are naturally obtained, such as proteins or polysaccharides, or synthetic, such as poloxamers. In order to be classified as biocompatible, these water-swollen networks can not trigger a toxic response once introduced into a biological or physiological environment and, therefore, must be immunoneutral. Hyaluronic acid hydrogels can be great candidates for tissue engineering applications as long as the cross-linking chemistry and process does not affect the biocompatibility of the natural protein matrix. Thermoreversible hydrogels have the advantage of undergoing a sol/gel phase transition at specific temperatures. Thus, they are excellent candidates for biomedical applications such as drug delivery systems, wound healing coatings or cellular scaffolds. Although these hydrogels can be used in their natural form without further modification or chemical alteration, the original protein or polymer matrix is often strengthened by the use of a crosslinking agent to achieve a specific set of properties. In the case of gelatin fibril formation at low temperatures or the micellization of triblock copolymers in solution with temperature increase, the natural phase transition is modified when crosslinkers are introduced to alter the biohydrogels properties and, ultimately, disturb the system's equilibrium. By using spectroscopy techniques, rheology and cryo-imaging we investigated several biocompatible polymeric networks in their natural form as well as their engineered structures to better understand the mechanisms of gelation and artificial internal re-organization of the networks. Natural and synthetic biohydrogels were designed and their mechanical properties were characterized before imaging. Models that better describe the relationship between network configuration and resulting mechanical properties showed great agreement with experimental mesh size observations. Finally, a novel set of hybrid gels was developed

Opportunities in plant synthetic biology.

Science.gov (United States)

Cook, Charis; Martin, Lisa; Bastow, Ruth

2014-05-01

Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

Interactive Environment Design in Smart City

Science.gov (United States)

Deng, DeXiang; Chen, LanSha; Zhou, Xi

2017-08-01

The interactive environment design of smart city is not just an interactive progress or interactive mode design, rather than generate an environment such as the “organic” life entity as human beings through interactive design, forming a smart environment with perception, memory, thinking, and reaction.

Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students†

OpenAIRE

Beach, Dale L.; Alvarez, Consuelo J.

2015-01-01

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniq...

Functional mimicry of a discontinuous antigenic site by a designed synthetic peptide

NARCIS (Netherlands)

Villen, J.; Borras, E.; Schaaper, W.M.M.; Meloen, R.H.; Davila, M.; Domingo, E.; Giralt, E.; Andreu, D.

2002-01-01

Functional reproduction of the discontinuous antigenic site D of foot-and-mouth disease virus (FMDV) has been achieved by means of synthetic peptide constructions that integrate each of the three protein loops that define the antigenic site into a single molecule. The site D mimics were designed on

Synergistic Synthetic Biology: Units in Concert

Science.gov (United States)

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

Synergistic Synthetic Biology: Units in Concert

International Nuclear Information System (INIS)

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device.

Science.gov (United States)

Ball, David A; Lux, Matthew W; Graef, Russell R; Peterson, Matthew W; Valenti, Jane D; Dileo, John; Peccoud, Jean

2010-01-01

The concept of co-design is common in engineering, where it is necessary, for example, to determine the optimal partitioning between hardware and software of the implementation of a system features. Here we propose to adapt co-design methodologies for synthetic biology. As a test case, we have designed an environmental sensing device that detects the presence of three chemicals, and returns an output only if at least two of the three chemicals are present. We show that the logical operations can be implemented in three different design domains: (1) the transcriptional domain using synthetically designed hybrid promoters, (2) the protein domain using bi-molecular fluorescence complementation, and (3) the fluorescence domain using spectral unmixing and relying on electronic processing. We discuss how these heterogeneous design strategies could be formalized to develop co-design algorithms capable of identifying optimal designs meeting user specifications.

A low cost, customizable turbidostat for use in synthetic circuit characterization.

Science.gov (United States)

Takahashi, Chris N; Miller, Aaron W; Ekness, Felix; Dunham, Maitreya J; Klavins, Eric

2015-01-16

Engineered biological circuits are often disturbed by a variety of environmental factors. In batch culture, where the majority of synthetic circuit characterization occurs, environmental conditions vary as the culture matures. Turbidostats are powerful characterization tools that provide static culture environments; however, they are often expensive, especially when purchased in custom configurations, and are difficult to design and construct in a lab. Here, we present a low cost, open source multiplexed turbidostat that can be manufactured and used with minimal experience in electrical or software engineering. We demonstrate the utility of this system to profile synthetic circuit behavior in S. cerevisiae. We also demonstrate the flexibility of the design by showing that a fluorometer can be easily integrated.

Synthetic analog computation in living cells.

Science.gov (United States)

Daniel, Ramiz; Rubens, Jacob R; Sarpeshkar, Rahul; Lu, Timothy K

2013-05-30

A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber's law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.

Generation of synthetic time histories compatible with multiple-damping design response spectra

International Nuclear Information System (INIS)

Lilhanand, K.; Tseng, W.S.

1987-01-01

Seismic design of nuclear power plants as currently practiced requires time history analyses be performed to generate floor response spectra for seismic qualification of piping, equipment, and components. Since design response spectra are normally prescribed in the form of smooth spectra, the generation of synthetic time histories whose response spectra closely match the ''target'' design spectra of multiple damping values, is often required for the seismic time history analysis purpose. Various methods of generation of synthetic time histories compatible with target response spectra have been proposed in the literature. Since the mathematical problem of determining a time history from a given set of response spectral values is not unique, an exact solution is not possible, and all the proposed methods resort to some forms of approximate solutions. In this paper, a new iteration scheme, is described which effectively removes the difficulties encountered by the existing methods. This new iteration scheme can not only improve the accuracy of spectrum matching for a single-damping target spectrum, but also automate the spectrum matching for multiple-damping target spectra. The applicability and limitations as well as the method adopted to improve the numerical stability of this new iteration scheme are presented. The effectiveness of this new iteration scheme is illustrated by two example applications

Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools

International Nuclear Information System (INIS)

Laganà, Alessandro; Shasha, Dennis; Croce, Carlo Maria

2014-01-01

The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.

Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools

Energy Technology Data Exchange (ETDEWEB)

Laganà, Alessandro [Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (United States); Shasha, Dennis [Courant Institute of Mathematical Sciences, New York University, New York, NY (United States); Croce, Carlo Maria [Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (United States)

2014-12-11

The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.

Experience with synthetic fluorinated fluid lubricants

Science.gov (United States)

Conley, Peter L.; Bohner, John J.

1990-01-01

Since the late 1970's, the wet lubricant of choice for space mechanisms has been one of the family of synthetic perfluoro polyalkylether (PFPE) compounds, namely Fomblin Z-25 (Bray-815Z) or DuPont's Krytox 143xx series. While offering the advantages of extremely low vapor pressures and wide temperature ranges, these oils and derived greases have a complex chemistry compared to the more familiar natural and synthetic hydrocarbons. Many aerospace companies have conducted test programs to characterize the behavior of these compounds in a space environment, resulting in a large body of hard knowledge as well as considerable space lore concerning the suitability of the lubricants for particular applications and techniques for successful application. The facts are summarized and a few myths about the compounds are dispelled, and some performance guidelines for the mechanism design engineer are provided.

Preparing Synthetic Biology for the World

Directory of Open Access Journals (Sweden)

Gerd H.G. Moe-Behrens

2013-01-01

Full Text Available Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or living devices. As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety.

Photocatalytic Role of Zinc Oxide Nanoparticles on Synthetic Activated Carbon to Remove Antibiotic from Aquatic Environment

Directory of Open Access Journals (Sweden)

Mohammad Reza Samarghandi

2017-10-01

Full Text Available Background & Aims of the Study: The presence of antibiotics in the environment, especially in aquatic environments is a major concern for health and the environment. The advanced oxidation process due to the ease of use, economical advantages and high performance have attracted a lot of attention. The purpose of this study was Evaluating of the photocatalytic role of zinc oxide on synthetic activated carbon to remove antibiotic from aquatic environment. Materials & Methods: This experimental study was done in batch reactor that has a 1 L volume. In this study effect of parameters such as initial pH (3-9, initial concentration of cefazolin (20-200 mg/L, modified photocatalyst concentration (20-100 mg/L and reaction time (10-60 min was investigated. In this study a low-pressure mercury lamp with the power of 55 watts in stainless case has been used. The cefazolin concentrations in different steps were measured using UV-Vis spectrophotometer in Wavelength of 262 nm. Results: The results showed that the highest removal efficiency (96% of cefazolin was at the pH=3, 0.1 mg/L of modified photocatalyst, retention time of 60 min and cefazolin concentrations of 100 mg/L. In the case of changing any of the above mentioned values, process efficiency was decreased. Conclusion: The results showed that the photocatalytic process of zinc oxide nanoparticles on synthetic activated carbon can be used as an advanced oxidation process to effectively remove pollutants like cefazolin and other similar pollutants.

Synthetic biology: an emerging engineering discipline.

Science.gov (United States)

Cheng, Allen A; Lu, Timothy K

2012-01-01

Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.

Design and management of sustainable built environments

CERN Document Server

2013-01-01

Climate change is believed to be a great challenge to built environment professionals in design and management. An integrated approach in delivering a sustainable built environment is desired by the built environment professional institutions. The aim of this book is to provide an advanced understanding of the key subjects required for the design and management of modern built environments to meet carbon emission reduction targets. In Design and Management of Sustainable Built Environments, an international group of experts provide comprehensive and the most up-to-date knowledge, covering sustainable urban and building design, management and assessment. The best practice case studies of the implementation of sustainable technology and management from the BRE Innovation Park are included. Design and Management of Sustainable Built Environments will be of interest to urban and building designers, environmental engineers, and building performance assessors.  It will be particularly useful as a reference book ...

RNEDE: Resilient Network Design Environment

Energy Technology Data Exchange (ETDEWEB)

Venkat Venkatasubramanian, Tanu Malik, Arun Giridh; Craig Rieger; Keith Daum; Miles McQueen

2010-08-01

Modern living is more and more dependent on the intricate web of critical infrastructure systems. The failure or damage of such systems can cause huge disruptions. Traditional design of this web of critical infrastructure systems was based on the principles of functionality and reliability. However, it is increasingly being realized that such design objectives are not sufficient. Threats, disruptions and faults often compromise the network, taking away the benefits of an efficient and reliable design. Thus, traditional network design parameters must be combined with self-healing mechanisms to obtain a resilient design of the network. In this paper, we present RNEDEa resilient network design environment that that not only optimizes the network for performance but tolerates fluctuations in its structure that result from external threats and disruptions. The environment evaluates a set of remedial actions to bring a compromised network to an optimal level of functionality. The environment includes a visualizer that enables the network administrator to be aware of the current state of the network and the suggested remedial actions at all times.

Life by design: Philosophical perspectives on synthetic biology

Directory of Open Access Journals (Sweden)

Bensaude Vincent Bernadette

2015-01-01

This paper outlines a number of distinctive features of this emerging field in the constellation of bionanotechnologies. It then insists on the variety of research agendas and strategies gathered under the umbrella “synthetic biology”. While redesigning life is the central goal, synthetic biologists do not develop a uniform view of living organisms.

A bio-synthetic interface for discovery of viral entry mechanisms.

Energy Technology Data Exchange (ETDEWEB)

Gutzler, Mike; Maar, Dianna; Negrete, Oscar; Hayden, Carl C.; Sasaki, Darryl Yoshio; Stachowiak, Jeanne C.; Wang, Julia

2010-09-01

Understanding and defending against pathogenic viruses is an important public health and biodefense challenge. The focus of our LDRD project has been to uncover the mechanisms enveloped viruses use to identify and invade host cells. We have constructed interfaces between viral particles and synthetic lipid bilayers. This approach provides a minimal setting for investigating the initial events of host-virus interaction - (i) recognition of, and (ii) entry into the host via membrane fusion. This understanding could enable rational design of therapeutics that block viral entry as well as future construction of synthetic, non-proliferating sensors that detect live virus in the environment. We have observed fusion between synthetic lipid vesicles and Vesicular Stomatitis virus particles, and we have observed interactions between Nipah virus-like particles and supported lipid bilayers and giant unilamellar vesicles.

Synthetic fibers in atmospheric fallout: A source of microplastics in the environment?

Science.gov (United States)

Dris, Rachid; Gasperi, Johnny; Saad, Mohamed; Mirande, Cécile; Tassin, Bruno

2016-03-15

Sources, pathways and reservoirs of microplastics, plastic particles smaller than 5mm, remain poorly documented in an urban context. While some studies pointed out wastewater treatment plants as a potential pathway of microplastics, none have focused on the atmospheric compartment. In this work, the atmospheric fallout of microplastics was investigated in two different urban and sub-urban sites. Microplastics were collected continuously with a stainless steel funnel. Samples were then filtered and observed with a stereomicroscope. Fibers accounted for almost all the microplastics collected. An atmospheric fallout between 2 and 355 particles/m(2)/day was highlighted. Registered fluxes were systematically higher at the urban than at the sub-urban site. Chemical characterization allowed to estimate at 29% the proportion of these fibers being all synthetic (made with petrochemicals), or a mixture of natural and synthetic material. Extrapolation using weight and volume estimates of the collected fibers, allowed a rough estimation showing that between 3 and 10 tons of fibers are deposited by atmospheric fallout at the scale of the Parisian agglomeration every year (2500 km(2)). These results could serve the scientific community working on the different sources of microplastic in both continental and marine environments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Energy and environment design guide

Energy Technology Data Exchange (ETDEWEB)

Harman, K. [Royal Australian Institute of Architects, Canberra, ACT (Australia)

1996-04-01

The Royal Australian Institute of Architects (RAIA) released an Environment Policy for architects in September 1994 which forms part of the RAIA Code of Professional Conduct. Prior to releasing the policy, it was recognised that members needed information and education in the area of energy and environment in order to adopt and implement the guide. This document is a report on the scope, work programme and achievements of a project to provide an easy reference resource for architects and other building designers, and bring together a wide range of information and research. It includes the Environment Policy as an appendix. The project produced 24 notes entitled the `Environment Design Guide - energy/environment notes` covering a wide range of topics, and four newsletters. Feedback received from architects to date indicates that the development of the notes has had a positive effect on their knowledge of these issues, resulting in the making of informed design decisions. The topics covered by the notes are expected to expand in 1996 with the preparation of additional notes which provide information on products and sustainable construction.

Building a Case-Based Design Assistant for Workplace Environment Design

NARCIS (Netherlands)

Mallory-Hill, S.M.; Timmermans, H.J.P.

1998-01-01

This paper reports on the early stages of development of a case-based design tool. The purpose of this tool, called the Workplace Environment Design Advisor (WEDA), is to support architects in the conceptual design of workplace environments. The objective of this system is to provide electronic

Rationally designed synthetic protein hydrogels with predictable mechanical properties.

Science.gov (United States)

Wu, Junhua; Li, Pengfei; Dong, Chenling; Jiang, Heting; Bin Xue; Gao, Xiang; Qin, Meng; Wang, Wei; Bin Chen; Cao, Yi

2018-02-12

Designing synthetic protein hydrogels with tailored mechanical properties similar to naturally occurring tissues is an eternal pursuit in tissue engineering and stem cell and cancer research. However, it remains challenging to correlate the mechanical properties of protein hydrogels with the nanomechanics of individual building blocks. Here we use single-molecule force spectroscopy, protein engineering and theoretical modeling to prove that the mechanical properties of protein hydrogels are predictable based on the mechanical hierarchy of the cross-linkers and the load-bearing modules at the molecular level. These findings provide a framework for rationally designing protein hydrogels with independently tunable elasticity, extensibility, toughness and self-healing. Using this principle, we demonstrate the engineering of self-healable muscle-mimicking hydrogels that can significantly dissipate energy through protein unfolding. We expect that this principle can be generalized for the construction of protein hydrogels with customized mechanical properties for biomedical applications.

The use of synthetic ligaments in the design of an enhanced stability total knee joint replacement.

Science.gov (United States)

Stokes, Michael D; Greene, Brendan C; Pietrykowski, Luke W; Gambon, Taylor M; Bales, Caroline E; DesJardins, John D

2018-03-01

Current total knee replacement designs work to address clinically desired knee stability and range of motion through a balance of retained anatomy and added implant geometry. However, simplified implant geometries such as bearing surfaces, posts, and cams are often used to replace complex ligamentous constraints that are sacrificed during most total knee replacement procedures. This article evaluates a novel total knee replacement design that incorporates synthetic ligaments to enhance the stability of the total knee replacement system. It was hypothesized that by incorporating artificial cruciate ligaments into a total knee replacement design at specific locations and lengths, the stability of the total knee replacement could be significantly altered while maintaining active ranges of motion. The ligament attachment mechanisms used in the design were evaluated using a tensile test, and determined to have a safety factor of three with respect to expected ligamentous loading in vivo. Following initial computational modeling of possible ligament orientations, a physical prototype was constructed to verify the function of the design by performing anterior/posterior drawer tests under physiologic load. Synthetic ligament configurations were found to increase total knee replacement stability up to 94% compared to the no-ligament case, while maintaining total knee replacement flexion range of motion between 0° and 120°, indicating that a total knee replacement that incorporates synthetic ligaments with calibrated location and lengths should be able to significantly enhance and control the kinematic performance of a total knee replacement system.

Where Synthetic Biology Meets ET

Science.gov (United States)

Rothschild, Lynn J.

2016-01-01

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

The prevalence of two ‘commonly’ encountered synthetic target fibres within a large urban environment

OpenAIRE

Palmer, Ray; Burnett, Elisabeth; Luff, Natalie; Wagner, Craig; Stinga, Georgia; Carney, Clare; Sheridan, Kelly

2015-01-01

A target fibre study was carried out to assess the random prevalence of two ostensibly commonly encountered synthetic fibre types; black acrylic and blue polyester. The study was performed in an environment which maximised the number of random contacts between textile garments in the population and specific surfaces, namely; seating relating to buses, public houses and cinemas found within a large urban conurbation.\\ud \\ud Surface debris tapings were collected from samples of bus seats (30), ...

Biocontainment of genetically modified organisms by synthetic protein design

Science.gov (United States)

Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T.; Takeuchi, Ryo; Kuznetsov, Gleb; Norville, Julie E.; Gregg, Christopher J.; Stoddard, Barry L.; Church, George M.

2015-02-01

Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

Science.gov (United States)

Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

2017-12-15

This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

40 CFR 721.3627 - Branched synthetic fatty acid.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Branched synthetic fatty acid. 721... Substances § 721.3627 Branched synthetic fatty acid. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as a branched synthetic fatty acid...

Application of fuzzy synthetic assessment to assess human factors design level on reactor control panel

International Nuclear Information System (INIS)

Peng Xuecheng

1999-01-01

Reactor control panel design level on human factors must be considered by designer. The author evaluated the human factor design level of arrangement and combinations including the switch buttons, meter dials and indication lamps on Minjiang Reactor and High-Flux Engineer Test Reactor (HFETR) critical device by application of fuzzy synthetic assessment method in mathematics. From the assessment results, the advantages and shortcomings are fount, and some modification suggestions have also been proposed

Designing an adaptive salutogenic care environment

OpenAIRE

Dalton, Cathy; Harrison, Jim D.

2011-01-01

Humans are profoundly affected by the surroundings which they inhabit. Environmental psychologists have produced numerous credible theories describing optimal human environments, based on the concept of congruence or “fit” (1, 2). Lack of person/environment fit can lead to stress-related illness and lack of psychosocial well-being (3). Conversely, appropriately designed environments can promote wellness (4) or “salutogenesis” (5). Increasingly, research in the area of Evidence-Based Design, l...

Chemical communication between synthetic and natural cells: a possible experimental design.

Directory of Open Access Journals (Sweden)

Livia Leoni

2013-09-01

Full Text Available The bottom-up construction of synthetic cells is one of the most intriguing and interesting research arenas in synthetic biology. Synthetic cells are built by encapsulating biomolecules inside lipid vesicles (liposomes, allowing the synthesis of one or more functional proteins. Thanks to the in situ synthesized proteins, synthetic cells become able to perform several biomolecular functions, which can be exploited for a large variety of applications. This paves the way to several advanced uses of synthetic cells in basic science and biotechnology, thanks to their versatility, modularity, biocompatibility, and programmability. In the previous WIVACE (2012 we presented the state-of-the-art of semi-synthetic minimal cell (SSMC technology and introduced, for the first time, the idea of chemical communication between synthetic cells and natural cells. The development of a proper synthetic communication protocol should be seen as a tool for the nascent field of bio/chemical-based Information and Communication Technologies (bio-chem-ICTs and ultimately aimed at building soft-wet-micro-robots. In this contribution (WIVACE, 2013 we present a blueprint for realizing this project, and show some preliminary experimental results. We firstly discuss how our research goal (based on the natural capabilities of biological systems to manipulate chemical signals finds a proper place in the current scientific and technological contexts. Then, we shortly comment on the experimental approaches from the viewpoints of (i synthetic cell construction, and (ii bioengineering of microorganisms, providing up-to-date results from our laboratory. Finally, we shortly discuss how autopoiesis can be used as a theoretical framework for defining synthetic minimal life, minimal cognition, and as bridge between synthetic biology and artificial intelligence.

Designer Drugs: A Synthetic Catastrophe

OpenAIRE

Fratantonio, James; Andrade, Lawrence; Febo, Marcelo

2015-01-01

Synthetic stimulants can cause hallucinations, aggressive behaviors, death and are sometimes legal. These substances are sold as plant food and bath salts that are "Not for Human Consumption", therefore skirting the 1986 Federal Analogue Act and giving a false pretense of safety. Studies have proved that these substances are toxic, have a high abuse potential, and are becoming extremely prevalent in the United States. This creates a dilemma for law enforcement agents, hospitals, and substance...

A Synthetic Algorithm for Tracking a Moving Object in a Multiple-Dynamic Obstacles Environment Based on Kinematically Planar Redundant Manipulators

Directory of Open Access Journals (Sweden)

Hongzhe Jin

2017-01-01

Full Text Available This paper presents a synthetic algorithm for tracking a moving object in a multiple-dynamic obstacles environment based on kinematically planar manipulators. By observing the motions of the object and obstacles, Spline filter associated with polynomial fitting is utilized to predict their moving paths for a period of time in the future. Several feasible paths for the manipulator in Cartesian space can be planned according to the predicted moving paths and the defined feasibility criterion. The shortest one among these feasible paths is selected as the optimized path. Then the real-time path along the optimized path is planned for the manipulator to track the moving object in real-time. To improve the convergence rate of tracking, a virtual controller based on PD controller is designed to adaptively adjust the real-time path. In the process of tracking, the null space of inverse kinematic and the local rotation coordinate method (LRCM are utilized for the arms and the end-effector to avoid obstacles, respectively. Finally, the moving object in a multiple-dynamic obstacles environment is thus tracked via real-time updating the joint angles of manipulator according to the iterative method. Simulation results show that the proposed algorithm is feasible to track a moving object in a multiple-dynamic obstacles environment.

Structure-activity-based design of a synthetic malaria peptide eliciting sporozoite inhibitory antibodies in a virosomal formulation.

NARCIS (Netherlands)

Okitsu, S.L.; Kienzl, U.; Moehle, K.; Silvie, O.; Peduzzi, E.; Mueller, M.S.; Sauerwein, R.W.; Matile, H.; Zurbriggen, R.; Mazier, D.; Robinson, J.A.; Pluschke, G.

2007-01-01

The circumsporozoite protein (CSP) of Plasmodium falciparum is a leading candidate antigen for inclusion in a malaria subunit vaccine. We describe here the design of a conformationally constrained synthetic peptide, designated UK-39, which has structural and antigenic similarity to the NPNA-repeat

Bottom-up synthetic biology: modular design for making artificial platelets

Science.gov (United States)

Majumder, Sagardip; Liu, Allen P.

2018-01-01

Engineering artificial cells to mimic one or multiple fundamental cell biological functions is an emerging area of synthetic biology. Reconstituting functional modules from biological components in vitro is a challenging yet an important essence of bottom-up synthetic biology. Here we describe the concept of building artificial platelets using bottom-up synthetic biology and the four functional modules that together could enable such an ambitious effort.

Control theory meets synthetic biology.

Science.gov (United States)

Del Vecchio, Domitilla; Dy, Aaron J; Qian, Yili

2016-07-01

The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology. © 2016 The Author(s).

Dynamic testing of horseshoe designs at impact on synthetic and dirt Thoroughbred racetrack materials.

Science.gov (United States)

Mahaffey, C A; Peterson, M L; Thomason, J J; McIlwraith, C W

2016-01-01

Different horseshoe designs have been developed in an attempt to optimise footing for equine athletes. Horseshoe performance is assumed to be dependent on the surface and gait, but there are limited data on horseshoe performance on different surfaces, independent of gait variation. To quantify the dynamic loading for 3 aluminium racing shoe designs on Thoroughbred racetrack surface materials, using a biomechanical surface tester. A flat racing plate, a serrated V-Grip and a shoe with a 6 mm toe grab and 10 mm heel calks were tested on synthetic and dirt surfaces under typical operating conditions of temperature and moisture content for the respective material samples. Samples were tested under laboratory conditions, replicating a track surface by compacting material into a latex-lined mould surrounded by silica sand for representative boundary conditions. Peak loading and loading rates were measured vertically and horizontally (craniocaudal), simulating aspects of primary and secondary impacts of the hoof in a galloping horse. Maximum vertical and shear loads and loading rates were not significantly different between shoe types, with the exception of a reduced craniocaudal loading rate for the V-Grip shoe on the synthetic surface. All other statistical significance was related to the surface material. These 3 different Thoroughbred racing shoes do not have a significant impact on loading and loading rate, with the exception of the V-Grip shoe on a synthetic surface. Although the V-Grip may reduce craniocaudal peak load rates in a synthetic material with relatively high wax and/or low oil content, the reduction in load rate is less than the difference found between materials. This study indicates that shoeing has little effect, and that a track's surface material and its preparation have a significant effect on the dynamic loading during the impact phase of the stance. © 2015 EVJ Ltd.

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

Science.gov (United States)

Toni, Tina; Tidor, Bruce

2013-01-01

Biological systems are inherently variable, with their dynamics influenced by intrinsic and extrinsic sources. These systems are often only partially characterized, with large uncertainties about specific sources of extrinsic variability and biochemical properties. Moreover, it is not yet well understood how different sources of variability combine and affect biological systems in concert. To successfully design biomedical therapies or synthetic circuits with robust performance, it is crucial to account for uncertainty and effects of variability. Here we introduce an efficient modeling and simulation framework to study systems that are simultaneously subject to multiple sources of variability, and apply it to make design decisions on small genetic networks that play a role of basic design elements of synthetic circuits. Specifically, the framework was used to explore the effect of transcriptional and post-transcriptional autoregulation on fluctuations in protein expression in simple genetic networks. We found that autoregulation could either suppress or increase the output variability, depending on specific noise sources and network parameters. We showed that transcriptional autoregulation was more successful than post-transcriptional in suppressing variability across a wide range of intrinsic and extrinsic magnitudes and sources. We derived the following design principles to guide the design of circuits that best suppress variability: (i) high protein cooperativity and low miRNA cooperativity, (ii) imperfect complementarity between miRNA and mRNA was preferred to perfect complementarity, and (iii) correlated expression of mRNA and miRNA – for example, on the same transcript – was best for suppression of protein variability. Results further showed that correlations in kinetic parameters between cells affected the ability to suppress variability, and that variability in transient states did not necessarily follow the same principles as variability in the steady

Models for synthetic biology.

Science.gov (United States)

Kaznessis, Yiannis N

2007-11-06

Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal.

Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology.

Science.gov (United States)

Toyoda, Tetsuro

2011-01-01

Synthetic biology requires both engineering efficiency and compliance with safety guidelines and ethics. Focusing on the rational construction of biological systems based on engineering principles, synthetic biology depends on a genome-design platform to explore the combinations of multiple biological components or BIO bricks for quickly producing innovative devices. This chapter explains the differences among various platform models and details a methodology for promoting open innovation within the scope of the statutory exemption of patent laws. The detailed platform adopts a centralized evaluation model (CEM), computer-aided design (CAD) bricks, and a freemium model. It is also important for the platform to support the legal aspects of copyrights as well as patent and safety guidelines because intellectual work including DNA sequences designed rationally by human intelligence is basically copyrightable. An informational platform with high traceability, transparency, auditability, and security is required for copyright proof, safety compliance, and incentive management for open innovation in synthetic biology. GenoCon, which we have organized and explained here, is a competition-styled, open-innovation method involving worldwide participants from scientific, commercial, and educational communities that aims to improve the designs of genomic sequences that confer a desired function on an organism. Using only a Web browser, a participating contributor proposes a design expressed with CAD bricks that generate a relevant DNA sequence, which is then experimentally and intensively evaluated by the GenoCon organizers. The CAD bricks that comprise programs and databases as a Semantic Web are developed, executed, shared, reused, and well stocked on the secure Semantic Web platform called the Scientists' Networking System or SciNetS/SciNeS, based on which a CEM research center for synthetic biology and open innovation should be established. Copyright © 2011 Elsevier Inc

Synthetic biological networks

International Nuclear Information System (INIS)

Archer, Eric; Süel, Gürol M

2013-01-01

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

Design of synthetic biological logic circuits based on evolutionary algorithm.

Science.gov (United States)

Chuang, Chia-Hua; Lin, Chun-Liang; Chang, Yen-Chang; Jennawasin, Tanagorn; Chen, Po-Kuei

2013-08-01

The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology. In this study, a real-structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis-regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting optimal design of these logic gates and circuits are established via the RSGA. The in silico computer-based modelling technology has been verified showing its great advantages in the purpose.

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

Science.gov (United States)

Ohno, Hirohisa; Saito, Hirohide

2016-01-01

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Engineering genetic circuit interactions within and between synthetic minimal cells

Science.gov (United States)

Adamala, Katarzyna P.; Martin-Alarcon, Daniel A.; Guthrie-Honea, Katriona R.; Boyden, Edward S.

2017-05-01

Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. We demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) to contain multiple-part genetic cascades, and that these cascades can be controlled by external signals as well as inter-liposomal communication without crosstalk. We also show that liposomes that contain different cascades can be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable a more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.

Synthetic biology: programming cells for biomedical applications.

Science.gov (United States)

Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

2012-01-01

The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.

Standardization of green building technologies for environment design

Directory of Open Access Journals (Sweden)

Benuzh Andrey

2016-01-01

Full Text Available The article describes the structure and field of standardization ISO / TC 205 “Building environment design”, provides examples of green building technologies. The main purpose of the article is to show the interaction between international ISO / TC 205 “Building environment design” and created in Russia in 2016 the Technical Committee of Standardization № 366 “Green technology of the build environment and green innovative products”. Both of these technical committees promote green building technologies for environment design, thereby deal with the negative impact on the environment and the reasons of global warming. Instead of buildings that attempt to suppress and overcome nature, why not design buildings that integrate with the environment, on every possible level? The international standardization work which ISO/TC 205 “Building environment design” performs seeks, in addition to lowering trade barriers for engineering design, to promote and facilitate the design of high performance buildings: higher performing as economic assets for their owners, higher performing as buildings that provide amenable indoor environment for their occupants, and higher performing with respect to resource utilization and environmental impact.

Environment, information divide and design

International Nuclear Information System (INIS)

Iwata, Shuichi

2007-01-01

Design of human environment is to be made with understanding human-human and human-environment relations and environmental behaviors of human beings, artifacts and natural things and overcoming their differences and contradictions. Information divide exists naturally due to various differences of human beings. Many problems in the area of nuclear energy seem to be derived from various differences and contradictions in central-local interests, between the particles concerned and unconcerned and also in human being-artifacts relations. In order to harmonize nuclear energy with the society, it is necessary to vanish differences and solve contradictions with redesigning environments of those problems in their context. Case studies are highly recommended with continuous efforts to develop more universal design methodology. Open access to information and data in science and technology is encouraged in the area of nuclear energy. (T. Tanaka)

A Design Framework for Personal Learning Environments

NARCIS (Netherlands)

Rahimi, E.

2015-01-01

The purpose of our research was to develop a PLE (personal learning environment) design framework for workplace settings. By doing such, the research has answered this research question, how should a technology-based personal learning environment be designed, aiming at supporting learners to gain

Characterization of Thermal Stability of Synthetic and Semi-Synthetic Engine Oils

Directory of Open Access Journals (Sweden)

Anand Kumar Tripathi

2015-03-01

Full Text Available Engine oils undergo oxidative degradation and wears out during service. Hence it is important to characterize ageing of engine oils at different simulated conditions to evaluate the performance of existing oils and also design new formulations. This work focuses on characterizing the thermo-oxidative degradation of synthetic and semi-synthetic engine oils aged at 120, 149 and 200 °C. Apparent activation energy of decomposition of aged oils evaluated using the isoconversional Kissinger-Akahira-Sunose technique was used as a thermal stability marker. The temporal variation of stability at different ageing temperatures was corroborated with kinematic viscosity, oxidation, sulfation and nitration indices, total base number, antiwear additive content and molecular structure of the organic species present in the oils. At the lowest temperature employed, synthetic oil underwent higher rate of oxidation, while semi-synthetic oil was stable for longer time periods. At higher temperatures, the initial rate of change of average apparent activation energy of synthetic oil correlated well with a similar variation in oxidation number. A mixture of long chain linear, branched, and cyclic hydrocarbons were observed when semi-synthetic oil was degraded at higher temperatures.

Synthetic biology: engineering molecular computers

CERN Multimedia

CERN. Geneva

2018-01-01

Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

From noise to synthetic nucleoli: can synthetic biology achieve new insights?

Science.gov (United States)

Ciechonska, Marta; Grob, Alice; Isalan, Mark

2016-04-18

Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."

The Ethics of Synthetic Biology

DEFF Research Database (Denmark)

Christiansen, Andreas

The dissertation analyses and discusses a number of ethical issues that have been raised in connection with the development of synthetic biology. Synthetic biology is a set of new techniques for DNA-level design and construction of living beings with useful properties. The dissertation especially...

Design of molecular imprinted polymers compatible with aqueous environment.

Science.gov (United States)

Piletska, Elena V; Guerreiro, Antonio R; Romero-Guerra, Maria; Chianella, Iva; Turner, Anthony P F; Piletsky, Sergey A

2008-01-21

The main problem of poor water compatibility of molecularly imprinted polymers (MIPs) was addressed in examples describing design of synthetic receptors with high affinity for drugs of abuse. An extensive potentiometric titration of 10 popular functional monomers and corresponding imprinted and blank polymers was conducted in order to evaluate the subtleties of functional groups ionisation under aqueous conditions. It was found that polymers prepared using 2-trifluoromethacrylic acid (TFMAA) in combination with toluene as porogen possess superior properties which make them suitable for effective template recognition in water. The potential impact of phase separation during polymerisation on formation of high quality imprints has been discussed. Three drugs of abuse such as cocaine, deoxyephedrine and methadone were used as template models in polymer preparation for the practical validation of obtained results. The polymer testing showed that synthesized molecularly imprinted polymers have high affinity and selectivity for corresponding templates in aqueous environment, with imprinting factors of 2.6 for cocaine and 1.4 for methadone and deoxyephedrine. Corresponding blank polymers were unable to differentiate between analytes, suggesting that imprinting phenomenon was responsible for the recognition properties.

A standard-enabled workflow for synthetic biology

KAUST Repository

Myers, Chris J.

2017-06-15

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

Designing Learning Resources in Synchronous Learning Environments

DEFF Research Database (Denmark)

Christiansen, Rene B

2015-01-01

Computer-mediated Communication (CMC) and synchronous learning environments offer new solutions for teachers and students that transcend the singular one-way transmission of content knowledge from teacher to student. CMC makes it possible not only to teach computer mediated but also to design...... and create new learning resources targeted to a specific group of learners. This paper addresses the possibilities of designing learning resources within synchronous learning environments. The empirical basis is a cross-country study involving students and teachers in primary schools in three Nordic...... Countries (Denmark, Sweden and Norway). On the basis of these empirical studies a set of design examples is drawn with the purpose of showing how the design fulfills the dual purpose of functioning as a remote, synchronous learning environment and - using the learning materials used and recordings...

A Distributed Feature-based Environment for Collaborative Design

Directory of Open Access Journals (Sweden)

Wei-Dong Li

2003-02-01

Full Text Available This paper presents a client/server design environment based on 3D feature-based modelling and Java technologies to enable design information to be shared efficiently among members within a design team. In this environment, design tasks and clients are organised through working sessions generated and maintained by a collaborative server. The information from an individual design client during a design process is updated and broadcast to other clients in the same session through an event-driven and call-back mechanism. The downstream manufacturing analysis modules can be wrapped as agents and plugged into the open environment to support the design activities. At the server side, a feature-feature relationship is established and maintained to filter the varied information of a working part, so as to facilitate efficient information update during the design process.

Cell-free synthetic biology for in vitro prototype engineering.

Science.gov (United States)

Moore, Simon J; MacDonald, James T; Freemont, Paul S

2017-06-15

Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).

Peptide/protein-polymer conjugates: synthetic strategies and design concepts.

Science.gov (United States)

Gauthier, Marc A; Klok, Harm-Anton

2008-06-21

This feature article provides a compilation of tools available for preparing well-defined peptide/protein-polymer conjugates, which are defined as hybrid constructs combining (i) a defined number of peptide/protein segments with uniform chain lengths and defined monomer sequences (primary structure) with (ii) a defined number of synthetic polymer chains. The first section describes methods for post-translational, or direct, introduction of chemoselective handles onto natural or synthetic peptides/proteins. Addressed topics include the residue- and/or site-specific modification of peptides/proteins at Arg, Asp, Cys, Gln, Glu, Gly, His, Lys, Met, Phe, Ser, Thr, Trp, Tyr and Val residues and methods for producing peptides/proteins containing non-canonical amino acids by peptide synthesis and protein engineering. In the second section, methods for introducing chemoselective groups onto the side-chain or chain-end of synthetic polymers produced by radical, anionic, cationic, metathesis and ring-opening polymerization are described. The final section discusses convergent and divergent strategies for covalently assembling polymers and peptides/proteins. An overview of the use of chemoselective reactions such as Heck, Sonogashira and Suzuki coupling, Diels-Alder cycloaddition, Click chemistry, Staudinger ligation, Michael's addition, reductive alkylation and oxime/hydrazone chemistry for the convergent synthesis of peptide/protein-polymer conjugates is given. Divergent approaches for preparing peptide/protein-polymer conjugates which are discussed include peptide synthesis from synthetic polymer supports, polymerization from peptide/protein macroinitiators or chain transfer agents and the polymerization of peptide side-chain monomers.

Towards a synthetic osteo-odonto-keratoprosthesis.

Science.gov (United States)

Viitala, Reeta; Franklin, Valerie; Green, David; Liu, Christopher; Lloyd, Andrew; Tighe, Brian

2009-01-01

Osteo-odonto-keratoprostheses (OOKP) is a unique form of keratoprosthesis involving surgical removal of a tooth root and surrounding bone from the patient which are then used to construct an osteo-odonto lamina into which an optical cylinder is cemented. The OOKP procedure is successful and capable of withstanding the very hostile ocular environments found in severe Stevens-Johnson syndrome, pemphigoid, chemical burns, trachoma and multiple corneal graft failure. The existing procedure is complex and time consuming in terms of operative time, and additionally involves sacrifice of the oral structures. This paper discusses the rational search for a "synthetic" analogue of the dental lamina, capable of mimicking those features of the natural system that are responsible for the success of OOKP. In this study the degradation of selected commercial and natural bioceramics was tested in vitro using a purpose-designed resorption assay. Degradation rate was compared with tooth and bone, which are currently used in OOKP lamina. At normal physiological pH the degradation of bioceramics was equivalent to tooth and bone; however, at pH 6.5-5.0, associated with infectious and inflamed tissues, the bioceramics degrade more rapidly. At lower pH the degradation rate decreased in the following order: calcium carbonate corals>biphasic calcium phosphates>hydroxyapatite. Porosity did not significantly influence these degradation rates. Such degradation is likely to compromise the stability and viability of the synthetic OOKP. Consequently more chemically stable materials are required that are optimized for the surrounding ocular environment.

Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

Directory of Open Access Journals (Sweden)

Lee Jack J

2009-01-01

Full Text Available Abstract Background Microbial communities are involved in many processes relevant to industrial and medical biotechnology, such as the formation of biofilms, lignocellulosic degradation, and hydrogen production. The manipulation of synthetic and natural microbial communities and their underlying ecological parameters, such as fitness, evolvability, and variation, is an increasingly important area of research for synthetic biology. Results Here, we explored how synthetic control of an endogenous circuit can be used to regulate a tradeoff between fitness in resource abundant and resource limited environments in a population of Saccharomyces cerevisiae. We found that noise in the expression of a key enzyme in ammonia assimilation, Gdh1p, mediated a tradeoff between growth in low nitrogen environments and stress resistance in high ammonia environments. We implemented synthetic control of an endogenous Gdh1p regulatory network to construct an engineered strain in which the fitness of the population was tunable in response to an exogenously-added small molecule across a range of ammonia environments. Conclusion The ability to tune fitness and biological tradeoffs will be important components of future efforts to engineer microbial communities.

A standard-enabled workflow for synthetic biology.

Science.gov (United States)

Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

2017-06-15

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Developments in the Tools and Methodologies of Synthetic Biology

Science.gov (United States)

Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.; Freemont, Paul

2014-01-01

Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community. PMID:25505788

Developments in the tools and methodologies of synthetic biology

Directory of Open Access Journals (Sweden)

Richard eKelwick

2014-11-01

Full Text Available Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices or systems. However, biological systems are generally complex and unpredictable and are therefore intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a ‘body of knowledge’ from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled and its functionality tested. At each stage of the design cycle an expanding repertoire of tools is being developed. In this review we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.

Design & Development of a High Mass Flow Piston Synthetic Jet Actuator

Directory of Open Access Journals (Sweden)

Ashraf Hamad Muhammad

2015-01-01

Full Text Available The idea of having a device that is capable of working in a systematic process allowing control of the boundary layer by means of operated on high-frequency, small-scale, and low energy actuators has caught the interest of the aerodynamicist community. With an eye on the available data and potential flow control advantages, our research team set out to manufacture a compact SJA (Synthetic Jet Actuator of its own, which would be capable of being installed inside an airfoil. It consists of components such as a single piston cylinder, with variable exit geometry along with the control system that has an electrical actuator which can be regulated in order for it to be capable of producing various operating frequencies. This paper consists of a study into the design of a single piston device SJA and will present all significant data both theoretical and computational regarding its design and performance.

GLobal Integrated Design Environment

Science.gov (United States)

Kunkel, Matthew; McGuire, Melissa; Smith, David A.; Gefert, Leon P.

2011-01-01

The GLobal Integrated Design Environment (GLIDE) is a collaborative engineering application built to resolve the design session issues of real-time passing of data between multiple discipline experts in a collaborative environment. Utilizing Web protocols and multiple programming languages, GLIDE allows engineers to use the applications to which they are accustomed in this case, Excel to send and receive datasets via the Internet to a database-driven Web server. Traditionally, a collaborative design session consists of one or more engineers representing each discipline meeting together in a single location. The discipline leads exchange parameters and iterate through their respective processes to converge on an acceptable dataset. In cases in which the engineers are unable to meet, their parameters are passed via e-mail, telephone, facsimile, or even postal mail. The result of this slow process of data exchange would elongate a design session to weeks or even months. While the iterative process remains in place, software can now exchange parameters securely and efficiently, while at the same time allowing for much more information about a design session to be made available. GLIDE is written in a compilation of several programming languages, including REALbasic, PHP, and Microsoft Visual Basic. GLIDE client installers are available to download for both Microsoft Windows and Macintosh systems. The GLIDE client software is compatible with Microsoft Excel 2000 or later on Windows systems, and with Microsoft Excel X or later on Macintosh systems. GLIDE follows the Client-Server paradigm, transferring encrypted and compressed data via standard Web protocols. Currently, the engineers use Excel as a front end to the GLIDE Client, as many of their custom tools run in Excel.

Synthetic biology and metabolic engineering.

Science.gov (United States)

Stephanopoulos, Gregory

2012-11-16

Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.

Design of a vascularized synthetic poly(ethylene glycol) macroencapsulation device for islet transplantation.

Science.gov (United States)

Weaver, Jessica D; Headen, Devon M; Hunckler, Michael D; Coronel, Maria M; Stabler, Cherie L; García, Andrés J

2018-07-01

The use of immunoisolating macrodevices in islet transplantation confers the benefit of safety and translatability by containing transplanted cells within a single retrievable device. To date, there has been limited development and characterization of synthetic poly(ethylene glycol) (PEG)-based hydrogel macrodevices for islet encapsulation and transplantation. Herein, we describe a two-component synthetic PEG hydrogel macrodevice system, designed for islet delivery to an extrahepatic islet transplant site, consisting of a hydrogel core cross-linked with a non-degradable PEG dithiol and a vasculogenic outer layer cross-linked with a proteolytically sensitive peptide to promote degradation and enhance localized vascularization. Synthetic PEG macrodevices exhibited equivalent passive molecular transport to traditional microencapsulation materials (e.g., alginate) and long-term stability in the presence of proteases in vitro and in vivo, out to 14 weeks in rats. Encapsulated islets demonstrated high viability within the device in vitro and the incorporation of RGD adhesive peptides within the islet encapsulating PEG hydrogel improved insulin responsiveness to a glucose challenge. In vivo, the implementation of a vasculogenic, degradable hydrogel layer at the outer interface of the macrodevice enhanced vascular density within the rat omentum transplant site, resulting in improved encapsulated islet viability in a syngeneic diabetic rat model. These results highlight the benefits of the facile PEG platform to provide controlled presentation of islet-supportive ligands, as well as degradable interfaces for the promotion of engraftment and overall graft efficacy. Copyright © 2018 Elsevier Ltd. All rights reserved.

Inputs and distributions of synthetic musk fragrances in an estuarine and coastal environment; a case study

International Nuclear Information System (INIS)

Sumner, Nicola R.; Guitart, Carlos; Fuentes, Gustavo; Readman, James W.

2010-01-01

Synthetic musks are ubiquitous contaminants in the environment. Compartmental distributions (dissolved, suspended particle associated and sedimentary) of the compounds throughout an axial estuarine transect and in coastal waters are reported. High concentrations of Galaxolide (HHCB) and Tonalide (AHTN) (987-2098 ng/L and 55-159 ng/L, respectively) were encountered in final effluent samples from sewage treatment plants (STPs) discharging into the Tamar and Plym Estuaries (UK), with lower concentrations of Celestolide (ADBI) (4-13 ng/L), Phantolide (AHMI) (6-9 ng/L), musk xylene (MX) (4-7 ng/L) and musk ketone (MK) (18-30 ng/L). Rapid dilution from the outfalls is demonstrated with resulting concentrations of HHCB spanning from 5 to 30 ng/L and those for AHTN from 3 to 15 ng/L. The other musks were generally not detected in the estuarine and coastal waters. The suspended particulate matter (SPM) and sedimentary profiles and compositions (HHCB:AHTN ratios) generally reflect the distribution in the water column with highest concentrations adjacent to sewage outfalls. - Synthetic musks were determined in coastal environmental compartments along an estuarine transect indicating their ubiquitous occurrence in transitional waters.

Inputs and distributions of synthetic musk fragrances in an estuarine and coastal environment; a case study

Energy Technology Data Exchange (ETDEWEB)

Sumner, Nicola R. [School of Earth, Ocean and Environmental Science, University of Plymouth, Drake Circus, Plymouth PL4 8AA (United Kingdom); Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH (United Kingdom); Guitart, Carlos, E-mail: guitart.carlos@gmail.co [Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH (United Kingdom); Fuentes, Gustavo [Instituto Universitario de Tecnologia del Mar (IUTEMAR), Fundacion La Salle de Ciencias Naturales, Margarita Island (Venezuela, Bolivarian Republic of); Readman, James W. [Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH (United Kingdom)

2010-01-15

Synthetic musks are ubiquitous contaminants in the environment. Compartmental distributions (dissolved, suspended particle associated and sedimentary) of the compounds throughout an axial estuarine transect and in coastal waters are reported. High concentrations of Galaxolide (HHCB) and Tonalide (AHTN) (987-2098 ng/L and 55-159 ng/L, respectively) were encountered in final effluent samples from sewage treatment plants (STPs) discharging into the Tamar and Plym Estuaries (UK), with lower concentrations of Celestolide (ADBI) (4-13 ng/L), Phantolide (AHMI) (6-9 ng/L), musk xylene (MX) (4-7 ng/L) and musk ketone (MK) (18-30 ng/L). Rapid dilution from the outfalls is demonstrated with resulting concentrations of HHCB spanning from 5 to 30 ng/L and those for AHTN from 3 to 15 ng/L. The other musks were generally not detected in the estuarine and coastal waters. The suspended particulate matter (SPM) and sedimentary profiles and compositions (HHCB:AHTN ratios) generally reflect the distribution in the water column with highest concentrations adjacent to sewage outfalls. - Synthetic musks were determined in coastal environmental compartments along an estuarine transect indicating their ubiquitous occurrence in transitional waters.

Coal conversion processes and analysis methodologies for synthetic fuels production. [technology assessment and economic analysis of reactor design for coal gasification

Science.gov (United States)

1979-01-01

Information to identify viable coal gasification and utilization technologies is presented. Analysis capabilities required to support design and implementation of coal based synthetic fuels complexes are identified. The potential market in the Southeast United States for coal based synthetic fuels is investigated. A requirements analysis to identify the types of modeling and analysis capabilities required to conduct and monitor coal gasification project designs is discussed. Models and methodologies to satisfy these requirements are identified and evaluated, and recommendations are developed. Requirements for development of technology and data needed to improve gasification feasibility and economies are examined.

[Research progress of mammalian synthetic biology in biomedical field].

Science.gov (United States)

Yang, Linfeng; Yin, Jianli; Wang, Meiyan; Ye, Haifeng

2017-03-25

Although still in its infant stage, synthetic biology has achieved remarkable development and progress during the past decade. Synthetic biology applies engineering principles to design and construct gene circuits uploaded into living cells or organisms to perform novel or improved functions, and it has been widely used in many fields. In this review, we describe the recent advances of mammalian synthetic biology for the treatment of diseases. We introduce common tools and design principles of synthetic gene circuits, and then we demonstrate open-loop gene circuits induced by different trigger molecules used in disease diagnosis and close-loop gene circuits used for biomedical applications. Finally, we discuss the perspectives and potential challenges of synthetic biology for clinical applications.

A Well Designed School Environment Facilitates Brain Learning.

Science.gov (United States)

Chan, Tak Cheung; Petrie, Garth

2000-01-01

Examines how school design facilitates learning by complementing how the brain learns. How the brain learns is discussed and how an artistic environment, spaciousness in the learning areas, color and lighting, and optimal thermal and acoustical environments aid student learning. School design suggestions conclude the article. (GR)

Fibrils from designed non-amyloid-related synthetic peptides induce AA-amyloidosis during inflammation in an animal model.

Directory of Open Access Journals (Sweden)

Per Westermark

Full Text Available BACKGROUND: Mouse AA-amyloidosis is a transmissible disease by a prion-like mechanism where amyloid fibrils act by seeding. Synthetic peptides with no amyloid relationship can assemble into amyloid-like fibrils and these may have seeding capacity for amyloid proteins. PRINCIPAL FINDINGS: Several synthetic peptides, designed for nanotechnology, have been examined for their ability to produce fibrils with Congo red affinity and concomitant green birefringence, affinity for thioflavin S and to accelerate AA-amyloidosis in mice. It is shown that some amphiphilic fibril-forming peptides not only produced Congo red birefringence and showed affinity for thioflavin S, but they also shortened the lag phase for systemic AA-amyloidosis in mice when they were given intravenously at the time of inflammatory induction with silver nitride. Peptides, not forming amyloid-like fibrils, did not have such properties. CONCLUSIONS: These observations should caution researchers and those who work with synthetic peptides and their derivatives to be aware of the potential health concerns.

Computer-aided biochemical programming of synthetic microreactors as diagnostic devices.

Science.gov (United States)

Courbet, Alexis; Amar, Patrick; Fages, François; Renard, Eric; Molina, Franck

2018-04-26

Biological systems have evolved efficient sensing and decision-making mechanisms to maximize fitness in changing molecular environments. Synthetic biologists have exploited these capabilities to engineer control on information and energy processing in living cells. While engineered organisms pose important technological and ethical challenges, de novo assembly of non-living biomolecular devices could offer promising avenues toward various real-world applications. However, assembling biochemical parts into functional information processing systems has remained challenging due to extensive multidimensional parameter spaces that must be sampled comprehensively in order to identify robust, specification compliant molecular implementations. We introduce a systematic methodology based on automated computational design and microfluidics enabling the programming of synthetic cell-like microreactors embedding biochemical logic circuits, or protosensors , to perform accurate biosensing and biocomputing operations in vitro according to temporal logic specifications. We show that proof-of-concept protosensors integrating diagnostic algorithms detect specific patterns of biomarkers in human clinical samples. Protosensors may enable novel approaches to medicine and represent a step toward autonomous micromachines capable of precise interfacing of human physiology or other complex biological environments, ecosystems, or industrial bioprocesses. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

Directory of Open Access Journals (Sweden)

Jason Gunther Lomnitz

2016-07-01

Full Text Available Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1 enumeration of the repertoire of model phenotypes, (2 prediction of values for the parameters for any model phenotype and (3 analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3 and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between 3 stable states by transient stimulation through one of two input channels: a positive channel that increases

Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

Science.gov (United States)

Lomnitz, Jason G.; Savageau, Michael A.

2016-01-01

Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2016-01-01

Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

Supporting design reviews with pre-meeting virtual reality environments

NARCIS (Netherlands)

van den Berg, Marc Casper; Hartmann, Timo; de Graaf, Robin S.

2017-01-01

The purpose of this paper is to explore how design reviews can be supported with pre-meeting virtual reality environments. Previous research has not systematically investigated how virtual environments can be used to communicate the design intent (to clients) and to communicate feedback (to design

Designing user models in a virtual cave environment

Energy Technology Data Exchange (ETDEWEB)

Brown-VanHoozer, S. [Argonne National Lab., Idaho Falls, ID (United States); Hudson, R. [Argonne National Lab., IL (United States); Gokhale, N. [Madge Networks, San Jose, CA (United States)

1995-12-31

In this paper, the results of a first study into the use of virtual reality for human factor studies and design of simple and complex models of control systems, components, and processes are described. The objective was to design a model in a virtual environment that would reflect more characteristics of the user`s mental model of a system and fewer of the designer`s. The technology of a CAVE{trademark} virtual environment and the methodology of Neuro Linguistic Programming were employed in this study.

Designing for the global environment

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-12-31

This document contains papers which were presented at the symposium entitled Designing for the Global Environment. Session topics included policy and the implementation of energy efficient technologies. Individual papers were processed separately for the Department of Energy databases.

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials.

Science.gov (United States)

Le Feuvre, Rosalind A; Scrutton, Nigel S

2018-06-01

Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials , where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal.

Synthetic metabolic engineering-a novel, simple technology for designing a chimeric metabolic pathway

Directory of Open Access Journals (Sweden)

Ye Xiaoting

2012-09-01

Full Text Available Abstract Background The integration of biotechnology into chemical manufacturing has been recognized as a key technology to build a sustainable society. However, the practical applications of biocatalytic chemical conversions are often restricted due to their complexities involving the unpredictability of product yield and the troublesome controls in fermentation processes. One of the possible strategies to overcome these limitations is to eliminate the use of living microorganisms and to use only enzymes involved in the metabolic pathway. Use of recombinant mesophiles producing thermophilic enzymes at high temperature results in denaturation of indigenous proteins and elimination of undesired side reactions; consequently, highly selective and stable biocatalytic modules can be readily prepared. By rationally combining those modules together, artificial synthetic pathways specialized for chemical manufacturing could be designed and constructed. Results A chimeric Embden-Meyerhof (EM pathway with balanced consumption and regeneration of ATP and ADP was constructed by using nine recombinant E. coli strains overproducing either one of the seven glycolytic enzymes of Thermus thermophilus, the cofactor-independent phosphoglycerate mutase of Pyrococcus horikoshii, or the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase of Thermococcus kodakarensis. By coupling this pathway with the Thermus malate/lactate dehydrogenase, a stoichiometric amount of lactate was produced from glucose with an overall ATP turnover number of 31. Conclusions In this study, a novel and simple technology for flexible design of a bespoke metabolic pathway was developed. The concept has been testified via a non-ATP-forming chimeric EM pathway. We designated this technology as “synthetic metabolic engineering”. Our technology is, in principle, applicable to all thermophilic enzymes as long as they can be functionally expressed in the host, and thus would be

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials

Directory of Open Access Journals (Sweden)

Rosalind A. Le Feuvre

2018-06-01

Full Text Available Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials, where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal. Keywords: Synthetic biology, Materials, Biological materials, Biomaterials, Advanced materials

Aerospace Systems Design in NASA's Collaborative Engineering Environment

Science.gov (United States)

Monell, Donald W.; Piland, William M.

1999-01-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g. manufacturing and systems operations). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often lead to the inability of assessing critical programmatic and technical issues (e.g., cost risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographically distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative

Aerospace Systems Design in NASA's Collaborative Engineering Environment

Science.gov (United States)

Monell, Donald W.; Piland, William M.

2000-07-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g., manufacturing and systems operations). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often led to the inability of assessing critical programmatic and technical issues (e.g., cost, risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographically distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative

Engineering of synthetic, stress-responsive yeast promoters

DEFF Research Database (Denmark)

Rajkumar, Arun Stephen; Liu, Guodong; Bergenholm, David

2016-01-01

Advances in synthetic biology and our understanding of the rules of promoter architecture have led to the development of diverse synthetic constitutive and inducible promoters in eukaryotes and prokaryotes. However, the design of promoters inducibleby specific endogenous or environmental conditions...

Numerical study of nozzle design for the hybrid synthetic jet actuator

Czech Academy of Sciences Publication Activity Database

Hsu, S.-S.; Chou, Y.-J.; Trávníček, Zdeněk; Lin, C.-F.; Wang, A. B.; Yen, R.H.

2015-01-01

Roč. 232, August (2015), s. 172-182 ISSN 0924-4247 R&D Projects: GA ČR GA14-08888S Institutional support: RVO:61388998 Keywords : synthetic jet * hybrid synthetic jet * numerical simulation Subject RIV: JU - Aeronautics, Aerodynamics, Aircrafts Impact factor: 2.201, year: 2015 http://www.sciencedirect.com/science/article/pii/S0924424715300091

Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.

Science.gov (United States)

Kosina, Suzanne M; Danielewicz, Megan A; Mohammed, Mujahid; Ray, Jayashree; Suh, Yumi; Yilmaz, Suzan; Singh, Anup K; Arkin, Adam P; Deutschbauer, Adam M; Northen, Trent R

2016-07-15

Synthetic microbial ecology has the potential to enhance the productivity and resiliency of biotechnology processes compared to approaches using single isolates. Engineering microbial consortia is challenging; however, one approach that has attracted significant attention is the creation of synthetic obligate mutualism using auxotrophic mutants that depend on each other for exchange or cross-feeding of metabolites. Here, we describe the integration of mutant library fitness profiling with mass spectrometry based exometabolomics as a method for constructing synthetic mutualism based on cross-feeding. Two industrially important species lacking known ecological interactions, Zymomonas mobilis and Escherichia coli, were selected as the test species. Amino acid exometabolites identified in the spent medium of Z. mobilis were used to select three corresponding E. coli auxotrophs (proA, pheA and IlvA), as potential E. coli counterparts for the coculture. A pooled mutant fitness assay with a Z. mobilis transposon mutant library was used to identify mutants with improved growth in the presence of E. coli. An auxotroph mutant in a gene (ZMO0748) with sequence similarity to cysteine synthase A (cysK), was selected as the Z. mobilis counterpart for the coculture. Exometabolomic analysis of spent E. coli medium identified glutathione related metabolites as potentially available for rescue of the Z. mobilis cysteine synthase mutant. Three sets of cocultures between the Z. mobilis auxotroph and each of the three E. coli auxotrophs were monitored by optical density for growth and analyzed by flow cytometry to confirm high cell counts for each species. Taken together, our methods provide a technological framework for creating synthetic mutualisms combining existing screening based methods and exometabolomics for both the selection of obligate mutualism partners and elucidation of metabolites involved in auxotroph rescue.

[Synthetic biology and rearrangements of microbial genetic material].

Science.gov (United States)

Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

2011-10-01

As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.

Synthetic Biology for Specialty Chemicals.

Science.gov (United States)

Markham, Kelly A; Alper, Hal S

2015-01-01

In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

The role of environment design in an educational Multi-User Virtual Environment

DEFF Research Database (Denmark)

Papachristos, Nikiforos; Vrellis, Ioannis; Natsis, Antonios

2014-01-01

This paper presents empirical results from an exploratory study conducted in an authentic educational situation with preservice education students enrolled in an undergraduate course, which was partially taught in Second Life. The study investigated the effect of environment design on presence, l...... necessary for all students to become familiar with the virtual environment and possible time losses due to technical issues. This study could act as support to construct and test hypotheses regarding the role of educational setting design in teaching and learning in MUVEs....

Antimicrobial activity predictors benchmarking analysis using shuffled and designed synthetic peptides.

Science.gov (United States)

Porto, William F; Pires, Állan S; Franco, Octavio L

2017-08-07

The antimicrobial activity prediction tools aim to help the novel antimicrobial peptides (AMP) sequences discovery, utilizing machine learning methods. Such approaches have gained increasing importance in the generation of novel synthetic peptides by means of rational design techniques. This study focused on predictive ability of such approaches to determine the antimicrobial sequence activities, which were previously characterized at the protein level by in vitro studies. Using four web servers and one standalone software, we evaluated 78 sequences generated by the so-called linguistic model, being 40 designed and 38 shuffled sequences, with ∼60 and ∼25% of identity to AMPs, respectively. The ab initio molecular modelling of such sequences indicated that the structure does not affect the predictions, as both sets present similar structures. Overall, the systems failed on predicting shuffled versions of designed peptides, as they are identical in AMPs composition, which implies in accuracies below 30%. The prediction accuracy is negatively affected by the low specificity of all systems here evaluated, as they, on the other hand, reached 100% of sensitivity. Our results suggest that complementary approaches with high specificity, not necessarily high accuracy, should be developed to be used together with the current systems, overcoming their limitations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthetic biology and occupational risk.

Science.gov (United States)

Howard, John; Murashov, Vladimir; Schulte, Paul

2017-03-01

Synthetic biology is an emerging interdisciplinary field of biotechnology that involves applying the principles of engineering and chemical design to biological systems. Biosafety professionals have done an excellent job in addressing research laboratory safety as synthetic biology and gene editing have emerged from the larger field of biotechnology. Despite these efforts, risks posed by synthetic biology are of increasing concern as research procedures scale up to industrial processes in the larger bioeconomy. A greater number and variety of workers will be exposed to commercial synthetic biology risks in the future, including risks to a variety of workers from the use of lentiviral vectors as gene transfer devices. There is a need to review and enhance current protection measures in the field of synthetic biology, whether in experimental laboratories where new advances are being researched, in health care settings where treatments using viral vectors as gene delivery systems are increasingly being used, or in the industrial bioeconomy. Enhanced worker protection measures should include increased injury and illness surveillance of the synthetic biology workforce; proactive risk assessment and management of synthetic biology products; research on the relative effectiveness of extrinsic and intrinsic biocontainment methods; specific safety guidance for synthetic biology industrial processes; determination of appropriate medical mitigation measures for lentiviral vector exposure incidents; and greater awareness and involvement in synthetic biology safety by the general occupational safety and health community as well as by government occupational safety and health research and regulatory agencies.

Synthetic aperture design for increased SAR image rate

Science.gov (United States)

Bielek, Timothy P [Albuquerque, NM; Thompson, Douglas G [Albuqerque, NM; Walker, Bruce C [Albuquerque, NM

2009-03-03

High resolution SAR images of a target scene at near video rates can be produced by using overlapped, but nevertheless, full-size synthetic apertures. The SAR images, which respectively correspond to the apertures, can be analyzed in sequence to permit detection of movement in the target scene.

Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis

Science.gov (United States)

Kim, Juhyun; Salvador, Manuel; Saunders, Elizabeth; González, Jaime; Avignone-Rossa, Claudio

2016-01-01

The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation. PMID:27903818

Synthetic Phage for Tissue Regeneration

Directory of Open Access Journals (Sweden)

So Young Yoo

2014-01-01

Full Text Available Controlling structural organization and signaling motif display is of great importance to design the functional tissue regenerating materials. Synthetic phage, genetically engineered M13 bacteriophage has been recently introduced as novel tissue regeneration materials to display a high density of cell-signaling peptides on their major coat proteins for tissue regeneration purposes. Structural advantages of their long-rod shape and monodispersity can be taken together to construct nanofibrous scaffolds which support cell proliferation and differentiation as well as direct orientation of their growth in two or three dimensions. This review demonstrated how functional synthetic phage is designed and subsequently utilized for tissue regeneration that offers potential cell therapy.

Kunst & de mens in dementie : Designing Environment

NARCIS (Netherlands)

Coumans, Anke; Schuffelers, Ingrid; Polstra, Louis

2016-01-01

The research project Designing Environment conducts research into how a different mind-set can be brought about concerning people with dementia, by intervening in care processes, and from the perspective of the participating observer. The objective is to create an environment for people with

Synthetic staggered architecture composites

International Nuclear Information System (INIS)

Dutta, Abhishek; Tekalur, Srinivasan Arjun

2013-01-01

Highlights: ► Composite design inspired by nature. ► Tuning microstructure via changing ceramic content and aspect ratio. ► Experimental display of structure–property correlationship in synthetic composites. - Abstract: Structural biocomposites (for example, nacre in seashells, bone, etc.) are designed according to the functional role they are delegated for. For instance, bone is primarily designed for withstanding time-dependent loading (for example, withstanding stresses while running, jumping, accidental fall) and hence the microstructure is designed primarily from enhanced toughness and moderate stiffness point of view. On the contrary, seashells (which lie in the abyss of oceans) apart from providing defense to the organism (it is hosting) against predatory attacks, are subjected to static loading (for example, enormous hydrostatic pressure). Hence, emphasis on the shell structure evolution is directed primarily towards providing enhanced stiffness. In order to conform between stiffness and toughness, nature precisely employs a staggered arrangement of inorganic bricks in a biopolymer matrix (at its most elementary level of architecture). Aspect ratio and content of ceramic bricks are meticulously used by nature to synthesize composites having varying degrees of stiffness, strength and toughness. Such an amazing capability of structure–property correlationship has rarely been demonstrated in synthetic composites. Therefore, in order to better understand the mechanical behavior of synthetic staggered composites, the problem becomes two-pronged: (a) synthesize composites with varying brick size and contents and (b) experimental investigation of the material response. In this article, an attempt has been made to synthesize and characterize staggered ceramic–polymer composites having varying aspect ratio and ceramic content using freeze-casting technique. This will in-turn help us in custom-design manufacture of hybrid bio-inspired composite materials

Design of New Food Technology: Social Shaping of Working Environment

DEFF Research Database (Denmark)

Broberg, Ole

2000-01-01

A five-year design process of a continuous process wok has been studied with the aim of elucidating the conditions for integrating working environment aspects. The design process is seen as a network building activity and as a social shaping process of the artefact. A working environment log...... is suggested as a tool designers can use to integrate considerations of future operators' working environment....

Synthetic Marijuana Induced Acute Nonischemic Left Ventricular Dysfunction.

Science.gov (United States)

Elsheshtawy, Moustafa; Sriganesh, Priatharsini; Virparia, Vasudev; Patel, Falgun; Khanna, Ashok

2016-01-01

Synthetic marijuana is an uptrending designer drug currently widely spread in the US. We report a case of acute deterioration of nonischemic left ventricular dysfunction after exposure to synthetic marijuana. This case illustrates the importance of history taking in cardiac patients and identifies a negative cardiovascular effect of synthetic marijuana known as K2, not yet well detected by urine toxicology screening tools.

Synthetic Marijuana Induced Acute Nonischemic Left Ventricular Dysfunction

OpenAIRE

Moustafa Elsheshtawy; Priatharsini Sriganesh; Vasudev Virparia; Falgun Patel; Ashok Khanna

2016-01-01

Synthetic marijuana is an uptrending designer drug currently widely spread in the US. We report a case of acute deterioration of nonischemic left ventricular dysfunction after exposure to synthetic marijuana. This case illustrates the importance of history taking in cardiac patients and identifies a negative cardiovascular effect of synthetic marijuana known as K2, not yet well detected by urine toxicology screening tools.

Instructional Design Issues in a Distributed Collaborative Engineering Design (CED) Instructional Environment

Science.gov (United States)

Koszalka, Tiffany A.; Wu, Yiyan

2010-01-01

Changes in engineering practices have spawned changes in engineering education and prompted the use of distributed learning environments. A distributed collaborative engineering design (CED) course was designed to engage engineering students in learning about and solving engineering design problems. The CED incorporated an advanced interactive…

From Extremophiles to Star Trek, The Use of Synthetic Biology in Astrobiology

Science.gov (United States)

Rothschild, Lynn J.; Fujishima, Kosuke; Lima, Ivan Paulino; Gentry, Diana; Phan, Samson; Navarette, Jesica; Palmer, Jesse; Burnier, Andre

2012-01-01

Synthetic biology – the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes – has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as bio-mining, human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

A Canadian refiner's perspective of synthetic crudes

International Nuclear Information System (INIS)

Halford, T.L.; McIntosh, A.P.; Rasmussen

1997-01-01

Some of the factors affecting a refiner's choice of crude oil include refinery hardware, particularly gas oil crackers, products slate and product specifications, crude availability, relative crude price and crude quality. An overview of synthetic crude, the use of synthetic crude combined with other crudes and a comparison of synthetic crude with conventional crude oil was given. The two main users of synthetic crude are basically two groups of refiners, those large groups who use synthetic crude combined with other crudes, and a smaller group who run synthetic crude on specially designed units as a sole feed. The effects of changes in fuel legislation were reviewed. It was predicted that the changes will have a mixed impact on the value of synthetic crude, but low sulphur diesel regulations and gasoline sulphur regulations will make current synthetic crudes attractive. The big future change with a negative impact will be diesel cetane increases to reduce engine emissions. This will reduce synthetic crude attractiveness due to distillate yields and quality and high gas oil yields. Similarly, any legislation limiting aromatics in diesel fuel will also make synthetic crudes less attractive. Problems experienced by refiners with hardware dedicated to synthetic crude (salt, naphthenic acid, fouling, quality variations) were also reviewed. 3 tabs

Research on the Design of Public Space Environment for Aging Society

Science.gov (United States)

Fang, Gu; Soo, Kim Chul

2018-03-01

This paper studies the living space environment suitable for the elderly, because the elderly and the disabled have become increasingly prominent social problems. Through the discussion of the humanistic environment design method of the elderly and the disabled, the paper puts forward a new environment design which has the traditional characteristics and adapts to the new society to care for the elderly (the disabled).By studying and analyzing the background of social aging, the theory of public space environment design and the needs of the elderly, it is pointed out that the design of public space environment in the aged society needs to be implemented in detail design. The number of elderly people in public space will increase, give full attention to the public space outdoor environment quality, for the elderly to provide a variety of environmental facilities have long-term significance.

Synthetic Marijuana Induced Acute Nonischemic Left Ventricular Dysfunction

Directory of Open Access Journals (Sweden)

Moustafa Elsheshtawy

2016-01-01

Full Text Available Synthetic marijuana is an uptrending designer drug currently widely spread in the US. We report a case of acute deterioration of nonischemic left ventricular dysfunction after exposure to synthetic marijuana. This case illustrates the importance of history taking in cardiac patients and identifies a negative cardiovascular effect of synthetic marijuana known as K2, not yet well detected by urine toxicology screening tools.

Synthetic detergents: 100 years of history

Directory of Open Access Journals (Sweden)

Ana Carolina Kogawa

2017-09-01

Full Text Available In the year 2016 the synthetic detergents complete 100 years and in this story they evolved as cleaners. They are already part of the routine of thousands of people worldwide. For a higher power of cleaning of the detergent, today, are added phosphates, the main responsible for environmental problems. After 100 years of synthetic detergents, the effect of the combination of various cleaners on the environment is a gap. Legislation and guidelines about the other components of the formula of cleaners still missing. Even the term biodegradable can be best placed on the diversity of products currently entitled biodegradable. A lot attitudes can still be taken to continuously improve the relationship between the parties involved, animals, plants, waters and men, so that in another 100 years continues to exist this interaction with the environment without destroying it. The marketing used by synthetic detergent companies evolved a lot over the years and showed maturity to deal with changes in theories and strategies for promotion and even with the constant social reform that its consumer lived, accompanying them intelligently to be able to capture their changing needs and desires, and so assemble the best way to connect to them. This paper focuses on the subject synthetic detergents as well as (i types and applications, (ii threats, (iii sustainability, (iv legislation, (v packaging and (vi marketing strategies.

Synthetic detergents: 100 years of history.

Science.gov (United States)

Kogawa, Ana Carolina; Cernic, Beatriz Gamberini; do Couto, Leandro Giovanni Domingos; Salgado, Hérida Regina Nunes

2017-09-01

In the year 2016 the synthetic detergents complete 100 years and in this story they evolved as cleaners. They are already part of the routine of thousands of people worldwide. For a higher power of cleaning of the detergent, today, are added phosphates, the main responsible for environmental problems. After 100 years of synthetic detergents, the effect of the combination of various cleaners on the environment is a gap. Legislation and guidelines about the other components of the formula of cleaners still missing. Even the term biodegradable can be best placed on the diversity of products currently entitled biodegradable. A lot attitudes can still be taken to continuously improve the relationship between the parties involved, animals, plants, waters and men, so that in another 100 years continues to exist this interaction with the environment without destroying it. The marketing used by synthetic detergent companies evolved a lot over the years and showed maturity to deal with changes in theories and strategies for promotion and even with the constant social reform that its consumer lived, accompanying them intelligently to be able to capture their changing needs and desires, and so assemble the best way to connect to them. This paper focuses on the subject synthetic detergents as well as (i) types and applications, (ii) threats, (iii) sustainability, (iv) legislation, (v) packaging and (vi) marketing strategies.

Cognitive mapping based on synthetic vision?

Science.gov (United States)

Helmetag, Arnd; Halbig, Christian; Kubbat, Wolfgang; Schmidt, Rainer

1999-07-01

The analysis of accidents focused our work on the avoidance of 'Controlled Flight Into Terrain' caused by insufficient situation awareness. Analysis of safety concepts led us to the design of the proposed synthetic vision system that will be described. Since most information on these 3D-Displays is shown in a graphical way, it can intuitively be understood by the pilot. What are the new possibilities using SVS enhancing situation awareness? First, detection of ground collision hazard is possible by monitoring a perspective Primary Flight Display. Under the psychological point of view it is based on the perception of expanding objects in the visual flow field. Supported by a Navigation Display a local conflict resolution can be mentally worked out very fast. Secondly, it is possible to follow a 3D flight path visualized as a 'Tunnel in the sky.' This can further be improved by using a flight path prediction. These are the prerequisites for a safe and adequate movement in any kind of spatial environment. However situation awareness requires the ability of navigation and spatial problem solving. Both abilities are based on higher cognitive functions in real as well as in a synthetic environment. In this paper the current training concept will be analyzed. Advantages resulting from the integration of a SVS concerning pilot training will be discussed and necessary requirements in terrain depiction will be pinpointed. Finally a modified Computer Based Training for the familiarization with Salzburg Airport for a SVS equipped aircraft will be presented. It is developed by Darmstadt University of Technology in co-operation with Lufthansa Flight Training.

Toward the First Data Acquisition Standard in Synthetic Biology.

Science.gov (United States)

Sainz de Murieta, Iñaki; Bultelle, Matthieu; Kitney, Richard I

2016-08-19

This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London.

DESIGN AND EVALUATION OF LOSARTAN POTASSIUM MATRIX TABLETS WITH NATURAL AND SYNTHETIC POLYMERS

OpenAIRE

R. L. C. Sasidhar et al.

2012-01-01

The objective of the study was to formulate controlled release matrix tablets of losartan Potassium by using a combination of hydrophilic synthetic polymer like poly (ethylene oxides) and natural gums like xanthan gum, karaya gum and guar gum. A combination of synthetic hydrophobic polymers like methacrylates with synthetic hydrophilic polymer like poly (ethylene oxide) was also used in the preparation of matrix tablets and evaluated for their influence on controlled drug release. The matrix ...

A standard-enabled workflow for synthetic biology

KAUST Repository

Myers, Chris J.; Beal, Jacob; Gorochowski, Thomas E.; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Gö ksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

2017-01-01

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select

FindPath: a Matlab solution for in silico design of synthetic metabolic pathways.

Science.gov (United States)

Vieira, Gilles; Carnicer, Marc; Portais, Jean-Charles; Heux, Stéphanie

2014-10-15

Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files. http://metasys.insa-toulouse.fr/software/findpath/. heux@insa-toulouse.fr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Paper-based synthetic gene networks.

Science.gov (United States)

Pardee, Keith; Green, Alexander A; Ferrante, Tom; Cameron, D Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J

2014-11-06

Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors.

Paper-based Synthetic Gene Networks

Science.gov (United States)

Pardee, Keith; Green, Alexander A.; Ferrante, Tom; Cameron, D. Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J.

2014-01-01

Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides a new venue for synthetic biologists to operate, and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze-dried onto paper, enabling the inexpensive, sterile and abiotic distribution of synthetic biology-based technologies for the clinic, global health, industry, research and education. For field use, we create circuits with colorimetric outputs for detection by eye, and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors. PMID:25417167

Recent advances in the molecular design of synthetic vaccines

Science.gov (United States)

Jones, Lyn H.

2015-12-01

Vaccines have typically been prepared using whole organisms. These are normally either attenuated bacteria or viruses that are live but have been altered to reduce their virulence, or pathogens that have been inactivated and effectively killed through exposure to heat or formaldehyde. However, using whole organisms to elicit an immune response introduces the potential for infections arising from a reversion to a virulent form in live pathogens, unproductive reactions to vaccine components or batch-to-batch variability. Synthetic vaccines, in which a molecular antigen is conjugated to a carrier protein, offer the opportunity to circumvent these problems. This Perspective will highlight the progress that has been achieved in developing synthetic vaccines using a variety of molecular antigens. In particular, the different approaches used to develop conjugate vaccines using peptide/proteins, carbohydrates and other small molecule haptens as antigens are compared.

Designing safer living environments support for local government

CSIR Research Space (South Africa)

Landman, K

1999-06-01

Full Text Available This paper addresses the built environment, the opportunities it presents for crime and the role city planners and urban designers have to play in the design of safer cities and towns. City planners and urban designers can play a role...

Frontiers in biomaterials the design, synthetic strategies and biocompatibility of polymer scaffolds for biomedical application

CERN Document Server

Cao, Shunsheng

2014-01-01

Frontiers in Biomaterials: The Design, Synthetic Strategies and Biocompatibility of Polymer Scaffolds for Biomedical Application, Volume 1" highlights the importance of biomaterials and their interaction with biological system. The need for the development of biomaterials as scaffold for tissue regeneration is driven by the increasing demands for materials that mimic functions of extracellular matrices of body tissues.This ebook covers the latest challenges on the biocompatibility of scaffold overtime after implantation and discusses the requirement of innovative technologies and strategies f

Design for a better environment

International Nuclear Information System (INIS)

Khan, Z.A.

2005-01-01

The paper discusses part of an ongoing study initiated at the Pakistan Navy Engineering College in Karachi. The study originated from the author's belief that design in this country is influenced by 'factors' other than considerations based on scientific knowledge and logical thinking. The same may be true for selection of materials for a particular application. The key thrust of the work is to explore how plastics and associated products affect the environment and the economy of the country, and the problems these may create. It also explores the role of people, government and industry in this regard. The study was planned to consist of case studies from the automotive sector in Pakistan. It was decided that plastic components manufactured in Pakistan would be studied and engineers and designers involved in 'design' would be interviewed. This paper focuses on the application of conceptual design techniques to the problem of sustainable design of a product in the automotive industry. It also attempts to focus on the role of this industry in the implementation of concepts related to sustainable development in engineering design. (author)

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Science.gov (United States)

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grünberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H; Myers, Chris; Sauro, Herbert; Wipat, Anil

2018-04-02

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL) Version 2.2.0

KAUST Repository

Cox, Robert Sidney

2018-04-04

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year\\'s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL Version 2.2.0

Directory of Open Access Journals (Sweden)

Cox Robert Sidney

2018-04-01

Full Text Available Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL) Version 2.2.0

KAUST Repository

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grunberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H.; Myers, Chris; Sauro, Herbert; Wipat, Anil

2018-01-01

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Is synthetic biology mechanical biology?

Science.gov (United States)

Holm, Sune

2015-12-01

A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

Design Rework Prediction in Concurrent Design Environment: Current Trends and Future Research Directions

OpenAIRE

Arundachawat, Panumas; Roy, Rajkumar; Al-Ashaab, Ahmed; Shehab, Essam

2009-01-01

Organised by: Cranfield University This paper aims to present state-of-the-art and formulate future research areas on design rework in concurrent design environment. Related literatures are analysed to extract the key factors which impact design rework. Design rework occurs due to changes from upstream design activities and/or by feedbacks from downstream design activities. Design rework is considered as negative iteration; therefore, value in design activities will be increase...

Synthetic greenhouse gases under control

International Nuclear Information System (INIS)

Horisberger, B.; Karlaganis, G.

2003-01-01

This article discusses new Swiss regulations on the use of synthetic materials that posses a considerable greenhouse-warming potential. Synthetic materials such as hydro-chlorofluorocarbons HCFCs, perfluoride-hydrocarbons and sulphur hexafluoride have, in recent years, replaced chlorofluorocarbons CFCs, which were banned on account of their ozone depletion characteristics. The use of these persistent substances is now being limited to applications where more environment-friendly alternatives are not available. The measures decreed in the legislation, which include a general ban on HCFCs as of 2004 and a ban on the export of installations and equipment that use ozone-depleting refrigerants are described. Details on the legislation's effects on the Swiss refrigeration industry are listed and discussed

Guiding bioprocess design by microbial ecology.

Science.gov (United States)

Volmer, Jan; Schmid, Andreas; Bühler, Bruno

2015-06-01

Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Smart therapeutics based on synthetic gene circuits].

Science.gov (United States)

Peng, Shuguang; Xie, Zhen

2017-03-25

Synthetic biology has an important impact on biology research since its birth. Applying the thought and methods that reference from electrical engineering, synthetic biology uncovers many regulatory mechanisms of life systems, transforms and expands a series of biological components. Therefore, it brings a wide range of biomedical applications, including providing new ideas for disease diagnosis and treatment. This review describes the latest advances in the field of disease diagnosis and therapy based on mammalian cell or bacterial synthetic gene circuits, and provides new ideas for future smart therapy design.

Towards a synthetic chloroplast.

Directory of Open Access Journals (Sweden)

Christina M Agapakis

2011-04-01

Full Text Available The evolution of eukaryotic cells is widely agreed to have proceeded through a series of endosymbiotic events between larger cells and proteobacteria or cyanobacteria, leading to the formation of mitochondria or chloroplasts, respectively. Engineered endosymbiotic relationships between different species of cells are a valuable tool for synthetic biology, where engineered pathways based on two species could take advantage of the unique abilities of each mutualistic partner.We explored the possibility of using the photosynthetic bacterium Synechococcus elongatus PCC 7942 as a platform for studying evolutionary dynamics and for designing two-species synthetic biological systems. We observed that the cyanobacteria were relatively harmless to eukaryotic host cells compared to Escherichia coli when injected into the embryos of zebrafish, Danio rerio, or taken up by mammalian macrophages. In addition, when engineered with invasin from Yersinia pestis and listeriolysin O from Listeria monocytogenes, S. elongatus was able to invade cultured mammalian cells and divide inside macrophages.Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.

Using software interoperability to achieve a virtual design environment

Science.gov (United States)

Gregory, G. Groot; Koshel, R. John

2005-09-01

A variety of simulation tools, including optical design and analysis, have benefited by many years of evolution in software functionality and computing power, thus making the notion of virtual design environments a reality. To simulate the optical characteristics of a system, one needs to include optical performance, mechanical design and manufacturing aspects simultaneously. To date, no single software program offers a universal solution. One approach to achieve an integrated environment is to select tools that offer a high degree of interoperability. This allows the selection of the best tools for each aspect of the design working in concert to solve the problem. This paper discusses the issues of how to assemble a design environment and provides an example of a combination of tools for illumination design. We begin by offering a broad definition of interoperability from an optical analysis perspective. This definition includes aspects of file interchange formats, software communications protocols and customized applications. One example solution is proposed by combining SolidWorks1 for computer-aided design (CAD), TracePro2 for optical analysis and MATLAB3 as the mathematical engine for tolerance analysis. The resulting virtual tool will be applied to a lightpipe design task to illustrate how such a system can be used.

Hydrothermal Gasification Of Synthetic Liquefied Wood To Methane

Energy Technology Data Exchange (ETDEWEB)

Waldner, M.H.; De Boni, E.; Vogel, F.

2005-03-01

Biomass can be effectively converted to synthetic natural gas (SNG) in a hydrothermal environment. Lower temperatures favor the production of methane rather than hydrogen. At around 420 C, catalysts are needed to ensure reasonable rates of reaction. They are tested in a new rig in terms of activity, selectivity and stability. Gold-plated surfaces ensure no interference from the stainless steel. Experiments were carried out using different feeds, such as ethanol and synthetic liquefied wood. (author)

Design of supply chain in fuzzy environment

Science.gov (United States)

Rao, Kandukuri Narayana; Subbaiah, Kambagowni Venkata; Singh, Ganja Veera Pratap

2013-05-01

Nowadays, customer expectations are increasing and organizations are prone to operate in an uncertain environment. Under this uncertain environment, the ultimate success of the firm depends on its ability to integrate business processes among supply chain partners. Supply chain management emphasizes cross-functional links to improve the competitive strategy of organizations. Now, companies are moving from decoupled decision processes towards more integrated design and control of their components to achieve the strategic fit. In this paper, a new approach is developed to design a multi-echelon, multi-facility, and multi-product supply chain in fuzzy environment. In fuzzy environment, mixed integer programming problem is formulated through fuzzy goal programming in strategic level with supply chain cost and volume flexibility as fuzzy goals. These fuzzy goals are aggregated using minimum operator. In tactical level, continuous review policy for controlling raw material inventories in supplier echelon and controlling finished product inventories in plant as well as distribution center echelon is considered as fuzzy goals. A non-linear programming model is formulated through fuzzy goal programming using minimum operator in the tactical level. The proposed approach is illustrated with a numerical example.

Waterproofing with polymeric geo synthetic barriers (GBR-P) in the manual for the design, construction, management and maintenance of reservoirs

International Nuclear Information System (INIS)

Blanco, M.; Cea, J. C.; Garcia, F.; Sanchez, F. J.; Castillo, F.; Mora, J.; Crespo, M. A.

2010-01-01

This article presents a part of Manual for the Design, Construction, Management and Maintenance of Reservoirs relative to waterproofing with Polymeric Geo synthetic Barriers (GBR-P). the nature materials of geo membranes is studied also theirs characteristics and specifications. (Author) 26 refs.

Design Quality in the Context of Healthcare Environments: A Scoping Review.

Science.gov (United States)

Anåker, Anna; Heylighen, Ann; Nordin, Susanna; Elf, Marie

2017-07-01

We explored the concept of design quality in relation to healthcare environments. In addition, we present a taxonomy that illustrates the wide range of terms used in connection with design quality in healthcare. High-quality physical environments can promote health and well-being. Developments in healthcare technology and methodology put high demands on the design quality of care environments, coupled with increasing expectations and demands from patients and staff that care environments be person centered, welcoming, and accessible while also supporting privacy and security. In addition, there are demands that decisions about the design of healthcare architecture be based on the best available information from credible research and the evaluation of existing building projects. The basic principles of Arksey and O'Malley's model of scoping review design were used. Data were derived from literature searches in scientific databases. A total of 18 articles and books were found that referred to design quality in a healthcare context. Design quality of physical healthcare environments involves three different themes: (i) environmental sustainability and ecological values, (ii) social and cultural interactions and values, and (iii) resilience of the engineering and building construction. Design quality was clarified herein with a definition. Awareness of what is considered design quality in relation to healthcare architecture could help to design healthcare environments based on evidence. To operationalize the concept, its definition must be clear and explicit and able to meet the complex needs of the stakeholders in a healthcare context, including patients, staff, and significant others.

Rapid Mission Design for Dynamically Complex Environments

Data.gov (United States)

National Aeronautics and Space Administration — Designing trajectories in dynamically complex environments is very challenging and easily becomes an intractable problem. More complex planning implies potentially...

The Role of Synthetic Biology in NASA's Missions

Science.gov (United States)

Rothschild, Lynn J.

2016-01-01

The time has come to for NASA to exploit synthetic biology in pursuit of its missions, including aeronautics, earth science, astrobiology and most notably, human exploration. Conversely, NASA advances the fundamental technology of synthetic biology as no one else can because of its unique expertise in the origin of life and life in extreme environments, including the potential for alternate life forms. This enables unique, creative "game changing" advances. NASA's requirement for minimizing upmass in flight will also drive the field toward miniaturization and automation. These drivers will greatly increase the utility of synthetic biology solutions for military, health in remote areas and commercial purposes. To this end, we have begun a program at NASA to explore the use of synthetic biology in NASA's missions, particular space exploration. As part of this program, we began hosting an iGEM team of undergraduates drawn from Brown and Stanford Universities to conduct synthetic biology research at NASA Ames Research Center. The 2011 team (http://2011.igem.org/Team:Brown-Stanford) produced an award-winning project on using synthetic biology as a basis for a human Mars settlement.

Assessment of synthetic image fidelity

Science.gov (United States)

Mitchell, Kevin D.; Moorhead, Ian R.; Gilmore, Marilyn A.; Watson, Graham H.; Thomson, Mitch; Yates, T.; Troscianko, Tomasz; Tolhurst, David J.

2000-07-01

Computer generated imagery is increasingly used for a wide variety of purposes ranging from computer games to flight simulators to camouflage and sensor assessment. The fidelity required for this imagery is dependent on the anticipated use - for example when used for camouflage design it must be physically correct spectrally and spatially. The rendering techniques used will also depend upon the waveband being simulated, spatial resolution of the sensor and the required frame rate. Rendering of natural outdoor scenes is particularly demanding, because of the statistical variation in materials and illumination, atmospheric effects and the complex geometric structures of objects such as trees. The accuracy of the simulated imagery has tended to be assessed subjectively in the past. First and second order statistics do not capture many of the essential characteristics of natural scenes. Direct pixel comparison would impose an unachievable demand on the synthetic imagery. For many applications, such as camouflage design, it is important that nay metrics used will work in both visible and infrared wavebands. We are investigating a variety of different methods of comparing real and synthetic imagery and comparing synthetic imagery rendered to different levels of fidelity. These techniques will include neural networks (ICA), higher order statistics and models of human contrast perception. This paper will present an overview of the analyses we have carried out and some initial results along with some preliminary conclusions regarding the fidelity of synthetic imagery.

A methodology to derive Synthetic Design Hydrographs for river flood management

Science.gov (United States)

Tomirotti, Massimo; Mignosa, Paolo

2017-12-01

The design of flood protection measures requires in many cases not only the estimation of the peak discharges, but also of the volume of the floods and its time distribution. A typical solution to this kind of problems is the formulation of Synthetic Design Hydrographs (SDHs). In this paper a methodology to derive SDHs is proposed on the basis of the estimation of the Flow Duration Frequency (FDF) reduction curve and of a Peak-Duration (PD) relationship furnishing respectively the quantiles of the maximum average discharge and the average peak position in each duration. The methodology is intended to synthesize the main features of the historical floods in a unique SDH for each return period. The shape of the SDH is not selected a priori but is a result of the behaviour of FDF and PD curves, allowing to account in a very convenient way for the variability of the shapes of the observed hydrographs at local time scale. The validation of the methodology is performed with reference to flood routing problems in reservoirs, lakes and rivers. The results obtained demonstrate the capability of the SDHs to describe the effects of different hydraulic systems on the statistical regime of floods, even in presence of strong modifications induced on the probability distribution of peak flows.

Synthetic fuels and the environment: an environmental and regulatory impacts analysis

Energy Technology Data Exchange (ETDEWEB)

None

1980-06-01

Since July 1979 when DOE/EV-0044 report Environmental Analysis of Synthetic Liquid fuels was published the synthetic fuels program proposals of the Administration have undergone significant modifications. The program year for which the development goal of 1.5 million barrels per day is to be reached has been changed from 1990 to 1995. The program plan is now proposed to have two stages to ensure, among other things, better environmental protection: an initial stage emphasizing applied research and development (R and D), including environmental research, followed by a second stage that would accelerate deployment of those synthetic fuel technologies then judged most ready for rapid deployment and economic operation within the environmental protection requirements. These program changes have significantly expanded the scope of technologies to be considered in this environmental analysis and have increased the likelihood that accelerated environmental R and D efforts will be successful in solving principal environmental and worker safety concerns for most technologies prior to the initiation of the second stage of the accelerated deployment plan. Information is presented under the following section headings: summary; study description; the technologies and their environmental concerns (including, coal liquefaction and gasification, oil shale production, biomass and urban waste conversion); regulatory and institutional analyses; and environmental impacts analysis (including air and water quaility analyses, impacts of carbon dioxide and acid rain, water availability, solid and hazardous wastes, coal mining environmental impacts, transportation issues, community growth and change, and regional impacts). Additional information is presented in seventeen appendixes. (JGB)

Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

Directory of Open Access Journals (Sweden)

Zhenyu Shi

2016-12-01

Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

Effects of synthetic and natural toxicants on livestock.

Science.gov (United States)

Shull, L R; Cheeke, P R

1983-07-01

Synthetic and natural toxicants are constituents of soil, air, water and foodstuffs. Their impact on animal agriculture has resulted from acute and chronic intoxication and residues transferred into meat, dairy and poultry products. Recent advances in analytical chemistry and the sciences associated with toxicology have allowed better assessment of the hazard of toxicants on animals including man. Historically, natural toxicants (phytotoxins, mycotoxins and minerals) that are associated with many common feedstuffs accounted for toxicity episodes of epidemic proportions. Most synthetic chemicals (pesticides, nonpesticidal organic chemicals and drugs) have been introduced in increasing numbers since the 1940's. In the 1960's and '70's, recognition of the need to control their environmental distribution stimulated the introduction of numerous laws and regulations. In the last decade, several problematic synthetic chemicals have been banned, particularly those found to persist in the environment or those confirmed or suspected as carcinogens in humans. At the farm level, the development of various preventative management strategies has decreased the exposure of livestock to natural toxicants. In the future, the impact of natural toxicants on animal agriculture is expected to lessen as their existence, etiology and toxicology are determined. On the other hand, synthetic chemicals will continue to threaten animal health as greater numbers and quantities are released into the environment. These challenges should stimulate a greater involvement of animal scientists in toxicology.

Physical and Emotional Benefits of Different Exercise Environments Designed for Treadmill Running.

Science.gov (United States)

Yeh, Hsiao-Pu; Stone, Joseph A; Churchill, Sarah M; Brymer, Eric; Davids, Keith

2017-07-11

(1) Background: Green physical activity promotes physical health and mental wellbeing and interesting questions concern effects of this information on designing indoor exercise environments. This study examined the physical and emotional effects of different nature-based environments designed for indoor treadmill running; (2) Methods: In a counterbalanced experimental design, 30 participants performed three, twenty-minute treadmill runs at a self-selected pace while viewing either a static nature image, a dynamic nature image or self-selected entertainment. Distance ran, heart rate (HR) and five pre-and post-exercise emotional states were measured; (3) Results: Participants ran farther, and with higher HRs, with self-selected entertainment compared to the two nature-based environment designs. Participants attained lowered anger, dejection, anxiety and increased excitement post exercise in all of the designed environments. Happiness increased during the two nature-based environment designs compared with self-selected entertainment; (4) Conclusions: Self-selected entertainment encouraged greater physical performances whereas running in nature-based exercise environments elicited greater happiness immediately after running.

Synthetic bedding and wheeze in childhood.

Science.gov (United States)

Ponsonby, Anne-Louise; Dwyer, Terence; Kemp, Andrew; Cochrane, Jennifer; Couper, David; Carmichael, Allan

2003-01-01

The reasons for the increase in childhood asthma over time are unclear. The indoor environment is of particular concern. An adverse role for synthetic bedding on asthma development in childhood has been suggested by cross-sectional studies that have found an association between synthetic pillow use and childhood wheeze. Prospective data on infant bedding have not been available. Bedding data at 1 month of age were available from an infant survey for children who were participating in a 1995 follow-up study (N = 863; 78% traced). The 1995 follow-up was embedded in a larger cross-sectional survey involving 6,378 seven year olds in Tasmania (N = 92% of eligible). Outcome measures included respiratory symptoms as defined in the International Study of Asthma and Allergies in Childhood protocol. Frequent wheeze was defined as more than 12 wheeze episodes over the past year compared with no wheeze. Synthetic pillow use at 1 month of age was associated with frequent wheeze at age 7 (adjusted relative risk [aRR] = 2.5; 95% confidence interval [CI] = 1.2-5.5) independent of childhood exposure. Current synthetic pillow and quilt use was strongly associated with frequent wheeze (aRR = 5.2; CI = 1.3-20.6). Substantial trends were evident for an association of increasing number of synthetic bedding items with frequent wheeze and with increasing wheeze frequency. Among children with asthma, the age of onset of asthma occurred earlier if synthetic bedding was used in infancy. In this cohort, synthetic bedding was strongly and consistently associated with frequent childhood wheeze. The association did not appear to be attributable to bedding choice as part of an asthma management strategy.

Designing persuasive interactive environments : a hands-on workshop to explore interactivity and persuasion in design

NARCIS (Netherlands)

Rozendaal, Marco; Bekker, Tilde; Vermeeren, Arnold; Kanis, Marije; Aprile, Walter; van der Helm, Aadjan; Middendorf, Wouter

2012-01-01

Ambient Intelligent environments are interactive environments that sense human behaviour and can respond intelligently. This workshop explores how interactive environments can be designed with persuasive quality, influencing human experience and behaviour. The workshop follows a

Multiply-Imputed Synthetic Data: Advice to the Imputer

Directory of Open Access Journals (Sweden)

Loong Bronwyn

2017-12-01

Full Text Available Several statistical agencies have started to use multiply-imputed synthetic microdata to create public-use data in major surveys. The purpose of doing this is to protect the confidentiality of respondents’ identities and sensitive attributes, while allowing standard complete-data analyses of microdata. A key challenge, faced by advocates of synthetic data, is demonstrating that valid statistical inferences can be obtained from such synthetic data for non-confidential questions. Large discrepancies between observed-data and synthetic-data analytic results for such questions may arise because of uncongeniality; that is, differences in the types of inputs available to the imputer, who has access to the actual data, and to the analyst, who has access only to the synthetic data. Here, we discuss a simple, but possibly canonical, example of uncongeniality when using multiple imputation to create synthetic data, which specifically addresses the choices made by the imputer. An initial, unanticipated but not surprising, conclusion is that non-confidential design information used to impute synthetic data should be released with the confidential synthetic data to allow users of synthetic data to avoid possible grossly conservative inferences.

Living closer to the environment: Housing design concept

Directory of Open Access Journals (Sweden)

Kosorić Vesna

2011-01-01

Full Text Available The main idea of this design concept is to strengthen the relationship and understanding between a man - resident and his environment. Residents are separated from the outdoor environment by glazing, which enables constant observation of environment from nearly all points of indoor space, encouraging positive feelings towards external world and understanding of the fragility of biosphere. Care for the environment should become a part of a man's nature and way of living, and it is the people who are expected to become the driving force of positive global changes towards sustainable development. The semisphere-like single family house of 14m in diameter has a multifunctional, multi-layer 'active' facade envelope. The envelope ensures constant visual contact of residents with the whole surroundings, while still providing comfort. The living space of the house reflects natural shapes which are organic rather than rectangular. Such indoor space becomes a part of the environment, rather than being protected, distanced and isolated from it. The house is designed to use solar energy 'passively' by absorption through insulated glazed envelope and 'actively' by outer skin layer on the first floor, made of stripes of flat semi-transparent polycrystalline photovoltaic (PV panels. In addition to its constructive role, the concrete core of the house acts as thermal mass and enables absorption and accumulation of thermal energy. The developed housing concept is applicable in different urban-design units and sets.

Ward design: creating a healing patient-environment.

Science.gov (United States)

Biley, F

The drive for cost-effectiveness in hospital design over the decades has meant that minimal thought has been given to the effect of environments on patients' health. The author draws on research evidence to demonstrate how the appearance and ambience of patient areas can have profound effects on recovery patterns, and suggests that the creation of environments more conducive to healing need not incur heavy expense in time or money.

Design of supply chain in fuzzy environment

OpenAIRE

Rao, Kandukuri Narayana; Subbaiah, Kambagowni Venkata; Singh, Ganja Veera Pratap

2013-01-01

Nowadays, customer expectations are increasing and organizations are prone to operate in an uncertain environment. Under this uncertain environment, the ultimate success of the firm depends on its ability to integrate business processes among supply chain partners. Supply chain management emphasizes cross-functional links to improve the competitive strategy of organizations. Now, companies are moving from decoupled decision processes towards more integrated design and control of their compone...

Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students.

Science.gov (United States)

Beach, Dale L; Alvarez, Consuelo J

2015-12-01

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic "parts," students construct a "reporter plasmid" expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a "sensor plasmid," the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.

Designing learning environments to teach interactive Quantum Physics

NARCIS (Netherlands)

Gómez Puente, S.M.; Swagten, H.J.M.

2012-01-01

This study aims at describing and analysing systematically an interactive learning environment designed to teach Quantum Physics, a second-year physics course. The instructional design of Quantum Physics is a combination of interactive lectures (using audience response systems), tutorials and

Protease-sensitive synthetic prions.

Directory of Open Access Journals (Sweden)

David W Colby

2010-01-01

Full Text Available Prions arise when the cellular prion protein (PrP(C undergoes a self-propagating conformational change; the resulting infectious conformer is designated PrP(Sc. Frequently, PrP(Sc is protease-resistant but protease-sensitive (s prions have been isolated in humans and other animals. We report here that protease-sensitive, synthetic prions were generated in vitro during polymerization of recombinant (rec PrP into amyloid fibers. In 22 independent experiments, recPrP amyloid preparations, but not recPrP monomers or oligomers, transmitted disease to transgenic mice (n = 164, denoted Tg9949 mice, that overexpress N-terminally truncated PrP. Tg9949 control mice (n = 174 did not spontaneously generate prions although they were prone to late-onset spontaneous neurological dysfunction. When synthetic prion isolates from infected Tg9949 mice were serially transmitted in the same line of mice, they exhibited sPrP(Sc and caused neurodegeneration. Interestingly, these protease-sensitive prions did not shorten the life span of Tg9949 mice despite causing extensive neurodegeneration. We inoculated three synthetic prion isolates into Tg4053 mice that overexpress full-length PrP; Tg4053 mice are not prone to developing spontaneous neurological dysfunction. The synthetic prion isolates caused disease in 600-750 days in Tg4053 mice, which exhibited sPrP(Sc. These novel synthetic prions demonstrate that conformational changes in wild-type PrP can produce mouse prions composed exclusively of sPrP(Sc.

WISB: Warwick Integrative Synthetic Biology Centre.

Science.gov (United States)

McCarthy, John

2016-06-15

Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).

TinkerCell: modular CAD tool for synthetic biology

Science.gov (United States)

Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

2009-01-01

Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. Results An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API). TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at . Conclusion An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled and analyzed computationally. TinkerCell can readily

TinkerCell: modular CAD tool for synthetic biology

Directory of Open Access Journals (Sweden)

Bergmann Frank T

2009-10-01

Full Text Available Abstract Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. Results An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at http://www.tinkercell.com. Conclusion An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Science.gov (United States)

Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

2017-03-28

Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Virtual environments for nuclear power plant design

International Nuclear Information System (INIS)

Brown-VanHoozer, S.A.; Singleterry, R.C. Jr.; King, R.W.

1996-01-01

In the design and operation of nuclear power plants, the visualization process inherent in virtual environments (VE) allows for abstract design concepts to be made concrete and simulated without using a physical mock-up. This helps reduce the time and effort required to design and understand the system, thus providing the design team with a less complicated arrangement. Also, the outcome of human interactions with the components and system can be minimized through various testing of scenarios in real-time without the threat of injury to the user or damage to the equipment. If implemented, this will lead to a minimal total design and construction effort for nuclear power plants (NPP)

Human-centered environment design in intensive care unit

OpenAIRE

Li, Y.; Albayrak, A.; Goossens, R.H.M.; Xiao, D.; Jakimowicz, J.J.

2013-01-01

Because of high risk and instability of the patients in Intensive care unit(ICU), the design of ICU is very difficult. ICU design, auxiliary building design, lighting design, noise control and other aspects can also enhance its management. In this paper, we compare ICU design in China and Holland based on related standards. We also premeditate the indoor environment from planning perspective, analyze patients, their families, medical staff and space requirement to conduct research in ICU desi...

Internet-centric collaborative design in a distributed environment

International Nuclear Information System (INIS)

Kim, Hyun; Kim, Hyoung Sun; Do, Nam Chul; Lee, Jae Yeol; Lee, Joo Haeng; Myong, Jae Hyong

2001-01-01

Recently, advanced information technologies including internet-related technology and distributed object technology have opened new possibilities for collaborative designs. In this paper, we discuss computer supports for collaborative design in a distributed environment. The proposed system is the internet-centric system composed of an engineering framework, collaborative virtual workspace and engineering service. It allows the distributed designers to more efficiently and collaboratively work their engineering tasks throughout the design process

Design and Structure-Function Characterization of 3D Printed Synthetic Porous Biomaterials for Tissue Engineering.

Science.gov (United States)

Kelly, Cambre N; Miller, Andrew T; Hollister, Scott J; Guldberg, Robert E; Gall, Ken

2018-04-01

3D printing is now adopted for use in a variety of industries and functions. In biomedical engineering, 3D printing has prevailed over more traditional manufacturing methods in tissue engineering due to its high degree of control over both macro- and microarchitecture of porous tissue scaffolds. However, with the improved flexibility in design come new challenges in characterizing the structure-function relationships between various architectures and both mechanical and biological properties in an assortment of clinical applications. Presently, the field of tissue engineering lacks a comprehensive body of literature that is capable of drawing meaningful relationships between the designed structure and resulting function of 3D printed porous biomaterial scaffolds. This work first discusses the role of design on 3D printed porous scaffold function and then reviews characterization of these structure-function relationships for 3D printed synthetic metallic, polymeric, and ceramic biomaterials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Creating Learning Environment Connecting Engineering Design and 3D Printing

Science.gov (United States)

Pikkarainen, Ari; Salminen, Antti; Piili, Heidi

Engineering education in modern days require continuous development in didactics, pedagogics and used practical methods. 3D printing provides excellent opportunity to connect different engineering areas into practice and produce learning by doing applications. The 3D-printing technology used in this study is FDM (Fused deposition modeling). FDM is the most used 3D-printing technology by commercial numbers at the moment and the qualities of the technology makes it popular especially in academic environments. For achieving the best result possible, students will incorporate the principles of DFAM (Design for additive manufacturing) into their engineering design studies together with 3D printing. This paper presents a plan for creating learning environment for mechanical engineering students combining the aspects of engineering design, 3D-CAD learning and AM (additive manufacturing). As a result, process charts for carrying out the 3D printing process from technological point of view and design process for AM from engineering design point of view were created. These charts are used in engineering design education. The learning environment is developed to work also as a platform for Bachelor theses, work-training environment for students, prototyping service centre for cooperation partners and source of information for mechanical engineering education in Lapland University of Applied Sciences.

The RHIC/AGS Online Model Environment: Design and Overview

International Nuclear Information System (INIS)

Satogata, T.; Brown, K.; Pilat, F.; Tafti Alai, A.; Tepikian, S.; Vanzeijtz

1999-01-01

An integrated online modeling environment is currently under development for use by AGS and RHIC physicists and commissioners. This environment combines the modeling efforts of both groups in a CDEV[1] client-server design, providing access to expected machine optics and physics parameters based on live and design machine settings. An abstract modeling interface has been designed as a set of adapters[2] around core computational modeling engines such as MAD and UAL/Teapot++[3]. This approach allows us to leverage existing survey, lattice, and magnet infrastructure, as well as easily incorporate new model engine developments. This paper describes the architecture of the RHIC/AGS modeling environment, including the application interface through CDEV and general tools for graphical interaction with the model using Tcl/Tk. Separate papers at this conference address the specifics of implementation and modeling experience for AGS and RHIC

Crime: impacts of urban design and environment

Directory of Open Access Journals (Sweden)

Paula Santana

2013-07-01

Full Text Available The criminal research has confirmed that there are clear patterns of crime, with concentrations in specific places at specific times. That is to say, incidence of crime are not distributed randomly; rather, there are certain areas in cities that are relatively small, but where crimes occur much more frequently than elsewhere (the so-called “hotspots”, making them highly vulnerable and predictable. Urban design and environment may play a part in the decision of whether or not to commit a crime; for example, the lack of natural vigilance, poor lighting and other variables mean that a small area may easily be transformed into a potential crime hotspot. The relationship between specific aspects of urban design and the formation of “hotspots” is present in the theory of “Crime Prevention through Environmental Design” (CPTED. This paper examines the relationship between the “hotspots” and the characteristics of the environment, in accordance with CPTED Index, in one city from the Lisbon Metropolitan Area (Amadora. The results highlight the need to reassess specific elements of urban design. This fact has drawn attention to the study of localities and urban design.

Designing discovery learning environments: process analysis and implications for designing an information system

NARCIS (Netherlands)

Pieters, Julius Marie; Limbach, R.; de Jong, Anthonius J.M.

2004-01-01

A systematic analysis of the design process of authors of (simulation based) discovery learning environments was carried out. The analysis aimed at identifying the design activities of authors and categorising knowledge gaps that they experience. First, five existing studies were systematically

DPL/Daedalus design environment (for VLSI)

Energy Technology Data Exchange (ETDEWEB)

Batali, J; Mayle, N; Shrobe, H; Sussman, G; Weise, D

1981-01-01

The DPL/Daedalus design environment is an interactive VLSI design system implemented at the MIT Artificial Intelligence Laboratory. The system consists of several components: a layout language called DPL (for design procedure language); an interactive graphics facility (Daedalus); and several special purpose design procedures for constructing complex artifacts such as PLAs and microprocessor data paths. Coordinating all of these is a generalized property list data base which contains both the data representing circuits and the procedures for constructing them. The authors first review the nature of the data base and then turn to DPL and Daedalus, the two most common ways of entering information into the data base. The next two sections review the specialized procedures for constructing PLAs and data paths; the final section describes a tool for hierarchical node extraction. 5 references.

Synthetic Genetic Targeting of Genome Instability in Cancer

International Nuclear Information System (INIS)

Sajesh, Babu V.; Guppy, Brent J.; McManus, Kirk J.

2013-01-01

Cancer is a leading cause of death throughout the World. A limitation of many current chemotherapeutic approaches is that their cytotoxic effects are not restricted to cancer cells, and adverse side effects can occur within normal tissues. Consequently, novel strategies are urgently needed to better target cancer cells. As we approach the era of personalized medicine, targeting the specific molecular defect(s) within a given patient’s tumor will become a more effective treatment strategy than traditional approaches that often target a given cancer type or sub-type. Synthetic genetic interactions are now being examined for their therapeutic potential and are designed to target the specific genetic and epigenetic phenomena associated with tumor formation, and thus are predicted to be highly selective. In general, two complementary approaches have been employed, including synthetic lethality and synthetic dosage lethality, to target aberrant expression and/or function associated with tumor suppressor genes and oncogenes, respectively. Here we discuss the concepts of synthetic lethality and synthetic dosage lethality, and explain three general experimental approaches designed to identify novel genetic interactors. We present examples and discuss the merits and caveats of each approach. Finally, we provide insight into the subsequent pre-clinical work required to validate novel candidate drug targets

Synthetic clay excels in 90Sr removal

International Nuclear Information System (INIS)

Komarneni, Sridhar; Kodama, Tatsuya; Paulus, William J.; Carlson, C.

2000-01-01

Tests with actual ground water from Hanford site, and fundamental studies of 2Na + →Sr 2+ exchange equilibria revealed that a synthetic clay is extremely selective for 90 Sr with a high capacity for uptake. Comparative studies with existing Sr selective ion exchangers clearly revealed that the present synthetic clay exhibited the best performance for 90 Sr removal from actual ground water collected from three different locations at Hanford. This novel Sr ion sieve is expected to be useful for the decontamination of the environment after accidental release and contamination with 90 Sr. (c) 2000 Materials Research Society

Design for the Environment Products (Raw Data)

Data.gov (United States)

U.S. Environmental Protection Agency — This dataset contains a list of products that carry the Design for the Environment (DfE) label. This mark enables consumers to quickly identify and choose products...

Design for the Environment Products (Online Search)

Data.gov (United States)

U.S. Environmental Protection Agency — This dataset contains a list of products that carry the Design for the Environment (DfE) label. This mark enables consumers to quickly identify and choose products...

POTENTIAL USE OF VIRTUAL ENVIRONMENTS IN DESIGN EDUCATION

OpenAIRE

SAGUN, Aysu

2011-01-01

This paper explores the potential use of Virtual Environments (VE) in design education. Recently, the way the designers form their mental concepts, develop and test their design is enhanced with the new computer technologies. Computer generated VE has a great potential to be used in the design process and collaborative studies because they enable manipulation of simulated products as well as interaction of people with each other and the simulated space for communication and col...

DESIGN COORDINATION IN DISTRIBUTED ENVIRONMENTS USING VIRTUAL REALITY SYSTEMS

Directory of Open Access Journals (Sweden)

Rusdi HA

2003-01-01

Full Text Available This paper presents a research project, which investigates the use of virtual reality and computer communication technology to facilitate building design coordination in distributed environments. The emphasis of the system, called VR-based DEsign COordination (VRDECO is providing a communication tool that can be used by remote designers for settling ideas before they fully engage in concurrent engineering environments. VRDECO provides the necessary design tools, library of building elements and communication procedures, for designers from remote places to perform and coordinate their initial tasks. It has been implemented using available commercial software packages, and is used in designing a simple house. VRDECO facilitates the creation a preliminary design and simple communication with the client. There are, however, some difficulties in the development of the full version of VRDECO, i.e.: creating an adequate number of building elements, building specification database with a sufficient number of choices, and establishing a systematic rule to determine the parts of a building that are updateable.

Characteristic Trends in Prevalence and Use of New Synthetic "Designer" Drugs over the Territory of the Republic of Bashkortostan

Science.gov (United States)

Asadullin, Azat R.; Yuldashev, Vladimir L.; Galeeva, Elena Kh.; Achmetova, Elvina A.; Nikolaev, Ivan V.

2016-01-01

The urgency of this study has become vivid in the light of the growing problem of prevalence and use of new synthetic drug types, incidence rate of comorbid states, and pathomorphism of psychoactive substances consumption. The aim of this paper consists in analysis and disclosure of the research data obtained on consumption of such designer drugs…

Cfd modeling of a synthetic jet actuator

International Nuclear Information System (INIS)

Dghim, Marouane; Ben Chiekh, Maher; Ben Nasrallah, Sassi

2009-01-01

Synthetic jet actuators show good promise as an enabling technology for innovative boundary layer flow control applied to external surfaces, like airplane wings, and to internal flows, like those occurring in a curved engine inlet. The appealing characteristics of a synthetic jet are zero-net-mass flux operation and an efficient control effect that takes advantages of unsteady fluid phenomena. The formation of a synthetic jet in a quiescent external air flow is only beginning to be understood and a rational understanding of these devices is necessary before they can be applied to the control of flows outside of the laboratory. The synthetic jet flow generated by a planar orifice is investigated here using computational approach. Computations of the 2D synthetic jet are performed with unsteady RANS modeled with the Realizable κ - ε turbulence model available in FLUENT environment. In this present work, the ability of the first order turbulence model, employed in our computations, to model the formation of the counter-rotating-vortex pair (CVP) that appears in the flow-field was investigated. Computational results were in good agreement with experimental measurements. The effectiveness of such control actuator was tested on separated boundary layer. Preliminary investigation were presented and discussed

[Applications of synthetic biology in materials science].

Science.gov (United States)

Zhao, Tianxin; Zhong, Chao

2017-03-25

Materials are the basis for human being survival and social development. To keep abreast with the increasing needs from all aspects of human society, there are huge needs in the development of advanced materials as well as high-efficiency but low-cost manufacturing strategies that are both sustainable and tunable. Synthetic biology, a new engineering principle taking gene regulation and engineering design as the core, greatly promotes the development of life sciences. This discipline has also contributed to the development of material sciences and will continuously bring new ideas to future new material design. In this paper, we review recent advances in applications of synthetic biology in material sciences, with the focus on how synthetic biology could enable synthesis of new polymeric biomaterials and inorganic materials, phage display and directed evolution of proteins relevant to materials development, living functional materials, engineered bacteria-regulated artificial photosynthesis system as well as applications of gene circuits for material sciences.

Using IMPRINT to Guide Experimental Design with Simulated Task Environments

Science.gov (United States)

2015-06-18

USING IMPRINT TO GUIDE EXPERIMENTAL DESIGN OF SIMULATED TASK ENVIRONMENTS THESIS Gregory...ENG-MS-15-J-052 USING IMPRINT TO GUIDE EXPERIMENTAL DESIGN WITH SIMULATED TASK ENVIRONMENTS THESIS Presented to the Faculty Department...Civilian, USAF June 2015 DISTRIBUTION STATEMENT A. APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED. AFIT-ENG-MS-15-J-052 USING IMPRINT

Multifunctional design of footwear for hot environment condition

Science.gov (United States)

Dragcevic, Z.; Vujasinovic, E.; Hursa Sajatovic, A.

2017-10-01

For some time design of a new product is not connected only with aesthetic, artistic appearance but moreover with functionality and engineering (from rightful selection of materials, construction, and technological concept to prototyping). One good example of this is design of multifunctional footwear as well as hiking footwear, footwear for soldiers, police officers, first responders etc. All mentioned kinds of footwear have lot of specific requirements to fulfil starting from maintaining and enhancing mobility to maximizing protection and eliminating or minimizing the risk for the wearer. Therefore, designing appropriate footwear represents a great challenge not only for designers but for engineers as well. Having that entire in mind few years ago, Faculty of Textile Technology University of Zagreb started the research with the aim to develop 21st century multifunctional footwear for e.g. military, police, first respondents or any special human forces for different weather environment. The paper presents how it was done in the case of boots for hot environment conditions

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

Science.gov (United States)

Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

2013-01-01

SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

Coating a polystyrene well-plate surface with synthetic hematite, goethite and aluminium hydroxide for cell mineral adhesion studies in a controlled environment

International Nuclear Information System (INIS)

Pouran, Hamid M.; Banwart, Steve A.; Romero-Gonzalez, Maria

2014-01-01

Highlights: • Hematite, goethite and aluminium hydroxide were synthesized and characterize. • Polystyrene cell culture well plates were coated with the synthetic metal oxides. • The coated well plates proven to be completely identical to the synthetic minerals. • The coating method is compatible with what occurs in aquifers with metal oxides. • This method provides a key experimental part for cell mineral adhesion studies. - Abstract: Iron and aluminium oxides are available in many climatic regions and play a vital role in many environmental processes, including the interactions of microorganisms in contaminated soils and groundwater with their ambient environment. Indigenous microorganisms in contaminated environments often have the ability to degrade or transform those contaminants, a concept that supports an in situ remediation approach and uses natural microbial populations in order to bio-remediate polluted sites. These metal oxides have a relatively high pH-dependent surface charge, which makes them good candidates for studying mineral–bacterial adhesion. Given the importance of understanding the reactions that occur at metal oxide and bacterial cell interfaces and to investigate this phenomenon further under well-characterized conditions, some of the most common iron and aluminium oxides; hematite, goethite and aluminium hydroxide, were synthesized and characterized and a coating method was developed to coat polystyrene well-plates as a surface exposable to bacterial adhesion with these minerals (non-treated polystyrene-12 well-plates which are used for cell cultures). The coating process was designed in a way that resembles naturally coated surfaces in aquifers. Hematite, Fe 2 O 3 , was synthesized from acidic FeCl 3 solution, while goethite, FeOOH, and aluminium hydroxide, Al(OH) 3 , were prepared from an alkaline solution of Fe(NO 3 ) 3 and Al(NO 3 ) 3 . They were further characterized using X-ray diffraction (XRD), Fourier transform infrared

Design research and the globalization of healthcare environments.

Science.gov (United States)

Shepley, Mardelle McCuskey; Song, Yilin

2014-01-01

Global healthcare practice has expanded in the past 20 years. At the same time the incorporation of research into the design process has gained prominence as a best practice among architects. The authors of this study investigated the status of design research in a variety of international settings. We intended to answer the question, "how pervasive is healthcare design research outside of the United States?" The authors reviewed the international literature on the design of healthcare facilities. More than 500 international studies and conference proceedings were incorporated in this literature review. A team of five research assistants searched multiple databases comparing approximately 16 keywords to geographic location. Some of those keywords included: evidence-based design, salutogenic design, design research, and healthcare environment. Additional articles were gathered by contacting prominent researchers and asking for their personal assessment of local health design research studies. While there are design researchers in most parts of the world, the majority of studies focus on the needs of populations in developed countries and generate guidelines that have significant cost and cultural implications that prohibit their implementation in developing countries. Additionally, the body of literature discussing the role of culture in healthcare environments is extremely limited. Design researchers must address the cultural implications of their studies. Additionally, we need to expand our research objectives to address healthcare design in countries that have not been previous considered. © 2014 Vendome Group, LLC.

Natural - synthetic - artificial!

DEFF Research Database (Denmark)

Nielsen, Peter E

2010-01-01

The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life.......The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life....

[How to be prudent with synthetic biology. Synthetic Biology and the precautionary principle].

Science.gov (United States)

Rodríguez López, Blanca

2014-01-01

Synthetic biology is a new discipline that is twofold: firstly it offers the promise to pay benefits that can alleviate some of the ills that plague mankind; On the other hand, like all technologies, holds risks. Given these, the most critical and concerned about the risks, invoke the application of the precautionary principle, common in cases where an activity or new technology creates risks to the environment and/or human health, but far from universally accepted happens to be currently one of the most controversial principles. In this paper the question of the risks and benefits of synthetic biology and the relevance of applying the precautionary principle are analyzed. To do this we proceed as follows. The first part focuses on synthetic biology. At first, this discipline is characterized, with special attention to what is novel compared to the known as "genetic engineering". In the second stage both the benefits and the risks associated with it are discussed. The first part concludes with a review of the efforts currently being made to control or minimize the risks. The second part aims to analyze the precautionary principle and its possible relevance to the case of Synthetic Biology. At first, the different versions and interpretations of the principle and the various criticisms of which has been the subject are reviewed. Finally, after discarding the Precautionary Principle as an useful tool, it is seen as more appropriate some recent proposals to treat technologies that take into account not only risks but also their benefits.

Designing Learning Environments to Teach Interactive Quantum Physics

Science.gov (United States)

Puente, Sonia M. Gomez; Swagten, Henk J. M.

2012-01-01

This study aims at describing and analysing systematically an interactive learning environment designed to teach Quantum Physics, a second-year physics course. The instructional design of Quantum Physics is a combination of interactive lectures (using audience response systems), tutorials and self-study in unit blocks, carried out with small…

Software support environment design knowledge capture

Science.gov (United States)

Dollman, Tom

1990-01-01

The objective of this task is to assess the potential for using the software support environment (SSE) workstations and associated software for design knowledge capture (DKC) tasks. This assessment will include the identification of required capabilities for DKC and hardware/software modifications needed to support DKC. Several approaches to achieving this objective are discussed and interim results are provided: (1) research into the problem of knowledge engineering in a traditional computer-aided software engineering (CASE) environment, like the SSE; (2) research into the problem of applying SSE CASE tools to develop knowledge based systems; and (3) direct utilization of SSE workstations to support a DKC activity.

Designing powerplants for today's competitive environment

International Nuclear Information System (INIS)

Makansi, J.

1994-01-01

Deregulation continues to unfold. Certainty about what the impact will be is as scarce as new US powerplant development opportunities. But one thing industry observers seem clear on is that the priorities for powerplant design will shift as competitive forces are rolled out. Powerplants will have to be developed, designed, and operated as a bottom-line business, not as part of a regulated industry. Thus, the design must enable the facility to accomplish this goal. In the emerging fully competitive environment, that bottom line applies to both the kilowatt and the kilowatt-hour. The entrepreneurial and business skills and talents of the independent power producer (IPP) have mostly been brought to bear on capital costs and project development thus far, with electricity sold under long-term power-purchase agreements. If retail wheeling takes hold, future plants must also be designed to merchandise power to a variety of customers scattered around the grid. This article provides insight into how powerplant design will accommodate new priorities

Personal Pervasive Environments: Practice and Experience

Directory of Open Access Journals (Sweden)

Enrique Soriano

2012-05-01

Full Text Available In this paper we present our experience designing and developing two different systems to enable personal pervasive computing environments, Plan B and the Octopus. These systems were fully implemented and have been used on a daily basis for years. Both are based on synthetic (virtual file system interfaces and provide mechanisms to adapt to changes in the context and reconfigure the system to support pervasive applications. We also present the main differences between them, focusing on architectural and reconfiguration aspects. Finally, we analyze the pitfalls and successes of both systems and review the lessons we learned while designing, developing, and using them.

Synthetic biology era: Improving antibiotic's world.

Science.gov (United States)

Guzmán-Trampe, Silvia; Ceapa, Corina D; Manzo-Ruiz, Monserrat; Sánchez, Sergio

2017-06-15

The emergence of antibiotic-resistant pathogen microorganisms is problematic in the context of the current spectrum of available medication. The poor specificity and the high toxicity of some available molecules have made imperative the search for new strategies to improve the specificity and to pursue the discovery of novel compounds with increased bioactivity. Using living cells as platforms, synthetic biology has counteracted this problem by offering novel pathways to create synthetic systems with improved and desired functions. Among many other biotechnological approaches, the advances in synthetic biology have made it possible to design and construct novel biological systems in order to look for new drugs with increased bioactivity. Advancements have also been made in the redesigning of RNA and DNA molecules in order to engineer antibiotic clusters for antibiotic overexpression. As for the production of these antibacterial compounds, yeasts and filamentous fungi as well as gene therapy are utilized to enhance protein solubility. Specific delivery is achieved by creating chimeras using plant genes into bacterial hosts. Some of these synthetic systems are currently in clinical trials, proving the proficiency of synthetic biology in terms of both pharmacological activities as well as an increase in the biosafety of treatments. It is possible that we may just be seeing the tip of the iceberg, and synthetic biology applications will overpass expectations beyond our present knowledge. Copyright © 2017. Published by Elsevier Inc.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Design and "As Flown" Radiation Environments for Materials in Low Earth Orbit

Science.gov (United States)

Minow, Joseph; McWilliams, Brett; Altstatt, Richard; Koontz, Steven

2006-01-01

A conservative design approach was adopted by the International Space Station Program for specifying total ionizing radiation dose requirements for use in selecting and qualifying materials for construction of the International Space Station. The total ionizing dose design environment included in SSP 30512 Space Station Ionizing Radiation Design Environment is based on trapped proton and electron fluence derived from the solar maximum versions of the AE-8 and AP-8 models, respectively, specified for a circular orbit at 500 km altitude and 51.7 degree inclination. Since launch, the range of altitudes utilized for Space Station operations vary from a minimum of approximately 330 km to a maximum of approximately 405 km with a mean operational altitude less than 400 km. The design environment, therefore, overestimates the radiation environment because the particle flux in the South Atlantic Anomaly is the primary contributor to radiation dose in low Earth orbit and flux within the Anomaly is altitude dependent. In addition, a 2X multiplier is often applied to the design environment to cover effects from the contributions of galactic cosmic rays, solar energetic particle events, geomagnetic storms, and uncertainties in the trapped radiation models which are not explicitly included in the design environment. Application of this environment may give radiation dose overestimates on the order of 1OX to 30X for materials exposed to the space environment, suggesting that materials originally qualified for ten year exposures on orbit may be used for longer periods without replacement. In this paper we evaluate the "as flown" radiation environments derived from historical records of the ISS flight trajectory since launch and compare the results with the SSP 30512 design environment to document the magnitude of the radiation dose overestimate provided by the design environment. "As flown" environments are obtained from application of the AE-8/AP-8 trapped particle models along

Design of Feedback in Interactive Multimedia Language Learning Environments

Directory of Open Access Journals (Sweden)

Vehbi Türel

2012-01-01

Full Text Available In interactive multimedia environments, different digital elements (i. e. video, audio, visuals, text, animations, graphics and glossary can be combined and delivered on the same digital computer screen (TDM 1997: 151, CCED 1987, Brett 1998: 81, Stenton 1998: 11, Mangiafico 1996: 46. This also enables effectively provision and presentation of feedback in pedagogically more efficient ways, which meets not only the requirement of different teaching and learning theories, but also the needs of language learners who vary in their learning-style preferences (Robinson 1991: 156, Peter 1994: 157f.. This study aims to bring out the pedagogical and design principles that might help us to more effectively design and customise feedback in interactive multimedia language learning environments. While so doing, some examples of thought out and customized computerised feedback from an interactive multimedia language learning environment, which were designed and created by the author of this study and were also used for language learning purposes, will be shown.

Design for the Environment Products (Online Search)

Science.gov (United States)

This dataset contains a list of products that carry the Design for the Environment (DfE) label. This mark enables consumers to quickly identify and choose products that can help protect the environment and are safer for families. When you see the DfE logo on a product it means that the DfE scientific review team has screened each ingredient for potential human health and environmental effects and that-based on currently available information, EPA predictive models, and expert judgment-the product contains only those ingredients that pose the least concern among chemicals in their class. Product manufacturers who become DfE partners, and earn the right to display the DfE logo on recognized products, have invested heavily in research, development and reformulation to ensure that their ingredients and finished product line up on the green end of the health and environmental spectrum while maintaining or improving product performance. EPA's Design for the Environment Program (DfE) has allowed use of their logo on over 2500 products. These products are formulated from the safest possible ingredients and have reduced the use of chemicals of concern by hundreds of millions of pounds.

Precision control of recombinant gene transcription for CHO cell synthetic biology.

Science.gov (United States)

Brown, Adam J; James, David C

2016-01-01

The next generation of mammalian cell factories for biopharmaceutical production will be genetically engineered to possess both generic and product-specific manufacturing capabilities that may not exist naturally. Introduction of entirely new combinations of synthetic functions (e.g. novel metabolic or stress-response pathways), and retro-engineering of existing functional cell modules will drive disruptive change in cellular manufacturing performance. However, before we can apply the core concepts underpinning synthetic biology (design, build, test) to CHO cell engineering we must first develop practical and robust enabling technologies. Fundamentally, we will require the ability to precisely control the relative stoichiometry of numerous functional components we simultaneously introduce into the host cell factory. In this review we discuss how this can be achieved by design of engineered promoters that enable concerted control of recombinant gene transcription. We describe the specific mechanisms of transcriptional regulation that affect promoter function during bioproduction processes, and detail the highly-specific promoter design criteria that are required in the context of CHO cell engineering. The relative applicability of diverse promoter development strategies are discussed, including re-engineering of natural sequences, design of synthetic transcription factor-based systems, and construction of synthetic promoters. This review highlights the potential of promoter engineering to achieve precision transcriptional control for CHO cell synthetic biology. Copyright © 2015. Published by Elsevier Inc.

Sky View Factors from Synthetic Fisheye Photos for Thermal Comfort Routing—A Case Study in Phoenix, Arizona

Directory of Open Access Journals (Sweden)

Ariane Middel

2017-03-01

Full Text Available The Sky View Factor (SVF is a dimension-reduced representation of urban form and one of the major variables in radiation models that estimate outdoor thermal comfort. Common ways of retrieving SVFs in urban environments include capturing fisheye photographs or creating a digital 3D city or elevation model of the environment. Such techniques have previously been limited due to a lack of imagery or lack of full scale detailed models of urban areas. We developed a web based tool that automatically generates synthetic hemispherical fisheye views from Google Earth at arbitrary spatial resolution and calculates the corresponding SVFs through equiangular projection. SVF results were validated using Google Maps Street View and compared to results from other SVF calculation tools. We generated 5-meter resolution SVF maps for two neighborhoods in Phoenix, Arizona to illustrate fine-scale variations of intra-urban horizon limitations due to urban form and vegetation. To demonstrate the utility of our synthetic fisheye approach for heat stress applications, we automated a radiation model to generate outdoor thermal comfort maps for Arizona State University’s Tempe campus for a hot summer day using synthetic fisheye photos and on-site meteorological data. Model output was tested against mobile transect measurements of the six-directional radiant flux density. Based on the thermal comfort maps, we implemented a pedestrian routing algorithm that is optimized for distance and thermal comfort preferences. Our synthetic fisheye approach can help planners assess urban design and tree planting strategies to maximize thermal comfort outcomes and can support heat hazard mitigation in urban areas.

LEVELS OF SYNTHETIC MUSKS COMPOUNDS IN AQUATIC ...

Science.gov (United States)

Synthetic musk compounds are consumer chemicals manufactured as fragrance materials Due to their high worldwide usage and release, they frequently occur in the aquatic and marine environments. The U.S. EPA (ORD, Las Vegas) developed surface-water monitoring methodology and conducted a one-year monthly monitoring of synthetic musks in water and biota from Lake Mead (Nevada) as well as from combined sewage effluent streams feeding Lake Mead. Presented are the overview of the chemistry, the monitoring methodology, and the significance of synthetic musk compounds in the aquatic environment. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-soluble pharmaceuticals in source waters at levels that could be environmentally significant (at concentrations less than p

User-centered virtual environment design for virtual rehabilitation

Directory of Open Access Journals (Sweden)

Rizzo Albert A

2010-02-01

Full Text Available Abstract Background As physical and cognitive rehabilitation protocols utilizing virtual environments transition from single applications to comprehensive rehabilitation programs there is a need for a new design cycle methodology. Current human-computer interaction designs focus on usability without benchmarking technology within a user-in-the-loop design cycle. The field of virtual rehabilitation is unique in that determining the efficacy of this genre of computer-aided therapies requires prior knowledge of technology issues that may confound patient outcome measures. Benchmarking the technology (e.g., displays or data gloves using healthy controls may provide a means of characterizing the "normal" performance range of the virtual rehabilitation system. This standard not only allows therapists to select appropriate technology for use with their patient populations, it also allows them to account for technology limitations when assessing treatment efficacy. Methods An overview of the proposed user-centered design cycle is given. Comparisons of two optical see-through head-worn displays provide an example of benchmarking techniques. Benchmarks were obtained using a novel vision test capable of measuring a user's stereoacuity while wearing different types of head-worn displays. Results from healthy participants who performed both virtual and real-world versions of the stereoacuity test are discussed with respect to virtual rehabilitation design. Results The user-centered design cycle argues for benchmarking to precede virtual environment construction, especially for therapeutic applications. Results from real-world testing illustrate the general limitations in stereoacuity attained when viewing content using a head-worn display. Further, the stereoacuity vision benchmark test highlights differences in user performance when utilizing a similar style of head-worn display. These results support the need for including benchmarks as a means of better

User-centered virtual environment design for virtual rehabilitation.

Science.gov (United States)

Fidopiastis, Cali M; Rizzo, Albert A; Rolland, Jannick P

2010-02-19

As physical and cognitive rehabilitation protocols utilizing virtual environments transition from single applications to comprehensive rehabilitation programs there is a need for a new design cycle methodology. Current human-computer interaction designs focus on usability without benchmarking technology within a user-in-the-loop design cycle. The field of virtual rehabilitation is unique in that determining the efficacy of this genre of computer-aided therapies requires prior knowledge of technology issues that may confound patient outcome measures. Benchmarking the technology (e.g., displays or data gloves) using healthy controls may provide a means of characterizing the "normal" performance range of the virtual rehabilitation system. This standard not only allows therapists to select appropriate technology for use with their patient populations, it also allows them to account for technology limitations when assessing treatment efficacy. An overview of the proposed user-centered design cycle is given. Comparisons of two optical see-through head-worn displays provide an example of benchmarking techniques. Benchmarks were obtained using a novel vision test capable of measuring a user's stereoacuity while wearing different types of head-worn displays. Results from healthy participants who performed both virtual and real-world versions of the stereoacuity test are discussed with respect to virtual rehabilitation design. The user-centered design cycle argues for benchmarking to precede virtual environment construction, especially for therapeutic applications. Results from real-world testing illustrate the general limitations in stereoacuity attained when viewing content using a head-worn display. Further, the stereoacuity vision benchmark test highlights differences in user performance when utilizing a similar style of head-worn display. These results support the need for including benchmarks as a means of better understanding user outcomes, especially for patient

Participatory design in the project of virtual learning environment of histology

OpenAIRE

Santa-Rosa, José Guilherme da Silva

2012-01-01

This present article describes a research on the development, under the approach of participatory design, a virtual teaching-learning of Histology in which students and teachers participated actively in all stages of development of the educational environment. We postulates that the development of virtual learning environment of Histology, through the Participatory Design approach, contributes to greater acceptance and use by students and that the adoption of virtual environment for teaching ...

Building biological foundries for next-generation synthetic biology.

Science.gov (United States)

Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

Transition of a Three-Dimensional Unsteady Viscous Flow Analysis from a Research Environment to the Design Environment

Science.gov (United States)

Dorney, Suzanne; Dorney, Daniel J.; Huber, Frank; Sheffler, David A.; Turner, James E. (Technical Monitor)

2001-01-01

The advent of advanced computer architectures and parallel computing have led to a revolutionary change in the design process for turbomachinery components. Two- and three-dimensional steady-state computational flow procedures are now routinely used in the early stages of design. Unsteady flow analyses, however, are just beginning to be incorporated into design systems. This paper outlines the transition of a three-dimensional unsteady viscous flow analysis from the research environment into the design environment. The test case used to demonstrate the analysis is the full turbine system (high-pressure turbine, inter-turbine duct and low-pressure turbine) from an advanced turboprop engine.

Designing Prediction Tasks in a Mathematics Software Environment

Science.gov (United States)

Brunström, Mats; Fahlgren, Maria

2015-01-01

There is a recognised need in mathematics teaching for new kinds of tasks which exploit the affordances provided by new technology. This paper focuses on the design of prediction tasks to foster student reasoning about exponential functions in a mathematics software environment. It draws on the first iteration of a design based research study…

CSBB: synthetic biology research at Newcastle University.

Science.gov (United States)

Goñi-Moreno, Angel; Wipat, Anil; Krasnogor, Natalio

2017-06-15

The Centre for Synthetic Biology and the Bioeconomy (CSBB) brings together a far-reaching multidisciplinary community across all Newcastle University's faculties - Medical Sciences, Science, Agriculture and Engineering, and Humanities, Arts and Social Sciences. The CSBB focuses on many different areas of Synthetic Biology, including bioprocessing, computational design and in vivo computation, as well as improving understanding of basic molecular machinery. Such breadth is supported by major national and international research funding, a range of industrial partners in the North East of England and beyond, as well as a large number of doctoral and post-doctoral researchers. The CSBB trains the next generation of scientists through a 1-year MSc in Synthetic Biology. © 2017 The Author(s).

The Next Generation of Synthetic Biology Chassis: Moving Synthetic Biology from the Laboratory to the Field.

Science.gov (United States)

Adams, Bryn L

2016-12-16

Escherichia coli (E. coli) has played a pivotal role in the development of genetics and molecular biology as scientific fields. It is therefore not surprising that synthetic biology (SB) was built upon E. coli and continues to dominate the field. However, scientific capabilities have advanced from simple gene mutations to the insertion of rationally designed, complex synthetic circuits and creation of entirely synthetic genomes. The point is rapidly approaching where E. coli is no longer an adequate host for the increasingly sophisticated genetic designs of SB. It is time to develop the next generation of SB chassis; robust organisms that can provide the advanced physiology novel synthetic circuits will require to move SB from the laboratory into fieldable technologies. This can be accomplished by developing chassis-specific genetic toolkits that are as extensive as those for E. coli. However, the holy grail of SB would be the development of a universal toolkit that can be ported into any chassis. This viewpoint article underscores the need for new bacterial chassis, as well as discusses some of the important considerations in their selection. It also highlights a few examples of robust, tractable bacterial species that can meet the demands of tomorrow's state-of-the-art in SB. Significant advances have been made in the first 15 years since this field has emerged. However, the advances over the next 15 years will occur not in laboratory organisms, but in fieldable species where the potential of SB can be fully realized in game changing technology.

Matte painting in stereoscopic synthetic imagery

Science.gov (United States)

Eisenmann, Jonathan; Parent, Rick

2010-02-01

While there have been numerous studies concerning human perception in stereoscopic environments, rules of thumb for cinematography in stereoscopy have not yet been well-established. To that aim, we present experiments and results of subject testing in a stereoscopic environment, similar to that of a theater (i.e. large flat screen without head-tracking). In particular we wish to empirically identify thresholds at which different types of backgrounds, referred to in the computer animation industry as matte paintings, can be used while still maintaining the illusion of seamless perspective and depth for a particular scene and camera shot. In monoscopic synthetic imagery, any type of matte painting that maintains proper perspective lines, depth cues, and coherent lighting and textures saves in production costs while still maintaining the illusion of an alternate cinematic reality. However, in stereoscopic synthetic imagery, a 2D matte painting that worked in monoscopy may fail to provide the intended illusion of depth because the viewer has added depth information provided by stereopsis. We intend to observe two stereoscopic perceptual thresholds in this study which will provide practical guidelines indicating when to use each of three types of matte paintings. We ran subject tests in two virtual testing environments, each with varying conditions. Data were collected showing how the choices of the users matched the correct response, and the resulting perceptual threshold patterns are discussed below.

Review of Opinions of Math Teachers Concerning the Learning Environment That They Design

Science.gov (United States)

Aydin, Bünyamin; Yavuz, Ayse

2016-01-01

Design of appropriate learning environment has a significant importance in creation of aims of the math teaching. In the design of learning environments, teachers play a significant role. The aim of this study is determination of opinions of the math teachers concerning the learning environment that they design. In accordance with this aim, an…

GLobal Integrated Design Environment (GLIDE): A Concurrent Engineering Application

Science.gov (United States)

McGuire, Melissa L.; Kunkel, Matthew R.; Smith, David A.

2010-01-01

The GLobal Integrated Design Environment (GLIDE) is a client-server software application purpose-built to mitigate issues associated with real time data sharing in concurrent engineering environments and to facilitate discipline-to-discipline interaction between multiple engineers and researchers. GLIDE is implemented in multiple programming languages utilizing standardized web protocols to enable secure parameter data sharing between engineers and researchers across the Internet in closed and/or widely distributed working environments. A well defined, HyperText Transfer Protocol (HTTP) based Application Programming Interface (API) to the GLIDE client/server environment enables users to interact with GLIDE, and each other, within common and familiar tools. One such common tool, Microsoft Excel (Microsoft Corporation), paired with its add-in API for GLIDE, is discussed in this paper. The top-level examples given demonstrate how this interface improves the efficiency of the design process of a concurrent engineering study while reducing potential errors associated with manually sharing information between study participants.

Urban Environment Development based on Universal Design Principles

Science.gov (United States)

Harsritanto, Bangun Ir

2018-02-01

Universal Design is a design which facilitated full range of human diversity. By applying Universal design principles, urban environment can be more functional and more user-friendly for everyone. This study examined five urban streets of South Korea as a country experienced on developing various urban street designs based on universal design. This study aimed to examine and compare the South Korea cases using seven principles of universal design. The research methods of this study are literature study, case study, and site observation. The results of this study are: South Korea cases are good practices, urgency of implementing the direction into local regulations; and change of urban development paradigm.

COVE: a visual environment for ocean observatory design

International Nuclear Information System (INIS)

Grochow, K; Lazowska, E; Stoermer, M; Kelley, D; Delaney, J

2008-01-01

Physical, chemical, and biological ocean processes play a crucial role in determining Earth's environment. Unfortunately, our knowledge of these processes is limited because oceanography is carried out today largely the way it was a century ago: as expeditionary science, going to sea in ships and measuring a relatively small number of parameters (e.g., temperature, salinity, and pressure) as time and budget allow. The NSF Ocean Observatories Initiative is a US$330 million project that will help transform oceanography from a data-poor to a data-rich science. A cornerstone of this project is the deep water Regional Scale Nodes (RSN) that will be installed off the coasts of Washington and Oregon. The RSN will include 1500 km of fiber optic cable providing power and bandwidth to the seafloor and throughout the water column. Thousands of sensors will be deployed to stream data and imagery to shore, where they will be available in real time for ocean scientists and the public at large. The design of the RSN is a complex undertaking, requiring a combination of many different interactive tools and areas of visualization: geographic visualization to see the available seafloor bathymetry, scientific visualization to examine existing geospatially located datasets, layout tools to place the sensors, and collaborative tools to communicate across the team during the design. COVE, the Common Observatory Visualization Environment, is a visualization environment designed to meet all these needs. COVE has been built by computer scientists working closely with the engineering and scientific teams who will build and use the RSN. This paper discusses the data and activities of cabled observatory design, the design of COVE, and results from its use across the team

ELISA, a demonstrator environment for information systems architecture design

Science.gov (United States)

Panem, Chantal

1994-01-01

This paper describes an approach of reusability of software engineering technology in the area of ground space system design. System engineers have lots of needs similar to software developers: sharing of a common data base, capitalization of knowledge, definition of a common design process, communication between different technical domains. Moreover system designers need to simulate dynamically their system as early as possible. Software development environments, methods and tools now become operational and widely used. Their architecture is based on a unique object base, a set of common management services and they host a family of tools for each life cycle activity. In late '92, CNES decided to develop a demonstrative software environment supporting some system activities. The design of ground space data processing systems was chosen as the application domain. ELISA (Integrated Software Environment for Architectures Specification) was specified as a 'demonstrator', i.e. a sufficient basis for demonstrations, evaluation and future operational enhancements. A process with three phases was implemented: system requirements definition, design of system architectures models, and selection of physical architectures. Each phase is composed of several activities that can be performed in parallel, with the provision of Commercial Off the Shelves Tools. ELISA has been delivered to CNES in January 94, currently used for demonstrations and evaluations on real projects (e.g. SPOT4 Satellite Control Center). It is on the way of new evolutions.

Multi-Disciplinary Multi-Fidelity Design Environment, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Phoenix Integration will develop a collaborative simulation and design environment that will seamlessly integrate the people, data, and tools required for analyzing...

Health by Design: Interweaving Health Promotion into Environments and Settings

Science.gov (United States)

Springer, Andrew E.; Evans, Alexandra E.; Ortuño, Jaquelin; Salvo, Deborah; Varela Arévalo, Maria Teresa

2017-01-01

The important influence of the environmental context on health and health behavior—which includes place, settings, and the multiple environments within place and settings—has directed health promotion planners from a focus solely on changing individuals, toward a focus on harnessing and changing context for individual and community health promotion. Health promotion planning frameworks such as Intervention Mapping provide helpful guidance in addressing various facets of the environmental context in health intervention design, including the environmental factors that influence a given health condition or behavior, environmental agents that can influence a population’s health, and environmental change methods. In further exploring how to harness the environmental context for health promotion, we examine in this paper the concept of interweaving of health promotion into context, defined as weaving or blending together health promotion strategies, practices, programs, and policies to fit within, complement, and build from existing settings and environments. Health promotion interweaving stems from current perspectives in health intervention planning, improvement science and complex systems thinking by guiding practitioners from a conceptualization of context as a backdrop to intervention, to one that recognizes context as integral to the intervention design and to the potential to directly influence health outcomes. In exploring the general approach of health promotion interweaving, we examine selected theoretical and practice-based interweaving concepts in relation to four key environments (the policy environment, the information environment, the social/cultural/organizational environment, and the physical environment), followed by evidence-based and practice-based examples of health promotion interweaving from the literature. Interweaving of health promotion into context is a common practice for health planners in designing health promotion interventions, yet

Synthetic biology between challenges and risks: suggestions for a model of governance and a regulatory framework, based on fundamental rights.

Science.gov (United States)

Colussi, Ilaria Anna

2013-01-01

This paper deals with the emerging synthetic biology, its challenges and risks, and tries to design a model for the governance and regulation of the field. The model is called of "prudent vigilance" (inspired by the report about synthetic biology, drafted by the U.S. Presidential Commission on Bioethics, 2010), and it entails (a) an ongoing and periodically revised process of assessment and management of all the risks and concerns, and (b) the adoption of policies - taken through "hard law" and "soft law" sources - that are based on the principle of proportionality (among benefits and risks), on a reasonable balancing between different interests and rights at stake, and are oriented by a constitutional frame, which is represented by the protection of fundamental human rights emerging in the field of synthetic biology (right to life, right to health, dignity, freedom of scientific research, right to environment). After the theoretical explanation of the model, its operability is "checked", by considering its application with reference to only one specific risk brought up by synthetic biology - biosecurity risk, i.e. the risk of bioterrorism.

DNA recognition by synthetic constructs.

Science.gov (United States)

Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L

2011-09-05

The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Requirements of Integrated Design Teams While Evaluating Advanced Energy Retrofit Design Options in Immersive Virtual Environments

Directory of Open Access Journals (Sweden)

Xue Yang

2015-12-01

Full Text Available One of the significant ways to save energy use in buildings is to implement advanced energy retrofits in existing buildings. Improving energy performance of buildings through advanced energy retrofitting requires a clear understanding of the cost and energy implications of design alternatives from various engineering disciplines when different retrofit options are considered. The communication of retrofit design alternatives and their energy implications is essential in the decision-making process, as it affects the final retrofit selections and hence the energy efficiency of the retrofitted buildings. The objective of the research presented here was to identify a generic list of information requirements that are needed to be shared and collectively analyzed by integrated design teams during advanced energy retrofit design review meetings held in immersive settings. While identifying such requirements, the authors used an immersive environment based iterative requirements elicitation approach. The technology was used as a means to better identify the information requirements of integrated design teams to be analyzed as a group. This paper provides findings on information requirements of integrated design teams when evaluating retrofit options in immersive virtual environments. The information requirements were identified through interactions with sixteen experts in design and energy modeling domain, and validated with another group of participants consisting of six design experts who were experienced in integrated design processes. Industry practitioners can use the findings in deciding on what information to share with integrated design team members during design review meetings that utilize immersive virtual environments.

DEFACTO: A Design Environment for Adaptive Computing Technology

National Research Council Canada - National Science Library

Hall, Mary

2003-01-01

This report describes the activities of the DEFACTO project, a Design Environment for Adaptive Computing Technology funded under the DARPA Adaptive Computing Systems and Just-In-Time-Hardware programs...

Quantifying shedding of synthetic fibers from textiles; a source of microplastics released into the environment.

Science.gov (United States)

Carney Almroth, Bethanie M; Åström, Linn; Roslund, Sofia; Petersson, Hanna; Johansson, Mats; Persson, Nils-Krister

2018-01-01

Microplastics in the environment are a subject of intense research as they pose a potential threat to marine organisms. Plastic fibers from textiles have been indicated as a major source of this type of contaminant, entering the oceans via wastewater and diverse non-point sources. Their presence is also documented in terrestrial samples. In this study, the amount of microfibers shedding from synthetic textiles was measured for three materials (acrylic, nylon, polyester), knit using different gauges and techniques. All textiles were found to shed, but polyester fleece fabrics shed the greatest amounts, averaging 7360 fibers/m -2 /L -1 in one wash, compared with polyester fabrics which shed 87 fibers/m -2 /L -1 . We found that loose textile constructions shed more, as did worn fabrics, and high twist yarns are to be preferred for shed reduction. Since fiber from clothing is a potentially important source of microplastics, we suggest that smarter textile construction, prewashing and vacuum exhaustion at production sites, and use of more efficient filters in household washing machines could help mitigate this problem.

Modular design of synthetic protein mimics. Characterization of the helical conformation of a 13-residue peptide in crystals

International Nuclear Information System (INIS)

Karle, I.L.; Flippen-Anderson, J.L.; Uma, K.; Balaram, P.

1989-01-01

The incorporation of α-aminoisobutyryl (Aib) residues into peptide sequences facilitates helical folding. Aib-containing sequences have been chosen for the design of rigid helical segments in a modular approach to the construction of a synthetic protein mimic. The helical conformation of the synthetic peptide Boc-Aib-(Val-Ala-Leu-Aib) 3 -OMe in crystals is established by X-ray diffraction. The 13-residue apolar peptide adopts a helical form in the crystal with seven α-type hydrogen bonds in the middle and 3 10 -type hydrogen bonds at either end. The helices stack in columns, zigzag rather than linear, by means of direct NH hor-ellipsis OC head to tail hydrogen bonds. Leucyl side chains are extended on one side of the helix and valyl side chains on the other side. Water molecules form hydrogen bonds with several backbone carbonyl oxygens that also participate in α-helix hydrogen bonds. There is no apparent distortion of the helix caused by hydration

Methods for preparing synthetic freshwaters.

Science.gov (United States)

Smith, E J; Davison, W; Hamilton-Taylor, J

2002-03-01

Synthetic solutions that emulate the major ion compositions of natural waters are useful in experiments aimed at understanding biogeochemical processes. Standard recipes exist for preparing synthetic analogues of seawater, with its relatively constant composition, but, due to the diversity of freshwaters, a range of compositions and recipes is required. Generic protocols are developed for preparing synthetic freshwaters of any desired composition. The major problems encountered in preparing hard and soft waters include dissolving sparingly soluble calcium carbonate, ensuring that the ionic components of each concentrated stock solution cannot form an insoluble salt and dealing with the supersaturation of calcium carbonate in many hard waters. For acidic waters the poor solubility of aluminium salts requires attention. These problems are overcome by preparing concentrated stock solutions according to carefully designed reaction paths that were tested using a combination of experiment and equilibrium modeling. These stock solutions must then be added in a prescribed order to prepare a final solution that is brought into equilibrium with the atmosphere. The example calculations for preparing hard, soft and acidic freshwater surrogates with major ion compositions the same as published analyses, are presented in a generalized fashion that should allow preparation of any synthetic freshwater according to its known analysis.

Synthetic polymers in the marine environment: a rapidly increasing, long-term threat.

Science.gov (United States)

Moore, Charles James

2008-10-01

Synthetic polymers, commonly known as plastics, have been entering the marine environment in quantities paralleling their level of production over the last half century. However, in the last two decades of the 20th Century, the deposition rate accelerated past the rate of production, and plastics are now one of the most common and persistent pollutants in ocean waters and beaches worldwide. Thirty years ago the prevailing attitude of the plastic industry was that "plastic litter is a very small proportion of all litter and causes no harm to the environment except as an eyesore" [Derraik, J.G.B., 2002. The pollution of the marine environment by plastic debris: a review. Mar. Pollut. Bull. 44(9), 842-852]. Between 1960 and 2000, the world production of plastic resins increased 25-fold, while recovery of the material remained below 5%. Between 1970 and 2003, plastics became the fastest growing segment of the US municipal waste stream, increasing nine-fold, and marine litter is now 60-80% plastic, reaching 90-95% in some areas. While undoubtedly still an eyesore, plastic debris today is having significant harmful effects on marine biota. Albatross, fulmars, shearwaters and petrels mistake floating plastics for food, and many individuals of these species are affected; in fact, 44% of all seabird species are known to ingest plastic. Sea turtles ingest plastic bags, fishing line and other plastics, as do 26 species of cetaceans. In all, 267 species of marine organisms worldwide are known to have been affected by plastic debris, a number that will increase as smaller organisms are assessed. The number of fish, birds, and mammals that succumb each year to derelict fishing nets and lines in which they become entangled cannot be reliably known; but estimates are in the millions. We divide marine plastic debris into two categories: macro, >5 mm and micro, plastic micro-debris by filter feeders at the base of the food web is known to occur, but has not been quantified

Collaborative design in virtual environments

CERN Document Server

Wang, Xiangyu

2011-01-01

Collaborative virtual environments (CVEs) are multi-user virtual realities which actively support communication and co-operation. This book offers a comprehensive reference volume to the state-of-the-art in the area of design studies in CVEs. It is an excellent mix of contributions from over 25 leading researcher/experts in multiple disciplines from academia and industry, providing up-to-date insight into the current research topics in this field as well as the latest technological advancements and the best working examples. Many of these results and ideas are also applicable to other areas su

Synthetic vision and memory model for virtual human - biomed 2010.

Science.gov (United States)

Zhao, Yue; Kang, Jinsheng; Wright, David

2010-01-01

This paper describes the methods and case studies of a novel synthetic vision and memory model for virtual human. The synthetic vision module simulates the biological / optical abilities and limitations of the human vision. The module is based on a series of collision detection between the boundary of virtual humans field of vision (FOV) volume and the surface of objects in a recreated 3D environment. The memory module simulates a short-term memory capability by employing a simplified memory structure (first-in-first-out stack). The synthetic vision and memory model has been integrated into a virtual human modelling project, Intelligent Virtual Modelling. The project aimed to improve the realism and autonomy of virtual humans.

Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2014

Energy Technology Data Exchange (ETDEWEB)

Voigt, Christopher [Massachusetts Institute of Technology

2014-07-01

SEED2014 focused on advances in the science and technology emerging from the field of synthetic biology. We broadly define this as technologies that accelerate the process of genetic engineering. It highlighted new tool development, as well as the application of these tools to diverse problems in biotechnology, including therapeutics, industrial chemicals and fuels, natural products, and agriculture. Systems spanned from in vitro experiments and viruses, through diverse bacteria, to eukaryotes (yeast, mammalian cells, plants).

Challenges for the European governance of synthetic biology for human health

NARCIS (Netherlands)

Stemerding, D.; Douglas, C.

2014-01-01

Synthetic biology is a series of scientific and technological practices involved in the application of engineering principles to the design and production of predictable and robust biological systems. While policy discussions abound in this area, emerging technologies like synthetic biology present

Design of magnetic coordination complexes for quantum computing.

Science.gov (United States)

Aromí, Guillem; Aguilà, David; Gamez, Patrick; Luis, Fernando; Roubeau, Olivier

2012-01-21

A very exciting prospect in coordination chemistry is to manipulate spins within magnetic complexes for the realization of quantum logic operations. An introduction to the requirements for a paramagnetic molecule to act as a 2-qubit quantum gate is provided in this tutorial review. We propose synthetic methods aimed at accessing such type of functional molecules, based on ligand design and inorganic synthesis. Two strategies are presented: (i) the first consists in targeting molecules containing a pair of well-defined and weakly coupled paramagnetic metal aggregates, each acting as a carrier of one potential qubit, (ii) the second is the design of dinuclear complexes of anisotropic metal ions, exhibiting dissimilar environments and feeble magnetic coupling. The first systems obtained from this synthetic program are presented here and their properties are discussed.

In Silico Synthesis of Synthetic Receptors: A Polymerization Algorithm.

Science.gov (United States)

Cowen, Todd; Busato, Mirko; Karim, Kal; Piletsky, Sergey A

2016-12-01

Molecularly imprinted polymer (MIP) synthetic receptors have proposed and applied applications in chemical extraction, sensors, assays, catalysis, targeted drug delivery, and direct inhibition of harmful chemicals and pathogens. However, they rely heavily on effective design for success. An algorithm has been written which mimics radical polymerization atomistically, accounting for chemical and spatial discrimination, hybridization, and geometric optimization. Synthetic ephedrine receptors were synthesized in silico to demonstrate the accuracy of the algorithm in reproducing polymers structures at the atomic level. Comparative analysis in the design of a synthetic ephedrine receptor demonstrates that the new method can effectively identify affinity trends and binding site selectivities where commonly used alternative methods cannot. This new method is believed to generate the most realistic models of MIPs thus produced. This suggests that the algorithm could be a powerful new tool in the design and analysis of various polymers, including MIPs, with significant implications in areas of biotechnology, biomimetics, and the materials sciences more generally. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthetic Cannabinoids

Directory of Open Access Journals (Sweden)

Aslihan Okan Ibiloglu

2017-09-01

Full Text Available Synthetic cannabinoids which is a subgroup of cannabinoids are commonly used for recreational drug use throughout the whole world. Although both marijuana and synthetic cannabinoids stimulate the same receptors, cannabinoid receptor 1 (CB1 and cannabinoid receptor 2 (CB2, studies have shown that synthetic cannabinoids are much more potent than marijuana. The longer use of synthetic cannabinoids can cause severe physical and psychological symptoms that might even result in death, similar to many known illicit drugs. Main treatment options mostly involve symptom management and supportive care. The aim of this article is to discuss clinical and pharmacological properties of the increasingly used synthetic cannabinoids. [Psikiyatride Guncel Yaklasimlar - Current Approaches in Psychiatry 2017; 9(3.000: 317-328

Sociotechnical design processes and working environment: The case of a continuous process wok

DEFF Research Database (Denmark)

Broberg, Ole

2000-01-01

A five-year design process of a continuous process wok has been studied with the aim of elucidating the conditions for integrating working environment aspects. The design process is seen as a network building activity and as a social shaping process of the artefact. A working environment log...... is suggested as a tool designers can use to integrate considerations of future operators' working environment....

The design of a study environment for acquiring academic and professional competence

NARCIS (Netherlands)

Kirschner, P.A.; Vilsteren, P. van

Proposes a framework for the design of a learning environment which encourages the acquisition of academic and professional competence. Definition of knowledge, cognitive skill and competence; Acquisition of competence; Designing an environment for competence acquisition; Implementation of study

An Experiential Exercise in Service Environment Design

Science.gov (United States)

Fowler, Kendra; Bridges, Eileen

2012-01-01

A new experiential exercise affords marketing students the opportunity to learn to design service environments. The exercise is appropriate for a variety of marketing courses and is especially beneficial in teaching services marketing because the proposed activity complements two other exercises widely used in this course. Service journal and…

Fictional space in participatory design of engaging interactive environments

DEFF Research Database (Denmark)

Dindler, Christian

2010-01-01

practices of visitors and museum knowledge. The second and larger part of the contribution addresses the issue of shaping design inquiries. This part is summarized through the overarching notion of fictional space denoting a perspective on the creation of a design space where established norms...... spaces for museums and science centres. The dissertation is composed of seven research papers framed by a general overview that summarises the arguments made in the papers and outlines related work and research method. The contribution reflects a dual yet intertwined concern for understanding engagement...... in exhibition spaces and shaping design inquiries around the notion of engaging interactive environments. The first part of the contribution relates to conceptualising aspects of engagement in relation to interactive environments. The perspective of participatory engagement is presented as an overarching...

Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering.

Science.gov (United States)

Knuuttila, Tarja; Loettgers, Andrea

2013-06-01

Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more "biology inspired." Copyright © 2013 Elsevier Ltd. All rights reserved.

Informing biological design by integration of systems and synthetic biology.

Science.gov (United States)

Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

Designing Second Generation Anti-Alzheimer Compounds as Inhibitors of Human Acetylcholinesterase: Computational Screening of Synthetic Molecules and Dietary Phytochemicals.

Directory of Open Access Journals (Sweden)

Hafsa Amat-Ur-Rasool

Full Text Available Alzheimer's disease (AD, a big cause of memory loss, is a progressive neurodegenerative disorder. The disease leads to irreversible loss of neurons that result in reduced level of acetylcholine neurotransmitter (ACh. The reduction of ACh level impairs brain functioning. One aspect of AD therapy is to maintain ACh level up to a safe limit, by blocking acetylcholinesterase (AChE, an enzyme that is naturally responsible for its degradation. This research presents an in-silico screening and designing of hAChE inhibitors as potential anti-Alzheimer drugs. Molecular docking results of the database retrieved (synthetic chemicals and dietary phytochemicals and self-drawn ligands were compared with Food and Drug Administration (FDA approved drugs against AD as controls. Furthermore, computational ADME studies were performed on the hits to assess their safety. Human AChE was found to be most approptiate target site as compared to commonly used Torpedo AChE. Among the tested dietry phytochemicals, berberastine, berberine, yohimbine, sanguinarine, elemol and naringenin are the worth mentioning phytochemicals as potential anti-Alzheimer drugs The synthetic leads were mostly dual binding site inhibitors with two binding subunits linked by a carbon chain i.e. second generation AD drugs. Fifteen new heterodimers were designed that were computationally more efficient inhibitors than previously reported compounds. Using computational methods, compounds present in online chemical databases can be screened to design more efficient and safer drugs against cognitive symptoms of AD.

Designing Second Generation Anti-Alzheimer Compounds as Inhibitors of Human Acetylcholinesterase: Computational Screening of Synthetic Molecules and Dietary Phytochemicals.

Science.gov (United States)

Amat-Ur-Rasool, Hafsa; Ahmed, Mehboob

2015-01-01

Alzheimer's disease (AD), a big cause of memory loss, is a progressive neurodegenerative disorder. The disease leads to irreversible loss of neurons that result in reduced level of acetylcholine neurotransmitter (ACh). The reduction of ACh level impairs brain functioning. One aspect of AD therapy is to maintain ACh level up to a safe limit, by blocking acetylcholinesterase (AChE), an enzyme that is naturally responsible for its degradation. This research presents an in-silico screening and designing of hAChE inhibitors as potential anti-Alzheimer drugs. Molecular docking results of the database retrieved (synthetic chemicals and dietary phytochemicals) and self-drawn ligands were compared with Food and Drug Administration (FDA) approved drugs against AD as controls. Furthermore, computational ADME studies were performed on the hits to assess their safety. Human AChE was found to be most approptiate target site as compared to commonly used Torpedo AChE. Among the tested dietry phytochemicals, berberastine, berberine, yohimbine, sanguinarine, elemol and naringenin are the worth mentioning phytochemicals as potential anti-Alzheimer drugs The synthetic leads were mostly dual binding site inhibitors with two binding subunits linked by a carbon chain i.e. second generation AD drugs. Fifteen new heterodimers were designed that were computationally more efficient inhibitors than previously reported compounds. Using computational methods, compounds present in online chemical databases can be screened to design more efficient and safer drugs against cognitive symptoms of AD.

Design considerations for medical devices in the home environment.

Science.gov (United States)

Kaufman-Rivi, Diana; Collins-Mitchell, Janette; Jetley, Raoul

2010-01-01

Patient demographics, economic forces, and technological advancements contribute to the rise in home care services. Advanced medical devices and equipment originally designed for use by trained personnel in hospitals and clinics are increasingly migrating into the home. Unlike the clinical setting, the home is an uncontrolled environment with additional hazards. The compatibility of the device with the recipient's knowledge, abilities, lifestyle, and home environment plays a significant role in their therapy and rehabilitation. The advent of new device technologies such as wireless devices and interoperability of systems lends a new and complex perspective for medical device use in the home that must also be addressed. Adequately assessing and matching the patient and their caregiver with the appropriate device technology while considering the suitability of the home environment for device operation and maintenance is a challenge that relies on good human factors principles. There is a need to address these challenges in the growing home care sector In this article, the authors take a look at some important considerations and design issues for medical devices used in the home care environment.

Exploring Synthetic and Systems Biology at the University of Edinburgh.

Science.gov (United States)

Fletcher, Liz; Rosser, Susan; Elfick, Alistair

2016-06-15

The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Intelligent Agents for Design and Synthesis Environments: My Summary

Science.gov (United States)

Norvig, Peter

1999-01-01

This presentation gives a summary of intelligent agents for design synthesis environments. We'll start with the conclusions, and work backwards to justify them. First, an important assumption is that agents (whatever they are) are good for software engineering. This is especially true for software that operates in an uncertain, changing environment. The "real world" of physical artifacts is like that: uncertain in what we can measure, changing in that things are always breaking down, and we must interact with non-software entities. The second point is that software engineering techniques can contribute to good design. There may have been a time when we wanted to build simple artifacts containing little or no software. But modern aircraft and spacecraft are complex, and rely on a great deal of software. So better software engineering leads to better designed artifacts, especially when we are designing a series of related artifacts and can amortize the costs of software development. The third point is that agents are especially useful for design tasks, above and beyond their general usefulness for software engineering, and the usefulness of software engineering to design.

Understanding Biological Regulation Through Synthetic Biology.

Science.gov (United States)

Bashor, Caleb J; Collins, James J

2018-03-16

Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function. Expected final online publication date for the Annual Review of Biophysics Volume 47 is May 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Designing presence for real locomotion in immersive virtual environments

DEFF Research Database (Denmark)

Turchet, Luca

2015-01-01

This paper describes a framework for designing systems for real locomotion in virtual environments (VEs) in order to achieve an intense sense of presence. The main outcome of the present research is a list of design features that the virtual reality technology should have in order to achieve...

[From synthetic biology to synthetic humankind].

Science.gov (United States)

Nouvel, Pascal

2015-01-01

In this paper, we propose an historical survey of the expression "synthetic biology" in order to identify its main philosophical components. The result of the analysis is then used to investigate the meaning of the notion of "synthetic man". It is shown that both notions share a common philosophical background that can be summed up by the short but meaningful assertion: "biology is technology". The analysis allows us to distinguish two notions that are often confused in transhumanist literature: the notion of synthetic man and the notion of renewed man. The consequences of this crucial distinction are discussed. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Design for the Environment Products (Raw Data)

Science.gov (United States)

This dataset contains a list of products that carry the Design for the Environment (DfE) label. This mark enables consumers to quickly identify and choose products that can help protect the environment and are safer for families. When you see the DfE logo on a product it means that the DfE scientific review team has screened each ingredient for potential human health and environmental effects and that-based on currently available information, EPA predictive models, and expert judgment-the product contains only those ingredients that pose the least concern among chemicals in their class. Product manufacturers who become DfE partners, and earn the right to display the DfE logo on recognized products, have invested heavily in research, development and reformulation to ensure that their ingredients and finished product line up on the green end of the health and environmental spectrum while maintaining or improving product performance. EPA's Design for the Environment Program (DfE) has allowed use of their logo on over 2500 products. These products are formulated from the safest possible ingredients and have reduced the use of chemicals of concern by hundreds of millions of pounds. A Spanish version of this dataset is available for download at http://www.epa.gov/dfe/pubs/products/list_of_labeled_products.html

Three-dimensional subsurface imaging synthetic aperture radar

International Nuclear Information System (INIS)

Moussally, G.J.

1995-01-01

The objective of this applied research and development project is to develop a system known as '3-D SISAR'. This system consists of a ground penetrating radar with software algorithms designed for the detection, location, and identification of buried objects in the underground hazardous waste environments found at DOE storage sites. Three-dimensional maps of the object locations will be produced which can assist the development of remediation strategies and the characterization of the digface during remediation operations. It is expected that the 3-D SISAR will also prove useful for monitoring hydrocarbon based contaminant migration after remediation. The underground imaging technique being developed under this contract utilizes a spotlight mode Synthetic Aperture Radar (SAR) approach which, due to its inherent stand-off capability, will permit the rapid survey of a site and achieve a high degree of productivity over large areas. When deployed from an airborne platform, the stand-off techniques is also seen as a way to overcome practical survey limitations encountered at vegetated sites

Design and Decorative Art in Shaping of Architectural Environment Image

Science.gov (United States)

Shabalina, N. M.

2017-11-01

The relevance of the topic is determined by the dynamic development of the promising branch, i.e. the architectural environment design, which requires, on the one hand, consideration of the morphology and typology of this art form, on the other hand, the specificity of the architectural environment artistic image. The intensive development of innovative computer technologies and materials in modern engineering, improvement of the information communications forms in their totality has led to the application of new methods in design and construction which, in their turn, have required the development of additional methods for content and context analysis in the integrated assessment of socially significant architectural environments. In the modern culture, correlative processes are steadily developing leading us to a new understanding of the interaction of architecture, decorative art and design. Their rapprochement at the morphological level has been noted which makes it possible to reveal a specific method of synthesis and similarity. The architecture of postmodern styles differs in its bionic form becoming an interactive part of the society and approaching its structural qualities with painting, sculpture, and design. In the modern world, these processes acquire multi-valued semantic nuances, expand the importance of associativity and dynamic processuality in the perception of environmental objects and demand the development of new approaches to the assessment of the architectural design environment. Within the framework of the universal paradigm of modern times the concept of the world develops as a set of systems that live according to the self-organization laws.

Islam and the healthcare environment: designing patient rooms.

Science.gov (United States)

Kopec, D A K; Han, Li

2008-01-01

Islam and the Muslim population are often the source of much misunderstanding and media-influenced misconceptions. Muslim patients who enter the healthcare environment are often weak and likely to experience feelings of vulnerability. Because of the complex and interwoven nature of culture and religion in a person's identity, it is important to consider patient belief systems and values when designing a patient's immediate environment. Through an exploration of literature related to culture and diversity and the beliefs and value system of the Muslim population, the authors were able to identify flexible design initiatives that could accommodate an array of cultural and spiritual practices. Islam and the Muslim population were chosen as the points of reference for this study because of the strong influence of the religion on the culture, and because of the many nuances that differ from the dominant culture within the United States. From these points of reference, a hypothetical design was developed for a patient room that considers differing notions of privacy, alternatives for cultural and religious practices, and ways to include symbolic meaning derived from attributes such as color.

A DBR Framework for Designing Mobile Virtual Reality Learning Environments

Science.gov (United States)

Cochrane, Thomas Donald; Cook, Stuart; Aiello, Stephen; Christie, Duncan; Sinfield, David; Steagall, Marcus; Aguayo, Claudio

2017-01-01

This paper proposes a design based research (DBR) framework for designing mobile virtual reality learning environments. The application of the framework is illustrated by two design-based research projects that aim to develop more authentic educational experiences and learner-centred pedagogies in higher education. The projects highlight the first…

A Computer Environment for Beginners' Learning of Sorting Algorithms: Design and Pilot Evaluation

Science.gov (United States)

Kordaki, M.; Miatidis, M.; Kapsampelis, G.

2008-01-01

This paper presents the design, features and pilot evaluation study of a web-based environment--the SORTING environment--for the learning of sorting algorithms by secondary level education students. The design of this environment is based on modeling methodology, taking into account modern constructivist and social theories of learning while at…

[Application of microelectronics CAD tools to synthetic biology].

Science.gov (United States)

Madec, Morgan; Haiech, Jacques; Rosati, Élise; Rezgui, Abir; Gendrault, Yves; Lallement, Christophe

2017-02-01

Synthetic biology is an emerging science that aims to create new biological functions that do not exist in nature, based on the knowledge acquired in life science over the last century. Since the beginning of this century, several projects in synthetic biology have emerged. The complexity of the developed artificial bio-functions is relatively low so that empirical design methods could be used for the design process. Nevertheless, with the increasing complexity of biological circuits, this is no longer the case and a large number of computer aided design softwares have been developed in the past few years. These tools include languages for the behavioral description and the mathematical modelling of biological systems, simulators at different levels of abstraction, libraries of biological devices and circuit design automation algorithms. All of these tools already exist in other fields of engineering sciences, particularly in microelectronics. This is the approach that is put forward in this paper. © 2017 médecine/sciences – Inserm.

Bio-treatment of phosphate from synthetic wastewater using ...

African Journals Online (AJOL)

Michael Horsfall

effect of carbon sources (glucose, starch, sucrose and lactose) at 0.5% on the ... to be maximum of 68 % in synthetic phosphate wastewater with glucose carbon ... possible entry of this ion into aquatic environment is ... Therefore it is essential to control the emission of ... Mumbai, India) was prepared and selected bacterial.

BrisSynBio: a BBSRC/EPSRC-funded Synthetic Biology Research Centre.

Science.gov (United States)

Sedgley, Kathleen R; Race, Paul R; Woolfson, Derek N

2016-06-15

BrisSynBio is the Bristol-based Biotechnology and Biological Sciences Research Council (BBSRC)/Engineering and Physical Sciences Research Council (EPSRC)-funded Synthetic Biology Research Centre. It is one of six such Centres in the U.K. BrisSynBio's emphasis is on rational and predictive bimolecular modelling, design and engineering in the context of synthetic biology. It trains the next generation of synthetic biologists in these approaches, to facilitate translation of fundamental synthetic biology research to industry and the clinic, and to do this within an innovative and responsible research framework. © 2016 The Author(s).

An Overview of NASA's Integrated Design and Engineering Analysis (IDEA) Environment

Science.gov (United States)

Robinson, Jeffrey S.

2011-01-01

Historically, the design of subsonic and supersonic aircraft has been divided into separate technical disciplines (such as propulsion, aerodynamics and structures), each of which performs design and analysis in relative isolation from others. This is possible, in most cases, either because the amount of interdisciplinary coupling is minimal, or because the interactions can be treated as linear. The design of hypersonic airbreathing vehicles, like NASA's X-43, is quite the opposite. Such systems are dominated by strong non-linear interactions between disciplines. The design of these systems demands that a multi-disciplinary approach be taken. Furthermore, increased analytical fidelity at the conceptual design phase is highly desirable, as many of the non-linearities are not captured by lower fidelity tools. Only when these systems are designed from a true multi-disciplinary perspective, can the real performance benefits be achieved and complete vehicle systems be fielded. Toward this end, the Vehicle Analysis Branch at NASA Langley Research Center has been developing the Integrated Design and Engineering Analysis (IDEA) Environment. IDEA is a collaborative environment for parametrically modeling conceptual and preliminary designs for launch vehicle and high speed atmospheric flight configurations using the Adaptive Modeling Language (AML) as the underlying framework. The environment integrates geometry, packaging, propulsion, trajectory, aerodynamics, aerothermodynamics, engine and airframe subsystem design, thermal and structural analysis, and vehicle closure into a generative, parametric, unified computational model where data is shared seamlessly between the different disciplines. Plans are also in place to incorporate life cycle analysis tools into the environment which will estimate vehicle operability, reliability and cost. IDEA is currently being funded by NASA?s Hypersonics Project, a part of the Fundamental Aeronautics Program within the Aeronautics

Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory.

Directory of Open Access Journals (Sweden)

Evgeni V Nikolaev

2016-04-01

Full Text Available Synthetic constructs in biotechnology, biocomputing, and modern gene therapy interventions are often based on plasmids or transfected circuits which implement some form of "on-off" switch. For example, the expression of a protein used for therapeutic purposes might be triggered by the recognition of a specific combination of inducers (e.g., antigens, and memory of this event should be maintained across a cell population until a specific stimulus commands a coordinated shut-off. The robustness of such a design is hampered by molecular ("intrinsic" or environmental ("extrinsic" noise, which may lead to spontaneous changes of state in a subset of the population and is reflected in the bimodality of protein expression, as measured for example using flow cytometry. In this context, a "majority-vote" correction circuit, which brings deviant cells back into the required state, is highly desirable, and quorum-sensing has been suggested as a way for cells to broadcast their states to the population as a whole so as to facilitate consensus. In this paper, we propose what we believe is the first such a design that has mathematically guaranteed properties of stability and auto-correction under certain conditions. Our approach is guided by concepts and theory from the field of "monotone" dynamical systems developed by M. Hirsch, H. Smith, and others. We benchmark our design by comparing it to an existing design which has been the subject of experimental and theoretical studies, illustrating its superiority in stability and self-correction of synchronization errors. Our stability analysis, based on dynamical systems theory, guarantees global convergence to steady states, ruling out unpredictable ("chaotic" behaviors and even sustained oscillations in the limit of convergence. These results are valid no matter what are the values of parameters, and are based only on the wiring diagram. The theory is complemented by extensive computational bifurcation analysis

Medium-Based Design: Extending a Medium to Create an Exploratory Learning Environment

Science.gov (United States)

Rick, Jochen; Lamberty, K. K.

2005-01-01

This article introduces "medium-based" design -- an approach to creating "exploratory learning environments" using the method of "extending a medium". First, the characteristics of exploratory learning environments and medium-based design are described and grounded in related work. Particular attention is given to "extending a medium" --…

'Synthetic lipase' production from a newly isolated Sporidiobolus pararoseus strain by submerged fermentation

Directory of Open Access Journals (Sweden)

Alessandra Smaniotto

2012-12-01

Full Text Available The lipase produced by a newly isolate Sporidiobolus pararoseus strain has potential catalysis ability for esterification reactions. In order to improve its synthetic activity, this work aimed at optimizing 'synthetic lipase' production by submerged fermentation of a conventional media based on peptone, yeast extract, NaCl and olive oil using experimental design technique. According to the results obtained in the first experimental design (2(4-1, yeast extract and NaCl concentrations were tested to further optimization by response surface methodology. The maximum 'synthetic lipase' activity obtained was 26.9 U/mL in the optimized media (5.0, 6.8, 7.0 and 1.0% (wt/v of peptone, yeast extract, NaCl and olive oil, respectively, representing a 6.36-fold increase compared to the initial medium. The time course of 'synthetic lipase' production in the optimized condition was evaluated in terms of synthetic activity, protease activity, biomass and total carbon and the maximum synthetic activity was observed during the stationary phase of growth.

Software Engineering Environment for Component-based Design of Embedded Software

DEFF Research Database (Denmark)

Guo, Yu

2010-01-01

as well as application models in a computer-aided software engineering environment. Furthermore, component models have been realized following carefully developed design patterns, which provide for an efficient and reusable implementation. The components have been ultimately implemented as prefabricated...... executable objects that can be linked together into an executable application. The development of embedded software using the COMDES framework is supported by the associated integrated engineering environment consisting of a number of tools, which support basic functionalities, such as system modelling......, validation, and executable code generation for specific hardware platforms. Developing such an environment and the associated tools is a highly complex engineering task. Therefore, this thesis has investigated key design issues and analysed existing platforms supporting model-driven software development...

Design as a way to develop a relevant urban environment ...

African Journals Online (AJOL)

Design as a way to develop a relevant urban environment. ... Futuristic ideas of young designers can become the first stage in solving these challenging tasks. ... the problems of a modern city: from space organization to leisure organization.

Agent-based modelling in synthetic biology.

Science.gov (United States)

Gorochowski, Thomas E

2016-11-30

Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

Bioinspired Chemical Communication between Synthetic Nanomotors.

Science.gov (United States)

Chen, Chuanrui; Chang, Xiaocong; Teymourian, Hazhir; Ramírez-Herrera, Doris E; Esteban-Fernández de Ávila, Berta; Lu, Xiaolong; Li, Jinxing; He, Sha; Fang, Chengcheng; Liang, Yuyan; Mou, Fangzhi; Guan, Jianguo; Wang, Joseph

2018-01-02

While chemical communication plays a key role in diverse natural processes, the intelligent chemical communication between synthetic nanomotors remains unexplored. The design and operation of bioinspired synthetic nanomotors is presented. Chemical communication between nanomotors is possible and has an influence on propulsion behavior. A chemical "message" is sent from a moving activator motor to a nearby activated (receiver) motor by release of Ag + ions from a Janus polystyrene/Ni/Au/Ag activator motor to the activated Janus SiO 2 /Pt nanomotor. The transmitted silver signal is translated rapidly into a dramatic speed change associated with the enhanced catalytic activity of activated motors. Selective and successive activation of multiple nanomotors is achieved by sequential localized chemical communications. The concept of establishing chemical communication between different synthetic nanomotors paves the way to intelligent nanoscale robotic systems that are capable of cooperating with each other. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Promoting Participation Through the Universal Design of Built Environments: Making it Happen

Directory of Open Access Journals (Sweden)

Valerie Watchorn

2014-12-01

Full Text Available Environmental design is a determinant of social inclusion and people’s participation in life roles. Design that does not cater for a diverse range of ages, abilities and cultures restricts people’s access to, and use of, domestic or public premises. Universal design is an approach that acknowledges diversity of populations and encourages designers to create objects and places that are usable by the greatest majority of users. Although there are potential benefits to the widest application of universal design within society, such application is not mandatory within Australia. This paper presents findings from an Australian qualitative study that explored universal design as a means of facilitating greater environmental access for all. The views of experts working within the field of architecture and environmental access were explored regarding factors that restrict or facilitate application of universal design to the design of built environments. Study findings revealed a number of themes relating to factors that may restrain, ‘what’s holding us back?’ and factors that may facilitate application of universal design, ‘making it happen’. These findings have direct relevance to those involved in the planning and design of built environments, policy developers and educators. Keywords: Universal design, architecture, occupational therapy, built environments, barriers, facilitators, inter-professional education

Executive control systems in the engineering design environment

Science.gov (United States)

Hurst, P. W.; Pratt, T. W.

1985-01-01

Executive Control Systems (ECSs) are software structures for the unification of various engineering design application programs into comprehensive systems with a central user interface (uniform access) method and a data management facility. Attention is presently given to the most significant determinations of a research program conducted for 24 ECSs, used in government and industry engineering design environments to integrate CAD/CAE applications programs. Characterizations are given for the systems' major architectural components and the alternative design approaches considered in their development. Attention is given to ECS development prospects in the areas of interdisciplinary usage, standardization, knowledge utilization, and computer science technology transfer.

Reward-based hypertension control by a synthetic brain-dopamine interface.

Science.gov (United States)

Rössger, Katrin; Charpin-El Hamri, Ghislaine; Fussenegger, Martin

2013-11-05

Synthetic biology has significantly advanced the design of synthetic trigger-controlled devices that can reprogram mammalian cells to interface with complex metabolic activities. In the brain, the neurotransmitter dopamine coordinates communication with target neurons via a set of dopamine receptors that control behavior associated with reward-driven learning. This dopamine transmission has recently been suggested to increase central sympathetic outflow, resulting in plasma dopamine levels that correlate with corresponding brain activities. By functionally rewiring the human dopamine receptor D1 (DRD1) via the second messenger cyclic adenosine monophosphate (cAMP) to synthetic promoters containing cAMP response element-binding protein 1(CREB1)-specific cAMP-responsive operator modules, we have designed a synthetic dopamine-sensitive transcription controller that reversibly fine-tunes specific target gene expression at physiologically relevant brain-derived plasma dopamine levels. Following implantation of circuit-transgenic human cell lines insulated by semipermeable immunoprotective microcontainers into mice, the designer device interfaced with dopamine-specific brain activities and produced a systemic expression response when the animal's reward system was stimulated by food, sexual arousal, or addictive drugs. Reward-triggered brain activities were able to remotely program peripheral therapeutic implants to produce sufficient amounts of the atrial natriuretic peptide, which reduced the blood pressure of hypertensive mice to the normal physiologic range. Seamless control of therapeutic transgenes by subconscious behavior may provide opportunities for treatment strategies of the future.

National design environment for pulp mills; Kansallinen paperitehtaan suunnitteluympaeristoe - PMST 03

Energy Technology Data Exchange (ETDEWEB)

Kaijaluoto, S. [VTT Energy, Jyvaeskylae (Finland)

1998-12-31

The research to be done in the CACTUS research programme produces new process models and generates new knowledge about the influence of various contaminants on the runnability and the quality of paper. The generated information calls for an environment where it can be analysed and utilised. The goal of the project is to build a design environment for papermaking processes. The environment will be composed of a number of tools, all integrated together, that can be used in process design from preliminary concept screening through detailed simulation studies to the design and tuning of control systems. The design environment is based on the Balas and APMS simulation programmes developed at VTT. Balas is a general steady-state simulation package for chemical processes with emphasis on pulp and paper. Recent applications include the analysis of the influence of new drying techniques on the energy and water management of a paper mill and the evaluation of new paper machine and water treatment concepts. APMS (Advanced Pulp and Paper Mill Simulator) is a new flexible tool intended for fast modelling and efficient simulation of the dynamic performance the various unit processes in pulp and paper mill, or even of the whole integrated mill. (orig.)

National design environment for pulp mills; Kansallinen paperitehtaan suunnitteluympaeristoe - PMST 03

Energy Technology Data Exchange (ETDEWEB)

Kaijaluoto, S [VTT Energy, Jyvaeskylae (Finland)

1999-12-31

The research to be done in the CACTUS research programme produces new process models and generates new knowledge about the influence of various contaminants on the runnability and the quality of paper. The generated information calls for an environment where it can be analysed and utilised. The goal of the project is to build a design environment for papermaking processes. The environment will be composed of a number of tools, all integrated together, that can be used in process design from preliminary concept screening through detailed simulation studies to the design and tuning of control systems. The design environment is based on the Balas and APMS simulation programmes developed at VTT. Balas is a general steady-state simulation package for chemical processes with emphasis on pulp and paper. Recent applications include the analysis of the influence of new drying techniques on the energy and water management of a paper mill and the evaluation of new paper machine and water treatment concepts. APMS (Advanced Pulp and Paper Mill Simulator) is a new flexible tool intended for fast modelling and efficient simulation of the dynamic performance the various unit processes in pulp and paper mill, or even of the whole integrated mill. (orig.)

Synthetic Biology and Human Health: Potential Applications for Spaceflight

Science.gov (United States)

Karouia, Fathi; Carr, Christopher; Cai, Yizhi; Chen, Y.; Grenon, Marlene; Larios-Sanz, Maia; Jones, Jeffrey A.; Santos, Orlando

2011-01-01

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. Spaceflight-related changes have been reported in the musculo-skeletal, cardiovascular, neurovestibular, endocrine, and immune systems. The spacecraft environment further subjects the traveler to noise and gravitational forces, as well as airborne chemical, microbiological contaminants, and radiation exposure. As humans prepare for longer duration missions effective countermeasures must be developed, verified, and implemented to ensure mission success. Over the past ten years, synthetic biology has opened new avenues for research and development in areas such as biological control, biomaterials, sustainable energy production, bioremediation, and biomedical therapies. The latter in particular is of great interest to the implementation of long-duration human spaceflight capabilities. This article discusses the effects of spaceflight on humans, and reviews current capabilities and potential needs associated with the health of the astronauts where synthetic biology could play an important role in the pursuit of space exploration.

Designing equipment for use in gamma radiation environments

International Nuclear Information System (INIS)

Vandergriff, K.U.

1990-05-01

High levels of gamma radiation are known to cause degradation in a variety of materials and components. When designing systems to operate in a high radiation environment, special precautions and procedures should be followed. This report (1) outlines steps that should be followed in designing equipment and (2) explains the general effects of radiation on various engineering materials and components. Much information exists in the literature on radiation effects upon materials. However, very little information is available to give the designer a step-by-step process for designing systems that will be subject to high levels of gamma radiation, such as those found in a nuclear fuel reprocessing facility. In this report, many radiation effect references are relied upon to aid in the design of components and systems. 11 refs., 4 tabs

Queueing-Based Synchronization and Entrainment for Synthetic Gene Oscillators

Science.gov (United States)

Mather, William; Butzin, Nicholas; Hochendoner, Philip; Ogle, Curtis

Synthetic gene oscillators have been a major focus of synthetic biology research since the beginning of the field 15 years ago. They have proven to be useful both for biotechnological applications as well as a testing ground to significantly develop our understanding of the design principles behind synthetic and native gene oscillators. In particular, the principles governing synchronization and entrainment of biological oscillators have been explored using a synthetic biology approach. Our work combines experimental and theoretical approaches to specifically investigate how a bottleneck for protein degradation, which is present in most if not all existing synthetic oscillators, can be leveraged to robustly synchronize and entrain biological oscillators. We use both the terminology and mathematical tools of queueing theory to intuitively explain the role of this bottleneck in both synchronization and entrainment, which extends prior work demonstrating the usefulness of queueing theory in synthetic and native gene circuits. We conclude with an investigation of how synchronization and entrainment may be sensitive to the presence of multiple proteolytic pathways in a cell that couple weakly through crosstalk. This work was supported by NSF Grant #1330180.

Data management in an object-oriented distributed aircraft conceptual design environment

Science.gov (United States)

Lu, Zhijie

In the competitive global market place, aerospace companies are forced to deliver the right products to the right market, with the right cost, and at the right time. However, the rapid development of technologies and new business opportunities, such as mergers, acquisitions, supply chain management, etc., have dramatically increased the complexity of designing an aircraft. Therefore, the pressure to reduce design cycle time and cost is enormous. One way to solve such a dilemma is to develop and apply advanced engineering environments (AEEs), which are distributed collaborative virtual design environments linking researchers, technologists, designers, etc., together by incorporating application tools and advanced computational, communications, and networking facilities. Aircraft conceptual design, as the first design stage, provides major opportunity to compress design cycle time and is the cheapest place for making design changes. However, traditional aircraft conceptual design programs, which are monolithic programs, cannot provide satisfactory functionality to meet new design requirements due to the lack of domain flexibility and analysis scalability. Therefore, we are in need of the next generation aircraft conceptual design environment (NextADE). To build the NextADE, the framework and the data management problem are two major problems that need to be addressed at the forefront. Solving these two problems, particularly the data management problem, is the focus of this research. In this dissertation, in light of AEEs, a distributed object-oriented framework is firstly formulated and tested for the NextADE. In order to improve interoperability and simplify the integration of heterogeneous application tools, data management is one of the major problems that need to be tackled. To solve this problem, taking into account the characteristics of aircraft conceptual design data, a robust, extensible object-oriented data model is then proposed according to the

Synchronous long-term oscillations in a synthetic gene circuit.

Science.gov (United States)

Potvin-Trottier, Laurent; Lord, Nathan D; Vinnicombe, Glenn; Paulsson, Johan

2016-10-27

Synthetically engineered genetic circuits can perform a wide variety of tasks but are generally less accurate than natural systems. Here we revisit the first synthetic genetic oscillator, the repressilator, and modify it using principles from stochastic chemistry in single cells. Specifically, we sought to reduce error propagation and information losses, not by adding control loops, but by simply removing existing features. We show that this modification created highly regular and robust oscillations. Furthermore, some streamlined circuits kept 14 generation periods over a range of growth conditions and kept phase for hundreds of generations in single cells, allowing cells in flasks and colonies to oscillate synchronously without any coupling between them. Our results suggest that even the simplest synthetic genetic networks can achieve a precision that rivals natural systems, and emphasize the importance of noise analyses for circuit design in synthetic biology.

Architectural Design and the Learning Environment: A Framework for School Design Research

Science.gov (United States)

Gislason, Neil

2010-01-01

This article develops a theoretical framework for studying how instructional space, teaching and learning are related in practice. It is argued that a school's physical design can contribute to the quality of the learning environment, but several non-architectural factors also determine how well a given facility serves as a setting for teaching…

Ethics, Design and Planning of the Built Environment

NARCIS (Netherlands)

Basta, C.; Moroni, S.

2013-01-01

The book proposes a set of original contributions in research areas shared by planning theory, architectural research, design and ethical inquiry. The contributors gathered in 2010 at the Ethics of the Built Environment seminar organized by the editors at Delft University of Technology. Both

Catalysts for synthetic liquid fuels

Energy Technology Data Exchange (ETDEWEB)

Bruce, L.A.; Turney, T.W.

1987-12-01

Fischer-Tropsch catalysts have been designed, characterized and tested for the selective production of hydrocarbons suitable as synthetic liquid transport fuels from synthesis gas (i.e., by the reduction of carbon monoxide with hydrogen). It was found that hydrocarbons in the middle distillate range, or suitable for conversion to that range, could be produced over several of the new catalyst systems. The various catalysts examined included: (1) synthetic cobalt clays, mainly cobalt chlorites; (2) cobalt hydrotalcites; (3) ruthenium metal supported on rare earth oxides of high surface area; and (4) a novel promoted cobalt catalyst. Active and selective catalysts have been obtained, in each category. With the exception of the clays, reproducibility of catalyst performance has been good. Catalysts in groups 2 and 4 have exhibited very high activity, with long lifetimes and easy regeneration.

Multivariate return periods in hydrology: a critical and practical review focusing on synthetic design hydrograph estimation

Directory of Open Access Journals (Sweden)

B. Gräler

2013-04-01

Full Text Available Most of the hydrological and hydraulic studies refer to the notion of a return period to quantify design variables. When dealing with multiple design variables, the well-known univariate statistical analysis is no longer satisfactory, and several issues challenge the practitioner. How should one incorporate the dependence between variables? How should a multivariate return period be defined and applied in order to yield a proper design event? In this study an overview of the state of the art for estimating multivariate design events is given and the different approaches are compared. The construction of multivariate distribution functions is done through the use of copulas, given their practicality in multivariate frequency analyses and their ability to model numerous types of dependence structures in a flexible way. A synthetic case study is used to generate a large data set of simulated discharges that is used for illustrating the effect of different modelling choices on the design events. Based on different uni- and multivariate approaches, the design hydrograph characteristics of a 3-D phenomenon composed of annual maximum peak discharge, its volume, and duration are derived. These approaches are based on regression analysis, bivariate conditional distributions, bivariate joint distributions and Kendall distribution functions, highlighting theoretical and practical issues of multivariate frequency analysis. Also an ensemble-based approach is presented. For a given design return period, the approach chosen clearly affects the calculated design event, and much attention should be given to the choice of the approach used as this depends on the real-world problem at hand.

Synthetic tracked aperture ultrasound imaging: design, simulation, and experimental evaluation.

Science.gov (United States)

Zhang, Haichong K; Cheng, Alexis; Bottenus, Nick; Guo, Xiaoyu; Trahey, Gregg E; Boctor, Emad M

2016-04-01

Ultrasonography is a widely used imaging modality to visualize anatomical structures due to its low cost and ease of use; however, it is challenging to acquire acceptable image quality in deep tissue. Synthetic aperture (SA) is a technique used to increase image resolution by synthesizing information from multiple subapertures, but the resolution improvement is limited by the physical size of the array transducer. With a large F-number, it is difficult to achieve high resolution in deep regions without extending the effective aperture size. We propose a method to extend the available aperture size for SA-called synthetic tracked aperture ultrasound (STRATUS) imaging-by sweeping an ultrasound transducer while tracking its orientation and location. Tracking information of the ultrasound probe is used to synthesize the signals received at different positions. Considering the practical implementation, we estimated the effect of tracking and ultrasound calibration error to the quality of the final beamformed image through simulation. In addition, to experimentally validate this approach, a 6 degree-of-freedom robot arm was used as a mechanical tracker to hold an ultrasound transducer and to apply in-plane lateral translational motion. Results indicate that STRATUS imaging with robotic tracking has the potential to improve ultrasound image quality.

Enhanced/Synthetic Vision Systems - Human factors research and implications for future systems

Science.gov (United States)

Foyle, David C.; Ahumada, Albert J.; Larimer, James; Sweet, Barbara T.

1992-01-01

This paper reviews recent human factors research studies conducted in the Aerospace Human Factors Research Division at NASA Ames Research Center related to the development and usage of Enhanced or Synthetic Vision Systems. Research discussed includes studies of field of view (FOV), representational differences of infrared (IR) imagery, head-up display (HUD) symbology, HUD advanced concept designs, sensor fusion, and sensor/database fusion and evaluation. Implications for the design and usage of Enhanced or Synthetic Vision Systems are discussed.

Global Military Operating Environments (GMOE) Phase I: Linking Natural Environments, International Security, and Military Operations

Science.gov (United States)

2013-01-30

diverse range of natural environments and will require that U.S. forces adapt to a wide range of terrain, climate, and associated hazards within these...Synthetic Environment Core Area), baseline terrain information, and application of remote‐sensing technologies for Warfighter and Chameleon . The

Mammalian synthetic biology for studying the cell.

Science.gov (United States)

Mathur, Melina; Xiang, Joy S; Smolke, Christina D

2017-01-02

Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

Design of plant safety model in plant enterprise engineering environment

International Nuclear Information System (INIS)

Gabbar, Hossam A.; Suzuki, Kazuhiko; Shimada, Yukiyasu

2001-01-01

Plant enterprise engineering environment (PEEE) is an approach aiming to manage the plant through its lifecycle. In such environment, safety is considered as the common objective for all activities throughout the plant lifecycle. One approach to achieve plant safety is to embed safety aspects within each function and activity within such environment. One ideal way to enable safety aspects within each automated function is through modeling. This paper proposes a theoretical approach to design plant safety model as integrated with the plant lifecycle model within such environment. Object-oriented modeling approach is used to construct the plant safety model using OO CASE tool on the basis of unified modeling language (UML). Multiple views are defined for plant objects to express static, dynamic, and functional semantics of these objects. Process safety aspects are mapped to each model element and inherited from design to operation stage, as it is naturally embedded within plant's objects. By developing and realizing the plant safety model, safer plant operation can be achieved and plant safety can be assured

Designing Environments for Handicapped Children: A Design Guide and Case Study. First Edition.

Science.gov (United States)

Moore, Gary T.; And Others

This guide addresses the planning and architectural design of play/learning environments for special needs children. The exceptional children discussed include those with most types of mild to severe handicaps and developmental disabilities. Specifically excluded from consideration are health impairments, severe psycho-emotional difficulties such…

Designing and Improving a Blended Synchronous Learning Environment: An Educational Design Research

Science.gov (United States)

Wang, Qiyun; Lang Quek, Choon; Hu, Xiaoyong

2017-01-01

In this study, a blended synchronous learning environment (BSLE) was created to support a group of graduate students when they were taking a course. Instruction was delivered to both face-to-face (F2F) and online students simultaneously. The purpose of this paper is to present how this BSLE was gradually designed, implemented, and improved by…

Synthetic Biology: Applications in the Food Sector.

Science.gov (United States)

Tyagi, Ashish; Kumar, Ashwani; Aparna, S V; Mallappa, Rashmi H; Grover, Sunita; Batish, Virender Kumar

2016-08-17

Synthetic biology also termed as "genomic alchemy" represents a powerful area of science that is based on the convergence of biological sciences with systems engineering. It has been fittingly described as "moving from reading the genetic code to writing it" as it focuses on building, modeling, designing and fabricating novel biological systems using customized gene components that result in artificially created genetic circuitry. The scientifically compelling idea of the technological manipulation of life has been advocated since long time. Realization of this idea has gained momentum with development of high speed automation and the falling cost of gene sequencing and synthesis following the completion of the human genome project. Synthetic biology will certainly be instrumental in shaping the development of varying areas ranging from biomedicine, biopharmaceuticals, chemical production, food and dairy quality monitoring, packaging, and storage of food and dairy products, bioremediation and bioenergy production, etc. However, potential dangers of using synthetic life forms have to be acknowledged and adoption of policies by the scientific community to ensure safe practice while making important advancements in the ever expanding field of synthetic biology is to be fully supported and implemented.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

Science.gov (United States)

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

Development of pedagogical design in technology-rich environments for language teaching and learning

OpenAIRE

Jalkanen, Juha

2015-01-01

This study explores the development of pedagogical design for language teaching and learning in increasingly technology-rich environments. More specifically, it focuses on the process of design, enactment and analysis of language and literacy pedagogies in technology-rich environments. Two substudies are reported in five articles, each of which approaches pedagogical design from a different perspective. The first substudy examined (a) what pedagogical choices language studen...

Research and Application of Integration Design Environment Faced to CSCD

Institute of Scientific and Technical Information of China (English)

ZHAO Han; LI Yanfeng; DONG Yude

2006-01-01

Computer supported collaborative design(CSCD) technology has been applied extensively with intensive market competition. The key technologies and problems of CSCD are analyzed and a CSCD design frame faced to product design is established. Then a CSCD system faced to radar key components is founded with Pro/INTRALINK software and re-exploiting technology. Some key processes are also designed, such as database management, workflow programming, information communication, file release, conflict identification and safety management. These will provide a reference for constructing a cooperative design environment.

Project Selection in the Design Studio: Absence of Learning Environments

Science.gov (United States)

Basa, Inci

2010-01-01

Project selection is an essential matter of design teaching. Based on observations of a specific curriculum, the author claims that a wide repertoire of subjects including offices, restaurants, hotels, and other public places are used to prepare design students, but that schools and other "learning environments/ schools" are similarly…

Approaches to Integrated Building Design Environments

DEFF Research Database (Denmark)

Bagger-Petersen, Susanne C; Andersen, Tom

1996-01-01

This report discusses functional requirements and specification which needs to be defined and fulfilled to initiate development of an integrated building design environment. The purpose is to outline specifications for further discussion and development. The report documents the first phase...... in an ongoing project at the Technical University of Denmark. The overall project objective is to provide a theoretically well-founded prototype of an integrated IT-system which can serve as a device of feedback from practice and as a test-bed for the developed concept and architecture....

Software Architecture Design for Spatially-Indexed Media in Smart Environments

Directory of Open Access Journals (Sweden)

SCHIPOR, O.-A.

2017-05-01

Full Text Available We introduce in this work a new software architecture design, based on well-established web communication protocols and scripting languages, for implementing spatially-indexed media in smart environments. We based our approach on specific design guidelines. Our concept of spatially-indexed media enables users to readily instantiate mappings between digital content and specific regions of the physical space. We present an implementation of the architecture using a motion capture system, a large visualization display, and several smart devices. We also present an experimental evaluation of our new software architecture by reporting response times function of changes in the complexity of physical-digital environment.

Characterization of high speed synthetic jet actuators

Science.gov (United States)

Pikcilingis, Lucia

Over the last 20 years, synthetic jets have been studied as a means for aerodynamic active flow control. Specifically, synthetic jets provide momentum transfer with zero-net mass flux, which has been proven to be effective for controlling flow fields. A synthetic jet is created by the periodic formation of vortex rings at its orifice due to the periodic motion of a piezoelectric disk(s). The present study seeks to optimize the performance of a synthetic jet actuator by utilizing different geometrical parameters such as disk thickness, orifice width and length, cavity height and cavity diameter, and different input parameters such as driving voltage and frequency. Two apparatuses were used with a cavity diameter of either 80 mm or 160 mm. Piezoelectric-based disks were provided by the Mide Corporation. Experiments were conducted using several synthetic jet apparatuses designed for various geometrical parameters utilizing a dual disk configuration. Velocity and temperature measurements were acquired at the center of the synthetic jet orifice using a temperature compensated hotwire and thermocouple probe. The disk(s) displacement was measured at the center of the disk with a laser displacement sensor. It was shown that the synthetic jets, having the 80 mm cavity diameter, are capable of exceeding peak velocities of 200 m/s with a relatively large orifice of dimensions AR = 12, hc* = 3, and hn* = 4. In addition, the conditions at which the disks were manufactured had minimal effect on the performance of the jet, except for the pair with overnight resting time as opposed to less than an hour resting time for the control units. Altering the tab style of the disks, where the tab allows the electrical circuit to be exposed for external power connection, showed that a thin fragile tab versus a tab of the same thickness as the disk has minimal effect on the performance but affects the durability of the disk due to the fragility or robustness of the tab. The synthetic jets

Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression.

Science.gov (United States)

Kabadi, Ami M; Gersbach, Charles A

2014-09-01

Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the development of a new class of gene therapies that alter the expression of endogenous genes. Designed transcription factors have entered clinical trials for the treatment of human diseases and others are in preclinical development. High-throughput and user-friendly platforms for designing synthetic DNA-binding proteins present innovative methods for deciphering cell biology and designing custom synthetic gene circuits. We review two platforms for designing synthetic transcription factors for manipulating gene expression: Transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. We present an overview of each technology and a guide for designing and assembling custom TALE- and CRISPR/Cas9-based transcription factors. We also discuss characteristics of each platform that are best suited for different applications. Copyright © 2014 Elsevier Inc. All rights reserved.

[Progress in synthetic biology of pinocembrin].

Science.gov (United States)

Guo, Lei; Kong, Jianqiang

2015-04-01

Pinocembrin, belonging to flavanons, was isolated from various plants. Pinocembrin has a variety of pharmacological activities, such as neuroprotective effect, antimicrobial activity, and antioxidant efficacy. Pinocembrin was approved as class I drugs to its phase II clinical trial by CFDA in 2009, mainly used for the treatment of ischemic stroke. As a promising compound, the manufacturing technologies of pinocembrin, including chemical synthesis, extraction from plant and synthetic biology, have attracted many attentions. Compared with the first two technologies, synthetic biology has many advantages, such as environment-friendly and low-cost. Construction of biosynthetic pathway in microorganism offers promising results for large scale pinocembrin production by fermentation after taking lots of effective strategies. This article reviews some of recent strategies in microorganisms to improve the yield, with focus on the selection of appropriate the key enzyme sources, the supply of precursors and cofactors by microorganisms, the choice of substance and the level of the key enzyme expression.

Enhancement of the Enterocin CRL35 Activity by a Synthetic Peptide Derived from the NH2-Terminal Sequence

Science.gov (United States)

Saavedra, Lucila; Minahk, Carlos; de Ruiz Holgado, Aída P.; Sesma, Fernando

2004-01-01

The enterocin CRL35 biosynthetic gene cluster was cloned and sequenced. The sequence was revealed to be highly identical to that of the mundticin KS gene cluster (S. Kawamoto, J. Shima, R. Sato, T. Eguchi, S. Ohmomo, J. Shibato, N. Horikoshi, K. Takeshita, and T. Sameshima, Appl. Environ. Microbiol. 68:3830-3840, 2002). Short synthetic peptides were designed based on the bacteriocin sequence and were evaluated in antimicrobial competitive assays. The peptide KYYGNGVSCNKKGCS produced an enhancement of enterocin CRL35 antimicrobial activity in a buffer system. PMID:15215149

A Synthetic Teammate for UAV Applications: A Prospective Look

National Research Council Canada - National Science Library

Gluck, Kevin A; Ball, Jerry T; Gunzelmann, Glenn; Krusmark, Michael A; Lyon, Don R; Cooke, Nancy J

2006-01-01

This report describes current progress and future plans for research and development in synthetic teammates for applications in training, analysis, and system design for Uninhabited Aerial Vehicle (UAV) operations...

Synthetic Musk Fragrances in a Conventional Drinking Water Treatment Plant with Lime Softening

OpenAIRE

Wombacher, William D.; Hornbuckle, Keri C.

2009-01-01

Synthetic musk fragrances are common personal care product additives and wastewater contaminants that are routinely detected in the environment. This study examines the presence eight synthetic musk fragrances (AHTN, HHCB, ATII, ADBI, AHMI, musk xylene, and musk ketone) in source water and the removal of these compounds as they flow through a Midwestern conventional drinking water plant with lime softening. The compounds were measured in water, waste sludge, and air throughout the plant. HHCB...

Co-culture systems and technologies: taking synthetic biology to the next level.

Science.gov (United States)

Goers, Lisa; Freemont, Paul; Polizzi, Karen M

2014-07-06

Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

On public space design for Chinese urban residential area based on integrated architectural physics environment evaluation

Science.gov (United States)

Dong, J. Y.; Cheng, W.; Ma, C. P.; Tan, Y. T.; Xin, L. S.

2017-04-01

The residential public space is an important part in designing the ecological residence, and a proper physics environment of public space is of greater significance to urban residence in China. Actually, the measure to apply computer aided design software into residential design can effectively avoid an inconformity of design intent with actual using condition, and a negative impact on users due to bad architectural physics environment of buildings, etc. The paper largely adopts a design method of analyzing architectural physics environment of residential public space. By analyzing and evaluating various physics environments, a suitability assessment is obtained for residential public space, thereby guiding the space design.

Towards a Development Environment for Model Based Test Design

OpenAIRE

Jing, Han

2008-01-01

Within the UP IP I&V organization there is high focus on increasing the ability to predict product quality in a cost efficient way. Test automation has therefore been an important enabler for us. The IP test design environment is continuously evolving and the investigations will show which improvements that is most important to implement in short and long term. In Ericsson UP IP I&V, the test automation framework environments are severed to complete some process by automated method, f...

Design A Situated Learning Environment Using Mixed Reality Technology - A Case Study

OpenAIRE

Rasimah Che Mohd Yusoff; Halimah Badioze Zaman; Azlina Ahmad

2010-01-01

Mixed Reality (MR) is one of the newest technologies explored in education. It promises the potential to promote teaching and learning and making learners- experience more "engaging". However, there still lack of research on designing a virtual learning environment using MR technology. In this paper, we describe the Mixed Reality technology, the characteristics of situated learning as instructional design for virtual environment using mixed reality technology. We also exp...

INCORPORATING THE BEHAVIORAL DIMENSION IN DESIGNING INCLUSIVE LEARNING ENVIRONMENT FOR AUTISM

Directory of Open Access Journals (Sweden)

Rachna Khare

2009-11-01

Full Text Available In last two decades environment and behavior studies has profoundly influenced the practice of architecture and there is growing trend towards people-centered and evidence-based design. The field has tremendous application in designing for special needs; most of the researches on designing for special groups, accessibility codes and design guidelines are based on the functional needs of the users, necessity to explore potential of behavioral aspects to design for people with cognitive limitations is felt though. In the present research, the systematic study of behavioral features in autism has provided a wealth of understanding that is applied to the process of design. There are several stages to this research project, in initial stage, learning behaviors of children, their strength and weakness in educational spaces helped in defining ‘enabling environment’ for autism, which is tested in the subsequent stages to provide evidence based body of knowledge that is expected to help architects and designers to design autism friendly inclusive educational spaces. The purpose of this paper is to present the enabling aspects of educational environment for children with autism and measure their affects on functional performance.

Synthetic biology and biomimetic chemistry as converging technologies fostering a new generation of smart biosensors.

Science.gov (United States)

Scognamiglio, Viviana; Antonacci, Amina; Lambreva, Maya D; Litescu, Simona C; Rea, Giuseppina

2015-12-15

Biosensors are powerful tunable systems able to switch between an ON/OFF status in response to an external stimulus. This extraordinary property could be engineered by adopting synthetic biology or biomimetic chemistry to obtain tailor-made biosensors having the desired requirements of robustness, sensitivity and detection range. Recent advances in both disciplines, in fact, allow to re-design the configuration of the sensing elements - either by modifying toggle switches and gene networks, or by producing synthetic entities mimicking key properties of natural molecules. The present review considered the role of synthetic biology in sustaining biosensor technology, reporting examples from the literature and reflecting on the features that make it a useful tool for designing and constructing engineered biological systems for sensing application. Besides, a section dedicated to bioinspired synthetic molecules as powerful tools to enhance biosensor potential is reported, and treated as an extension of the concept of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules. Thus, the design of synthetic molecules, such as aptamers, biomimetics, molecular imprinting polymers, peptide nucleic acids, and ribozymes were encompassed as "products" of biomimetic chemistry. Copyright © 2015 Elsevier B.V. All rights reserved.

Learning Environments Designed According to Learning Styles and Its Effects on Mathematics Achievement

Science.gov (United States)

Özerem, Aysen; Akkoyunlu, Buket

2015-01-01

Problem Statement: While designing a learning environment it is vital to think about learner characteristics (learning styles, approaches, motivation, interests… etc.) in order to promote effective learning. The learning environment and learning process should be designed not to enable students to learn in the same manner and at the same level,…

Synthetic

Directory of Open Access Journals (Sweden)

Anna Maria Manferdini

2010-06-01

Full Text Available Traditionally materials have been associated with a series of physical properties that can be used as inputs to production and manufacturing. Recently we witnessed an interest in materials considered not only as ‘true matter’, but also as new breeds where geometry, texture, tooling and finish are able to provoke new sensations when they are applied to a substance. These artificial materials can be described as synthetic because they are the outcome of various qualities that are not necessarily true to the original matter, but they are the combination of two or more parts, whether by design or by natural processes. The aim of this paper is to investigate the potential of architectural surfaces to produce effects through the invention of new breeds of artificial matter, using micro-scale details derived from Nature as an inspiration.

Rewiring protein synthesis: From natural to synthetic amino acids.

Science.gov (United States)

Fan, Yongqiang; Evans, Christopher R; Ling, Jiqiang

2017-11-01

The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthetic sustained gene delivery systems.

Science.gov (United States)

Agarwal, Ankit; Mallapragada, Surya K

2008-01-01

Gene therapy today is hampered by the need of a safe and efficient gene delivery system that can provide a sustained therapeutic effect without cytotoxicity or unwanted immune responses. Bolus gene delivery in solution results in the loss of delivered factors via lymphatic system and may cause undesired effects by the escape of bioactive molecules to distant sites. Controlled gene delivery systems, acting as localized depot of genes, provide an extended sustained release of genes, giving prolonged maintenance of the therapeutic level of encoded proteins. They also limit the DNA degradation in the nuclease rich extra-cellular environment. While attempts have been made to adapt existing controlled drug delivery technologies, more novel approaches are being investigated for controlled gene delivery. DNA encapsulated in nano/micro spheres of polymers have been administered systemically/orally to be taken up by the targeted tissues and provide sustained release once internalized. Alternatively, DNA entrapped in hydrogels or scaffolds have been injected/implanted in tissues/cavities as platforms for gene delivery. The present review examines these different modalities for sustained delivery of viral and non-viral gene-delivery vectors. Design parameters and release mechanisms of different systems made with synthetic or natural polymers are presented along with their prospective applications and opportunities for continuous development.

Comparison of Nonlinear Model Results Using Modified Recorded and Synthetic Ground Motions

International Nuclear Information System (INIS)

Spears, Robert E.; Wilkins, J. Kevin

2011-01-01

A study has been performed that compares results of nonlinear model runs using two sets of earthquake ground motion time histories that have been modified to fit the same design response spectra. The time histories include applicable modified recorded earthquake ground motion time histories and synthetic ground motion time histories. The modified recorded earthquake ground motion time histories are modified from time history records that are selected based on consistent magnitude and distance. The synthetic ground motion time histories are generated using appropriate Fourier amplitude spectrums, Arias intensity, and drift correction. All of the time history modification is performed using the same algorithm to fit the design response spectra. The study provides data to demonstrate that properly managed synthetic ground motion time histories are reasonable for use in nonlinear seismic analysis.

Factors related to the design and implementation of an 'design for environment' process

DEFF Research Database (Denmark)

Skelton, Kristen; Knitl, Teresa

2013-01-01

In the last two decades, Siemens AG has systematically built up the topic of environmental protection within its core functions. The company is currently expanding its focus by including additional product and supply related environmental activities to enable strategic and inclusive decisions. Most...... recently, the Energy Sector of Siemens AG developed a Design for Environment (DfE) process based on ISO/TR 14062 to integrate environmental issues into product design and development. This paper briefly presents the DfE process and the feedback that was gathered from engineers as input to improve...

A design method of bilateral control system with uncertain dynamics of environments

International Nuclear Information System (INIS)

Yamada, Kou; Iida, Noriyuki; Kudou, Naoki

2002-01-01

In the present paper, we examine a design method for master-slave systems of bilateral control systems. In master-slave systems, human operator works to achieve tasks via the master and the salve system. The salve system contacts the environment and works the tasks. According to past studies, when the dynamics of environment is treated as uncertainties, the number of unstable poles of the slave system is required to be equivalent to that of the slave system with the dynamics of the environment. In some cases, the number of unstable poles of the slave system with the dynamics of environment is different from that of the slave system. We propose a simple design method of bilateral control systems such that the number of unstable poles of the slave system with the dynamics of environmental is different from that of the slave system without the dynamics of the environment. (author)

Squidy : a Zoomable Design Environment for Natural User Interfaces

OpenAIRE

König, Werner A.; Rädle, Roman; Reiterer, Harald

2009-01-01

We introduce the interaction library Squidy, which eases the design of natural user interfaces by unifying relevant frameworks and toolkits in a common library. Squidy provides a central design environment based on high-level visual data flow programming combined with zoomable user interface concepts. The user interface offers a Simple visual language and a collection of ready-to-use devices, filters and interaction techniques. The concept of semantic zooming enables nevertheless access to mo...

Thermal Insulating Concrete Wall Panel Design for Sustainable Built Environment

Science.gov (United States)

Zhou, Ao; Wong, Kwun-Wah

2014-01-01

Air-conditioning system plays a significant role in providing users a thermally comfortable indoor environment, which is a necessity in modern buildings. In order to save the vast energy consumed by air-conditioning system, the building envelopes in envelope-load dominated buildings should be well designed such that the unwanted heat gain and loss with environment can be minimized. In this paper, a new design of concrete wall panel that enhances thermal insulation of buildings by adding a gypsum layer inside concrete is presented. Experiments have been conducted for monitoring the temperature variation in both proposed sandwich wall panel and conventional concrete wall panel under a heat radiation source. For further understanding the thermal effect of such sandwich wall panel design from building scale, two three-story building models adopting different wall panel designs are constructed for evaluating the temperature distribution of entire buildings using finite element method. Both the experimental and simulation results have shown that the gypsum layer improves the thermal insulation performance by retarding the heat transfer across the building envelopes. PMID:25177718

The Integrated Design for Micro - environment Monitoring System of Showcase in Museum

Directory of Open Access Journals (Sweden)

Dong Chan

2017-01-01

Full Text Available In order to improve the current environment quality of cultural relics in museum and make them preserved for a long time, the paper proposes the integrated design for micro - environment monitoring system of showcase in museum, the system mainly monitors the micro-environment of heritage, such as ultraviolet, light, formaldehyde, CO2, TVOC, PM 2.5, choosing cotex-M3 ARM microcontroller STM32F103ZET6 as the control core. Based on the concept of integration, the system integrates the single air monitoring instruments. The design of circuit mainly includes the process of digital power supply and analog power supply, the acquisition and processing of 5 analog signals from sensors, and the design of reserved interface. In the aspect of interaction, the serial port lcd module was uesd for the display and control, which can get rid of the control of PC and achieve the functions of environmental monitoring, environmental warning, environmental assessment, historical data query. The integrated design for Micro-environment of Showcase in Museum achieves a monitoring platform successfully which is easy for users’ operation and access to display information conveniently. The advantages of the system are strong portability, low cost and short development cycle.

POTENTIATION OF COPAÍBA OIL-RESIN WITH SYNTHETIC INSECTICIDES TO CONTROL OF FALL ARMYWORM

OpenAIRE

ALMEIDA, WALDIANE ARAÚJO DE; SILVA, IGOR HONORATO LEDUÍNO DA; SANTOS, ANA CLÁUDIA VIEIRA DOS; BARROS JÚNIOR, AURÉLIO PAES; SOUSA, ADALBERTO HIPÓLITO DE

2017-01-01

ABSTRACT The control of Spodoptera frugiperda (J. E. SMITH) (Lepidoptera: Noctuidae) has been carried out mainly with pyrethroids and organophosphates insecticides. The continuous and indiscriminate use of synthetic insecticides, for decades, has led to the selection of resistant populations and has caused concerns for human health and the environment. An alternative is the use of botanical insecticides, including through the mixtures with synthetic insecticides. This study aimed to investiga...

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

Science.gov (United States)

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

OpenAIRE

Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

2015-01-01

First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

The Designed Environment and How it Affects Brain Morphology and Mental Health.

Science.gov (United States)

Golembiewski, Jan A

2016-01-01

The environment is inextricably related to mental health. Recent research replicates findings of a significant, linear correlation between a childhood exposure to the urban environment and psychosis. Related studies also correlate the urban environment and aberrant brain morphologies. These findings challenge common beliefs that the mind and brain remain neutral in the face of worldly experience. There is a signature within these neurological findings that suggests that specific features of design cause and trigger mental illness. The objective in this article is to work backward from the molecular dynamics to identify features of the designed environment that may either trigger mental illness or protect against it. This review analyzes the discrete functions putatively assigned to the affected brain areas and a neurotransmitter called dopamine, which is the primary target of most antipsychotic medications. The intention is to establish what the correlations mean in functional terms, and more specifically, how this relates to the phenomenology of urban experience. In doing so, environmental mental illness risk factors are identified. Having established these relationships, the review makes practical recommendations for those in public health who wish to use the environment itself as a tool to improve the mental health of a community through design. © The Author(s) 2015.

Stayin Alive: What are Persistent Synthetic Environments

Science.gov (United States)

2014-10-01

worlds (vWorlds) and Massive Multiplayer Online Games ( MMORPGs ) or Online Role-Playing Games. In these commercial products, the requirements for...extremely attractive. Of these two technologies, vWorlds is the more general, while MMORPGs can be seen as a sub-set instantiated for a specific...Second Life is largely built and operated by its users and has a wide variety of environments. MMORPGs [7], on the other hand, have typically

Experimental Design of Electrocoagulation and Magnetic Technology for Enhancing Suspended Solids Removal from Synthetic Wastewater

Directory of Open Access Journals (Sweden)

Moh Faiqun Ni'am

2014-10-01

Full Text Available Design of experiments (DOE is one of the statistical method that is used as a tool to enhance and improve experimental quality. The changes to the variables of a process or system is supposed to give the optimal result (response and quite satisfactory. Experimental design can defined as a test or series of test series by varying the input variables (factors of a process that can known to cause changes in output (response. This paper presents the results of experimental design of wastewater treatment by electrocoagulation (EC technique. A combined magnet and electrocoagulation (EC technology were designed to increase settling velocity and to enhance suspended solid removal efficiencies from wastewater samples. In this experiment, a synthetic wastewater samples were prepared by mixing 700 mg of the milk powder in one litre of water and treated by using an acidic buffer solution. The monopolar iron (Fe plate anodes and cathodes were employed as electrodes. Direct current was varied in a range of between 0.5 and 1.1 A, and flowrate in a range of between 1.00 to 3.50 mL/s. One permanent magnets namely AlNiCo with a magnetic strength of 0.16T was used in this experiment. The results show that the magnetic field and the flowrate have major influences on suspended solids removal. The efficiency removals of suspended solids, turbidity and COD removal efficiencies at optimum conditions were found to be more than 85%, 95%, and 75%, respectively.

The prevalence of two 'commonly' encountered synthetic target fibres within a large urban environment.

Science.gov (United States)

Palmer, R; Burnett, E; Luff, N; Wagner, C; Stinga, G; Carney, C; Sheridan, K

2015-03-01

A target fibre study was carried out to assess the random prevalence of two ostensibly commonly encountered synthetic fibre types; black acrylic and blue polyester. The study was performed in an environment which maximised the number of random contacts between textile garments in the population and specific surfaces, namely; seating relating to buses, public houses and cinemas found within a large urban conurbation. Surface debris tapings were collected from samples of bus seats (30), pub seats (54) and cinema seats (53). Using low power stereomicroscopy, a total of 114 and 68 fibres, superficially similar to the respective black acrylic and blue polyester target fibres, were recovered from these tapings. The full range of comparative microscopical and instrumental analysis used in operational forensic laboratories was performed on the recovered fibres. No matches were found with either of the target fibres. These findings are in accordance with similar studies which show that the probability of an 'adventitious' match with a particular fibre type/colour combination is extremely low. In addition, the findings demonstrate that the current techniques and instrumentation employed by operational forensic laboratories are fit for purpose. Importantly, the findings demonstrate that databases and surveys (e.g. fibre population studies) which do not consider the analytical/comparison processes, must not be used in isolation when evaluating fibre evidence at source level. Copyright © 2015 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

[New materia medica project: synthetic biology based bioactive metabolites research in medicinal plant].

Science.gov (United States)

Wang, Yong

2017-03-25

In the last decade, synthetic biology research has been gradually transited from monocellular parts or devices toward more complex multicellular systems. The emerging plant synthetic biology is regarded as the "next chapter" of synthetic biology. The complex and diverse plant metabolism as the entry point, plant synthetic biology research not only helps us understand how real life is working, but also facilitates us to learn how to design and construct more complex artificial life. Bioactive compounds innovation and large-scale production are expected to be breakthrough with the redesigned plant metabolism as well. In this review, we discuss the research progress in plant synthetic biology and propose the new materia medica project to lift the level of traditional Chinese herbal medicine research.

Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

Prediction and evaluation method of wind environment in the early design stage using BIM-based CFD simulation

International Nuclear Information System (INIS)

Lee, Sumi; Song, Doosam

2010-01-01

Drastic urbanization and manhattanization are causing various problems in wind environment. This study suggests a CFD simulation method to evaluate wind environment in the early design stage of high-rise buildings. The CFD simulation of this study is not a traditional in-depth simulation, but a method to immediately evaluate wind environment for each design alternative and provide guidelines for design modification. Thus, the CFD simulation of this study to evaluate wind environments uses BIM-based CFD tools to utilize building models in the design stage. This study examined previous criteria to evaluate wind environment for pedestrians around buildings and selected evaluation criteria applicable to the CFD simulation method of this study. Furthermore, proper mesh generation method and CPU time were reviewed to find a meaningful CFD simulation result for determining optimal design alternative from the perspective of wind environment in the design stage. In addition, this study is to suggest a wind environment evaluation method through a BIM-based CFD simulation.

Synthetic Biology: A Unifying View and Review Using Analog Circuits.

Science.gov (United States)

Teo, Jonathan J Y; Woo, Sung Sik; Sarpeshkar, Rahul

2015-08-01

We review the field of synthetic biology from an analog circuits and analog computation perspective, focusing on circuits that have been built in living cells. This perspective is well suited to pictorially, symbolically, and quantitatively representing the nonlinear, dynamic, and stochastic (noisy) ordinary and partial differential equations that rigorously describe the molecular circuits of synthetic biology. This perspective enables us to construct a canonical analog circuit schematic that helps unify and review the operation of many fundamental circuits that have been built in synthetic biology at the DNA, RNA, protein, and small-molecule levels over nearly two decades. We review 17 circuits in the literature as particular examples of feedforward and feedback analog circuits that arise from special topological cases of the canonical analog circuit schematic. Digital circuit operation of these circuits represents a special case of saturated analog circuit behavior and is automatically incorporated as well. Many issues that have prevented synthetic biology from scaling are naturally represented in analog circuit schematics. Furthermore, the deep similarity between the Boltzmann thermodynamic equations that describe noisy electronic current flow in subthreshold transistors and noisy molecular flux in biochemical reactions has helped map analog circuit motifs in electronics to analog circuit motifs in cells and vice versa via a `cytomorphic' approach. Thus, a body of knowledge in analog electronic circuit design, analysis, simulation, and implementation may also be useful in the robust and efficient design of molecular circuits in synthetic biology, helping it to scale to more complex circuits in the future.

Building, Using, Sharing and Reusing Environment Concept Models

National Research Council Canada - National Science Library

Chadbourne, Christopher; Clark, Douglas

2006-01-01

.... The Environment Concept Model (ECM) is an object-oriented documentation technique. The technique is tailored for system engineers who must deliver a consistent synthetic environment representation, on time and within budget...

Synthetic biology expands chemical control of microorganisms.

Science.gov (United States)

Ford, Tyler J; Silver, Pamela A

2015-10-01

The tools of synthetic biology allow researchers to change the ways engineered organisms respond to chemical stimuli. Decades of basic biology research and new efforts in computational protein and RNA design have led to the development of small molecule sensors that can be used to alter organism function. These new functions leap beyond the natural propensities of the engineered organisms. They can range from simple fluorescence or growth reporting to pathogen killing, and can involve metabolic coordination among multiple cells or organisms. Herein, we discuss how synthetic biology alters microorganisms' responses to chemical stimuli resulting in the development of microbes as toxicity sensors, disease treatments, and chemical factories. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hydrothermal synthetic strategies of inorganic semiconducting nanostructures.

Science.gov (United States)

Shi, Weidong; Song, Shuyan; Zhang, Hongjie

2013-07-07

Because of their unique chemical and physical properties, inorganic semiconducting nanostructures have gradually played a pivotal role in a variety of research fields, including electronics, chemical reactivity, energy conversion, and optics. A major feature of these nanostructures is the quantum confinement effect, which strongly depends on their size, shape, crystal structure and polydispersity. Among all developed synthetic methods, the hydrothermal method based on a water system has attracted more and more attention because of its outstanding advantages, such as high yield, simple manipulation, easy control, uniform products, lower air pollution, low energy consumption and so on. Precise control over the hydrothermal synthetic conditions is a key to the success of the preparation of high-quality inorganic semiconducting nanostructures. In this review, only the representative hydrothermal synthetic strategies of inorganic semiconducting nanostructures are selected and discussed. We will introduce the four types of strategies based on exterior reaction system adjustment, namely organic additive- and template-free hydrothermal synthesis, organic additive-assisted hydrothermal synthesis, template-assisted hydrothermal synthesis and substrate-assisted hydrothermal synthesis. In addition, the two strategies based on exterior reaction environment adjustment, including microwave-assisted and magnetic field-assisted hydrothermal synthesis, will be also described. Finally, we conclude and give the future prospects of this research area.

METABOLIC MODELLING IN THE DEVELOPMENT OF CELL FACTORIES BY SYNTHETIC BIOLOGY

Directory of Open Access Journals (Sweden)

Paula Jouhten

2012-10-01

Full Text Available Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory.

A Method to Design Synthetic Cell-Cycle Networks

International Nuclear Information System (INIS)

Ke-Ke, Miao

2009-01-01

The interactions among proteins, DNA and RNA in an organism form elaborate cell-cycle networks which govern cell growth and proliferation. Understanding the common structure of cell-cycle networks will be of great benefit to science research. Here, inspired by the importance of the cell-cycle regulatory network of yeast which has been studied intensively, we focus on small networks with 11 nodes, equivalent to that of the cell-cycle regulatory network used by Li et al. [Proc. Natl. Acad. Sci. USA 101(2004)4781] Using a Boolean model, we study the correlation between structure and function, and a possible common structure. It is found that cascade-like networks with a great number of interactions between nodes are stable. Based on these findings, we are able to construct synthetic networks that have the same functions as the cell-cycle regulatory network. (condensed matter: structure, mechanical and thermal properties)

Learning How to Design a Technology Supported Inquiry-Based Learning Environment

Science.gov (United States)

Hakverdi-Can, Meral; Sonmez, Duygu

2012-01-01

This paper describes a study focusing on pre-service teachers' experience of learning how to design a technology supported inquiry-based learning environment using the Internet. As part of their elective course, pre-service science teachers were asked to develop a WebQuest environment targeting middle school students. A WebQuest is an…

Design Environment for Multifidelity and Multidisciplinary Components

Science.gov (United States)

Platt, Michael

2014-01-01

One of the greatest challenges when developing propulsion systems is predicting the interacting effects between the fluid loads, thermal loads, and structural deflection. The interactions between technical disciplines often are not fully analyzed, and the analysis in one discipline often uses a simplified representation of other disciplines as an input or boundary condition. For example, the fluid forces in an engine generate static and dynamic rotor deflection, but the forces themselves are dependent on the rotor position and its orbit. It is important to consider the interaction between the physical phenomena where the outcome of each analysis is heavily dependent on the inputs (e.g., changes in flow due to deflection, changes in deflection due to fluid forces). A rigid design process also lacks the flexibility to employ multiple levels of fidelity in the analysis of each of the components. This project developed and validated an innovative design environment that has the flexibility to simultaneously analyze multiple disciplines and multiple components with multiple levels of model fidelity. Using NASA's open-source multidisciplinary design analysis and optimization (OpenMDAO) framework, this multifaceted system will provide substantially superior capabilities to current design tools.

Design of GNSS Performance Analysis and Simulation Tools as a Web Portal

Directory of Open Access Journals (Sweden)

S. Tadic

2014-11-01

Full Text Available This paper considers design of a web-portal for the validation of behavior of GNSS applications in different environments. The tool provides the positioning performance analysis and a comparison to benchmark devices. Web-portal incorporates a 3D synthetic data generator to compute the propagation and the reception of radio-navigation signals in a 3D virtual environment. This radio propagation simulator uses ray-tracing to calculate interactions between the GNSS signal and the local environment. For faster execution on a GPU platform, the simulator uses BVH optimization. The work is verified in field trials and by using reference software.

Launch Vehicle Design and Optimization Methods and Priority for the Advanced Engineering Environment

Science.gov (United States)

Rowell, Lawrence F.; Korte, John J.

2003-01-01

NASA's Advanced Engineering Environment (AEE) is a research and development program that will improve collaboration among design engineers for launch vehicle conceptual design and provide the infrastructure (methods and framework) necessary to enable that environment. In this paper, three major technical challenges facing the AEE program are identified, and three specific design problems are selected to demonstrate how advanced methods can improve current design activities. References are made to studies that demonstrate these design problems and methods, and these studies will provide the detailed information and check cases to support incorporation of these methods into the AEE. This paper provides background and terminology for discussing the launch vehicle conceptual design problem so that the diverse AEE user community can participate in prioritizing the AEE development effort.

Designing for social interaction in open-ended play environments

NARCIS (Netherlands)

de Valk, L.; Bekker, T.; Eggen, J.H.

2015-01-01

Interactive technology is becoming more strongly integrated in innovative play solutions. As play is often a social experience, understanding the dynamic social context in which such play takes place is an essential step in designing new interactive play environments. In this paper, we explore the

Knowledge management in an integrated design and engineering environment

NARCIS (Netherlands)

Reefman, R.J.B.; Van Nederveen, G.A.

2012-01-01

Organisations and / or disciplines in Building and Construction projects are usually working in their own design and engineering environments and using their own Building Information Models (BIM). The discipline models are merged into a project BIM which is mainly used to check for interferences or

Liner shipping hub network design in a competitive environment

DEFF Research Database (Denmark)

Gelareh, Shahin; Nickel, Stefan; Pisinger, David

2010-01-01

A mixed integer programming formulation is proposed for hub-and-spoke network design in a competitive environment. It addresses the competition between a newcomer liner service provider and an existing dominating operator, both operating on hub-and-spoke networks. The newcomer company maximizes i...

Designing an Interactive Multimedia Environment for Learning and Aiding Troubleshooting

National Research Council Canada - National Science Library

Kolodner, Janet

1997-01-01

.... However troubleshooting is a complex process both to learn and perform. This report examines the prospects for designing an interactive learning environment that helps users acquire and engage in effective troubleshooting...

Understanding and Designing Military Organizations for a Complex Dynamic Environment

National Research Council Canada - National Science Library

Hicks, Christopher E

2008-01-01

.... The two theories will be used to describe the external environment and how it relates to DoD organizations, current DoD organizational structures, and transformational concepts related to organizational design...

The Sustainable Expression of Ecological Concept in the Urban Landscape Environment Design

Science.gov (United States)

Dong, Junyan; Zhou, Tiejun; Xin, Lisen; Tan, Yuetong; Wang, Zhigang

2018-02-01

Urbanization is an inevitable trend of development of human society, also the inevitable outcome of economic development and scientific and technological progress, while urbanization process in promoting the development of human civilization, also no doubt, urban landscape has been a corresponding impact. Urban environment has suffered unprecedented damage, the urban population density, traffic congestion, shortage of resources, environmental pollution, ecological degradation, has become the focus of human society. In order to create an environment of ecological and harmonious, beautiful, sustainable development in the urban landscape, This paper discusses the concept of ecological design combined with the urban landscape design and sustainable development of urban landscape design.

Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces.

Science.gov (United States)

Boehm, Markus; Wu, Tong-Ying; Claussen, Holger; Lemmen, Christian

2008-04-24

Large collections of combinatorial libraries are an integral element in today's pharmaceutical industry. It is of great interest to perform similarity searches against all virtual compounds that are synthetically accessible by any such library. Here we describe the successful application of a new software tool CoLibri on 358 combinatorial libraries based on validated reaction protocols to create a single chemistry space containing over 10 (12) possible products. Similarity searching with FTrees-FS allows the systematic exploration of this space without the need to enumerate all product structures. The search result is a set of virtual hits which are synthetically accessible by one or more of the existing reaction protocols. Grouping these virtual hits by their synthetic protocols allows the rapid design and synthesis of multiple follow-up libraries. Such library ideas support hit-to-lead design efforts for tasks like follow-up from high-throughput screening hits or scaffold hopping from one hit to another attractive series.

Design of wireless communication systems for nuclear power plant environments

International Nuclear Information System (INIS)

Kadri, A.

2007-01-01

The problem of low-SNR (Signal-to-Noise ratio) digital communication system design in man-made electromagnetic environment within a nuclear power plant is addressed. A canonical structure of the low-SNR receiver is derived and analyzed for its bit error rate performance. The parameters that affect the error rate performance are identified and illustrated. Several well-known digital modulations are considered. It is shown that the receiver structure is dependent on the first-order probability density function of the noise environment. Thus, we offer comments for its robust implementation and its effect on bit error rate performance. We model the EM environment within the nuclear power plant to be e - mixture model, the parameters of which can be estimated to fit the environment. (author)

SYNTHETIC FRAGRANCES IN THE ENVIRONMENT ...

Science.gov (United States)

There is no abstract available for this product. If further information is requested, please refer to the bibliographic citation and contact the person listed under Contact field. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-soluble pharmaceuticals in source waters at levels that could be environmentally significant (at concentrations less than parts per billion, ppb). IAG with USGS ends in FY05. APM 20 due in FY05.Subtask 2: Coordination of interagency research and public outreach activities for PPCPs. Participate on NSTC Health and Environment subcommittee working group on PPCPs. Web site maintenance and expansion, invited technical presentations, invited articles for peer-reviewed journals, interviews for media, responding to public inquiries. S

Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project.

Science.gov (United States)

Sliva, Anna; Yang, Huanming; Boeke, Jef D; Mathews, Debra J H

2015-08-01

First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) PROJECT is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with this field of research and operate under a common set of principles. In this commentary, we survey the current ethics and regulatory landscape of synthetic biology and present the Sc2.0 Statement of Ethics and Governance to which all members of the project adhere. This statement focuses on four aspects of the Sc2.0 PROJECT: societal benefit, intellectual property, safety, and self-governance. We propose that such project-level agreements are an important, valuable, and flexible model of self-regulation for similar global, large-scale synthetic biology projects in order to maximize the benefits and minimize potential harms. Copyright © 2015 by the Genetics Society of America.

Design for Environment as a Tool for the Development of a Sustainable Supply Chain

CERN Document Server

Bevilacqua, Maurizio; Giacchetta, Giancarlo

2012-01-01

Environmental Design is becoming an increasingly significant agenda for many manufacturing companies and yet there is no standard to their approaches, strategies or their levels of execution. Applying Design for Environment (DfE) methodologies to develop a more sustainable supply chain has formed procedures and techniques which allow designers to integrate these methods with environmental supply chain management. Design for Environment as a Tool for the Development of a Sustainable Supply Chain aims to define relevant target specifications for a product throughout its life cycle; from conception and design to the end of its operating life.  Be considering this new approach to the supply chain, environmental responsiveness can work in tandem with sounds business management. The usual focus on suppliers, manufacturers and customers is expanded in Design for Environment as a Tool for the Development of a Sustainable Supply Chain to include stakeholders such as government bodies and recycling companies. The infl...

BISRU: Synthetic Microbes for Moon, Mars and Beyond

Science.gov (United States)

Cumbers, J.; Rothchild, L.

2010-04-01

Synthetic biology and genomics will bring a new range of designer organisms into being and give us new tools for the manipulation and control of these organisms. BISRU or biological in situ resource utilization is the use of such genetically modified organisms in space.

Analog synthetic biology.

Science.gov (United States)

Sarpeshkar, R

2014-03-28

We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.

A Framework for Adaptive Learning Design in a Web-Conferencing Environment

Science.gov (United States)

Bower, Matt

2016-01-01

Many recent technologies provide the ability to dynamically adjust the interface depending on the emerging cognitive and collaborative needs of the learning episode. This means that educators can adaptively re-design the learning environment during the lesson, rather than purely relying on preemptive learning design thinking. Based on a…

Interface design for health care environments: the role of cognitive science.

OpenAIRE

Patel, V. L.; Kushniruk, A. W.

1998-01-01

An important challenge in the development of computer-based health care environments is the design of effective user interfaces. In this paper we consider a number of aspects of interface design related to the study of human-computer interaction from a cognitive perspective. It is argued that user interfaces must be designed with consideration of the information requirements, cognitive capabilities and limitations of the end users. Greater concern for fundamental research in design of user in...

Diels-Alder reactions for the rational design of benzo[b]thiophenes: DFT-based guidelines for synthetic chemists

Science.gov (United States)

Brasca, Romina; Kneeteman, María N.; Mancini, Pedro M. E.; Fabian, Walter M. F.

2012-02-01

In this work we studied the capability of several diene/dienophile pairs to undergo Diels-Alder (DA) reactions leading to benzo[b]thiophenes. A variety of synthetically and commercially available nitrothiophenes were chosen as dienophiles. Methyl 5-nitro-3-thiophenecarboxylate was selected as a potential strong electrophilic candidate based on some DFT-based properties and the substitution pattern of the expected product. The mechanistic details concerning the participation of this dienophile in polar DA reactions were investigated through a theoretical point of view. The results were compared with the experimental outcomes. This methodology should allow synthetic chemists to analyze DA reactions in detail in a stage prior to the synthetic job.

Synthetic biology devices for in vitro and in vivo diagnostics.

Science.gov (United States)

Slomovic, Shimyn; Pardee, Keith; Collins, James J

2015-11-24

There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging pathogens or be applied to orphan diseases. Synthetic biology, with its rational and short design-to-production cycles, has the potential to overcome many of these limitations. Synthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagnostics, expanding the molecular detection palette, creating dynamic sensors, and untethering reactions from laboratory equipment. The field is also beginning to move toward in vivo diagnostics, which could provide near real-time surveillance of multiple pathological conditions. Here, we describe current efforts in synthetic biology, focusing on the translation of promising technologies into pragmatic diagnostic tools and platforms.

Designing a Virtual-Reality-Based, Gamelike Math Learning Environment

Science.gov (United States)

Xu, Xinhao; Ke, Fengfeng

2016-01-01

This exploratory study examined the design issues related to a virtual-reality-based, gamelike learning environment (VRGLE) developed via OpenSimulator, an open-source virtual reality server. The researchers collected qualitative data to examine the VRGLE's usability, playability, and content integration for math learning. They found it important…

Synthetic Adhesive Attachment Discs based on Spider Pyriform Silk Architecture

Science.gov (United States)

Jain, Dharamdeep; Sahni, Vasav; Dhinojwala, Ali

2014-03-01

Among the variety of silks produced by spiders, pyriform silk is used in conjunction with the dragline silk to attach webs to different surfaces. Cob weaver spiders employ different architectural patterns to utilize the pyriform silk and form attachment joints with each pattern having a characteristic adhesive performance. The staple pin architecture is a one of the strongest attachment designs employed by spiders to attach their webs. Here we use a synthetic approach to create the a similar patterned architecture attachment discs on aluminum substrate using thermoplastic polyurethane. Measurable pull off forces are generated when the synthetic discs are peeled off a surface. This innovative adhesive strategy can be a source of design in various biomedical applications. Financial Support from National Science Foundation.

Instructional Designers' Media Selection Practices for Distributed Problem-Based Learning Environments

Science.gov (United States)

Fells, Stephanie

2012-01-01

The design of online or distributed problem-based learning (dPBL) is a nascent, complex design problem. Instructional designers are challenged to effectively unite the constructivist principles of problem-based learning (PBL) with appropriate media in order to create quality dPBL environments. While computer-mediated communication (CMC) tools and…

Hybrid protein-synthetic polymer nanoparticles for drug delivery.

Science.gov (United States)

Koseva, Neli S; Rydz, Joanna; Stoyanova, Ekaterina V; Mitova, Violeta A

2015-01-01

Among the most common nanoparticulate systems, the polymeric nanocarriers have a number of key benefits, which give a great choice of delivery platforms. Nevertheless, polymeric nanoparticles possess some limitations that include use of toxic solvents in the production process, polymer degradation, drug leakage outside the diseased tissue, and polymer cytotoxicity. The combination of polymers of biological and synthetic origin is an appealing modern strategy for the production of novel nanocarriers with unprecedented properties. Proteins' interface can play an important role in determining bioactivity and toxicity and gives perspective for future development of the polymer-based nanoparticles. The design of hybrid constructs composed of synthetic polymer and biological molecules such as proteins can be considered as a straightforward tool to integrate a broad spectrum of properties and biofunctions into a single device. This review discusses hybrid protein-synthetic polymer nanoparticles with different structures and levels in complexity and functionality, in view of their applications as drug delivery systems. © 2015 Elsevier Inc. All rights reserved.

Emerging Insights into Directed Assembly: Taking Examples from Nature to Design Synthetic Processes

Science.gov (United States)

de Pablo, Juan J.

There is considerable interest in controlling the assembly of polymeric material in order to create highly ordered materials for applications. Such materials are often trapped in metastable, non-equilibrium states, and the processes through which they assemble become an important aspect of the materials design strategy. An example is provided by di-block copolymer directed self-assembly, where a decade of work has shown that, through careful choice of process variables, it is possible to create ordered structures whose degree of perfection meets the constraints of commercial semiconductor manufacturing. As impactful as that work has been, it has focused on relatively simple materials neutral polymers, consisting of two or at most three blocks. Furthermore, the samples that have been produced have been limited to relatively thin films, and the assembly has been carried out on ideal, two-dimensional substrates. The question that arises now is whether one can translate those achievements to polymeric materials having a richer sequence, to monomers that include charges, to three-dimensional substrates, or to active systems that are in a permanent non-equilibrium state. Building on discoveries from the biophysics literature, this presentation will review recent work from our group and others that explains how nature has evolved to direct the assembly of nucleic acids into intricate, fully three-dimensional macroscopic functional materials that are not only active, but also responsive to external cues. We will discuss how principles from polymer physics serve to explain those assemblies, and how one might design a new generation of synthetic systems that incorporate some of those principles.

Chlorine-36 abundance in natural and synthetic perchlorate

Energy Technology Data Exchange (ETDEWEB)

Heikoop, Jeffrey M [Los Alamos National Laboratory; Dale, M [NON LANL; Sturchio, Neil C [UNIV OF ILLIONOIS; Caffee, M [PURDUE UNIV; Belosa, A D [UNIV OF ILLINOIS; Heraty, Jr., L J [UNIV OF ILLINOIS; Bohike, J K [RESTON, VA; Hatzinger, P B [SHAW ENIVIORNMENTAL C0.; Jackson, W A [TEXAS TECH; Gu, B [ORNL

2009-01-01

Perchlorate (ClO{sub 4}{sup -}) is ubiquitous in the environment. It occurs naturally as a product of atmospheric photochemical reactions, and is synthesized for military, aerospace, and industrial applications. Nitrate-enriched soils of the Atacama Desert (Chile) contain high concentrations of natural ClO{sub 4}{sup -}; nitrate produced from these soils has been exported worldwide since the mid-1800's for use in agriculture. The widespread introduction of synthetic and agricultural ClO{sub 4}{sup -} into the environment has complicated attempts to understand the geochemical cycle of ClO{sub 4}{sup -}. Natural ClO{sub 4}{sup -} samples from the southwestern United States have relatively high {sup 36}Cl abundances ({sup 36}Cl/Cl = 3,100 x 10{sup -15} to 28,800 x 10{sup -15}), compared with samples of synthetic ({sup 36}Cl/Cl = 0.0 x 10{sup -15} to 40 x 10{sup -15}) and Atacama Desert ({sup 36}Cl/Cl = 0.9 x 10{sup -15} to 590 x 10{sup -15}) ClO{sub 4}{sup -}. These data give a lower limit for the initial {sup 36}Cl abundance of natural ClO{sub 4}{sup -} and provide temporal and other constraints on its geochemical cycle.

Evaluating the Physical Environment of Design Studios: A Case study in Malaysian Private Architecture Schools

Directory of Open Access Journals (Sweden)

Shanthi Muniandy

2015-09-01

Full Text Available Understanding the notion of learner’s experiences in the design of physical environment of an architecture design studio is a necessity as it contains certain values of influence. It is due to the unique learning experiences which are accrued particularly in design studio that is continued during professional practice as well. Most architectural campuses in Malaysian Private Higher Education Institutions (MPHEI are devoid of certain important elements and this issue needs to be looked into seriously. Apparently, most architectural design studios today have different physical settings, and have developed their own learning culture based on the typical space that they have. Reviewing the physical environment and how it contributes to the social environ-ment in MPHEI’s architectural context requires certain understanding on the learner’s psycho-logical needs, expectations and in the same time to meet the educational objective which is never an easy task. Hence, this paper reviewed the studies of the possible physical environment approaches in connecting the learner’s connections in architecture studio learning environ-ment. A questionnaire survey with Likert-scale components, and semi-structured interview on learners of five distinguished Private Architectural schools in Malaysia unveiled several signifi-cant findings that can lead entrepreneurs to upgrade the physical environment of these MPHEIs in order to cope with the demands of the stakeholders.

Restorative Virtual Environment Design for Augmenting Nursing Home Rehabilitation

DEFF Research Database (Denmark)

Bruun-Pedersen, Jon Ram; Serafin, Stefania; Kofoed, Lise

2016-01-01

do, but more studies on content and design of proper custom designs for RVEs is necessary. This paper reviews the background for RVE design, describes four custom RVE designs for recreational VE exploration and presents user preferences among nursing home users concerning content and other pivotal......With increasing age, muscle strength decreases excessively rapidly if physical activity is not maintained. However, physical activity is increasingly difficult with age, due to balance, strength or coordination difficulties, arthritis, etc. Moreover, many nursing home residents become unable...... to experience natural surroundings. Augmenting a conventional biking exercise with a recreational virtual environment (RVE) has shown to serve as an intrinsic motivation contributor to exercise for nursing home residents. RVEs might be able to provide some of the health benefits that regular nature experiences...

Introducing an attractive method for total biomimetic creation of a synthetic biodegradable bioactive bone scaffold based on statistical experimental design.

Science.gov (United States)

Shahbazi, Sara; Zamanian, Ali; Pazouki, Mohammad; Jafari, Yaser

2018-05-01

A new total biomimetic technique based on both the water uptake and degradation processes is introduced in this study to provide an interesting procedure to fabricate a bioactive and biodegradable synthetic scaffold, which has a good mechanical and structural properties. The optimization of effective parameters to scaffold fabrication was done by response surface methodology/central composite design (CCD). With this method, a synthetic scaffold was fabricated which has a uniform and open-interconnected porous structure with the largest pore size of 100-200μm. The obtained compressive ultimate strength of ~35MPa and compression modulus of 58MPa are similar to some of the trabecular bone. The pore morphology, size, and distribution of the scaffold were characterized using a scanning electron microscope and mercury porosimeter. Fourier transform infrared spectroscopy, EDAX and X-ray diffraction analyses were used to determine the chemical composition, Ca/P element ratio of mineralized microparticles, and the crystal structure of the scaffolds, respectively. The optimum biodegradable synthetic scaffold based on its raw materials of polypropylene fumarate, hydroxyethyl methacrylate and nano bioactive glass (PPF/HEMA/nanoBG) as 70/30wt/wt%, 20wt%, and 1.5wt/wt% (PHB.732/1.5) with desired porosity, pore size, and geometry were created by 4weeks immersion in SBF. This scaffold showed considerable biocompatibility in the ranging from 86 to 101% for the indirect and direct contact tests and good osteoblast cell attachment when studied with the bone-like cells. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthetic genome engineering forging new frontiers for wine yeast.

Science.gov (United States)

Pretorius, Isak S

2017-02-01

Over the past 15 years, the seismic shifts caused by the convergence of biomolecular, chemical, physical, mathematical, and computational sciences alongside cutting-edge developments in information technology and engineering have erupted into a new field of scientific endeavor dubbed Synthetic Biology. Recent rapid advances in high-throughput DNA sequencing and DNA synthesis techniques are enabling the design and construction of new biological parts (genes), devices (gene networks) and modules (biosynthetic pathways), and the redesign of biological systems (cells and organisms) for useful purposes. In 2014, the budding yeast Saccharomyces cerevisiae became the first eukaryotic cell to be equipped with a fully functional synthetic chromosome. This was achieved following the synthesis of the first viral (poliovirus in 2002 and bacteriophage Phi-X174 in 2003) and bacterial (Mycoplasma genitalium in 2008 and Mycoplasma mycoides in 2010) genomes, and less than two decades after revealing the full genome sequence of a laboratory (S288c in 1996) and wine (AWRI1631 in 2008) yeast strain. A large international project - the Synthetic Yeast Genome (Sc2.0) Project - is now underway to synthesize all 16 chromosomes (∼12 Mb carrying ∼6000 genes) of the sequenced S288c laboratory strain by 2018. If successful, S. cerevisiae will become the first eukaryote to cross the horizon of in silico design of complex cells through de novo synthesis, reshuffling, and editing of genomes. In the meantime, yeasts are being used as cell factories for the semi-synthetic production of high-value compounds, such as the potent antimalarial artemisinin, and food ingredients, such as resveratrol, vanillin, stevia, nootkatone, and saffron. As a continuum of previously genetically engineered industrially important yeast strains, precision genome engineering is bound to also impact the study and development of wine yeast strains supercharged with synthetic DNA. The first taste of what the future

Induction of Fish Biomarkers by Synthetic-Based Drilling Muds

Science.gov (United States)

Gagnon, Marthe Monique; Bakhtyar, Sajida

2013-01-01

The study investigated the effects of chronic exposure of pink snapper (Pagrus auratus Forster), to synthetic based drilling muds (SBMs). Fish were exposed to three mud systems comprised of three different types of synthetic based fluids (SBFs): an ester (E), an isomerized olefin (IO) and linear alpha olefin (LAO). Condition factor (CF), liver somatic index (LSI), hepatic detoxification (EROD activity), biliary metabolites, DNA damage and stress proteins (HSP-70) were determined. Exposure to E caused biologically significant effects by increasing CF and LSI, and triggered biliary metabolite accumulation. While ester-based SBFs have a rapid biodegradation rate in the environment, they caused the most pronounced effects on fish health. IO induced EROD activity and biliary metabolites and LAO induced EROD activity and stress protein levels. The results demonstrate that while acute toxicity of SBMs is generally low, chronic exposure to weathering cutting piles has the potential to affect fish health. The study illustrates the advantages of the Western Australian government case-by-case approach to drilling fluid management, and highlights the importance of considering the receiving environment in the selection of SBMs. PMID:23894492

Engineering synthetic vaccines using cues from natural immunity

Science.gov (United States)

Irvine, Darrell J.; Swartz, Melody A.; Szeto, Gregory L.

2013-11-01

Vaccines aim to protect against or treat diseases through manipulation of the immune response, promoting either immunity or tolerance. In the former case, vaccines generate antibodies and T cells poised to protect against future pathogen encounter or attack diseased cells such as tumours; in the latter case, which is far less developed, vaccines block pathogenic autoreactive T cells and autoantibodies that target self tissue. Enormous challenges remain, however, as a consequence of our incomplete understanding of human immunity. A rapidly growing field of research is the design of vaccines based on synthetic materials to target organs, tissues, cells or intracellular compartments; to co-deliver immunomodulatory signals that control the quality of the immune response; or to act directly as immune regulators. There exists great potential for well-defined materials to further our understanding of immunity. Here we describe recent advances in the design of synthetic materials to direct immune responses, highlighting successes and challenges in prophylactic, therapeutic and tolerance-inducing vaccines.

On Beyond Star Trek, the Role of Synthetic Biology in Nasa's Missions

Science.gov (United States)

Rothschild, Lynn J.

2016-01-01

The time has come to for NASA to exploit the nascent field of synthetic biology in pursuit of its mission, including aeronautics, earth science, astrobiology and notably, human exploration. Conversely, NASA advances the fundamental technology of synthetic biology as no one else can because of its unique expertise in the origin of life and life in extreme environments, including the potential for alternate life forms. This enables unique, creative "game changing" advances. NASA's requirement for minimizing upmass in flight will also drive the field toward miniaturization and automation. These drivers will greatly increase the utility of synthetic biology solutions for military, health in remote areas and commercial purposes. To this end, we have begun a program at NASA to explore the use of synthetic biology in NASA's missions, particularly space exploration. As part of this program, we began hosting an iGEM team of undergraduates drawn from Brown and Stanford Universities to conduct synthetic biology research at NASA Ames Research Center. The 2011 team (http://2011.igem.org/Team:Brown-Stanford) produced an award-winning project on using synthetic biology as a basis for a human Mars settlement and the 2012 team has expanded the use of synthetic biology to estimate the potential for life in the clouds of other planets (http://2012.igem.org/Team:Stanford-Brown; http://www.calacademy.org/sciencetoday/igem-competition/). More recent projects from the Stanford-Brown team have expanded our ideas of how synthetic biology can aid NASA's missions from "Synthetic BioCommunication" (http://2013.igem.org/Team:Stanford-Brown) to a "Biodegradable UAS (drone)" in collaboration with Spelman College (http://2014.igem.org/Team:StanfordBrownSpelman#SBS%20iGEM) and most recently, "Self-Folding Origami" (http://2015.igem.org/Team:Stanford-Brown), the winner of the 2015 award for Manufacturing.

Deep functional analysis of synII, a 770 kb synthetic yeast chromosome

OpenAIRE

Shen, Yue; Wang, Yun; Chen, Tai; Gao, Feng; Gong, Jianhui; Abramczyk, Dariusz; Walker, Roy; Zhao, Hongcui; Chen, Shihong; Liu, Wei; Luo, Yisha; Müller, Carolin A.; Paul-Dubois-Taine, Adrien; Alver, Bonnie; Stracquadanio, Giovanni

2017-01-01

Herein we report the successful design, construction and characterization of a 770 kb synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels, including phenomics, transcriptomics, proteomics, chromosome segregation and replication analysis to provide a thorough and comprehensive analysis of a synthetic chromosome. Our “Trans-Omics” analyses reveal a modest but potentially significant pervasive up-regulation of translational machinery observed in synI...

The population genetics of X-autosome synthetic lethals and steriles.

Science.gov (United States)

Lachance, Joseph; Johnson, Norman A; True, John R

2011-11-01

Epistatic interactions are widespread, and many of these interactions involve combinations of alleles at different loci that are deleterious when present in the same individual. The average genetic environment of sex-linked genes differs from that of autosomal genes, suggesting that the population genetics of interacting X-linked and autosomal alleles may be complex. Using both analytical theory and computer simulations, we analyzed the evolutionary trajectories and mutation-selection balance conditions for X-autosome synthetic lethals and steriles. Allele frequencies follow a set of fundamental trajectories, and incompatible alleles are able to segregate at much higher frequencies than single-locus expectations. Equilibria exist, and they can involve fixation of either autosomal or X-linked alleles. The exact equilibrium depends on whether synthetic alleles are dominant or recessive and whether fitness effects are seen in males, females, or both sexes. When single-locus fitness effects and synthetic incompatibilities are both present, population dynamics depend on the dominance of alleles and historical contingency (i.e., whether X-linked or autosomal mutations occur first). Recessive synthetic lethality can result in high-frequency X-linked alleles, and dominant synthetic lethality can result in high-frequency autosomal alleles. Many X-autosome incompatibilities in natural populations may be cryptic, appearing to be single-locus effects because one locus is fixed. We also discuss the implications of these findings with respect to standing genetic variation and the origins of Haldane's rule.

Interactive tool that empowers structural understanding and enables FEM analysis in a parametric design environment

DEFF Research Database (Denmark)

Christensen, Jesper Thøger; Parigi, Dario; Kirkegaard, Poul Henning

2014-01-01

This paper introduces an interactive tool developed to integrate structural analysis in the architectural design environment from the early conceptual design stage. The tool improves exchange of data between the design environment of Rhino Grasshopper and the FEM analysis of Autodesk Robot...... Structural Analysis. Further the tool provides intuitive setup and visual aids in order to facilitate the process. Enabling students and professionals to quickly analyze and evaluate multiple design variations. The tool has been developed inside the Performance Aided Design course at the Master...... of Architecture and Design at Aalborg University...

Liner Shipping Hub Network Design in a Competitive Environment

DEFF Research Database (Denmark)

Gelareh, Shahin; Nickel, Stefan; Pisinger, David

A new mixed integer programming formulation is proposed for hub-and-spoke network design in a competitive environment. It addresses competition between a newcomer liner service provider and an alliance, both operating on hub-and-spoke networks. The newcomer company maximizes its market share...... — proportional to service time and transportation cost —by locating a predefined number of hubs at candidate ports and designing its network. While general-purpose solvers do not solve instances of even small size, an accelerated lagrangian method coupled with a primal heuristic obtains very good bounds. Our...

ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.

Science.gov (United States)

Wood, Christopher W; Heal, Jack W; Thomson, Andrew R; Bartlett, Gail J; Ibarra, Amaurys Á; Brady, R Leo; Sessions, Richard B; Woolfson, Derek N

2017-10-01

The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the 'dark matter of protein-fold space'. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. d.n.woolfson@bristol.ac.uk or chris.wood@bristol.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

In silico design and functional assessment of semisynthetic genes that confer tolerance to phosphinothricin

Directory of Open Access Journals (Sweden)

Jenny Paola Jiménez

2016-07-01

Full Text Available Herbicide tolerance is one of the features most used in GM crops, which has shown positive results for farmers and the environment. The starting point is the development of expression cassettes that express the characteristic of interest, they are initially constructed by standard molecular biology techniques. Currently, by bioinformatics and synthetic biology tools, it is possible to design and test the construct in silico, and then hire their synthesis. This approach allows optimizing expression by modifying the codon usage. In this work there were designed and evaluated semi-synthetic versions of genes in Nicotiana benthamiana, these genes confer tolerance to the herbicide phosphinothricin. It was made an analysis of freedom to operate in order to ensure that the designed constructs not violate intellectual property in Colombia. There were obtained two expression cassettes with freedom to operate, which express versions of the bar gene.

Controlling Ionic Transport for Device Design in Synthetic Nanopores

Science.gov (United States)

Kalman, Eric Boyd

Polymer nanopores present a number of behaviors not seen in microscale systems, such as ion current rectification, ionic selectivity, size exclusion and potential dependent ion concentrations in and near the pore. The existence of these effects stems from the small size of nanopores with respect to the characteristic length scales of surface interactions at the interface between the nanopore surface and the solution within it. The large surface-to-volume ratio due to the nanoscale geometry of a nanopore, as well as similarity in scale between geometry and interaction demands the solution interact with the nanopore walls. As surfaces in solution almost always carry residual charge, these surface forces are primarily the electrostatic interactions between the charge groups on the pore surface and the ions in solution. These interactions may be used by the experimentalist to control ionic transport through synthetic nanopores, and use them as a template for the construction of devices. In this research, we present our work on creating a number of ionic analogs to seminal electronic devices, specifically diodes, and transistors, by controlling ionic transport through the electrostatic interactions between a single synthetic nanopore and ions. Control is achieved by "doping" the effective charge carrier concentration in specific regions of the nanopore through manipulation of the pore's surface charge. This manipulation occurs through two mechanisms: chemical modification of the surface charge and electrostatic manipulation of the local internal nanopore potential using a gate electrode. Additionally, the innate selectivity of the charged nanopores walls allows for the separation of charges in solution. This well-known effect, which spawns measureable quantities, the streaming potential and current, has been used to create nanoscale water desalination membranes. We attempt to create a device using membranes with large nanopore densities for the desalination of water

Teachers as Participatory Designers: Two Case Studies with Technology-Enhanced Learning Environments