WorldWideScience

Sample records for biological engineers asabe

  1. 100 Years of Cotton Production, Harvesting and Ginning Systems Engineering: 1907 - 2007

    Science.gov (United States)

    The American Society of Agricultural and Biological Engineers (ASABE) celebrated its centennial year during 2007. As part of the ASABE centennial, the authors were asked to describe agricultural engineering accomplishments in U.S. cotton production, harvesting and ginning over the past 100 years. ...

  2. Multiplexed Engineering in Biology.

    Science.gov (United States)

    Rogers, Jameson K; Church, George M

    2016-03-01

    Biotechnology is the manufacturing technology of the future. However, engineering biology is complex, and many possible genetic designs must be evaluated to find cells that produce high levels of a desired drug or chemical. Recent advances have enabled the design and construction of billions of genetic variants per day, but evaluation capacity remains limited to thousands of variants per day. Here we evaluate biological engineering through the lens of the design–build–test cycle framework and highlight the role that multiplexing has had in transforming the design and build steps. We describe a multiplexed solution to the ‘test’ step that is enabled by new research. Achieving a multiplexed test step will permit a fully multiplexed engineering cycle and boost the throughput of biobased product development by up to a millionfold.

  3. 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.

  4. Synthetic biology: engineering molecular computers

    CERN Document Server

    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...

  5. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  6. 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.

  7. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  8. Biology: An Important Agricultural Engineering Mechanism

    Science.gov (United States)

    Henderson, S. M.

    1974-01-01

    Describes the field of bioengineering with particular emphasis on agricultural engineering, and presents the results of a survey of schools that combine biology and engineering in their curricula. (JR)

  9. Synthetic Biological Engineering of Photosynthesis

    Science.gov (United States)

    2015-11-16

    sink’, allowing a greater utilization of solar energy under conditions of excess light. The engineered microalgae exhibit a 25-30% enhancement in...the cellular ‘metabolic sink’, allowing a greater utilization of solar energy under conditions of excess light. The engineered microalgae exhibit a

  10. Synthetic Biology to Engineer Bacteriophage Genomes.

    Science.gov (United States)

    Rita Costa, Ana; Milho, Catarina; Azeredo, Joana; Pires, Diana Priscila

    2018-01-01

    Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Bacteriophages have been engineered towards a wide range of applications including pathogen control and detection, targeted drug delivery, or even assembly of new materials.In this chapter, two strategies that have been successfully used to genetically engineer bacteriophage genomes are addressed: a yeast-based platform and bacteriophage recombineering of electroporated DNA.

  11. Engineering reduced evolutionary potential for synthetic biology

    Science.gov (United States)

    Renda, Brian A.; Hammerling, Michael J.

    2014-01-01

    The field of synthetic biology seeks to engineer reliable and predictable behaviors in organisms from collections of standardized genetic parts. However, unlike other types of machines, genetically encoded biological systems are prone to changes in their designed sequences due to mutations in their DNA sequences after these devices are constructed and deployed. Thus, biological engineering efforts can be confounded by undesired evolution that rapidly breaks the functions of parts and systems, particularly when they are costly to the host cell to maintain. Here, we explain the fundamental properties that determine the evolvability of biological systems. Then, we use this framework to review current efforts to engineer the DNA sequences that encode synthetic biology devices and the genomes of their microbial hosts to reduce their ability to evolve and therefore increase their genetic reliability so that they maintain their intended functions over longer timescales. PMID:24556867

  12. Synthetic biology approaches to engineer T cells.

    Science.gov (United States)

    Wu, Chia-Yung; Rupp, Levi J; Roybal, Kole T; Lim, Wendell A

    2015-08-01

    There is rapidly growing interest in learning how to engineer immune cells, such as T lymphocytes, because of the potential of these engineered cells to be used for therapeutic applications such as the recognition and killing of cancer cells. At the same time, our knowhow and capability to logically engineer cellular behavior is growing rapidly with the development of synthetic biology. Here we describe how synthetic biology approaches are being used to rationally alter the behavior of T cells to optimize them for therapeutic functions. We also describe future developments that will be important in order to construct safe and precise T cell therapeutics. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Biological Systems Thinking for Control Engineering Design

    Directory of Open Access Journals (Sweden)

    D. J. Murray-Smith

    2004-01-01

    Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

  14. An engineering design approach to systems biology.

    Science.gov (United States)

    Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

    2017-07-17

    Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

  15. Enabling plant synthetic biology through genome engineering.

    Science.gov (United States)

    Baltes, Nicholas J; Voytas, Daniel F

    2015-02-01

    Synthetic biology seeks to create new biological systems, including user-designed plants and plant cells. These systems can be employed for a variety of purposes, ranging from producing compounds of industrial or therapeutic value, to reducing crop losses by altering cellular responses to pathogens or climate change. To realize the full potential of plant synthetic biology, techniques are required that provide control over the genetic code - enabling targeted modifications to DNA sequences within living plant cells. Such control is now within reach owing to recent advances in the use of sequence-specific nucleases to precisely engineer genomes. We discuss here the enormous potential provided by genome engineering for plant synthetic biology. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Micromechanics of engineered and biological systems

    Indian Academy of Sciences (India)

    Microsystems are good examples of integrated engineered systems of small size. Although this .... In develop- mental biology, the application of controlled forces on growing embryos is shown to help in under- standing ..... Optimization is a useful tool for synthesis. Many optimal synthesis methods have been developed for.

  17. Engineering Liposomes and Nanoparticles for Biological Targeting

    DEFF Research Database (Denmark)

    Jølck, Rasmus Irming; Feldborg, Lise Nørkjær; Andersen, Simon

    2011-01-01

    Our ability to engineer nanomaterials for biological and medical applications is continuously increasing, and nanomaterial designs are becoming more and more complex. One very good example of this is the drug delivery field where nanoparticle systems can be used to deliver drugs specifically...... to diseased tissue. In the early days, the design of the nanoparticles was relatively simple, but today we can surface functionalize and manipulate material properties to target diseased tissue and build highly complex drug release mechanisms into our designs. One of the most promising strategies in drug...

  18. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

  19. Advancing metabolic engineering through systems biology of industrial microorganisms

    DEFF Research Database (Denmark)

    Dai, Zongjie; Nielsen, Jens

    2015-01-01

    resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

  20. Engineering and Biology: Counsel for a Continued Relationship

    Science.gov (United States)

    Levy, Arnon; Siegal, Mark L.; Soyer, Orkun S.; Wagner, Andreas

    2015-01-01

    Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology. PMID:26085824

  1. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Nielsen, Jens; Jewett, Michael Christopher

    2008-01-01

    in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

  2. Challenges and opportunities in synthetic biology for chemical engineers

    Energy Technology Data Exchange (ETDEWEB)

    Luo, YZ; Lee, JK; Zhao, HM

    2013-11-15

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. (C) 2012 Elsevier Ltd. All rights reserved.

  3. International Conference on Medical and Biological Engineering 2017

    CERN Document Server

    2017-01-01

    This volume presents the proceedings of the International Conference on Medical and Biological Engineering held from 16 to 18 March 2017 in Sarajevo, Bosnia and Herzegovina. Focusing on the theme of ‘Pursuing innovation. Shaping the future’, it highlights the latest advancements in Biomedical Engineering and also presents the latest findings, innovative solutions and emerging challenges in this field. Topics include: - Biomedical Signal Processing - Biomedical Imaging and Image Processing - Biosensors and Bioinstrumentation - Bio-Micro/Nano Technologies - Biomaterials - Biomechanics, Robotics and Minimally Invasive Surgery - Cardiovascular, Respiratory and Endocrine Systems Engineering - Neural and Rehabilitation Engineering - Molecular, Cellular and Tissue Engineering - Bioinformatics and Computational Biology - Clinical Engineering and Health Technology Assessment - Health Informatics, E-Health and Telemedicine - Biomedical Engineering Education - Pharmaceutical Engineering.

  4. IntegromeDB: an integrated system and biological search engine.

    Science.gov (United States)

    Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

    2012-01-19

    With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

  5. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  6. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  7. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-10-11

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  8. A transatlantic perspective on 20 emerging issues in biological engineering.

    Science.gov (United States)

    Wintle, Bonnie C; Boehm, Christian R; Rhodes, Catherine; Molloy, Jennifer C; Millett, Piers; Adam, Laura; Breitling, Rainer; Carlson, Rob; Casagrande, Rocco; Dando, Malcolm; Doubleday, Robert; Drexler, Eric; Edwards, Brett; Ellis, Tom; Evans, Nicholas G; Hammond, Richard; Haseloff, Jim; Kahl, Linda; Kuiken, Todd; Lichman, Benjamin R; Matthewman, Colette A; Napier, Johnathan A; ÓhÉigeartaigh, Seán S; Patron, Nicola J; Perello, Edward; Shapira, Philip; Tait, Joyce; Takano, Eriko; Sutherland, William J

    2017-11-14

    Advances in biological engineering are likely to have substantial impacts on global society. To explore these potential impacts we ran a horizon scanning exercise to capture a range of perspectives on the opportunities and risks presented by biological engineering. We first identified 70 potential issues, and then used an iterative process to prioritise 20 issues that we considered to be emerging, to have potential global impact, and to be relatively unknown outside the field of biological engineering. The issues identified may be of interest to researchers, businesses and policy makers in sectors such as health, energy, agriculture and the environment.

  9. Engineering Biology by Controlling Tissue Folding.

    Science.gov (United States)

    Hookway, Tracy A

    2018-04-01

    Achieving complex self-organization in vitro has remained a fundamental challenge in tissue engineering. A recent study in Developmental Cell by Hughes and colleagues uses computational and experimental approaches to understand and control the morphogenic process of tissue folding. These approaches provide an engineering framework to reproducibly control tissue shape. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Accessing Nature's diversity through metabolic engineering and synthetic biology.

    Science.gov (United States)

    King, Jason R; Edgar, Steven; Qiao, Kangjian; Stephanopoulos, Gregory

    2016-01-01

    In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through "scaffold diversification", and subsequent "derivatization" of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the "privileged" chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.

  11. Advancing metabolic engineering through systems biology of industrial microorganisms.

    Science.gov (United States)

    Dai, Zongjie; Nielsen, Jens

    2015-12-01

    Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Synthetic biology and its alternatives. Descartes, Kant and the idea of engineering biological machines.

    Science.gov (United States)

    Kogge, Werner; Richter, Michael

    2013-06-01

    The engineering-based approach of synthetic biology is characterized by an assumption that 'engineering by design' enables the construction of 'living machines'. These 'machines', as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes's and Kant's thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology's engineering paradigm. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Challenges of medical and biological engineering and science

    International Nuclear Information System (INIS)

    Magjarevic, R.

    2004-01-01

    All aspects of biomedical engineering and science, from research and development, education and training, implementation in health care systems, internationalisation and globalisation, and other, new issues are present in the strategy and in action plans of the International Federation for Medical and Biological Engineering (IFMBE) which, with help of a large number of highly motivated volunteers, will stay in leading position in biomedical engineering and science

  14. 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.

  15. XIV Mediterranean Conference on Medical and Biological Engineering and Computing

    CERN Document Server

    Christofides, Stelios; Pattichis, Constantinos

    2016-01-01

    This volume presents the proceedings of Medicon 2016, held in Paphos, Cyprus. Medicon 2016 is the XIV in the series of regional meetings of the International Federation of Medical and Biological Engineering (IFMBE) in the Mediterranean. The goal of Medicon 2016 is to provide updated information on the state of the art on Medical and Biological Engineering and Computing under the main theme “Systems Medicine for the Delivery of Better Healthcare Services”. Medical and Biological Engineering and Computing cover complementary disciplines that hold great promise for the advancement of research and development in complex medical and biological systems. Research and development in these areas are impacting the science and technology by advancing fundamental concepts in translational medicine, by helping us understand human physiology and function at multiple levels, by improving tools and techniques for the detection, prevention and treatment of disease. Medicon 2016 provides a common platform for the cross fer...

  16. 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.

  17. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    NARCIS (Netherlands)

    He, F.; Murabito, E.; Westerhoff, H.V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

  18. Tissue Engineering Organs for Space Biology Research

    Science.gov (United States)

    Vandenburgh, H. H.; Shansky, J.; DelTatto, M.; Lee, P.; Meir, J.

    1999-01-01

    Long-term manned space flight requires a better understanding of skeletal muscle atrophy resulting from microgravity. Atrophy most likely results from changes at both the systemic level (e.g. decreased circulating growth hormone, increased circulating glucocorticoids) and locally (e.g. decreased myofiber resting tension). Differentiated skeletal myofibers in tissue culture have provided a model system over the last decade for gaining a better understanding of the interactions of exogenous growth factors, endogenous growth factors, and muscle fiber tension in regulating protein turnover rates and muscle cell growth. Tissue engineering these cells into three dimensional bioartificial muscle (BAM) constructs has allowed us to extend their use to Space flight studies for the potential future development of countermeasures.

  19. Biological process of soil improvement in civil engineering: A review

    Directory of Open Access Journals (Sweden)

    Murtala Umar

    2016-10-01

    Full Text Available The concept of using biological process in soil improvement which is known as bio-mediated soil improvement technique has shown greater potential in geotechnical engineering applications in terms of performance and environmental sustainability. This paper presents a review on the soil microorganisms responsible for this process, and factors that affect their metabolic activities and geometric compatibility with the soil particle sizes. Two mechanisms of biomineralization, i.e. biologically controlled and biologically induced mineralization, were also discussed. Environmental and other factors that may be encountered in situ during microbially induced calcite precipitation (MICP and their influences on the process were identified and presented. Improvements in the engineering properties of soil such as strength/stiffness and permeability as evaluated in some studies were explored. Potential applications of the process in geotechnical engineering and the challenges of field application of the process were identified.

  20. Microenvironmental Regulation of Tumor Angiogenesis: Biological and Engineering Considerations

    Science.gov (United States)

    Infanger, David W.; Pathi, Siddharth P.; Fischbach, Claudia

    Tumor angiogenesis is fundamental to tumor growth and metastasis, and antiangiogenic therapies have been developed to target this process. However, the clinical success of these treatments has been limited, which may be due, in part, to an incomplete understanding of cell-microenvironment interactions and their role in tumor angiogenesis. Traditionally, two-dimensional (2D) culture approaches have been used to study tumor progression in vitro, but these systems fail to faithfully recreate tumor microenvironmental conditions contributing to tumor angiogenesis in vivo. By integrating cancer biology with tissue engineering and drug delivery approaches, the development of biologically inspired tumor models has emerged. Such 3D model systems allow studying the specific role of soluble factor signaling, cell-extracellular matrix (ECM) interactions, cell-cell interactions, mechanical cues, and metabolic stress. This chapter discusses specific biological and engineering design considerations for tissue-engineered tumor models and highlights their application for defining the underpinnings of tumor angiogenesis.

  1. Abstracts of the 17. world congress of the International Commission of Agriculture and Biosystems Engineering (CIGR) : sustainable biosystems through engineering

    Energy Technology Data Exchange (ETDEWEB)

    Savoie, P.; Villeneuve, J.; Morisette, R. [Agriculture and Agri-Food Canada, Quebec City, PQ (Canada). Soils and Crops Research and Development Centre] (eds.)

    2010-07-01

    This international conference provided a forum to discuss methods to produce agricultural products more efficiently through improvements in engineering and technology. It was attended by engineers and scientists working from different perspectives on biosystems. Beyond food, farms and forests can provide fibre, bio-products and renewable energy. Seven sections of CIGR were organized in the following technical sessions: (1) land and water engineering, (2) farm buildings, equipment, structures and environment, (3) equipment engineering for plants, (4) energy in agriculture, (5) management, ergonomics and systems engineering, (6) post harvest technology and process engineering, and (7) information systems. The Canadian Society of Bioengineering (CSBE) merged its technical program within the 7 sections of CIGR. Four other groups also held their activities during the conference. The American Society of Agricultural and Biological Engineers (ASABE) organized its 9th international drainage symposium and the American Ecological Engineering Society (AEES) held its 10th annual meeting. The International Network for Information Technology in Agriculture (INFITA), and the 8th world congress on computers in agriculture also joined CIGR 2010.

  2. Recent applications of synthetic biology tools for yeast metabolic engineering

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Keasling, Jay

    2015-01-01

    The last 20 years of metabolic engineering has enabled bio-based production of fuels and chemicals from renewable carbon sources using cost-effective bioprocesses. Much of this work has been accomplished using engineered microorganisms that act as chemical factories. Although the time required...... to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together...... with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed...

  3. Genome modularity and synthetic biology: Engineering systems.

    Science.gov (United States)

    Mol, Milsee; Kabra, Ritika; Singh, Shailza

    2018-01-01

    Whole genome sequencing projects running in various laboratories around the world has generated immense data. A systematic phylogenetic analysis of this data shows that genome complexity goes on decreasing as it evolves, due to its modular nature. This modularity can be harnessed to minimize the genome further to reduce it with the bare minimum essential genes. A reduced modular genome, can fuel progress in the area of synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Applying elastic fibre biology in vascular tissue engineering

    OpenAIRE

    Kielty, Cay M; Stephan, Simon; Sherratt, Michael J; Williamson, Matthew; Shuttleworth, C. Adrian

    2007-01-01

    For the treatment of vascular disease, the major cause of death in Western society, there is an urgent need for tissue-engineered, biocompatible, small calibre artery substitutes that restore biological function. Vascular tissue engineering of such grafts involves the development of compliant synthetic or biomaterial scaffolds that incorporate vascular cells and extracellular matrix. Elastic fibres are major structural elements of arterial walls that can enhance vascular graft design and pate...

  5. A discussion of molecular biology methods for protein engineering.

    Science.gov (United States)

    Zawaira, Alexander; Pooran, Anil; Barichievy, Samantha; Chopera, Denis

    2012-05-01

    A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. We discuss the basic principles of these methods in a repertoire that may be used to achieve the elemental steps in protein engineering. These include site-directed, deletion and insertion mutagenesis. We provide detailed case studies, drawn from our own experiences, packaged together with conceptual discussions and include an analysis of the techniques presented with regards to their uses in protein engineering.

  6. Transcription control engineering and applications in synthetic biology

    Directory of Open Access Journals (Sweden)

    Michael D. Engstrom

    2017-09-01

    Full Text Available In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein, a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators (cis-factors were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators (trans-factors, giving examples of how cis- and trans-acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli, we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

  7. Transcription control engineering and applications in synthetic biology.

    Science.gov (United States)

    Engstrom, Michael D; Pfleger, Brian F

    2017-09-01

    In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein), a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity) levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators ( cis -factors) were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators ( trans- factors), giving examples of how cis- and trans -acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli , we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

  8. Biological augmentation and tissue engineering approaches in meniscus surgery.

    Science.gov (United States)

    Moran, Cathal J; Busilacchi, Alberto; Lee, Cassandra A; Athanasiou, Kyriacos A; Verdonk, Peter C

    2015-05-01

    The purpose of this review was to evaluate the role of biological augmentation and tissue engineering strategies in meniscus surgery. Although clinical (human), preclinical (animal), and in vitro tissue engineering studies are included here, we have placed additional focus on addressing preclinical and clinical studies reported during the 5-year period used in this review in a systematic fashion while also providing a summary review of some important in vitro tissue engineering findings in the field over the past decade. A search was performed on PubMed for original works published from 2009 to March 31, 2014 using the term "meniscus" with all the following terms: "scaffolds," "constructs," "cells," "growth factors," "implant," "tissue engineering," and "regenerative medicine." Inclusion criteria were the following: English-language articles and original clinical, preclinical (in vivo), and in vitro studies of tissue engineering and regenerative medicine application in knee meniscus lesions published from 2009 to March 31, 2014. Three clinical studies and 18 preclinical studies were identified along with 68 tissue engineering in vitro studies. These reports show the increasing promise of biological augmentation and tissue engineering strategies in meniscus surgery. The role of stem cell and growth factor therapy appears to be particularly useful. A review of in vitro tissue engineering studies found a large number of scaffold types to be of promise for meniscus replacement. Limitations include a relatively low number of clinical or preclinical in vivo studies, in addition to the fact there is as yet no report in the literature of a tissue-engineered meniscus construct used clinically. Neither does the literature provide clarity on the optimal meniscus scaffold type or biological augmentation with which meniscus repair or replacement would be best addressed in the future. There is increasing focus on the role of mechanobiology and biomechanical and

  9. Biological process of soil improvement in civil engineering: A review

    OpenAIRE

    Murtala Umar; Khairul Anuar Kassim; Kenny Tiong Ping Chiet

    2016-01-01

    The concept of using biological process in soil improvement which is known as bio-mediated soil improvement technique has shown greater potential in geotechnical engineering applications in terms of performance and environmental sustainability. This paper presents a review on the soil microorganisms responsible for this process, and factors that affect their metabolic activities and geometric compatibility with the soil particle sizes. Two mechanisms of biomineralization, i.e. biologically co...

  10. The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

    Science.gov (United States)

    Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

    2012-01-01

    Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

  11. Engineering Titanium for Improved Biological Response

    Energy Technology Data Exchange (ETDEWEB)

    Orme, C; Bearinger, J; Dimasi, E; Gilbert, J

    2002-01-23

    The human body and its aggressive environment challenge the survival of implanted foreign materials. Formidable biocompatibility issues arise from biological, chemical, electrical, and tribological origins. The body's electrolytic solution provides the first point of contact with any kind of implant, and is responsible for transport, healing, integration, or attack. Therefore, determining how to successfully control the integration of a biomaterial should begin with an analysis of the early interfacial dynamics involved. setting, a complicated feedback system of solution chemistry, pH, ions, and solubility exists. The introduction of a fixation device instantly confounds this system. The body is exposed to a range of voltages, and wear can bring about significant shifts in potentials across an implant. In the environment of a new implant the solution pH becomes acidic, ionic concentrations shift, cathodic currents can lead to corrosion, and oxygen levels can be depleted; all of these impact the ability of the implant to retain its protective oxide layer and to present a stable interface for the formation of a biolayer. Titanium has been used in orthopedic and maxilofacial surgery for many years due to its reputation as being biocompatible and its ability to osseointegrate. Osseointegration is defined as direct structural and functional connection between ordered, living bone, and the surface of a load carrying implant. Branemark discovered this phenomenon in the 60's while examining titanium juxtaposed to bone. The mechanism by which titanium and its passivating oxide encourage osseosynthetic activity remains unknown. However in general terms the oxide film serves two purposes: first to provide a kinetic barrier that prevents titanium from corroding and second to provide a substrate that allows the constituents of bone (calcium phosphate crystals, cells, proteins, and collagen) to bond to it. We believe that the electrochemical environment dictates the

  12. Towards Engineering Biological Systems in a Broader Context.

    Science.gov (United States)

    Venturelli, Ophelia S; Egbert, Robert G; Arkin, Adam P

    2016-02-27

    Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Reverse engineering development: Crosstalk opportunities between developmental biology and tissue engineering.

    Science.gov (United States)

    Marcucio, Ralph S; Qin, Ling; Alsberg, Eben; Boerckel, Joel D

    2017-11-01

    The fields of developmental biology and tissue engineering have been revolutionized in recent years by technological advancements, expanded understanding, and biomaterials design, leading to the emerging paradigm of "developmental" or "biomimetic" tissue engineering. While developmental biology and tissue engineering have long overlapping histories, the fields have largely diverged in recent years at the same time that crosstalk opportunities for mutual benefit are more salient than ever. In this perspective article, we will use musculoskeletal development and tissue engineering as a platform on which to discuss these emerging crosstalk opportunities and will present our opinions on the bright future of these overlapping spheres of influence. The multicellular programs that control musculoskeletal development are rapidly becoming clarified, represented by shifting paradigms in our understanding of cellular function, identity, and lineage specification during development. Simultaneously, advancements in bioartificial matrices that replicate the biochemical, microstructural, and mechanical properties of developing tissues present new tools and approaches for recapitulating development in tissue engineering. Here, we introduce concepts and experimental approaches in musculoskeletal developmental biology and biomaterials design and discuss applications in tissue engineering as well as opportunities for tissue engineering approaches to inform our understanding of fundamental biology. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2356-2368, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  14. Cell-free synthetic biology forin vitroprototype 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).

  15. Plant synthetic biology for molecular engineering of signalling and development.

    Science.gov (United States)

    Nemhauser, Jennifer L; Torii, Keiko U

    2016-03-02

    Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.

  16. Genome-scale engineering for systems and synthetic biology

    Science.gov (United States)

    Esvelt, Kevin M; Wang, Harris H

    2013-01-01

    Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering. PMID:23340847

  17. Engineering plant metabolism into microbes: from systems biology to synthetic biology.

    Science.gov (United States)

    Xu, Peng; Bhan, Namita; Koffas, Mattheos A G

    2013-04-01

    Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Recent applications of synthetic biology tools for yeast metabolic engineering.

    Science.gov (United States)

    Jensen, Michael K; Keasling, Jay D

    2015-02-01

    The last 20 years of metabolic engineering has enabled bio-based production of fuels and chemicals from renewable carbon sources using cost-effective bioprocesses. Much of this work has been accomplished using engineered microorganisms that act as chemical factories. Although the time required to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  19. A Synthetic Biology Approach to Engineering Living Photovoltaics.

    Science.gov (United States)

    Schuergers, N; Werlang, C; Ajo-Franklin, C M; Boghossian, A A

    2017-05-01

    The ability to electronically interface living cells with electron accepting scaffolds is crucial for the development of next-generation biophotovoltaic technologies. Although recent studies have focused on engineering synthetic interfaces that can maximize electronic communication between the cell and scaffold, the efficiency of such devices is limited by the low conductivity of the cell membrane. This review provides a materials science perspective on applying a complementary, synthetic biology approach to engineering membrane-electrode interfaces. It focuses on the technical challenges behind the introduction of foreign extracellular electron transfer pathways in bacterial host cells and the past and future efforts to engineer photosynthetic organisms with artificial electron-export capabilities for biophotovoltaic applications. The article highlights advances in engineering protein-based, electron-exporting conduits in a model host organism, E. coli, before reviewing state-of-the-art biophotovoltaic technologies that use both unmodified and bioengineered photosynthetic bacteria with improved electron transport capabilities. A thermodynamic analysis is used to propose an energetically feasible pathway for extracellular electron transport in engineered cyanobacteria and identify metabolic bottlenecks amenable to protein engineering techniques. Based on this analysis, an engineered photosynthetic organism expressing a foreign, protein-based electron conduit yields a maximum theoretical solar conversion efficiency of 6-10% without accounting for additional bioengineering optimizations for light-harvesting.

  20. Advances and Computational Tools towards Predictable Design in Biological Engineering

    Directory of Open Access Journals (Sweden)

    Lorenzo Pasotti

    2014-01-01

    Full Text Available The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated.

  1. Applying elastic fibre biology in vascular tissue engineering.

    Science.gov (United States)

    Kielty, Cay M; Stephan, Simon; Sherratt, Michael J; Williamson, Matthew; Shuttleworth, C Adrian

    2007-08-29

    For the treatment of vascular disease, the major cause of death in Western society, there is an urgent need for tissue-engineered, biocompatible, small calibre artery substitutes that restore biological function. Vascular tissue engineering of such grafts involves the development of compliant synthetic or biomaterial scaffolds that incorporate vascular cells and extracellular matrix. Elastic fibres are major structural elements of arterial walls that can enhance vascular graft design and patency. In blood vessels, they endow vessels with the critical property of elastic recoil. They also influence vascular cell behaviour through direct interactions and by regulating growth factor activation. This review addresses physiological elastic fibre assembly and contributions to vessel structure and function, and how elastic fibre biology is now being exploited in small diameter vascular graft design.

  2. 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).

  3. CellNet: network biology applied to stem cell engineering.

    Science.gov (United States)

    Cahan, Patrick; Li, Hu; Morris, Samantha A; Lummertz da Rocha, Edroaldo; Daley, George Q; Collins, James J

    2014-08-14

    Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Charusanti, Pep; Lee, Sang Yup

    2016-01-01

    Metabolic engineering using systems biology tools is increasingly applied to overproduce secondary metabolites for their potential industrial production. In this Highlight, recent relevant metabolic engineering studies are analyzed with emphasis on host selection and engineering approaches for th...

  5. Engineered ion channels as emerging tools for chemical biology.

    Science.gov (United States)

    Mayer, Michael; Yang, Jerry

    2013-12-17

    Over the last 25 years, researchers have developed exogenously expressed, genetically engineered, semi-synthetic, and entirely synthetic ion channels. These structures have sufficient fidelity to serve as unique tools that can reveal information about living organisms. One of the most exciting success stories is optogenetics: the use of light-gated channels to trigger action potentials in specific neurons combined with studies of the response from networks of cells or entire live animals. Despite this breakthrough, the use of molecularly engineered ion channels for studies of biological systems is still in its infancy. Historically, researchers studied ion channels in the context of their own function in single cells or in multicellular signaling and regulation. Only recently have researchers considered ion channels and pore-forming peptides as responsive tools to report on the chemical and physical changes produced by other biochemical processes and reactions. This emerging class of molecular probes has a number of useful characteristics. For instance, these structures can greatly amplify the signal of chemical changes: the binding of one molecule to a ligand-gated ion channel can result in flux of millions of ions across a cell membrane. In addition, gating occurs on sub-microsecond time scales, resulting in fast response times. Moreover, the signal is complementary to existing techniques because the output is ionic current rather than fluorescence or radioactivity. And finally, ion channels are also localized at the membrane of cells where essential processes such as signaling and regulation take place. This Account highlights examples, mostly from our own work, of uses of ion channels and pore-forming peptides such as gramicidin in chemical biology. We discuss various strategies for preparing synthetically tailored ion channels that range from de novo designed synthetic molecules to genetically engineered or simply exogenously expressed or reconstituted wild

  6. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

    Science.gov (United States)

    He, Fei; Murabito, Ettore; Westerhoff, Hans V

    2016-04-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. © 2016 The Author(s).

  7. From biology to mathematical models and back: teaching modeling to biology students, and biology to math and engineering students.

    Science.gov (United States)

    Chiel, Hillel J; McManus, Jeffrey M; Shaw, Kendrick M

    2010-01-01

    We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a "live" textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology.

  8. Engineered Ribosomes for Basic Science and Synthetic Biology.

    Science.gov (United States)

    d'Aquino, Anne E; Kim, Do Soon; Jewett, Michael C

    2018-03-28

    The ribosome is the cell's factory for protein synthesis. With protein synthesis rates of up to 20 amino acids per second and at an accuracy of 99.99%, the extraordinary catalytic capacity of the bacterial translation machinery has attracted extensive efforts to engineer, reconstruct, and repurpose it for biochemical studies and novel functions. Despite these efforts, the potential for harnessing the translation apparatus to manufacture bio-based products beyond natural limits remains underexploited, and fundamental constraints on the chemistry that the ribosome's RNA-based active site can carry out are unknown. This review aims to cover the past and present advances in ribosome design and engineering to understand the fundamental biology of the ribosome to facilitate the construction of synthetic manufacturing machines. The prospects for the development of engineered, or designer, ribosomes for novel polymer synthesis are reviewed, future challenges are considered, and promising advances in a variety of applications are discusse Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering Volume 9 is June 7, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  9. Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials.

    Science.gov (United States)

    Esensten, Jonathan H; Bluestone, Jeffrey A; Lim, Wendell A

    2017-01-24

    Engineered T cells are currently in clinical trials to treat patients with cancer, solid organ transplants, and autoimmune diseases. However, the field is still in its infancy. The design, and manufacturing, of T cell therapies is not standardized and is performed mostly in academic settings by competing groups. Reliable methods to define dose and pharmacokinetics of T cell therapies need to be developed. As of mid-2016, there are no US Food and Drug Administration (FDA)-approved T cell therapeutics on the market, and FDA regulations are only slowly adapting to the new technologies. Further development of engineered T cell therapies requires advances in immunology, synthetic biology, manufacturing processes, and government regulation. In this review, we outline some of these challenges and discuss the contributions that pathologists can make to this emerging field.

  10. Is nanotechnology the key to unravel and engineer biological processes?

    Science.gov (United States)

    Navarro, Melba; Planell, Josep A

    2012-01-01

    Regenerative medicine is an emerging field aiming to the development of new reparative strategies to treat degenerative diseases, injury, and trauma through developmental pathways in order to rebuild the architecture of the original injured organ and take over its functionality. Most of the processes and interactions involved in the regenerative process take place at subcellular scale. Nanotechnology provides the tools and technology not only to detect, to measure, or to image the interactions between the different biomolecules and biological entities, but also to control and guide the regenerative process. The relevance of nanotechnology for the development of regenerative medicine as well as an overview of the different tools that contribute to unravel and engineer biological systems are presented in this chapter. In addition, general data about the social impact and global investment in nanotechnology are provided.

  11. Engineering the robustness of industrial microbes through synthetic biology.

    Science.gov (United States)

    Zhu, Linjiang; Zhu, Yan; Zhang, Yanping; Li, Yin

    2012-02-01

    Microbial fermentations and bioconversions play a central role in the production of pharmaceuticals, enzymes and chemicals. To meet the demands of industrial production, it is desirable that microbes maintain a maximized carbon flux towards target metabolites regardless of fluctuations in intracellular or extracellular environments. This requires cellular systems that maintain functional stability and dynamic homeostasis in a given physiological state, or manipulate transitions between different physiological states. Stable maintenance or smooth transition can be achieved through engineering of dynamic controllability, modular and hierarchical organization, or functional redundancy, three key features of biological robustness in a cellular system. This review summarizes how synthetic biology can be used to improve the robustness of industrial microbes. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Systems biology for understanding and engineering of heterotrophic oleaginous microorganisms.

    Science.gov (United States)

    Park, Beom Gi; Kim, Minsuk; Kim, Joonwon; Yoo, Heewang; Kim, Byung-Gee

    2017-01-01

    Heterotrophic oleaginous microorganisms continue to draw interest as they can accumulate a large amount of lipids which is a promising feedstock for the production of biofuels and oleochemicals. Nutrient limitation, especially nitrogen limitation, is known to effectively trigger the lipid production in these microorganisms. For the aim of developing improved strains, the mechanisms behind the lipid production have been studied for a long time. Nowadays, system-level understanding of their metabolism and associated metabolic switches is attainable with modern systems biology tools. This work reviews the systems biology studies, based on (i) top-down, large-scale 'omics' tools, and (ii) bottom-up, mathematical modeling methods, on the heterotrophic oleaginous microorganisms with an emphasis on further application to metabolic engineering. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Simple glycolipids of microbes: Chemistry, biological activity and metabolic engineering

    Directory of Open Access Journals (Sweden)

    Ahmad Mohammad Abdel-Mawgoud

    2018-03-01

    Full Text Available Glycosylated lipids (GLs are added-value lipid derivatives of great potential. Besides their interesting surface activities that qualify many of them to act as excellent ecological detergents, they have diverse biological activities with promising biomedical and cosmeceutical applications. Glycolipids, especially those of microbial origin, have interesting antimicrobial, anticancer, antiparasitic as well as immunomodulatory activities. Nonetheless, GLs are hardly accessing the market because of their high cost of production. We believe that experience of metabolic engineering (ME of microbial lipids for biofuel production can now be harnessed towards a successful synthesis of microbial GLs for biomedical and other applications. This review presents chemical groups of bacterial and fungal GLs, their biological activities, their general biosynthetic pathways and an insight on ME strategies for their production.

  14. PREFACE: Nanobiology: from physics and engineering to biology

    Science.gov (United States)

    Nussinov, Ruth; Alemán, Carlos

    2006-03-01

    Biological systems are inherently nano in scale. Unlike nanotechnology, nanobiology is characterized by the interplay between physics, materials science, synthetic organic chemistry, engineering and biology. Nanobiology is a new discipline, with the potential of revolutionizing medicine: it combines the tools, ideas and materials of nanoscience and biology; it addresses biological problems that can be studied and solved by nanotechnology; it devises ways to construct molecular devices using biomacromolecules; and it attempts to build molecular machines utilizing concepts seen in nature. Its ultimate aim is to be able to predictably manipulate these, tailoring them to specified needs. Nanobiology targets biological systems and uses biomacromolecules. Hence, on the one hand, nanobiology is seemingly constrained in its scope as compared to general nanotechnology. Yet the amazing intricacy of biological systems, their complexity, and the richness of the shapes and properties provided by the biological polymers, enrich nanobiology. Targeting biological systems entails comprehension of how they work and the ability to use their components in design. From the physical standpoint, ultimately, if we are to understand biology we need to learn how to apply physical principles to figure out how these systems actually work. The goal of nanobiology is to assist in probing these systems at the appropriate length scale, heralding a new era in the biological, physical and chemical sciences. Biology is increasingly asking quantitative questions. Quantitation is essential if we are to understand how the cell works, and the details of its regulation. The physical sciences provide tools and strategies to obtain accurate measurements and simulate the information to allow comprehension of the processes. Nanobiology is at the interface of the physical and the biological sciences. Biology offers to the physical sciences fascinating problems, sophisticated systems and a rich repertoire of

  15. A model of engineering materials inspired by biological tissues

    Directory of Open Access Journals (Sweden)

    Holeček M.

    2009-12-01

    Full Text Available The perfect ability of living tissues to control and adapt their mechanical properties to varying external conditions may be an inspiration for designing engineering materials. An interesting example is the smooth muscle tissue since this "material" is able to change its global mechanical properties considerably by a subtle mechanism within individual muscle cells. Multi-scale continuum models may be useful in designing essentially simpler engineering materials having similar properties. As an illustration we present the model of an incompressible material whose microscopic structure is formed by flexible, soft but incompressible balls connected mutually by linear springs. This simple model, however, shows a nontrivial nonlinear behavior caused by the incompressibility of balls and is very sensitive on some microscopic parameters. It may elucidate the way by which "small" changes in biopolymer networks within individual muscular cells may control the stiffness of the biological tissue, which outlines a way of designing similar engineering materials. The 'balls and springs' material presents also prestress-induced stiffening and allows elucidating a contribution of extracellular fluids into the tissue’s viscous properties.

  16. PGASO: A synthetic biology tool for engineering a cellulolytic yeast

    Directory of Open Access Journals (Sweden)

    Chang Jui-Jen

    2012-07-01

    Full Text Available Abstract Background To achieve an economical cellulosic ethanol production, a host that can do both cellulosic saccharification and ethanol fermentation is desirable. However, to engineer a non-cellulolytic yeast to be such a host requires synthetic biology techniques to transform multiple enzyme genes into its genome. Results A technique, named Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO, that employs overlapping oligonucleotides for recombinatorial assembly of gene cassettes with individual promoters, was developed. PGASO was applied to engineer Kluyveromycesmarxianus KY3, which is a thermo- and toxin-tolerant yeast. We obtained a recombinant strain, called KR5, that is capable of simultaneously expressing exoglucanase and endoglucanase (both of Trichodermareesei, a beta-glucosidase (from a cow rumen fungus, a neomycin phosphotransferase, and a green fluorescent protein. High transformation efficiency and accuracy were achieved as ~63% of the transformants was confirmed to be correct. KR5 can utilize beta-glycan, cellobiose or CMC as the sole carbon source for growth and can directly convert cellobiose and beta-glycan to ethanol. Conclusions This study provides the first example of multi-gene assembly in a single step in a yeast species other than Saccharomyces cerevisiae. We successfully engineered a yeast host with a five-gene cassette assembly and the new host is capable of co-expressing three types of cellulase genes. Our study shows that PGASO is an efficient tool for simultaneous expression of multiple enzymes in the kefir yeast KY3 and that KY3 can serve as a host for developing synthetic biology tools.

  17. Biologically active and biomimetic dual gelatin scaffolds for tissue engineering.

    Science.gov (United States)

    Sánchez, P; Pedraz, J L; Orive, G

    2017-05-01

    We have designed, developed and optimized Genipin cross-linked 3D gelatin scaffolds that were biologically active and biomimetic, show a dual activity both for growth factor and cell delivery. Type B gelatin powder was dissolved in DI water. 100mg of genipin was dissolved in 10ml of DI water. Three genipin concentrations were prepared: 0.1%, 0.2% and 0.3% (w/v). Solutions were mixed at 40°C and under stirring and then left crosslinking for 72h. Scaffolds were obtained by punching 8 mm-cylinders into ethanol 70% solution for 10min and then freeze-drying. Scaffolds were biologically, biomechanically and morphologically evaluated. Cell adhesion and morphology of D1-Mesenchymal stem cells (MSCs) and L-929 fibroblast was studied. Vascular endothelial grwoth factor (VEGF) and Sonic hedgehog (SHH) were used as model proteins. Swelling ratio increased and younǵs module decreased along with the concentration of genipin. All scaffolds were biocompatible according to the toxicity test. MSC and L-929 cell adhesion improved in 0.2% of genipin, obtaining better results with MSCs. VEGF and SHH were released from the gels. This preliminary study suggest that the biologically active and dual gelatin scaffolds may be used for tissue engineering approaches like bone regeneration. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Experiential Engineering through iGEM--An Undergraduate Summer Competition in Synthetic Biology

    Science.gov (United States)

    Mitchell, Rudolph; Dori, Yehudit Judy; Kuldell, Natalie H.

    2011-01-01

    Unlike students in other engineering disciplines, undergraduates in biological engineering typically have limited opportunity to develop design competencies, and even fewer chances to implement their designed projects. The international Genetically Engineered Machines (iGEM) competition is a student Synthetic Biology competition that, in 2009,…

  19. 1st Global Conference on Biomedical Engineering & 9th Asian-Pacific Conference on Medical and Biological Engineering

    CERN Document Server

    Wang, Shyh-Hau; Yeh, Ming-Long

    2015-01-01

    This volume presents the proceedings of the 9th Asian-Pacific Conference on Medical and Biological Engineering (APCMBE 2014). The proceedings address a broad spectrum of topics from Bioengineering and Biomedicine, like Biomaterials, Artificial Organs, Tissue Engineering, Nanobiotechnology and Nanomedicine, Biomedical Imaging, Bio MEMS, Biosignal Processing, Digital Medicine, BME Education. It helps medical and biological engineering professionals to interact and exchange their ideas and experiences.

  20. Tissue Engineering a Biological Repair Strategy for Lumbar Disc Herniation

    Science.gov (United States)

    O'Connell, Grace D.; Leach, J. Kent; Klineberg, Eric O.

    2015-01-01

    Abstract The intervertebral disc is a critical part of the intersegmental soft tissue of the spinal column, providing flexibility and mobility, while absorbing large complex loads. Spinal disease, including disc herniation and degeneration, may be a significant contributor to low back pain. Clinically, disc herniations are treated with both nonoperative and operative methods. Operative treatment for disc herniation includes removal of the herniated material when neural compression occurs. While this strategy may have short-term advantages over nonoperative methods, the remaining disc material is not addressed and surgery for mild degeneration may have limited long-term advantage over nonoperative methods. Furthermore, disc herniation and surgery significantly alter the mechanical function of the disc joint, which may contribute to progression of degeneration in surrounding tissues. We reviewed recent advances in tissue engineering and regenerative medicine strategies that may have a significant impact on disc herniation repair. Our review on tissue engineering strategies focuses on cell-based and inductive methods, each commonly combined with material-based approaches. An ideal clinically relevant biological repair strategy will significantly reduce pain and repair and restore flexibility and motion of the spine. PMID:26634189

  1. Engineering the mechanical and biological properties of nanofibrous vascular grafts for in situ vascular tissue engineering.

    Science.gov (United States)

    Henry, Jeffrey J D; Yu, Jian; Wang, Aijun; Lee, Randall; Fang, Jun; Li, Song

    2017-08-17

    Synthetic small diameter vascular grafts have a high failure rate, and endothelialization is critical for preventing thrombosis and graft occlusion. A promising approach is in situ tissue engineering, whereby an acellular scaffold is implanted and provides stimulatory cues to guide the in situ remodeling into a functional blood vessel. An ideal scaffold should have sufficient binding sites for biomolecule immobilization and a mechanical property similar to native tissue. Here we developed a novel method to blend low molecular weight (LMW) elastic polymer during electrospinning process to increase conjugation sites and to improve the mechanical property of vascular grafts. LMW elastic polymer improved the elasticity of the scaffolds, and significantly increased the amount of heparin conjugated to the micro/nanofibrous scaffolds, which in turn increased the loading capacity of vascular endothelial growth factor (VEGF) and prolonged the release of VEGF. Vascular grafts were implanted into the carotid artery of rats to evaluate the in vivo performance. VEGF treatment significantly enhanced endothelium formation and the overall patency of vascular grafts. Heparin coating also increased cell infiltration into the electrospun grafts, thus increasing the production of collagen and elastin within the graft wall. This work demonstrates that LMW elastic polymer blending is an approach to engineer the mechanical and biological property of micro/nanofibrous vascular grafts for in situ vascular tissue engineering.

  2. Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions.

    Science.gov (United States)

    Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

    By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Integration of systems biology with bioprocess engineering: L: -threonine production by systems metabolic engineering of Escherichia coli.

    Science.gov (United States)

    Lee, Sang Yup; Park, Jin Hwan

    2010-01-01

    Random mutation and selection or targeted metabolic engineering without consideration of its impact on the entire metabolic and regulatory networks can unintentionally cause genetic alterations in the region, which is not directly related to the target metabolite. This is one of the reasons why strategies for developing industrial strains are now shifted towards targeted metabolic engineering based on systems biology, which is termed systems metabolic engineering. Using systems metabolic engineering strategies, all the metabolic engineering works are conducted in systems biology framework, whereby entire metabolic and regulatory networks are thoroughly considered in an integrated manner. The targets for purposeful engineering are selected after all possible effects on the entire metabolic and regulatory networks are thoroughly considered. Finally, the strain, which is capable of producing the target metabolite to a high level close to the theoretical maximum value, can be constructed. Here we review strategies and applications of systems biology successfully implemented on bioprocess engineering, with particular focus on developing L: -threonine production strains of Escherichia coli.

  4. Designing a 'neotissue' using the principles of biology, chemistry and engineering.

    Science.gov (United States)

    Nannaparaju, Madhusudhan; Oragui, Emeka; Khan, Wasim S

    2012-01-01

    The traditional methods of treating musculoskeletal injuries and disorders are not completely effective and have several limitations. Tissue engineering involves using the principles of biology, chemistry and engineering to design a 'neotissue' that augments a malfunctioning in vivo tissue. The main requirements for functional engineered tissue include reparative cellular components that proliferate on a scaffold grown within a bioreactor that provides specific biochemical and physical signals to regulate cell differentiation and tissue assembly. In this review we provide an overview of the biology of common musculoskeletal tissue and discuss their common pathologies. We also describe the commonly used stem cells, scaffolds and bioreactors and evaluate their role in issue engineering.

  5. 6th European Conference of the International Federation for Medical and Biological Engineering

    CERN Document Server

    Vasic, Darko

    2015-01-01

    This volume presents the Proceedings of the 6th European Conference of the International Federation for Medical and Biological Engineering (MBEC2014), held in Dubrovnik September 7 – 11, 2014. The general theme of MBEC 2014 is "Towards new horizons in biomedical engineering" The scientific discussions in these conference proceedings include the following themes: - Biomedical Signal Processing - Biomedical Imaging and Image Processing - Biosensors and Bioinstrumentation - Bio-Micro/Nano Technologies - Biomaterials - Biomechanics, Robotics and Minimally Invasive Surgery - Cardiovascular, Respiratory and Endocrine Systems Engineering - Neural and Rehabilitation Engineering - Molecular, Cellular and Tissue Engineering - Bioinformatics and Computational Biology - Clinical Engineering and Health Technology Assessment - Health Informatics, E-Health and Telemedicine - Biomedical Engineering Education

  6. A review on biological adaptation: with applications in engineering science

    Directory of Open Access Journals (Sweden)

    LiMin Luo

    2014-06-01

    Full Text Available Biological adaptation refers to that organisms change themselves at morphological, physiological, behavioral and molecular level to better survive in a changing environment. It includes phenotype adaptation and molecular adaptation. Biological adaptation is a driving force of evolution. Biological adaptation was described from Darwinian theory of evolution to the theory of molecular evolution in present paper. Adaptive control and adaptive filtering were briefly described also.

  7. Reformulating General Engineering and Biological Systems Engineering Programs at Virginia Tech

    Science.gov (United States)

    Lohani, Vinod K.; Wolfe, Mary Leigh; Wildman, Terry; Mallikarjunan, Kumar; Connor, Jeffrey

    2011-01-01

    In 2004, a group of engineering and education faculty at Virginia Tech received a major curriculum reform and engineering education research grant under the department-level reform (DLR) program of the NSF. This DLR project laid the foundation of sponsored research in engineering education in the Department of Engineering Education. The DLR…

  8. Accessing Nature’s diversity through metabolic engineering and synthetic biology [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Jason R. King

    2016-03-01

    Full Text Available In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.

  9. Accessing Nature’s diversity through metabolic engineering and synthetic biology

    Science.gov (United States)

    King, Jason R.; Edgar, Steven; Qiao, Kangjian; Stephanopoulos, Gregory

    2016-01-01

    In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents. PMID:27081481

  10. Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

    Science.gov (United States)

    Oerther, Daniel B.

    2002-01-01

    Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

  11. Engineering Design of an Adaptive Leg Prosthesis Using Biological Principles

    DEFF Research Database (Denmark)

    Lenau, Torben Anker; Dentel, Andy; Invarsdottir, Thorunn

    2010-01-01

    The biomimetic design process is explored through a design case: An adaptive leg prosthesis. The aim is to investigate if the biomimetic design process can be carried out with a minimum of biological knowledge and without using advanced design methods. In the design case biomimetic design was suc...... was successfully carried out using library search resulting in 14 biological analogies for the design problem 'shape adaption'. It is proposed that search results are handled using special cards describing the biological phenomena and the functional principles....

  12. Advancing the science of forest hydrology A challenge to agricultural and biological engineers

    Science.gov (United States)

    Devendra Amatya; Wayne Skaggs; Carl Trettin

    2009-01-01

    For more than a century, agricultural and biological engineers have provided major advances in science, engineering, and technology to increase food and fiber production to meet the demands of a rapidly growing global population. The land base for these technological advances has originated largely from forested lands, which have experienced dramatic declines over the...

  13. Biological production of monoethanolamine by engineered Pseudomonas putida S12

    NARCIS (Netherlands)

    Foti, M.J.; Médici, R.; Ruijssenaars, H.J.

    2013-01-01

    Pseudomonas putida S12 was engineered for the production of monoethanolamine (MEA) from glucose via the decarboxylation of the central metabolite l-serine, which is catalyzed by the enzyme l-serine decarboxylase (SDC).The host was first evaluated for its tolerance towards MEA as well as its

  14. Review of Microfluidic Photobioreactor Technology for Metabolic Engineering and Synthetic Biology of Cyanobacteria and Microalgae

    Directory of Open Access Journals (Sweden)

    Ya-Tang Yang

    2016-10-01

    Full Text Available One goal of metabolic engineering and synthetic biology for cyanobacteria and microalgae is to engineer strains that can optimally produce biofuels and commodity chemicals. However, the current workflow is slow and labor intensive with respect to assembly of genetic parts and characterization of production yields because of the slow growth rates of these organisms. Here, we review recent progress in the microfluidic photobioreactors and identify opportunities and unmet needs in metabolic engineering and synthetic biology. Because of the unprecedented experimental resolution down to the single cell level, long-term real-time monitoring capability, and high throughput with low cost, microfluidic photobioreactor technology will be an indispensible tool to speed up the development process, advance fundamental knowledge, and realize the full potential of metabolic engineering and synthetic biology for cyanobacteria and microalgae.

  15. Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

    Science.gov (United States)

    Villaverde, Alejandro F; Banga, Julio R

    2014-02-06

    The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?

  16. Micropropagation, genetic engineering, and molecular biology of Populus

    Science.gov (United States)

    N. B. Klopfenstein; Y. W. Chun; M. -S. Kim; M. A. Ahuja; M. C. Dillon; R. C. Carman; L. G. Eskew

    1997-01-01

    Thirty-four Populus biotechnology chapters, written by 85 authors, are comprised in 5 sections: 1) in vitro culture (micropropagation, somatic embryogenesis, protoplasts, somaclonal variation, and germplasm preservation); 2) transformation and foreign gene expression; 3) molecular biology (molecular/genetic characterization); 4) biotic and abiotic resistance (disease,...

  17. Harnessing systems biology approaches to engineer functional microvascular networks.

    Science.gov (United States)

    Sefcik, Lauren S; Wilson, Jennifer L; Papin, Jason A; Botchwey, Edward A

    2010-06-01

    Microvascular remodeling is a complex process that includes many cell types and molecular signals. Despite a continued growth in the understanding of signaling pathways involved in the formation and maturation of new blood vessels, approximately half of all compounds entering clinical trials will fail, resulting in the loss of much time, money, and resources. Most pro-angiogenic clinical trials to date have focused on increasing neovascularization via the delivery of a single growth factor or gene. Alternatively, a focus on the concerted regulation of whole networks of genes may lead to greater insight into the underlying physiology since the coordinated response is greater than the sum of its parts. Systems biology offers a comprehensive network view of the processes of angiogenesis and arteriogenesis that might enable the prediction of drug targets and whether or not activation of the targets elicits the desired outcome. Systems biology integrates complex biological data from a variety of experimental sources (-omics) and analyzes how the interactions of the system components can give rise to the function and behavior of that system. This review focuses on how systems biology approaches have been applied to microvascular growth and remodeling, and how network analysis tools can be utilized to aid novel pro-angiogenic drug discovery.

  18. Cell-Free Synthetic Biology: Engineering Beyond the Cell.

    Science.gov (United States)

    Perez, Jessica G; Stark, Jessica C; Jewett, Michael C

    2016-12-01

    Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

  19. A discussion of molecular biology methods for protein engineering

    CSIR Research Space (South Africa)

    Zawaira, A

    2011-09-01

    Full Text Available A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. The authors discuss the basic principles of these methods in a repertoire that may be used to achieve...

  20. Importance of systems biology in engineering microbes for biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Mukhopadhyay, Aindrila; Redding, Alyssa M.; Rutherford, Becky J.; Keasling, Jay D.

    2009-12-02

    Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.

  1. Research and engineering assessment of biological solubilization of phosphate

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, R.D.; McIlwain, M.E.; Losinski, S.J.; Taylor, D.D.

    1993-03-01

    This research and engineering assessment examined a microbial phosphate solubilization process as a method of recovering phosphate from phosphorus containing ore compared to the existing wet acid and electric arc methods. A total of 860 microbial isolates, collected from a range of natural environments were tested for their ability to solubilize phosphate from rock phosphate. A bacterium (Pseudomonas cepacia) was selected for extensive characterization and evaluation of the mechanism of phosphate solubilization and of process engineering parameters necessary to recover phosphate from rock phosphate. These studies found that concentration of hydrogen ion and production of organic acids arising from oxidation of the carbon source facilitated microbial solubilization of both pure chemical insoluble phosphate compounds and phosphate rock. Genetic studies found that phosphate solubilization was linked to an enzyme system (glucose dehydrogenase). Process-related studies found that a critical solids density of 1% by weight (ore to liquid) was necessary for optimal solubilization. An engineering analysis evaluated the cost and energy requirements for a 2 million ton per year sized plant, whose size was selected to be comparable to existing wet acid plants.

  2. Genetically engineered biological agents in therapy for systemic lupus erythematosus

    Directory of Open Access Journals (Sweden)

    Elena Aleksandrovna Aseeva

    2013-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototype for chronic autoimmune disease. Its prevalence is 20 to 70 cases per 100,000 women and varies by race and ethnicity. Despite considerable progress in traditional therapy, many problems associated with the management of these patients need to be immediately solved: thus, 50-80% are found to have activity signs and/or frequent exacerbations and about 30% of the patients have to stop work; Class IV lupus nephritis increases the risk of terminalrenal failure. In the past 20 years great progress has been made in studying the pathogenesis of SLE: biological targets to affect drugs have been sought and fundamentally new therapeutic goals defined. Belimumab is the first genetically biological agent specially designed to treat SLE, which is rightly regarded as one of the most important achievements of rheumatology in the past 50 years.

  3. Synthetic biology for engineering acetyl coenzyme a metabolism in yeast

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2014-01-01

    The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels, chemicals, and pharmaceuticals. The use of this cell factory for cost-efficient production of novel fuels and chemicals requires high yields and low by-product production. Many industrially interesting...... chemicals are biosynthesized from acetyl coenzyme A (acetyl-CoA), which serves as a central precursor metabolite in yeast. To ensure high yields in production of these chemicals, it is necessary to engineer the central carbon metabolism so that ethanol production is minimized (or eliminated) and acetyl......-CoA can be formed from glucose in high yield. Here the perspective of generating yeast platform strains that have such properties is discussed in the context of a major breakthrough with expression of a functional pyruvate dehydrogenase complex in the cytosol....

  4. Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops.

    Science.gov (United States)

    Shih, Patrick M; Liang, Yan; Loqué, Dominique

    2016-07-01

    The Green Revolution has fuelled an exponential growth in human population since the mid-20th century. Due to population growth, food and energy demands will soon surpass supply capabilities. To overcome these impending problems, significant improvements in genetic engineering will be needed to complement breeding efforts in order to accelerate the improvement of agronomical traits. The new field of plant synthetic biology has emerged in recent years and is expected to support rapid, precise, and robust engineering of plants. In this review, we present recent advances made in the field of plant synthetic biology, specifically in genome editing, transgene expression regulation, and bioenergy crop engineering, with a focus on traits related to lignocellulose, oil, and soluble sugars. Ultimately, progress and innovation in these fields may facilitate the development of beneficial traits in crop plants to meet society's bioenergy needs. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  5. Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Laura R. Jarboe

    2010-01-01

    Full Text Available Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.

  6. Biomaterials — where biology, physics, chemistry, engineering and medicine meet

    Science.gov (United States)

    Hing, K. A.

    2008-03-01

    The success or failure of an implant material in the body depends on a complex interaction between a synthetic 'foreign body' and the 'host tissue'. These interactions occur at many levels from the sub-microscopic level, where subtle changes in the surface physio-chemistry can substantially alter the nature of the biomaterial-host tissue interface, through the microscopical level (e.g. sensitivity to surface topography) to the macrostructural level (e.g. dependence on scaffold porosity). Thus the factors that control these responses are not only biologically determined but also mechanically, physically and chemically mediated, although identifying where one starts and the other finishes can be difficult. Design of a successful medical device has therefore to call on expertise within a wide range of disciplines. In terms of both investigating the basic science behind the factors which orchestrate a biological response and developing research tools that enable study of these responses. However, a medical device must also meet the economic and practical demands of health care professionals who will ultimately be using it in the clinic. Bone graft substitute materials are used in orthopaedics as an alternative or adjunct to autografting, a practice where the patient 'donates' bone from a healthy site to aid bone repair at a damaged or diseased site. These materials are used in a wide range of procedures from total hip revision to spinal fusion and their evolution over the last 10 years illustrates how an interdisciplinary approach has benefited their development and may lead to further innovation in the future.

  7. Reproducibility of fluorescent expression from engineered biological constructs in E. coli

    OpenAIRE

    Beal, Jacob; Haddock-Angelli, Traci; Gershater, Markus; De Mora, Kim; Lizarazo, Meagan; Hollenhorst, Jim; Rettberg, Randy; Demling, Philipp; Hanke, Rene; Osthege, Michael; Schechtel, Anna; Sudarsan, Suresh; Zimmermann, Arne; Gabryelczyk, Bartosz; Ikonen, Martina

    2016-01-01

    We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1....

  8. 5th European Conference of the International Federation for Medical and Biological Engineering

    CERN Document Server

    European IFMBE MBEC : Cooperation for Effective Healthcare

    2012-01-01

    This volume presents the 5th European Conference of the International Federation for Medical and Biological Engineering (EMBEC),  held in Budapest, 14-18 September, 2011. The scientific discussion on the conference and in this conference proceedings include the following issues: - Signal & Image Processing - ICT - Clinical Engineering and Applications - Biomechanics and Fluid Biomechanics - Biomaterials and Tissue Repair - Innovations and Nanotechnology - Modeling and Simulation - Education and Professional

  9. Biologically improved nanofibrous scaffolds for cardiac tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Bhaarathy, V. [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore); Department of Nanoscience and Technology, School of Physical Sciences, Bharathiar University, Coimbatore 641046 (India); Lee Kong Chian School of Medicine, Nanyang Technological University, 138673 (Singapore); Venugopal, J., E-mail: nnijrv@nus.edu.sg [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore); Gandhimathi, C. [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore); Ponpandian, N.; Mangalaraj, D. [Department of Nanoscience and Technology, School of Physical Sciences, Bharathiar University, Coimbatore 641046 (India); Ramakrishna, S. [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore)

    2014-11-01

    Nanofibrous structure developed by electrospinning technology provides attractive extracellular matrix conditions for the anchorage, migration and differentiation of stem cells, including those responsible for regenerative medicine. Recently, biocomposite nanofibers consisting of two or more polymeric blends are electrospun more tidily in order to obtain scaffolds with desired functional and mechanical properties depending on their applications. The study focuses on one such an attempt of using copolymer Poly(L-lactic acid)-co-poly (ε-caprolactone) (PLACL), silk fibroin (SF) and Aloe Vera (AV) for fabricating biocomposite nanofibrous scaffolds for cardiac tissue engineering. SEM micrographs of fabricated electrospun PLACL, PLACL/SF and PLACL/SF/AV nanofibrous scaffolds are porous, beadless, uniform nanofibers with interconnected pores and obtained fibre diameter in the range of 459 ± 22 nm, 202 ± 12 nm and 188 ± 16 nm respectively. PLACL, PLACL/SF and PLACL/SF/AV electrospun mats obtained at room temperature with an elastic modulus of 14.1 ± 0.7, 9.96 ± 2.5 and 7.0 ± 0.9 MPa respectively. PLACL/SF/AV nanofibers have more desirable properties to act as flexible cell supporting scaffolds compared to PLACL for the repair of myocardial infarction (MI). The PLACL/SF and PLACL/SF/AV nanofibers had a contact angle of 51 ± 12° compared to that of 133 ± 15° of PLACL alone. Cardiac cell proliferation was increased by 21% in PLACL/SF/AV nanofibers compared to PLACL by day 6 and further increased to 42% by day 9. Confocal analysis for cardiac expression proteins myosin and connexin 43 was observed better by day 9 compared to all other nanofibrous scaffolds. The results proved that the fabricated PLACL/SF/AV nanofibrous scaffolds have good potentiality for the regeneration of infarcted myocardium in cardiac tissue engineering. - Highlights: • Fabricated nanofibrous scaffolds are porous, beadless and uniform structures. • PLACL/SF/AV nanofibers improve the

  10. Biologically improved nanofibrous scaffolds for cardiac tissue engineering

    International Nuclear Information System (INIS)

    Bhaarathy, V.; Venugopal, J.; Gandhimathi, C.; Ponpandian, N.; Mangalaraj, D.; Ramakrishna, S.

    2014-01-01

    Nanofibrous structure developed by electrospinning technology provides attractive extracellular matrix conditions for the anchorage, migration and differentiation of stem cells, including those responsible for regenerative medicine. Recently, biocomposite nanofibers consisting of two or more polymeric blends are electrospun more tidily in order to obtain scaffolds with desired functional and mechanical properties depending on their applications. The study focuses on one such an attempt of using copolymer Poly(L-lactic acid)-co-poly (ε-caprolactone) (PLACL), silk fibroin (SF) and Aloe Vera (AV) for fabricating biocomposite nanofibrous scaffolds for cardiac tissue engineering. SEM micrographs of fabricated electrospun PLACL, PLACL/SF and PLACL/SF/AV nanofibrous scaffolds are porous, beadless, uniform nanofibers with interconnected pores and obtained fibre diameter in the range of 459 ± 22 nm, 202 ± 12 nm and 188 ± 16 nm respectively. PLACL, PLACL/SF and PLACL/SF/AV electrospun mats obtained at room temperature with an elastic modulus of 14.1 ± 0.7, 9.96 ± 2.5 and 7.0 ± 0.9 MPa respectively. PLACL/SF/AV nanofibers have more desirable properties to act as flexible cell supporting scaffolds compared to PLACL for the repair of myocardial infarction (MI). The PLACL/SF and PLACL/SF/AV nanofibers had a contact angle of 51 ± 12° compared to that of 133 ± 15° of PLACL alone. Cardiac cell proliferation was increased by 21% in PLACL/SF/AV nanofibers compared to PLACL by day 6 and further increased to 42% by day 9. Confocal analysis for cardiac expression proteins myosin and connexin 43 was observed better by day 9 compared to all other nanofibrous scaffolds. The results proved that the fabricated PLACL/SF/AV nanofibrous scaffolds have good potentiality for the regeneration of infarcted myocardium in cardiac tissue engineering. - Highlights: • Fabricated nanofibrous scaffolds are porous, beadless and uniform structures. • PLACL/SF/AV nanofibers improve the

  11. The future of metabolic engineering and synthetic biology: towards a systematic practice.

    Science.gov (United States)

    Yadav, Vikramaditya G; De Mey, Marjan; Lim, Chin Giaw; Ajikumar, Parayil Kumaran; Stephanopoulos, Gregory

    2012-05-01

    Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as 'multivariate modular metabolic engineering' (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Can an engineer fix an immune system?--Rethinking theoretical biology.

    Science.gov (United States)

    Mattiussi, Claudio

    2013-06-01

    In an instant classic paper (Lazebnik, in Cancer Cell 2(3); 2002: 179-182) biologist Yuri Lazebnik deplores the poor effectiveness of the approach adopted by biologists to understand and "fix" biological systems. Lazebnik suggests that to remedy this state of things biologist should take inspiration from the approach used by engineers to design, understand, and troubleshoot technological systems. In the present paper I substantiate Lazebnik's analysis by concretely showing how to apply the engineering approach to biological problems. I use an actual example of electronic circuit troubleshooting to ground the thesis that, in engineering, the crucial phases of any non-trivial troubleshooting process are aimed at generating a mechanistic explanation of the functioning of the system, which makes extensive recourse to problem-driven qualitative reasoning possibly based on cognitive artifacts applied to systems that are known to have been designed for function. To show how to translate these findings into biological practice I consider a concrete example of biological model building and "troubleshooting", aimed at the identification of a "fix" for the human immune system in presence of progressing cancer, autoimmune disease, and transplant rejection. The result is a novel immune system model--the danger model with regulatory cells--and new, original hypotheses concerning the development, prophylaxis, and therapy of these unwanted biological processes. Based on the manifest efficacy of the proposed approach, I suggest a refocusing of the activity of theoretical biologists along the engineering-inspired lines illustrated in the paper.

  13. Biological aspects of application of nanomaterials in tissue engineering

    Directory of Open Access Journals (Sweden)

    Markovic Dejan

    2016-01-01

    Full Text Available Millions of patients worldwide need surgery to repair or replace tissue that has been damaged through trauma or disease. To solve the problem of lost tissue, a major emphasis of tissue engineering (TE is on tissue regeneration. Stem cells and highly porous biomaterials used as cell carriers (scaffolds have an essential role in the production of new tissue by TE. Cellular component is important for the generation and establishment of the extracellular matrix, while a scaffold is necessary to determine the shape of the newly formed tissue and facilitate migration of cells into the desired location, as well as their growth and differentiation. This review describes the types, characteristics and classification of stem cells. Furthermore, it includes functional features of cell carriers - biocompatibility, biodegradability and mechanical properties of biomaterials used in developing state-of-the-art scaffolds for TE applications, as well as suitability for different tissues. Moreover, it explains the importance of nanotechnology and defines the challenges and the purpose of future research in this rapidly advancing field. [Projekat Ministarstva nauke Republike Srbije, br. 41030 i br. 172026

  14. On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

    Science.gov (United States)

    Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

    2017-12-05

    The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

  15. Can Man Control His Biological Evolution? A Symposium on Genetic Engineering. Genetic Engineering

    Science.gov (United States)

    Ramsey, Paul

    1972-01-01

    Presented are issues related to genetic engineering. Increased knowledge of techniques to manipulate genes are apt to create confusion about moral values in relation to unborn babies and other living organisms on earth. Human beings may use this knowledge to disturb the balance maintained by nature. (PS)

  16. Recent advances in synthetic biology for engineering isoprenoid production in yeast.

    Science.gov (United States)

    Vickers, Claudia E; Williams, Thomas C; Peng, Bingyin; Cherry, Joel

    2017-10-01

    Isoprenoids (terpenes/terpenoids) have many useful industrial applications, but are often not produced at industrially viable level in their natural sources. Synthetic biology approaches have been used extensively to reconstruct metabolic pathways in tractable microbial hosts such as yeast and re-engineer pathways and networks to increase yields. Here we review recent advances in this field, focusing on central carbon metabolism engineering to increase precursor supply, re-directing carbon flux for production of C10, C15, or C20 isoprenoids, and chemical decoration of high value diterpenoids (C20). We also overview other novel synthetic biology strategies that have potential utility in yeast isoprenoid pathway engineering. Finally, we address the question of what is required in the future to move the field forwards. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. The emerging role of systems biology for engineering protein production in CHO cells.

    Science.gov (United States)

    Kuo, Chih-Chung; Chiang, Austin Wt; Shamie, Isaac; Samoudi, Mojtaba; Gutierrez, Jahir M; Lewis, Nathan E

    2017-12-06

    To meet the ever-growing demand for effective, safe, and affordable protein therapeutics, decades of intense efforts have aimed to maximize the quantity and quality of recombinant proteins produced in CHO cells. Bioprocessing innovations and cell engineering efforts have improved product titer; however, uncharacterized cellular processes and gene regulatory mechanisms still hinder cell growth, specific productivity, and protein quality. Herein, we summarize recent advances in systems biology and data-driven approaches aiming to unravel how molecular pathways, cellular processes, and extrinsic factors (e.g. media supplementation) influence recombinant protein production. In particular, as the available omics data for CHO cells continue to grow, predictive models and screens will be increasingly used to unravel the biological drivers of protein production, which can be used with emerging genome editing technologies to rationally engineer cells to further control the quantity, quality and affordability of many biologic drugs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. A comparison of the role of beamwidth in biological and engineered sonar.

    Science.gov (United States)

    Todd, Bryan Donald; Mueller, Rolf

    2017-11-13

    Sonar is an important sensory modality for engineers as well as in nature. In engineering, sonar is the dominating modality for underwater sensing. In nature, biosonar is likely to have been a central factor behind the unprecedented evolutionary success of bats, a highly diverse group that accounts for over 20% of all mammal species. However, it remains unclear to what extent engineered and biosonar follow similar design and operational principles. In the current work, the key sonar design characteristic of beamwidth is examined in technical and biosonar. To this end, beamwidth data has been obtained for 23 engineered sonar systems and from numerical beampattern predictions for 151 emission and reception elements (noseleaves and ears) representing bat biosonar. Beamwidth data from these sources is compared to the beamwidth of a planar ellipsoidal transducer as a reference. The results show that engineered and biological both obey the basic physical limit on beamwidth as a function of the ratio of aperture size and wavelength. However, beyond that, the beamwidth data revealed very different behaviors between the engineered and the biological sonar systems. Whereas the beamwidths of the technical sonar systems were very close to the planar transducer limit, the biological samples showed a very wide scatter away from this limit. This scatter was as large, if not wider, than what was seen in a small reference data set obtained with random aluminum cones. A possible interpretation of these differences in the variability could be that whereas sonar engineers try to minimize beamwidth subject to constraints on device size, the evolutionary optimization of bat biosonar beampatterns has been directed at other factors that have left beamwidth as a byproduct. Alternatively, the biosonar systems may require beamwidth values that are larger than the physical limit and differ between species and their sensory ecological niches. © 2017 IOP Publishing Ltd.

  19. Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes.

    Science.gov (United States)

    Kang, Zhen; Zhang, Junli; Jin, Peng; Yang, Sen

    2015-01-01

    Owing to our limited understanding of the relationship between sequence and function and the interaction between intracellular pathways and regulatory systems, the rational design of enzyme-coding genes and de novo assembly of a brand-new artificial genome for a desired functionality or phenotype are difficult to achieve. As an alternative approach, directed evolution has been widely used to engineer genomes and enzyme-coding genes. In particular, significant developments toward DNA synthesis, DNA assembly (in vitro or in vivo), recombination-mediated genetic engineering, and high-throughput screening techniques in the field of synthetic biology have been matured and widely adopted, enabling rapid semi-rational genome engineering to generate variants with desired properties. In this commentary, these novel tools and their corresponding applications in the directed evolution of genomes and enzymes are discussed. Moreover, the strategies for genome engineering and rapid in vitro enzyme evolution are also proposed.

  20. Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

    Energy Technology Data Exchange (ETDEWEB)

    Kuk Lee, Sung; Chou, Howard; Ham, Timothy S.; Soon Lee, Taek; Keasling, Jay D.

    2009-12-02

    The ability to generate microorganisms that can produce biofuels similar to petroleum-based transportation fuels would allow the use of existing engines and infrastructure and would save an enormous amount of capital required for replacing the current infrastructure to accommodate biofuels that have properties significantly different from petroleum-based fuels. Several groups have demonstrated the feasibility of manipulating microbes to produce molecules similar to petroleum-derived products, albeit at relatively low productivity (e.g. maximum butanol production is around 20 g/L). For cost-effective production of biofuels, the fuel-producing hosts and pathways must be engineered and optimized. Advances in metabolic engineering and synthetic biology will provide new tools for metabolic engineers to better understand how to rewire the cell in order to create the desired phenotypes for the production of economically viable biofuels.

  1. Rabi model as a quantum coherent heat engine: From quantum biology to superconducting circuits

    OpenAIRE

    Altintas, Ferdi; Hardal, Ali Ü. C.; Müstecaplıoğlu, Özgür E.

    2014-01-01

    We propose a multilevel quantum heat engine with a working medium described by a generalized Rabi model which consists of a two-level system coupled to a single-mode bosonic field. The model is constructed to be a continuum limit of a quantum biological description of light-harvesting complexes so that it can amplify quantum coherence by a mechanism which is a quantum analog of classical Huygens clocks. The engine operates in a quantum Otto cycle where the working medium is coupled to classic...

  2. The mismeasure of machine: Synthetic biology and the trouble with engineering metaphors.

    Science.gov (United States)

    Boudry, Maarten; Pigliucci, Massimo

    2013-12-01

    The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the "blueprint" of an organism, organisms are "reverse engineered" to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on "designs" that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with "programming" the right "software" would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes-isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms-pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for "engineering" a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic "instructions" is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these

  3. Synthetic biology and metabolic engineering for marine carotenoids: new opportunities and future prospects.

    Science.gov (United States)

    Wang, Chonglong; Kim, Jung-Hun; Kim, Seon-Won

    2014-09-17

    Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations.

  4. Synthetic Biology and Metabolic Engineering for Marine Carotenoids: New Opportunities and Future Prospects

    Directory of Open Access Journals (Sweden)

    Chonglong Wang

    2014-09-01

    Full Text Available Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations.

  5. Synthetic Biology and Metabolic Engineering for Marine Carotenoids: New Opportunities and Future Prospects

    Science.gov (United States)

    Wang, Chonglong; Kim, Jung-Hun; Kim, Seon-Won

    2014-01-01

    Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations. PMID:25233369

  6. 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

  7. Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

    Science.gov (United States)

    Tadmor, Brigitta; Tidor, Bruce

    2005-09-01

    Progress in the life sciences, including genome sequencing and high-throughput experimentation, offers an opportunity for understanding biology and medicine from a systems perspective. This 'new view', which complements the more traditional component-based approach, involves the integration of biological research with approaches from engineering disciplines and computer science. The result is more than a new set of technologies. Rather, it promises a fundamental reconceptualization of the life sciences based on the development of quantitative and predictive models to describe crucial processes. To achieve this change, learning communities are being formed at the interface of the life sciences, engineering and computer science. Through these communities, research and education will be integrated across disciplines and the challenges associated with multidisciplinary team-based science will be addressed.

  8. Proceedings of the 8. Mediterranean Conference on Medical and Biological Engineering and Computing (Medicon '98)

    International Nuclear Information System (INIS)

    Christofides, Stelios; Pattichis, Constantinos; Schizas, Christos; Keravnou-Papailiou, Elpida; Kaplanis, Prodromos; Spyros, Spyrou; Christodoulides, George; Theodoulou, Yiannis

    1998-01-01

    Medicon '98 is the eighth in the series of regional meetings of the International Federation of Medical and Biological Engineering (IFMBE) in the Mediterranean. The goal of Medicon '98 is to provide updated information on the state of the art on medical and biological engineering and computing. Medicon '98 was held in Lemesos, Cyprus, between 14-17 June, 1998. The full papers of the proceedings were published on CD and consisted of 190 invited and submitted papers. A book of abstracts was also published in paper form and was available to all the participants. Twenty seven papers fall within the scope of INIS and are dealing with Nuclear Medicine,Computerized Tomography, Radiology, Radiotherapy, Magnetic Resonance Imaging and Personnel Dosimetry (eds)

  9. Polymer-Based Microfluidic Devices for Pharmacy, Biology and Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Kerstin Ramser

    2012-07-01

    Full Text Available This paper reviews microfluidic technologies with emphasis on applications in the fields of pharmacy, biology, and tissue engineering. Design and fabrication of microfluidic systems are discussed with respect to specific biological concerns, such as biocompatibility and cell viability. Recent applications and developments on genetic analysis, cell culture, cell manipulation, biosensors, pathogen detection systems, diagnostic devices, high-throughput screening and biomaterial synthesis for tissue engineering are presented. The pros and cons of materials like polydimethylsiloxane (PDMS, polymethylmethacrylate (PMMA, polystyrene (PS, polycarbonate (PC, cyclic olefin copolymer (COC, glass, and silicon are discussed in terms of biocompatibility and fabrication aspects. Microfluidic devices are widely used in life sciences. Here, commercialization and research trends of microfluidics as new, easy to use, and cost-effective measurement tools at the cell/tissue level are critically reviewed.

  10. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

    Science.gov (United States)

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

    2016-04-01

    Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.

  11. Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli

    International Nuclear Information System (INIS)

    Whitaker, W. Brian; Bennett, R. Kyle

    2016-01-01

    Methanol is an attractive substrate for biological production of chemicals and fuels. Engineering methylotrophic Escherichia coli as a platform organism for converting methanol to metabolites is desirable. Prior efforts to engineer methylotrophic E. coli were limited by methanol dehydrogenases (Mdhs) with unfavorable enzyme kinetics. We engineered E. coli to utilize methanol using a superior NAD-dependent Mdh from Bacillus stearothermophilus and ribulose monophosphate (RuMP) pathway enzymes from B. methanolicus. Using 13 C-labeling, we demonstrate this E. coli strain converts methanol into biomass components. For example, the key TCA cycle intermediates, succinate and malate, exhibit labeling up to 39%, while the lower glycolytic intermediate, 3-phosphoglycerate, up to 53%. Multiple carbons are labeled for each compound, demonstrating a cycling RuMP pathway for methanol assimilation to support growth. In conclusion, by incorporating the pathway to synthesize the flavanone naringenin, we demonstrate the first example of in vivo conversion of methanol into a specialty chemical in E. coli.

  12. Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications.

    Science.gov (United States)

    Bober, Josef R; Beisel, Chase L; Nair, Nikhil U

    2018-03-12

    An increasing number of studies have strongly correlated the composition of the human microbiota with many human health conditions and, in several cases, have shown that manipulating the microbiota directly affects health. These insights have generated significant interest in engineering indigenous microbiota community members and nonresident probiotic bacteria as biotic diagnostics and therapeutics that can probe and improve human health. In this review, we discuss recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes, and we provide our perspective on the future potential of these technologies. 277 Expected final online publication date for the Annual Review of Biomedical Engineering Volume 20 is June 4, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  13. Dental pulp stem cells. Biology and use for periodontal tissue engineering.

    Science.gov (United States)

    Ashri, Nahid Y; Ajlan, Sumaiah A; Aldahmash, Abdullah M

    2015-12-01

    Inflammatory periodontal disease is a major cause of loss of tooth-supporting structures. Novel approaches for regeneration of periodontal apparatus is an area of intensive research. Periodontal tissue engineering implies the use of appropriate regenerative cells, delivered through a suitable scaffold, and guided through signaling molecules. Dental pulp stem cells have been used in an increasing number of studies in dental tissue engineering. Those cells show mesenchymal (stromal) stem cell-like properties including self-renewal and multilineage differentiation potentials, aside from their relative accessibility and pleasant handling properties. The purpose of this article is to review the biological principles of periodontal tissue engineering, along with the challenges facing the development of a consistent and clinically relevant tissue regeneration platform. This article includes an updated review on dental pulp stem cells and their applications in periodontal regeneration, in combination with different scaffolds and growth factors.

  14. Dental pulp stem cells. Biology and use for periodontal tissue engineering

    Directory of Open Access Journals (Sweden)

    Nahid Y. Ashri

    2015-12-01

    Full Text Available Inflammatory periodontal disease is a major cause of loss of tooth-supporting structures. Novel approaches for regeneration of periodontal apparatus is an area of intensive research. Periodontal tissue engineering implies the use of appropriate regenerative cells, delivered through a suitable scaffold, and guided through signaling molecules. Dental pulp stem cells have been used in an increasing number of studies in dental tissue engineering. Those cells show mesenchymal (stromal stem cell-like properties including self-renewal and multilineage differentiation potentials, aside from their relative accessibility and pleasant handling properties. The purpose of this article is to review the biological principles of periodontal tissue engineering, along with the challenges facing the development of a consistent and clinically relevant tissue regeneration platform. This article includes an updated review on dental pulp stem cells and their applications in periodontal regeneration, in combination with different scaffolds and growth factors.

  15. Metabolic engineering and synthetic biology approaches driving isoprenoid production in Escherichia coli.

    Science.gov (United States)

    Wang, Chonglong; Zada, Bakht; Wei, Gongyuan; Kim, Seon-Won

    2017-10-01

    Isoprenoids comprise the largest family of natural organic compounds with many useful applications in the pharmaceutical, nutraceutical, and industrial fields. Rapid developments in metabolic engineering and synthetic biology have facilitated the engineering of isoprenoid biosynthetic pathways in Escherichia coli to induce high levels of production of many different isoprenoids. In this review, the stem pathways for synthesizing isoprene units as well as the branch pathways deriving diverse isoprenoids from the isoprene units have been summarized. The review also highlights the metabolic engineering efforts made for the biosynthesis of hemiterpenoids, monoterpenoids, sesquiterpenoids, diterpenoids, carotenoids, retinoids, and coenzyme Q 10 in E. coli. Perspectives and future directions for the synthesis of novel isoprenoids, decoration of isoprenoids using cytochrome P450 enzymes, and secretion or storage of isoprenoids in E. coli have also been included. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Engineering C4 photosynthesis into C3 chassis in the synthetic biology age.

    Science.gov (United States)

    Schuler, Mara L; Mantegazza, Otho; Weber, Andreas P M

    2016-07-01

    C4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long-standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon-concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  17. Building better bone: The weaving of biologic and engineering strategies for managing bone loss.

    Science.gov (United States)

    Schwartz, Andrew M; Schenker, Mara L; Ahn, Jaimo; Willett, Nick J

    2017-09-01

    Segmental bone loss remains a challenging clinical problem for orthopaedic trauma surgeons. In addition to the missing bone itself, the local tissues (soft tissue, vascular) are often highly traumatized as well, resulting in a less than ideal environment for bone regeneration. As a result, attempts at limb salvage become a highly expensive endeavor, often requiring multiple operations and necessitating the use of every available strategy (autograft, allograft, bone graft substitution, Masquelet, bone transport, etc.) to achieve bony union. A cost-sensitive, functionally appropriate, and volumetrically adequate engineered substitute would be practice-changing for orthopaedic trauma surgeons and these patients with difficult clinical problems. In tissue engineering and bone regeneration fields, numerous research efforts continue to make progress toward new therapeutic interventions for segmental bone loss, including novel biomaterial development as well as cell-based strategies. Despite an ever-evolving literature base of these new therapeutic and engineered options, there remains a disconnect with the clinical practice, with very few translating into clinical use. A symposium entitled "Building better bone: The weaving of biologic and engineering strategies for managing bone loss," was presented at the 2016 Orthopaedic Research Society Conference to further explore this engineering-clinical disconnect, by surveying basic, translational, and clinical researchers along with orthopaedic surgeons and proposing ideas for pushing the bar forward in the field of segmental bone loss. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1855-1864, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  18. Rabi model as a quantum coherent heat engine: From quantum biology to superconducting circuits

    Science.gov (United States)

    Altintas, Ferdi; Hardal, Ali Ü. C.; Müstecaplıoǧlu, Özgür E.

    2015-02-01

    We propose a multilevel quantum heat engine with a working medium described by a generalized Rabi model which consists of a two-level system coupled to a single-mode bosonic field. The model is constructed to be a continuum limit of a quantum biological description of light-harvesting complexes so that it can amplify quantum coherence by a mechanism which is a quantum analog of classical Huygens clocks. The engine operates in a quantum Otto cycle where the working medium is coupled to classical heat baths in the isochoric processes of the four-stroke cycle, while either the coupling strength or the resonance frequency is changed in the adiabatic stages. We found that such an engine can produce work with an efficiency close to the Carnot bound when it operates at low temperatures and in the ultrastrong-coupling regime. The interplay of the effects of quantum coherence and quantum correlations on the engine performance is discussed in terms of second-order coherence, quantum mutual information, and the logarithmic negativity of entanglement. We point out that the proposed quantum Otto engine can be implemented experimentally with modern circuit quantum electrodynamic systems where flux qubits can be coupled ultrastrongly to superconducting transmission-line resonators.

  19. EMT-inducing biomaterials for heart valve engineering: taking cues from developmental biology

    Science.gov (United States)

    Sewell-Loftin, M.K.; Chun, Young Wook; Khademhosseini, Ali; Merryman, W. David

    2012-01-01

    Although artificial prostheses for diseased heart valves have been around for several decades, viable heart valve replacements have yet to be developed due to their complicated nature. The majority of research in heart valve replacement technology seeks to improve decellularization techniques for porcine valves or bovine pericardium as an effort to improve current clinically used valves. The drawback of clinically used valves is that they are nonviable and thus do not grow or remodel once implanted inside patients. This is particularly detrimental for pediatric patients, who will likely need several reoperations over the course of their lifetimes to implant larger valves as the patient grows. Due to this limitation, additional biomaterials, both synthetic and natural in origin, are also being investigated as novel scaffolds for tissue engineered heart valves, specifically for the pediatric population. Here, we provide a brief overview of valves in clinical use as well as of the materials being investigated as novel tissue engineered heart valve scaffolds. Additionally, we focus on natural-based biomaterials for promoting cell behavior that is indicative of the developmental biology process that occurs in the formation of heart valves in utero, such as epithelial-to-mesenchymal transition or transformation (EMT). By engineering materials that promote native developmental biology cues and signaling, while also providing mechanical integrity once implanted, a viable tissue engineered heart valve may one day be realized. A viable tissue engineered heart valve, capable of growing and remodeling actively inside a patient, could reduce risks and complications associated with current valve replacement options and improve overall quality of life in the thousands of patients who received such valves each year, particularly for children. PMID:21751069

  20. EMT-inducing biomaterials for heart valve engineering: taking cues from developmental biology.

    Science.gov (United States)

    Sewell-Loftin, M K; Chun, Young Wook; Khademhosseini, Ali; Merryman, W David

    2011-10-01

    Although artificial prostheses for diseased heart valves have been around for several decades, viable heart valve replacements have yet to be developed due to their complicated nature. The majority of research in heart valve replacement technology seeks to improve decellularization techniques for porcine valves or bovine pericardium as an effort to improve current clinically used valves. The drawback of clinically used valves is that they are nonviable and thus do not grow or remodel once implanted inside patients. This is particularly detrimental for pediatric patients, who will likely need several reoperations over the course of their lifetimes to implant larger valves as the patient grows. Due to this limitation, additional biomaterials, both synthetic and natural in origin, are also being investigated as novel scaffolds for tissue-engineered heart valves, specifically for the pediatric population. Here, we provide a brief overview of valves in clinical use as well as of the materials being investigated as novel tissue-engineered heart valve scaffolds. Additionally, we focus on natural-based biomaterials for promoting cell behavior that is indicative of the developmental biology process that occurs in the formation of heart valves in utero, such as epithelial-to-mesenchymal transition or transformation. By engineering materials that promote native developmental biology cues and signaling, while also providing mechanical integrity once implanted, a viable tissue-engineered heart valve may one day be realized. A viable tissue-engineered heart valve, capable of growing and remodeling actively inside a patient, could reduce risks and complications associated with current valve replacement options and improve overall quality of life in the thousands of patients who received such valves each year, particularly for children.

  1. BioCarian: search engine for exploratory searches in heterogeneous biological databases.

    Science.gov (United States)

    Zaki, Nazar; Tennakoon, Chandana

    2017-10-02

    There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search

  2. Biological and mechanical evaluation of a Bio-Hybrid scaffold for autologous valve tissue engineering.

    Science.gov (United States)

    Jahnavi, S; Saravanan, U; Arthi, N; Bhuvaneshwar, G S; Kumary, T V; Rajan, S; Verma, R S

    2017-04-01

    Major challenge in heart valve tissue engineering for paediatric patients is the development of an autologous valve with regenerative capacity. Hybrid tissue engineering approach is recently gaining popularity to design scaffolds with desired biological and mechanical properties that can remodel post implantation. In this study, we fabricated aligned nanofibrous Bio-Hybrid scaffold made of decellularized bovine pericardium: polycaprolactone-chitosan with optimized polymer thickness to yield the desired biological and mechanical properties. CD44 + , αSMA + , Vimentin + and CD105 - human valve interstitial cells were isolated and seeded on these Bio-Hybrid scaffolds. Subsequent biological evaluation revealed interstitial cell proliferation with dense extra cellular matrix deposition that indicated the viability for growth and proliferation of seeded cells on the scaffolds. Uniaxial mechanical tests along axial direction showed that the Bio-Hybrid scaffolds has at least 20 times the strength of the native valves and its stiffness is nearly 3 times more than that of native valves. Biaxial and uniaxial mechanical studies on valve interstitial cells cultured Bio-Hybrid scaffolds revealed that the response along the axial and circumferential direction was different, similar to native valves. Overall, our findings suggest that Bio-Hybrid scaffold is a promising material for future development of regenerative heart valve constructs in children. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli.

    Science.gov (United States)

    Whitaker, W Brian; Jones, J Andrew; Bennett, R Kyle; Gonzalez, Jacqueline E; Vernacchio, Victoria R; Collins, Shannon M; Palmer, Michael A; Schmidt, Samuel; Antoniewicz, Maciek R; Koffas, Mattheos A; Papoutsakis, Eleftherios T

    2017-01-01

    Methanol is an attractive substrate for biological production of chemicals and fuels. Engineering methylotrophic Escherichia coli as a platform organism for converting methanol to metabolites is desirable. Prior efforts to engineer methylotrophic E. coli were limited by methanol dehydrogenases (Mdhs) with unfavorable enzyme kinetics. We engineered E. coli to utilize methanol using a superior NAD-dependent Mdh from Bacillus stearothermophilus and ribulose monophosphate (RuMP) pathway enzymes from B. methanolicus. Using 13 C-labeling, we demonstrate this E. coli strain converts methanol into biomass components. For example, the key TCA cycle intermediates, succinate and malate, exhibit labeling up to 39%, while the lower glycolytic intermediate, 3-phosphoglycerate, up to 53%. Multiple carbons are labeled for each compound, demonstrating a cycling RuMP pathway for methanol assimilation to support growth. By incorporating the pathway to synthesize the flavanone naringenin, we demonstrate the first example of in vivo conversion of methanol into a specialty chemical in E. coli. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  4. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    . With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available...... for an increasing number of microorganisms. This has resulted in substantial research efforts in assigning function to all identified open reading frames - referred to as functional genomics. In both metabolic engineering and functional genomics there is a trend towards application of a macroscopic view on cell......Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function...

  5. Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals.

    Science.gov (United States)

    Jullesson, David; David, Florian; Pfleger, Brian; Nielsen, Jens

    2015-11-15

    Industrial bio-processes for fine chemical production are increasingly relying on cell factories developed through metabolic engineering and synthetic biology. The use of high throughput techniques and automation for the design of cell factories, and especially platform strains, has played an important role in the transition from laboratory research to industrial production. Model organisms such as Saccharomyces cerevisiae and Escherichia coli remain widely used host strains for industrial production due to their robust and desirable traits. This review describes some of the bio-based fine chemicals that have reached the market, key metabolic engineering tools that have allowed this to happen and some of the companies that are currently utilizing these technologies for developing industrial production processes. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli.

    Directory of Open Access Journals (Sweden)

    Jacob Beal

    Full Text Available We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.

  7. Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals

    DEFF Research Database (Denmark)

    Jullesson, David; David, Florian; Pfleger, Brian

    2015-01-01

    Industrial bio-processes for fine chemical production are increasingly relying on cell factories developed through metabolic engineering and synthetic biology. The use of high throughput techniques and automation for the design of cell factories, and especially platform strains, has played...... an important role in the transition from laboratory research to industrial production. Model organisms such as Saccharomyces cerevisiae and Escherichia coli remain widely used host strains for industrial production due to their robust and desirable traits. This review describes some of the bio-based fine...... chemicals that have reached the market, key metabolic engineering tools that have allowed this to happen and some of the companies that are currently utilizing these technologies for developing industrial production processes....

  8. The rise of nanotoxicology: A successful collaboration between engineering and biology

    Directory of Open Access Journals (Sweden)

    Kristen K. Comfort

    2016-07-01

    Full Text Available The field of nanotechnology has grown exponentially in the last decade, due to increasing capabilities in material science which allows for the precise and reproducible synthesis of nanomaterials (NMs. However, the unique physicochemical properties of NMs that make them attractive for nanotechnological applications also introduce serious health and safety concerns; thus giving rise to the field of nanotoxicology. Initial efforts focused on evaluating the toxic potential of NMs, however, it became clear that due to their distinctive characteristics it was necessary to design and develop new assessment metrics. Through a prolific collaboration, engineering practices and principles were applied to nanotoxicology in order to accurately evaluate NM behavior, characterize the nano-cellular interface, and measure biological responses within a cellular environment. This review discusses three major areas in which the field of nanotoxicology progressed as a result of a strong engineering-biology partnership: 1 the establishment of standardized characterization tools and techniques, 2 the examination of NM dosimetry and the development of mathematical, predictive models, and 3 the generation of physiologically relevant exposure systems that incorporate fluid dynamics and high-throughput mechanisms. The goal of this review is to highlight the multidisciplinary efforts behind the successes of nanotoxicology and celebrate the partnerships that have emerged from this research field.

  9. Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course.

    Science.gov (United States)

    Dymond, Jessica S; Scheifele, Lisa Z; Richardson, Sarah; Lee, Pablo; Chandrasegaran, Srinivasan; Bader, Joel S; Boeke, Jef D

    2009-01-01

    A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into approximately 750-bp fragments. Once trained in assembly of such DNA "building blocks" by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular "lab meeting" sessions help prepare them for future roles in laboratory science.

  10. Reverse engineering biological networks :applications in immune responses to bio-toxins.

    Energy Technology Data Exchange (ETDEWEB)

    Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Thomas, Edward Victor; Slepoy, Alexander; Zhang, Zhaoduo; May, Elebeoba Eni; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-12-01

    Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

  11. Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology.

    Science.gov (United States)

    Dvořák, Pavel; Nikel, Pablo I; Damborský, Jiří; de Lorenzo, Víctor

    2017-11-15

    Elimination or mitigation of the toxic effects of chemical waste released to the environment by industrial and urban activities relies largely on the catalytic activities of microorganisms-specifically bacteria. Given their capacity to evolve rapidly, they have the biochemical power to tackle a large number of molecules mobilized from their geological repositories through human action (e.g., hydrocarbons, heavy metals) or generated through chemical synthesis (e.g., xenobiotic compounds). Whereas naturally occurring microbes already have considerable ability to remove many environmental pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow revisiting the same environmental pollution challenges through fresh and far more powerful approaches. The focus on contaminated sites and chemicals has been broadened by the phenomenal problems of anthropogenic emissions of greenhouse gases and the accumulation of plastic waste on a global scale. In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering workflow. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Survey of French research in biological and medical engineering - aims, means, results

    International Nuclear Information System (INIS)

    Teissier, J.

    1975-01-01

    A review of the aims and means available is followed by an outline of the results of French research in biological and medical engineering. Most of the work undertaken has given very positive results from the scientific view-point, followed up by industrial applications. Scintigraphic image processing research has led to CINE 200. A study of heart output quantification in real time has produced a haemodynamic investigation system, the Sysconoram, now commercialized. The study of heart signal recording methods has led to a marketable and reliable system for the detection of pathological heart conditions. Research in neurosurgery on the use of pressure transducers in integrated technology, using a piezoelectric detector associated with a field effect amplifier, has enabled two types of extradural pressure transducer and one cervical intraventricular pressure transducer to be industrialized. Finally the study of a gamma detector combined with a light-amplifier tube has led to the development of camera giving quite exceptional results [fr

  13. Harnessing biological motors to engineer systems for nanoscale transport and assembly.

    Science.gov (United States)

    Goel, Anita; Vogel, Viola

    2008-08-01

    Living systems use biological nanomotors to build life's essential molecules--such as DNA and proteins--as well as to transport cargo inside cells with both spatial and temporal precision. Each motor is highly specialized and carries out a distinct function within the cell. Some have even evolved sophisticated mechanisms to ensure quality control during nanomanufacturing processes, whether to correct errors in biosynthesis or to detect and permit the repair of damaged transport highways. In general, these nanomotors consume chemical energy in order to undergo a series of shape changes that let them interact sequentially with other molecules. Here we review some of the many tasks that biomotors perform and analyse their underlying design principles from an engineering perspective. We also discuss experiments and strategies to integrate biomotors into synthetic environments for applications such as sensing, transport and assembly.

  14. Biologically inspired robotic inspectors: the engineering reality and future outlook (Keynote address)

    Science.gov (United States)

    Bar-Cohen, Yoseph

    2005-04-01

    Human errors have long been recognized as a major factor in the reliability of nondestructive evaluation results. To minimize such errors, there is an increasing reliance on automatic inspection tools that allow faster and consistent tests. Crawlers and various manipulation devices are commonly used to perform variety of inspection procedures that include C-scan with contour following capability to rapidly inspect complex structures. The emergence of robots has been the result of the need to deal with parts that are too complex to handle by a simple automatic system. Economical factors are continuing to hamper the wide use of robotics for inspection applications however technology advances are increasingly changing this paradigm. Autonomous robots, which may look like human, can potentially address the need to inspect structures with configuration that are not predetermined. The operation of such robots that mimic biology may take place at harsh or hazardous environments that are too dangerous for human presence. Biomimetic technologies such as artificial intelligence, artificial muscles, artificial vision and numerous others are increasingly becoming common engineering tools. Inspired by science fiction, making biomimetic robots is increasingly becoming an engineering reality and in this paper the state-of-the-art will be reviewed and the outlook for the future will be discussed.

  15. 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.

  16. 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.

  17. Biological evaluation of porous aliphatic polyurethane/hydroxyapatite composite scaffolds for bone tissue engineering.

    Science.gov (United States)

    Yang, Wanxun; Both, Sanne K; Zuo, Yi; Birgani, Zeinab Tahmasebi; Habibovic, Pamela; Li, Yubao; Jansen, John A; Yang, Fang

    2015-07-01

    Biomaterial scaffolds meant to function as supporting structures to osteogenic cells play a pivotal role in bone tissue engineering. Recently, we synthesized an aliphatic polyurethane (PU) scaffold via a foaming method using non-toxic components. Through this procedure a uniform interconnected porous structure was created. Furthermore, hydroxyapatite (HA) particles were introduced into this process to increase the bioactivity of the PU matrix. To evaluate the biological performances of these PU-based scaffolds, their influence on in vitro cellular behavior and in vivo bone forming capacity of the engineered cell-scaffold constructs was investigated in this study. A simulated body fluid test demonstrated that the incorporation of 40 wt % HA particles significantly promoted the biomineralization ability of the PU scaffolds. Enhanced in vitro proliferation and osteogenic differentiation of the seeded mesenchymal stem cells were also observed on the PU/HA composite. Next, the cell-scaffold constructs were implanted subcutaneously in a nude mice model. After 8 weeks, a considerable amount of vascularized bone tissue with initial marrow stroma development was generated in both PU and PU/HA40 scaffold. In conclusion, the PU/HA composite is a potential scaffold for bone regeneration applications. © 2014 Wiley Periodicals, Inc.

  18. Use of Mesothelial Cells and Biological Matrices for Tissue Engineering of Simple Epithelium Surrogates

    Directory of Open Access Journals (Sweden)

    Christian Claude Lachaud

    2015-08-01

    Full Text Available Tissue engineering technologies have progressed rapidly through last decades resulting in the manufacture of quite complex bioartificial tissues with potential use for human organ and tissue regeneration. The manufacture of avascular monolayered tissues such as simple squamous epithelia was initiated a few decades ago and is attracting increasing interest. Their relative morphostructural simplicity makes of their biomimetization a goal, which is currently accessible. The mesothelium is a simple squamous epithelium in nature and is the monolayered tissue lining the walls of large coelomic cavities (peritoneal, pericardial and pleural and internal organs housed inside. Interestedly, mesothelial cells can be harvested in clinically relevant numbers from several anatomical sources and not less important, they also display high transdifferentiation capacities and are low immunogenic, characteristics, which endow these cells with therapeutic interest. Their combination with a suitable scaffold (biocompatible, degradable and non-immunogenic may allow the manufacture of tailored serosal membranes biomimetics with potential spanning a wide range of therapeutic applications, principally for the regeneration of simple squamous-like epithelia such as the visceral and parietal mesothelium vascular endothelium and corneal endothelium among others. Herein, we review recent research progresses in mesothelial cells biology and their clinical sources. We make a particular emphasis on reviewing the different types of biological scaffolds suitable for the manufacture of serosal mesothelial membranes biomimetics. Finally, we also review progresses made in mesothelial cells-based therapeutic applications and propose some possible future directions.

  19. Nanodimensional and Nanocrystalline Apatites and Other Calcium Orthophosphates in Biomedical Engineering, Biology and Medicine

    Directory of Open Access Journals (Sweden)

    Sergey V. Dorozhkin

    2009-11-01

    Full Text Available Recent developments in biomineralization have already demonstrated that nanosized particles play an important role in the formation of hard tissues of animals. Namely, the basic inorganic building blocks of bones and teeth of mammals are nanodimensional and nanocrystalline calcium orthophosphates (in the form of apatites of a biological origin. In mammals, tens to hundreds nanocrystals of a biological apatite were found to be combined into self-assembled structures under the control of various bioorganic matrixes. In addition, the structures of both dental enamel and bones could be mimicked by an oriented aggregation of nanosized calcium orthophosphates, determined by the biomolecules. The application and prospective use of nanodimensional and nanocrystalline calcium orthophosphates for a clinical repair of damaged bones and teeth are also known. For example, a greater viability and a better proliferation of various types of cells were detected on smaller crystals of calcium orthophosphates. Thus, the nanodimensional and nanocrystalline forms of calcium orthophosphates have a great potential to revolutionize the field of hard tissue engineering starting from bone repair and augmentation to the controlled drug delivery devices. This paper reviews current state of knowledge and recent developments of this subject starting from the synthesis and characterization to biomedical and clinical applications. More to the point, this review provides possible directions of future research and development.

  20. Prospects and progress in the production of valuable carotenoids: Insights from metabolic engineering, synthetic biology, and computational approaches.

    Science.gov (United States)

    Sankari, Mohan; Rao, Priya Rajendra; Hemachandran, Hridya; Pullela, Phani Kumar; Doss C, George Priya; Tayubi, Iftikhar Aslam; Subramanian, Babu; Gothandam, K M; Singh, Pooja; Ramamoorthy, Siva

    2018-01-20

    Carotenoids are isoprenoid pigments synthesized exclusively by plants and microorganisms and play critical roles in light harvesting, photoprotection, attracting pollinators and phytohormone production. In recent years, carotenoids have been used for their health benefits due to their high antioxidant activity and are extensively utilized in food, pharmaceutical, and nutraceutical industries. Regulation of carotenoid biosynthesis occurs throughout the life cycle of plants, with vibrant changes in composition based on developmental needs and responses to external environmental stimuli. With advancements in metabolic engineering techniques, there has been tremendous progress in the production of industrially valuable secondary metabolites such as carotenoids. Application of metabolic engineering and synthetic biology has become essential for the successful and improved production of carotenoids. Synthetic biology is an emerging discipline; metabolic engineering approaches may provide insights into novel ideas for biosynthetic pathways. In this review, we discuss the current knowledge on carotenoid biosynthetic pathways and genetic engineering of carotenoids to improve their nutritional value. In addition, we investigated synthetic biological approaches for the production of carotenoids. Theoretical biology approaches that may aid in understanding the biological sciences are discussed in this review. A combination of theoretical knowledge and experimental strategies may improve the production of industrially relevant secondary metabolites. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Proceedings of the Joint Conference of Australasian College of Physical Scientists and Engineers in Medicine and IEAust College of Biomedical Engineers; Asia/Pacific Region of the IEEE Engineering in Medicine and Biology Society

    International Nuclear Information System (INIS)

    1996-01-01

    This is a celebration of the centenary of Rontgen''s discovery of Xrays. It is also the 50th anniversary of the first hospital physicist appointment in New Zealand. The historical element of the programme will complement the emphasis on current applications of the physical and engineering sciences to medicine and an anticipation of future developments. For the first time the Australasian College of Physical Scientists and Engineers in Medicine, together with the IEAust College of Biomedical Engineers, are joined by the Asia/Pacific Region of the IEEE Engineering in Medicine and Biology Society to make this a truly international conference. The proceedings include many papers on radiology and radiotherapy

  2. Chitosan fibers with improved biological and mechanical properties for tissue engineering applications.

    Science.gov (United States)

    Albanna, Mohammad Z; Bou-Akl, Therese H; Blowytsky, Oksana; Walters, Henry L; Matthew, Howard W T

    2013-04-01

    The low mechanical properties of hydrogel materials such as chitosan hinder their broad utility for tissue engineering applications. Previous research efforts improved the mechanical properties of chitosan fiber through chemical and physical modifications; however, unfavorable toxicity effects on cells were reported. In this paper, we report the preparation of chitosan fibers with improved mechanical and biocompatibility properties. The structure-property relationships of extruded chitosan fibers were explored by varying acetic acid (AA) concentration, ammonia concentration, annealing temperature and degree of heparin crosslinking. Results showed that optimizing AA concentration to 2vol% improved fiber strength and stiffness by 2-fold. Extruding chitosan solution into 25wt% of ammonia solution reduced fiber diameters and improved fiber strength by 2-fold and stiffness by 3-fold, due to an increase in crystallinity as confirmed by XRD. Fiber annealing further reduced fiber diameter and improved fiber strength and stiffness as temperature increased. Chitosan fibers crosslinked with heparin had increased diameter but lower strength and stiffness properties and higher breaking strain values. When individual parameters were combined, further improvement in fiber mechanical properties was achieved. All mechanically improved fibers and heparin crosslinked fibers promoted valvular interstitial cells (VIC) attachment and growth over 10 day cultures. Our results demonstrate the ability to substantially improve the mechanical properties of chitosan fibers without adversely affecting their biological properties. The investigated treatments offer numerous advantages over previous physical/chemical modifications and thus are expected to expand the utility of chitosan fibers with tunable mechanical properties in various tissue engineering applications. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Hybrid printing of mechanically and biologically improved constructs for cartilage tissue engineering applications

    International Nuclear Information System (INIS)

    Xu Tao; Binder, Kyle W; Albanna, Mohammad Z; Dice, Dennis; Zhao Weixin; Yoo, James J; Atala, Anthony

    2013-01-01

    Bioprinting is an emerging technique used to fabricate viable, 3D tissue constructs through the precise deposition of cells and hydrogels in a layer-by-layer fashion. Despite the ability to mimic the native properties of tissue, printed 3D constructs that are composed of naturally-derived biomaterials still lack structural integrity and adequate mechanical properties for use in vivo, thus limiting their development for use in load-bearing tissue engineering applications, such as cartilage. Fabrication of viable constructs using a novel multi-head deposition system provides the ability to combine synthetic polymers, which have higher mechanical strength than natural materials, with the favorable environment for cell growth provided by traditional naturally-derived hydrogels. However, the complexity and high cost associated with constructing the required robotic system hamper the widespread application of this approach. Moreover, the scaffolds fabricated by these robotic systems often lack flexibility, which further restrict their applications. To address these limitations, advanced fabrication techniques are necessary to generate complex constructs with controlled architectures and adequate mechanical properties. In this study, we describe the construction of a hybrid inkjet printing/electrospinning system that can be used to fabricate viable tissues for cartilage tissue engineering applications. Electrospinning of polycaprolactone fibers was alternated with inkjet printing of rabbit elastic chondrocytes suspended in a fibrin–collagen hydrogel in order to fabricate a five-layer tissue construct of 1 mm thickness. The chondrocytes survived within the printed hybrid construct with more than 80% viability one week after printing. In addition, the cells proliferated and maintained their basic biological properties within the printed layered constructs. Furthermore, the fabricated constructs formed cartilage-like tissues both in vitro and in vivo as evidenced by the

  4. Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology.

    Science.gov (United States)

    Pandey, Ramesh Prasad; Parajuli, Prakash; Koffas, Mattheos A G; Sohng, Jae Kyung

    2016-01-01

    In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.

    Science.gov (United States)

    Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth

    2017-03-01

    Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  6. Oxygen diffusivity of biologic and synthetic scaffold materials for tissue engineering.

    Science.gov (United States)

    Valentin, Jolene E; Freytes, Donald O; Grasman, Jonathan M; Pesyna, Colin; Freund, John; Gilbert, Thomas W; Badylak, Stephen F

    2009-12-15

    Scaffolds for tissue engineering and regenerative medicine applications are commonly manufactured from synthetic materials, intact or isolated components of extracellular matrix (ECM), or a combination of such materials. After surgical implantation, the metabolic requirements of cells that populate the scaffold depend upon adequate gas and nutrient exchange with the surrounding microenvironment. The present study measured the oxygen transfer through three biologic scaffold materials composed of ECM including small intestinal submucosa (SIS), urinary bladder submucosa (UBS), and urinary bladder matrix (UBM), and one synthetic biomaterial, Dacron. The oxygen diffusivity was calculated from Fick's first law of diffusion. Each material permitted measurable oxygen diffusion. The diffusivity of SIS was found to be dependent on the direction of oxygen transfer; the oxygen transfer in the abluminal-to-luminal direction was significantly greater than the luminal-to-abluminal direction. The oxygen diffusivity of UBM and UBS were similar despite the presence of an intact basement membrane on the luminal surface of UBM. Dacron showed oxygen diffusivity values seven times greater than the ECM biomaterials. The current study showed that each material has unique oxygen diffusivity values, and these values may be dependent on the scaffold's ultrastructure.

  7. The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.

    Science.gov (United States)

    Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Gur, Tamer; Cowley, Andrew; Li, Weizhong; Uludag, Mahmut; Pundir, Sangya; Cham, Jennifer A; McWilliam, Hamish; Lopez, Rodrigo

    2015-07-01

    The European Bioinformatics Institute (EMBL-EBI-https://www.ebi.ac.uk) provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present the EBI Search engine, referred to here as 'EBI Search', an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Preliminary report of biological intrusion studies at the Idaho National Engineering Laboratory subsurface disposal area

    International Nuclear Information System (INIS)

    Reynolds, T.D.; Arthur, W.J.

    1983-01-01

    As part of a larger study on the effects of biological intrusion of plants and animals into the soil cover placed over low-level radioactive wastes stored at the Idaho National Engineering Laboratory Subsurface Disposal Area (SDA), research was initiated in the summer of 1982 to determine the burrow characteristics and movement patterns of several small mammal species, and the rooting depths of various plants. The depth, length, and volume of burrows were determined for four small mammal species: deer mouse (Peromyscus maniculatus), Ord's kangaroo rat (Dipodomys ordii), montane vole (Microtus montanus), and Townsend's ground squirrel (Spermophilis townsendii). The latter species excavated the greatest mean burrow depth (39 cm), length (404 cm), and volume (14.8 1). Movement patterns of three species were determined by radiotelemetry. The mean area of use for P. maniculatus, D. ordii, and M. montanus was 2.3, 1.5, and 1.2 ha respectively. Limited data on rooting depths of various native and introduced plant species at the SDA were obtained by literature review and excavation. During FY-83, experiments will be conducted, using the information obtained from the first year of this study, to evaluate the impact of burrowing mammals and root intrusion on the integrity of the soil cover currently existing at the SDA. Details of these experimental studies are presented

  9. Morphology of Filamentous Fungi: Linking Cellular Biology to Process Engineering Using Aspergillus niger

    Science.gov (United States)

    Krull, Rainer; Cordes, Christiana; Horn, Harald; Kampen, Ingo; Kwade, Arno; Neu, Thomas R.; Nörtemann, Bernd

    In various biotechnological processes, filamentous fungi, e.g. Aspergillus niger, are widely applied for the production of high value-added products due to their secretion efficiency. There is, however, a tangled relationship between the morphology of these microorganisms, the transport phenomena and the related productivity. The morphological characteristics vary between freely dispersed mycelia and distinct pellets of aggregated biomass. Hence, advantages and disadvantages for mycel or pellet cultivation have to be balanced out carefully. Due to this inadequate understanding of morphogenesis of filamentous microorganisms, fungal morphology, along with reproducibility of inocula of the same quality, is often a bottleneck of productivity in industrial production. To obtain an optimisation of the production process it is of great importance to gain a better understanding of the molecular and cell biology of these microorganisms as well as the approaches in biochemical engineering and particle technique, in particular to characterise the interactions between the growth conditions, cell morphology, spore-hyphae-interactions and product formation. Advances in particle and image analysis techniques as well as micromechanical devices and their applications to fungal cultivations have made available quantitative morphological data on filamentous cells. This chapter provides the ambitious aspects of this line of action, focussing on the control and characterisation of the morphology, the transport gradients and the approaches to understand the metabolism of filamentous fungi. Based on these data, bottlenecks in the morphogenesis of A. niger within the complex production pathways from gene to product should be identified and this may improve the production yield.

  10. Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

    Energy Technology Data Exchange (ETDEWEB)

    Madhavan, Aravind [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Rajiv Gandhi Centre for Biotechnology, Trivandrum (India); Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran, E-mail: sindhurgcb@gmail.com; Sukumaran, Rajeev K. [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Pandey, Ashok [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Center for Innovative and Applied Bioprocessing, Mohali, Punjab (India); Castro, Galliano Eulogio [Dpt. Ingeniería Química, Ambiental y de los Materiales Edificio, Universidad de Jaén, Jaén (Spain)

    2017-04-25

    The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

  11. Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

    Directory of Open Access Journals (Sweden)

    Raveendran Sindhu

    2017-04-01

    Full Text Available The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

  12. Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

    International Nuclear Information System (INIS)

    Madhavan, Aravind; Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran; Sukumaran, Rajeev K.; Pandey, Ashok; Castro, Galliano Eulogio

    2017-01-01

    The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

  13. Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices.

    Directory of Open Access Journals (Sweden)

    Lorenzo Pasotti

    Full Text Available BACKGROUND: Modularity is a crucial issue in the engineering world, as it enables engineers to achieve predictable outcomes when different components are interconnected. Synthetic Biology aims to apply key concepts of engineering to design and construct new biological systems that exhibit a predictable behaviour. Even if physical and measurement standards have been recently proposed to facilitate the assembly and characterization of biological components, real modularity is still a major research issue. The success of the bottom-up approach strictly depends on the clear definition of the limits in which biological functions can be predictable. RESULTS: The modularity of transcription-based biological components has been investigated in several conditions. First, the activity of a set of promoters was quantified in Escherichia coli via different measurement systems (i.e., different plasmids, reporter genes, ribosome binding sites relative to an in vivo reference promoter. Second, promoter activity variation was measured when two independent gene expression cassettes were assembled in the same system. Third, the interchangeability of input modules (a set of constitutive promoters and two regulated promoters connected to a fixed output device (a logic inverter expressing GFP was evaluated. The three input modules provide tunable transcriptional signals that drive the output device. If modularity persists, identical transcriptional signals trigger identical GFP outputs. To verify this, all the input devices were individually characterized and then the input-output characteristic of the logic inverter was derived in the different configurations. CONCLUSIONS: Promoters activities (referred to a standard promoter can vary when they are measured via different reporter devices (up to 22%, when they are used within a two-expression-cassette system (up to 35% and when they drive another device in a functionally interconnected circuit (up to 44%. This paper

  14. Ecological engineering to control bioclogging: an original field study coupling infiltration and biological measurements

    Science.gov (United States)

    Gette-bouvarot, Morgane; Mermillod-Blondin, Florian; Lassabatere, Laurent; Lemoine, Damien; Delolme, Cécile; Volatier, Laurence

    2014-05-01

    biomass, bacterial abundances, microbial enzymatic activities, EPS composition, and photosynthetic efficiency) with in situ hydraulic conductivity measurements (falling head method, five measures per enclosure at t0 and tf). Our results showed that some treatments could regulate benthic biofilm growth and improve infiltration rate. For instance, V. viviparus treatment resulted in a decrease in chlorophyll-a, EPS sugar and protein contents and an associated increase of infiltration rate, while it decreased in the control treatment. These results are very promising for the future development of ecological engineering solutions to prevent biological clogging in systems dedicated to infiltration. To our knowledge, this study is the first to highlight such potential role of macro-organisms under field conditions.

  15. Synthesis and characterization of polyglycerols dendrimers for applications in tissue engineering biological

    International Nuclear Information System (INIS)

    Passos, E.D.; Queiroz, A.A.A. de

    2014-01-01

    Full text: Introduction: Over the last twenty years is the growing development in the manufacture of synthetic scaffold in tissue engineering applications. These new materials are based on polyglycerol dendrimers (PGLD's). PGLD's are highly functional polymers with hydroxymethyl side groups, fulfill all structural prerequisites to replace poly(ethylene glycol)s in medical applications. Furthermore, since these materials are based on naturally occurring compounds that degrades over time in the body and can be safely excreted. The objective of this work was the synthesis, physicochemical, biological characterization of HPGL's with potential use as scaffolds in tissue engineering. HPGL's with oligomeric cores, of diglycerol triglycerol and tetraglycerol was used. Theoretical and Experimental Simulation Details: The synthesis of PGLD procedures involves the etherification of glycerol through anionic polymerization of glycidol. The PGLD's were characterized by chromatographic techniques (SEC and HPLC), spectroscopic (FTIR, 1H-NMR and 13C - NMR) electrochemical (zeta potential) and thermal analysis (DSC and TGA) techniques. The structure- activity relationships (SAR's) of compound prototype and its analogs were studied to determine the generation number (G) of the molecule responsible for the biological activity on the adhesion and cell proliferation process. A detailed study of the structure of PGLD's of G=0-4 was performed using the Hyperchem 7. 5 and Gromacs 4 software packages. The biocompatibility studies were studied by scanning electron microscopy (SEM) and fluorescence microscopy (EPF) technique after PGLD (G=0-4) blood contact. The overall electro-negativity/total charge density, dipole moment, frontier orbital's (HOMO - LUMO) and electrostatic potential maps (EPM) were calculated. The most stable form of the resulting compounds was determined by estimating the hydration energy and energy conformation. Results and

  16. Molecular Biology: Conference on Genetic Engineering Techniques (2nd) Held in London (United Kingdom) on 20-21 November 1986.

    Science.gov (United States)

    1987-05-27

    A181 T5 MOLECULAR BIOLOGY CONFERENCE O GENETIC ENGINEERING 1/ TECNIQUES (2ND) HEL (U) OFFICE OF NAVAL RESEARCH LONDON (ENGLAND) C F ZOMZELY-NEURATH...represented both genetic diseases. For example, Hunting- academic and industrial organizations in ton’s Chorea, Cystic Fibrosis , and a 1:1 ratio...be cloned in available vicinity of the Huntington’s Chorea and vectors or easily analyzed by standard Cystic Fibrosis mutations in human, and 3

  17. Promoting convergence: The integrated graduate program in physical and engineering biology at Yale University, a new model for graduate education.

    Science.gov (United States)

    Noble, Dorottya B; Mochrie, Simon G J; O'Hern, Corey S; Pollard, Thomas D; Regan, Lynne

    2016-11-12

    In 2008, we established the Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) at Yale University. Our goal was to create a comprehensive graduate program to train a new generation of scientists who possess a sophisticated understanding of biology and who are capable of applying physical and quantitative methodologies to solve biological problems. Here we describe the framework of the training program, report on its effectiveness, and also share the insights we gained during its development and implementation. The program features co-teaching by faculty with complementary specializations, student peer learning, and novel hands-on courses that facilitate the seamless blending of interdisciplinary research and teaching. It also incorporates enrichment activities to improve communication skills, engage students in science outreach, and foster a cohesive program cohort, all of which promote the development of transferable skills applicable in a variety of careers. The curriculum of the graduate program is integrated with the curricular requirements of several Ph.D.-granting home programs in the physical, engineering, and biological sciences. Moreover, the wide-ranging recruiting activities of the IGPPEB serve to enhance the quality and diversity of students entering graduate school at Yale. We also discuss some of the challenges we encountered in establishing and optimizing the program, and describe the institution-level changes that were catalyzed by the introduction of the new graduate program. The goal of this article is to serve as both an inspiration and as a practical "how to" manual for those who seek to establish similar programs at their own institutions. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):537-549, 2016. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

  18. Using Mathematics and Engineering to Solve Problems in Secondary Level Biology

    Science.gov (United States)

    Cox, Charles; Reynolds, Birdy; Schunn, Christian; Schuchardt, Anita

    2016-01-01

    There are strong classroom ties between mathematics and the sciences of physics and chemistry, but those ties seem weaker between mathematics and biology. Practicing biologists realize both that there are interesting mathematics problems in biology, and that viewing classroom biology in the context of another discipline could support students'…

  19. Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research

    Directory of Open Access Journals (Sweden)

    Toshitsugu Fujita

    2015-09-01

    Full Text Available Engineered DNA-binding molecules such as transcription activator-like effector (TAL or TALE proteins and the clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated proteins (Cas (CRISPR/Cas system have been used extensively for genome editing in cells of various types and species. The sequence-specific DNA-binding activities of these engineered DNA-binding molecules can also be utilized for other purposes, such as transcriptional activation, transcriptional repression, chromatin modification, visualization of genomic regions, and isolation of chromatin in a locus-specific manner. In this review, we describe applications of these engineered DNA-binding molecules for biological purposes other than genome editing.

  20. An Interdisciplinary Approach for Biology, Technology, Engineering and Mathematics (BTEM to Enhance 21st Century Skills in Malaysia.

    Directory of Open Access Journals (Sweden)

    Lee Chuo Hiong

    2015-07-01

    Full Text Available An interdisciplinary approach for Biology, Technology, Engineering and Mathematics (BTEM is suggested to develop 21st century skills in the Malaysian context. BTEM allows students to master biological knowledge and at the same time to be adroit in other sub discipline skills. Students master factual knowledge of biology and skills of the 21st century simultaneously. The two main teaching and learning strategies applied in BTEM are problem-based learning and inquiry-based learning. Students are exposed to real world problems that require them to undergo inquiry processes to discover the inventive solutions. The content knowledge of biology adheres to the Malaysian Integrated Curriculum for Secondary Schools. The essence of engineering is inventive problem solving. Incorporation of information communication technologies in teaching and learning will be able to fulfil the needs of the current Net Generation. Mathematics plays an important role as computational tools, especially in analysing data. The highlighted 21st century skills in BTEM include digital literacy, inventive thinking, effective communication, high productivity, and spiritual and noble values.

  1. Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization.

    Science.gov (United States)

    Whitaker, William B; Sandoval, Nicholas R; Bennett, Robert K; Fast, Alan G; Papoutsakis, Eleftherios T

    2015-06-01

    Synthetic methylotrophy is the development of non-native methylotrophs that can utilize methane and methanol as sole carbon and energy sources or as co-substrates with carbohydrates to produce metabolites as biofuels and chemicals. The availability of methane (from natural gas) and its oxidation product, methanol, has been increasing, while prices have been decreasing, thus rendering them as attractive fermentation substrates. As they are more reduced than most carbohydrates, methane and methanol, as co-substrates, can enhance the yields of biologically produced metabolites. Here we discuss synthetic biology and metabolic engineering strategies based on the native biology of aerobic methylotrophs for developing synthetic strains grown on methanol, with Escherichia coli as the prototype. Copyright © 2015. Published by Elsevier Ltd.

  2. Using Biographies of Outstanding Women in Bioengineering to Dispel Biology Teachers' Misperceptions of Engineers

    Science.gov (United States)

    Hoh, Yin Kiong

    2009-01-01

    The perception that engineers and scientists are intelligent Caucasian men who are socially inept and absent-minded people is prevalent among students of all levels, from elementary school to college. While the media may, by chance or choice, promote this image, the reality is that most engineers are men. These stereotypical images of engineers…

  3. Numerical Techniques for Chemical and Biological Engineers Using MATLAB A Simple Bifurcation Approach

    CERN Document Server

    Elnashaie, Said SEH; Affane, Chadia

    2007-01-01

    All reactive chemical and biological processes are highly nonlinear allowing for multiple steady states. This book addresses the bifurcation characteristics of chemical and biological processes as the general case and treats systems with a unique steady state as special cases. It includes a CD-ROM which contains nearly 100 MATLAB programs.

  4. Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing.

    Science.gov (United States)

    Chakravarti, Deboki; Cho, Jang Hwan; Weinberg, Benjamin H; Wong, Nicole M; Wong, Wilson W

    2016-04-18

    Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.

  5. Promoting convergence: The integrated graduate program in physical and engineering biology at Yale University, a new model for graduate education

    Science.gov (United States)

    Noble, Dorottya B.; Mochrie, Simon G. J.; O'Hern, Corey S.; Pollard, Thomas D.

    2016-01-01

    Abstract In 2008, we established the Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) at Yale University. Our goal was to create a comprehensive graduate program to train a new generation of scientists who possess a sophisticated understanding of biology and who are capable of applying physical and quantitative methodologies to solve biological problems. Here we describe the framework of the training program, report on its effectiveness, and also share the insights we gained during its development and implementation. The program features co‐teaching by faculty with complementary specializations, student peer learning, and novel hands‐on courses that facilitate the seamless blending of interdisciplinary research and teaching. It also incorporates enrichment activities to improve communication skills, engage students in science outreach, and foster a cohesive program cohort, all of which promote the development of transferable skills applicable in a variety of careers. The curriculum of the graduate program is integrated with the curricular requirements of several Ph.D.‐granting home programs in the physical, engineering, and biological sciences. Moreover, the wide‐ranging recruiting activities of the IGPPEB serve to enhance the quality and diversity of students entering graduate school at Yale. We also discuss some of the challenges we encountered in establishing and optimizing the program, and describe the institution‐level changes that were catalyzed by the introduction of the new graduate program. The goal of this article is to serve as both an inspiration and as a practical “how to” manual for those who seek to establish similar programs at their own institutions. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):537–549, 2016. PMID:27292366

  6. Comparing Two Definitions of Work for a Biological Quantum Heat Engine

    International Nuclear Information System (INIS)

    Xu You-Yang; Zhao Shun-Cai; Liu Juan

    2015-01-01

    Systems of photosynthetic reaction centres have been modelled as heat engines, while it has also been reported that the efficiency and power of such heat engines can be enhanced by quantum interference — a trait that has attracted much interest. We compare two definitions of the work of such a photosynthetic heat engine, i.e. definition A used by Weimer et al. and B by Dorfman et al. We also introduce a coherent interaction between donor and acceptor (CIDA) to demonstrate a reversible energy transport. We show that these two definitions of work can impart contradictory results, that is, CIDA enhances the power and efficiency of the photosynthetic heat engine with definition B but not with A. Additionally, we find that both reversible and irreversible excitation-energy transport can be described with definition A, but definition B can only model irreversible transport. As a result, we conclude that definition A is more suitable for photosynthetic systems than definition B. (paper)

  7. Biology

    Indian Academy of Sciences (India)

    I am particularly happy that the Academy is bringing out this document by Professor M S. Valiathan on Ayurvedic Biology. It is an effort to place before the scientific community, especially that of India, the unique scientific opportunities that arise out of viewing Ayurveda from the perspective of contemporary science, its tools ...

  8. Synthetic biology of metabolism: using natural variation to reverse engineer systems.

    Science.gov (United States)

    Kliebenstein, Daniel J

    2014-06-01

    A goal of metabolic engineering is to take a plant and introduce new or modify existing pathways in a directed and predictable fashion. However, existing data does not provide the necessary level of information to allow for predictive models to be generated. One avenue to reverse engineer the necessary information is to study the genetic control of natural variation in plant primary and secondary metabolism. These studies are showing that any engineering model will have to incorporate information about 1000s of genes in both the nuclear and organellar genome to optimize the function of the introduced pathway. Further, these genes may interact in an unpredictable fashion complicating any engineering approach as it moves from the one or two gene manipulation to higher order stacking efforts. Finally, metabolic engineering may be influenced by a previously unrecognized potential for a plant to measure the metabolites within it. In combination, these observations from natural variation provide a beginning to help improve current efforts at metabolic engineering. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. BioTCM-SE: a semantic search engine for the information retrieval of modern biology and traditional Chinese medicine.

    Science.gov (United States)

    Chen, Xi; Chen, Huajun; Bi, Xuan; Gu, Peiqin; Chen, Jiaoyan; Wu, Zhaohui

    2014-01-01

    Understanding the functional mechanisms of the complex biological system as a whole is drawing more and more attention in global health care management. Traditional Chinese Medicine (TCM), essentially different from Western Medicine (WM), is gaining increasing attention due to its emphasis on individual wellness and natural herbal medicine, which satisfies the goal of integrative medicine. However, with the explosive growth of biomedical data on the Web, biomedical researchers are now confronted with the problem of large-scale data analysis and data query. Besides that, biomedical data also has a wide coverage which usually comes from multiple heterogeneous data sources and has different taxonomies, making it hard to integrate and query the big biomedical data. Embedded with domain knowledge from different disciplines all regarding human biological systems, the heterogeneous data repositories are implicitly connected by human expert knowledge. Traditional search engines cannot provide accurate and comprehensive search results for the semantically associated knowledge since they only support keywords-based searches. In this paper, we present BioTCM-SE, a semantic search engine for the information retrieval of modern biology and TCM, which provides biologists with a comprehensive and accurate associated knowledge query platform to greatly facilitate the implicit knowledge discovery between WM and TCM.

  10. BioTCM-SE: A Semantic Search Engine for the Information Retrieval of Modern Biology and Traditional Chinese Medicine

    Directory of Open Access Journals (Sweden)

    Xi Chen

    2014-01-01

    Full Text Available Understanding the functional mechanisms of the complex biological system as a whole is drawing more and more attention in global health care management. Traditional Chinese Medicine (TCM, essentially different from Western Medicine (WM, is gaining increasing attention due to its emphasis on individual wellness and natural herbal medicine, which satisfies the goal of integrative medicine. However, with the explosive growth of biomedical data on the Web, biomedical researchers are now confronted with the problem of large-scale data analysis and data query. Besides that, biomedical data also has a wide coverage which usually comes from multiple heterogeneous data sources and has different taxonomies, making it hard to integrate and query the big biomedical data. Embedded with domain knowledge from different disciplines all regarding human biological systems, the heterogeneous data repositories are implicitly connected by human expert knowledge. Traditional search engines cannot provide accurate and comprehensive search results for the semantically associated knowledge since they only support keywords-based searches. In this paper, we present BioTCM-SE, a semantic search engine for the information retrieval of modern biology and TCM, which provides biologists with a comprehensive and accurate associated knowledge query platform to greatly facilitate the implicit knowledge discovery between WM and TCM.

  11. Human or animal homograft: could they have a future as a biological scaffold for engineered heart valves?

    Science.gov (United States)

    Dainese, L; Biglioli, P

    2010-06-01

    Tissue-engineered heart valves (TEHVs) promise to be the ideal heart valve replacement: they have the potential to grow and repair within the host, to minimise inflammatory and immunological responses and to limit thromboembolism. Viable cells included in TEHVs can theoretically adapt to a growing and changing environment exactly as a native biological structure. This could be extremely important in case of paediatric applications, where reoperations are frequently required to replace failed valve substitutes or to accommodate the growth of the patient. At present time the biological matrix from allogenic or xenogenic decellularized valves represents an appropriate valve scaffold in TEHVs, showing theoretically an ability to grow and repair within the host. Viable cells included in extracellular valve matrix can theoretically adapt to a growing and changing environment like the native biological structure. The aim of this paper is to present a review concerning the use of homograft and allograft valves as an ideal substrate for cardiac engineered tissue valves that represent an exciting possibility for in situ regeneration and repair of heart valves.

  12. Can Man Control His Biological Evolution? A Symposium on Genetic Engineering. Man's Responsibility to His Future

    Science.gov (United States)

    Hoagland, Hudson

    1972-01-01

    Biological evolution can be carried out in the laboratory. With new knowledge available in genetics, possibilities are raised that genetic characters can be transferred in the future to embryos according to a predetermined plan. (PS)

  13. Proceedings of the ninth annual conference of the IEEE Engineering in Medicine and Biology Society

    International Nuclear Information System (INIS)

    Anon.

    1987-01-01

    This book contains over 100 papers. Some of the titles are: Angular integrations and inter-projections correlation effects in CT reconstruction; Supercomputing environment for biomedical research; Program towards a computational molecular biology; Current problems in molecular biology computing; Signal averaging applied to positron emission tomography; First experimental results from a high spatial resolution PET prototype; and A coherent approach in computer-aided radiotherapy

  14. Suitability of a PLCL fibrous scaffold for soft tissue engineering applications: A combined biological and mechanical characterisation.

    Science.gov (United States)

    Laurent, Cédric P; Vaquette, Cédryck; Liu, Xing; Schmitt, Jean-François; Rahouadj, Rachid

    2018-04-01

    Poly(lactide-co-ε-caprolactone) (PLCL) has been reported to be a good candidate for tissue engineering because of its good biocompatibility. Particularly, a braided PLCL scaffold (PLL/PCL ratio = 85/15) has been recently designed and partially validated for ligament tissue engineering. In the present study, we assessed the in vivo biocompatibility of acellular and cellularised scaffolds in a rat model. We then determined its in vitro biocompatibility using stem cells issued from both bone marrow and Wharton Jelly. From a biological point of view, the scaffold was shown to be suitable for tissue engineering in all these cases. Secondly, while the initial mechanical properties of this scaffold have been previously reported to be adapted to load-bearing applications, we studied the evolution in time of the mechanical properties of PLCL fibres due to hydrolytic degradation. Results for isolated PLCL fibres were extrapolated to the fibrous scaffold using a previously developed numerical model. It was shown that no accumulation of plastic strain was to be expected for a load-bearing application such as anterior cruciate ligament tissue engineering. However, PLCL fibres exhibited a non-expected brittle behaviour after two months. This may involve a potential risk of premature failure of the scaffold, unless tissue growth compensates this change in mechanical properties. This combined study emphasises the need to characterise the properties of biomaterials in a pluridisciplinary approach, since biological and mechanical characterisations led in this case to different conclusions concerning the suitability of this scaffold for load-bearing applications.

  15. Systems biology and metabolic engineering of lactic acid bacteria for improved fermented foods

    NARCIS (Netherlands)

    Flahaut, N.A.L.; Vos, de W.M.

    2014-01-01

    Lactic acid bacteria have long been used in industrial dairy and other food fermentations that make use of their metabolic activities leading to products with specific organoleptic properties. Metabolic engineering is a rational approach to steer fermentations toward the production of desired

  16. Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System

    Science.gov (United States)

    Weiss, J.; Egea-Cortines, M.

    2008-01-01

    We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

  17. Enhancing the Internationalisation of Distance Education in the Biological Sciences: The DUNE Project and Genetic Engineering.

    Science.gov (United States)

    Leach, C. K.; And Others

    1997-01-01

    Describes the Distance Educational Network of Europe (DUNE) project that aims at enhancing the development of distance education in an international context. Highlights issues relating to the delivery of distance-learning courses in a transnational forum. Describes the genetic engineering course that aims at explaining the core techniques of…

  18. Biology versus engineering: the TMI accident as a case study in problems of dosimetry

    International Nuclear Information System (INIS)

    Aamodt, N.O.

    2000-01-01

    Contradictions between official results of studying impact on the environment arising from the Three-Mile-Island (TMI) accident in 1979 and scarce information about biological objects irradiation years later are considered. It is shown that some populations (public and animals) underwent radiation exposure by several orders exceeding the previously calculated doses, which is confirmed by cytogenetic and immune tests. The use of meteorological models, which do not consider complicated topography, gives rise to incorrect results. The situation that took shape around TMI provides a unique potentiality for biological dosimetry to demonstrate its efficiency and advantages in technical reconstruction of radiation exposure doses [ru

  19. 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.

    Science.gov (United States)

    Shi, Zhenyu; Vickers, Claudia E

    2016-12-01

    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.

  20. Finite element analysis (FEA): applying an engineering method to functional morphology in anthropology and human biology.

    Science.gov (United States)

    Panagiotopoulou, O

    2009-01-01

    A fundamental research question for morphologists is how morphological variation in the skeleton relates to function. Traditional approaches have advanced our understanding of form-function relationships considerably but have limitations. Strain gauges can only record strains on a surface, and the geometry of the structure can limit where they can be bonded. Theoretical approaches, such as geometric abstractions, work well on problems with simple geometries and material properties but biological structures typically have neither of these. Finite element analysis (FEA) is a method that overcomes these problems by reducing a complex geometry into a finite number of elements with simple geometries. In addition, FEA allows strain to be modelled across the entire surface of the structure and throughout the internal structure. With advances in the processing power of computers, FEA has become more accessible and as such is becoming an increasingly popular tool to address questions about form-function relationships in development and evolution, as well as human biology generally. This paper provides an introduction to FEA including a review of the sequence of steps needed for the generation of biologically accurate finite element models that can be used for the testing of biological and functional morphology hypotheses.

  1. Recent developments in systems biology and metabolic engineering of plant microbe interactions

    Directory of Open Access Journals (Sweden)

    Vishal Kumar

    2016-09-01

    Full Text Available Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant microbe interactions using gene editing and system biology tools towards the comprehension in improvement of plant traits. Further, system biology tools like FBA, OptKnock and constrain based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g. single nucleotide polymorphism (SNP detection, RNA-seq, proteomics and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.

  2. Convergent Inquiry in Science & Engineering: The Use of Atomic Force Microscopy in a Biology Class

    Science.gov (United States)

    Lee, Il-Sun; Byeon, Jung-Ho; Kwon, Yong-Ju

    2013-01-01

    The purpose of this study was to design a teaching method suitable for science high school students using atomic force microscopy. During their scientific inquiry procedure, high school students observed a micro-nanostructure of a biological sample, which is unobservable via an optical microscope. The developed teaching method enhanced students'…

  3. Food engineering and predictive microbiology: on the necessity to combine biological and physical kinetics.

    Science.gov (United States)

    Mafart, P

    2005-04-15

    Predictive microbiology is mainly applied in the area of risk assessment, but unusually regarded as a tool for the optimisation of processes, which needs the implementation of food engineering. Combination of predictive microbiology and food engineering allows both the assessment of a process in relation to risk and its optimisation. Intrinsic comparison between processes in relation to risk, on one hand, and the development of process optimisation tools on the other hand, necessitates the implementation of new concepts and the involvement of simplified and standard calculations based upon reference target strains and environmental conditions. Some conventional concepts related to heat treatments are extended, while some new ones related to bacterial growth are derived from the gamma concept of Marcel Zwietering.

  4. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production.

    Science.gov (United States)

    Bi, Changhao; Su, Peter; Müller, Jana; Yeh, Yi-Chun; Chhabra, Swapnil R; Beller, Harry R; Singer, Steven W; Hillson, Nathan J

    2013-11-13

    The chemoautotrophic bacterium Ralstonia eutropha can utilize H2/CO2 for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhydroxybutyrate) directly from CO2, little work has been done to develop genetic part libraries to enable such endeavors. We report the development of a toolbox for the metabolic engineering of Ralstonia eutropha H16. We have constructed a set of broad-host-range plasmids bearing a variety of origins of replication, promoters, 5' mRNA stem-loop structures, and ribosomal binding sites. Specifically, we analyzed the origins of replication pCM62 (IncP), pBBR1, pKT (IncQ), and their variants. We tested the promoters P(BAD), T7, P(xyls/PM), P(lacUV5), and variants thereof for inducible expression. We also evaluated a T7 mRNA stem-loop structure sequence and compared a set of ribosomal binding site (RBS) sequences derived from Escherichia coli, R. eutropha, and a computational RBS design tool. Finally, we employed the toolbox to optimize hydrocarbon production in R. eutropha and demonstrated a 6-fold titer improvement using the appropriate combination of parts. We constructed and evaluated a versatile synthetic biology toolbox for Ralstonia eutropha metabolic engineering that could apply to other microbial hosts as well.

  5. Towards biologically relevant synthetic designer matrices in 3D bioprinting for tissue engineering and regenerative medicine

    KAUST Repository

    Costa, Rúben M.

    2017-05-12

    3D bioprinting is one of the most promising technologies in tissue engineering and regenerative medicine. As new printing techniques and bioinks are getting developed, new cellular constructs with high resolution and functionality arise. Different to bioinks of animal, algal or plant origin, synthesized bioinks are proposed as superior biomaterials because their characteristics are fully under control. In this review, we will highlight the potential of synthetic biomaterials to be used as bioinks in 3D bioprinting to produce functionally enhanced matrices.

  6. In Vitro Biological Evaluation of Electrospun Polycaprolactone/Gelatine Nanofibrous Scaffold for Tissue Engineering

    OpenAIRE

    Lim, Mim Mim; Sun, Tao; Sultana, Naznin

    2015-01-01

    The fabrication of biocompatible and biodegradable scaffolds which mimic the native extracellular matrix of tissues to promote cell adhesion and growth is emphasized recently. Many polymers have been utilized in scaffold fabrication, but there is still a need to fabricate hydrophilic nanosized fibrous scaffolds with an appropriate degradation rate for skin tissue engineering applications. In this study, nanofibrous scaffolds of a biodegradable synthetic polymer, polycaprolactone (PCL), and bl...

  7. Reverse engineering: A key component of systems biology to unravel global abiotic stress cross-talk

    Directory of Open Access Journals (Sweden)

    Swetlana eFriedel

    2012-12-01

    Full Text Available Understanding the global abiotic stress response is an important stepping stone for the development of universal stress tolerance in plants in the era of climate change. Although co-occurrence of several stress factors (abiotic and biotic in nature is found to be frequent, current attempts are poor to understand the complex physiological processes impacting plant growth under combinatory factors. In this review article, we discuss the recent advances of reverse engineering approaches that led to seminal discoveries of key candidate regulatory genes involved in cross-talk of abiotic stress responses and summarised the available tools of reverse-engineering and its relevant application. Among the universally induced regulators involved in various abiotic stress responses, we highlight the importance of (i abscisic acid (ABA and jasmonic acid (JA hormonal cross-talks and (ii the central role of WRKY transcription factors, potentially mediating both abiotic and biotic stress responses. Such interactome networks help not only to derive hypotheses but also play a vital role in identifying key regulatory targets and interconnected hormonal responses. To explore the full potential of gene network inference in the area of abiotic stress tolerance, we need to validate hypotheses by implementing time-dependent gene expression data from genetically engineered plants with modulated expression of target genes. We further propose to combine information on gene-by-gene interactions with data from physical interaction platforms such as protein-protein or transcription factor (TF-gene networks.

  8. Biomimeticity in tissue engineering scaffolds through synthetic peptide modifications-altering chemistry for enhanced biological response.

    Science.gov (United States)

    Sreejalekshmi, Kumaran G; Nair, Prabha D

    2011-02-01

    Biomimetic and bioactive biomaterials are desirable as tissue engineering scaffolds by virtue of their capability to mimic natural environments of the extracellular matrix. Biomimeticity has been achieved by the incorporation of synthetic short peptide sequences into suitable materials either by surface modification or by bulk incorporation. Research in this area has identified several novel synthetic peptide segments, some of them with cell-specific interactions, which may serve as potential candidates for use in explicit tissue applications. This review focuses on the developments and prospective directions of incorporating short synthetic peptide sequences onto scaffolds for tissue engineering, with emphasis on the chemistry of peptide immobilization and subsequent cell responses toward modified scaffolds. The article provides a decision-tree-type flow chart indicating the most probable cellular events on a given peptide-modified scaffold along with the consolidated list of synthetic peptide sequences, supports as well as cell types used in various tissue engineering studies, and aims to serve as a quick reference guide to peptide chemists and material scientists interested in the field. 2010 Wiley Periodicals, Inc.

  9. Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering

    Directory of Open Access Journals (Sweden)

    Maiwald Thomas

    2009-10-01

    Full Text Available Abstract Background Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics of complex pathologies like cancer: acquiring information for a system understanding of complex reaction networks is time consuming and expensive. Stimulus response experiments (SRE have been used to gain a deeper insight into the details of biochemical mechanisms underlying cell life and functioning. Optimisation of the input time-profile, however, still remains a major area of research due to the complexity of the problem and its relevance for the task of information retrieval in systems biology-related experiments. Results We have addressed the problem of quantifying the information associated to an experiment using the Fisher Information Matrix and we have proposed an optimal experimental design strategy based on evolutionary algorithm to cope with the problem of information gathering in Systems Biology. On the basis of the theoretical results obtained in the field of control systems theory, we have studied the dynamical properties of the signals to be used in cell stimulation. The results of this study have been used to develop a microfluidic device for the automation of the process of cell stimulation for system identification. Conclusion We have applied the proposed approach to the Epidermal Growth Factor Receptor pathway and we observed that it minimises the amount of parametric uncertainty associated to the identified model. A statistical framework based on Monte-Carlo estimations of the uncertainty ellipsoid confirmed the superiority of optimally designed experiments over canonical inputs. The proposed approach can be easily extended to multiobjective formulations that can also take advantage of identifiability

  10. Microstructured surfaces engineered using biological templates: a facile approach for the fabrication of superhydrophobic surfaces

    Directory of Open Access Journals (Sweden)

    DUSAN LOSIC

    2008-10-01

    Full Text Available The fabrication of microstructured surfaces using biological templates was investigated with the aim of exploring of a facile and low cost approach for the fabrication of structured surfaces with superhydrophobic properties. Two soft lithographic techniques, i.e., replica moulding and nano-imprinting, were used to replicate the surfaces of a biological substrate. Leaves of the Agave plant (Agave attenuate, a cost-free biological template, were used as a model of a biosurface with superhydrophobic properties. The replication process was performed using two polymers: an elastomeric polymer, poly(dimethylsiloxane (PDMS, and a polyurethane (PU based, UV-curable polymer (NOA 60. In the first replication step, negative polymer replicas of the surface of leaves were fabricated, which were used as masters to fabricate positive polymer replicas by moulding and soft imprinting. The pattern with micro and nanostructures of the surface of the leaf possesses superhydrophobic properties, which was successfully replicated into both polymers. Finally, the positive replicas were coated with a thin gold film and modified with self-assembled monolayers (SAMs to verify the importance of the surface chemistry on the hydrophobic properties of the fabricated structures. Wetting (contact angle and structural (light microscopy and scanning electron microscopy characterisation was performed to confirm the hydrophobic properties of the fabricated surfaces (> 150°, as well as the precision and reproducibility of the replication process.

  11. Genome Engineering of Stem Cells for Autonomously Regulated, Closed-Loop Delivery of Biologic Drugs

    Directory of Open Access Journals (Sweden)

    Jonathan M. Brunger

    2017-05-01

    Full Text Available Chronic inflammatory diseases such as arthritis are characterized by dysregulated responses to pro-inflammatory cytokines such as interleukin-1 (IL-1 and tumor necrosis factor α (TNF-α. Pharmacologic anti-cytokine therapies are often effective at diminishing this inflammatory response but have significant side effects and are used at high, constant doses that do not reflect the dynamic nature of disease activity. Using the CRISPR/Cas9 genome-engineering system, we created stem cells that antagonize IL-1- or TNF-α-mediated inflammation in an autoregulated, feedback-controlled manner. Our results show that genome engineering can be used successfully to rewire endogenous cell circuits to allow for prescribed input/output relationships between inflammatory mediators and their antagonists, providing a foundation for cell-based drug delivery or cell-based vaccines via a rapidly responsive, autoregulated system. The customization of intrinsic cellular signaling pathways in stem cells, as demonstrated here, opens innovative possibilities for safer and more effective therapeutic approaches for a wide variety of diseases.

  12. In Vitro Biological Evaluation of Electrospun Polycaprolactone/Gelatine Nanofibrous Scaffold for Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Mim Mim Lim

    2015-01-01

    Full Text Available The fabrication of biocompatible and biodegradable scaffolds which mimic the native extracellular matrix of tissues to promote cell adhesion and growth is emphasized recently. Many polymers have been utilized in scaffold fabrication, but there is still a need to fabricate hydrophilic nanosized fibrous scaffolds with an appropriate degradation rate for skin tissue engineering applications. In this study, nanofibrous scaffolds of a biodegradable synthetic polymer, polycaprolactone (PCL, and blends of PCL with a natural polymer, gelatine (Ge, in three different compositions: 85 : 15, 70 : 30, and 50 : 50 were fabricated via an electrospinning technique. The nanofibrous scaffold prepared from 14% w/v PCL/Ge (70 : 30 exhibited more balanced properties of homogeneous nanofibres with an average fibre diameter of 155.60 ± 41.13 nm, 83% porosity, and surface roughness of 176.27 ± 2.53 nm. In vitro cell culture study using human skin fibroblasts (HSF demonstrated improved cell attachment with a flattened morphology on the PCL/Ge (70 : 30 nanofibrous scaffold and accelerated proliferation on day 3 compared to the PCL nanofibrous scaffold. These results show that the PCL/Ge (70 : 30 nanofibrous scaffold was more favourable and has the potential to be a promising scaffold for skin tissue engineering applications.

  13. A Novel Application of Synthetic Biology and Directed Evolution to Engineer Phage-based Antibiotics

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Meiye [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2014-09-01

    The emergence of multiple drug resistant bacteria poses threats to human health, agriculture and food safety. Annually over 100,000 deaths and up to $20 billion loss to the U.S. economy are attributed to multiple drug resistant bacteria. With only four new chemical antibiotics in the drug development pipeline, we are in dire need of new solutions to address the emerging threat of multiple drug resistance. We propose a paradigm-changing approach to address the multi-drug resistant bacteria problem by utilizing Synthetic Biology (SynBio) methodologies to create and evolve “designer” bacteriophages or phages – viruses that specifically infect bacteria – to infect and kill newly emerging pathogenic bacterial strains WITHOUT the need for chemical antibiotics. A major advantage of using phage to combat pathogenic bacteria is that phages can co-evolve with their bacterial host, and Sandia can be the first in the world to establish an industrial scale Synthetic Biology pipeline for phage directed evolution for safe, targeted, customizable solution to bacterial drug resistance. Since there is no existing phage directed evolution effort within or outside of Sandia, this proposal is suitable as a high-risk LDRD effort to create the first pipeline for such an endeavor. The high potential reward nature of this proposal will be the immediate impact in decontamination and restoration of surfaces and infrastructure, with longer term impact in human or animal therapeutics. The synthetic biology and screening approaches will lead to fundamental knowledge of phage/bacteria co-evolution, making Sandia a world leader in directed evolution of bacteriophages.

  14. Engineered Breast Cancer Cell Spheroids Reproduce Biologic Properties of Solid Tumors.

    Science.gov (United States)

    Ham, Stephanie L; Joshi, Ramila; Luker, Gary D; Tavana, Hossein

    2016-11-01

    Solid tumors develop as 3D tissue constructs. As tumors grow larger, spatial gradients of nutrients and oxygen and inadequate diffusive supply to cells distant from vasculature develops. Hypoxia initiates signaling and transcriptional alterations to promote survival of cancer cells and generation of cancer stem cells (CSCs) that have self-renewal and tumor-initiation capabilities. Both hypoxia and CSCs are associated with resistance to therapies and tumor relapse. This study demonstrates that 3D cancer cell models, known as tumor spheroids, generated with a polymeric aqueous two-phase system (ATPS) technology capture these important biological processes. Similar to solid tumors, spheroids of triple negative breast cancer cells deposit major extracellular matrix proteins. The molecular analysis establishes presence of hypoxic cells in the core region and expression of CSC gene and protein markers including CD24, CD133, and Nanog. Importantly, these spheroids resist treatment with chemotherapy drugs. A combination treatment approach using a hypoxia-activated prodrug, TH-302, and a chemotherapy drug, doxorubicin, successfully targets drug resistant spheroids. This study demonstrates that ATPS spheroids recapitulate important biological and functional properties of solid tumors and provide a unique model for studies in cancer research. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering

    Directory of Open Access Journals (Sweden)

    Kevin B. Reed

    2018-03-01

    Full Text Available Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.

  16. The EBI search engine: EBI search as a service-making biological data accessible for all.

    Science.gov (United States)

    Park, Young M; Squizzato, Silvano; Buso, Nicola; Gur, Tamer; Lopez, Rodrigo

    2017-07-03

    We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing 'Search as a Service' capabilities, which are the main topic of this article. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. The EBI search engine: EBI search as a service—making biological data accessible for all

    Science.gov (United States)

    Park, Young M.; Squizzato, Silvano; Buso, Nicola; Gur, Tamer

    2017-01-01

    Abstract We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL–EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing ‘Search as a Service’ capabilities, which are the main topic of this article. PMID:28472374

  18. Biological detoxification of the mycotoxin deoxynivalenol and its use in genetically engineered crops and feed additives.

    Science.gov (United States)

    Karlovsky, Petr

    2011-08-01

    Deoxynivalenol (DON) is the major mycotoxin produced by Fusarium fungi in grains. Food and feed contaminated with DON pose a health risk to humans and livestock. The risk can be reduced by enzymatic detoxification. Complete mineralization of DON by microbial cultures has rarely been observed and the activities turned out to be unstable. The detoxification of DON by reactions targeting its epoxide group or hydroxyl on carbon 3 is more feasible. Microbial strains that de-epoxidize DON under anaerobic conditions have been isolated from animal digestive system. Feed additives claimed to de-epoxidize trichothecenes enzymatically are on the market but their efficacy has been disputed. A new detoxification pathway leading to 3-oxo-DON and 3-epi-DON was discovered in taxonomically unrelated soil bacteria from three continents; the enzymes involved remain to be identified. Arabidopsis, tobacco, wheat, barley, and rice were engineered to acetylate DON on carbon 3. In wheat expressing DON acetylation activity, the increase in resistance against Fusarium head blight was only moderate. The Tri101 gene from Fusarium sporotrichioides was used; Fusarium graminearum enzyme which possesses higher activity towards DON would presumably be a better choice. Glycosylation of trichothecenes occurs in plants, contributing to the resistance of wheat to F. graminearum infection. Marker-assisted selection based on the trichothecene-3-O-glucosyltransferase gene can be used in breeding for resistance. Fungal acetyltransferases and plant glucosyltransferases targeting carbon 3 of trichothecenes remain promising candidates for engineering resistance against Fusarium head blight. Bacterial enzymes catalyzing oxidation, epimerization, and less likely de-epoxidation of DON may extend this list in future.

  19. An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system

    Directory of Open Access Journals (Sweden)

    Yusuke Kato

    2015-09-01

    Full Text Available Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8 per 105 cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3.

  20. Biological properties of coral GFP-type proteins provide clues for engineering novel optical probes and biosensors

    Science.gov (United States)

    Salih, Anya; Larkum, Anthony W.; Cronin, Thomas W.; Wiedenmann, Joerg; Szymczak, Ron; Cox, Guy C.

    2004-06-01

    In recent years, a variety of Green Fluorescent Protein (GFP)-like pigments have been discovered from corals and other marine organisms. They are widely used to expand the range of available GFP-type proteins in imaging applications, such as in vivo markers for gene expression and protein localization studies, FRET-based (Förster resonance energy transfer) multicolor imaging and biosensors. They have known diverse optical and biochemical properties but their in vivo spectral properties and biological function in marine organisms is only beginning to be understood. We have investigated their spectral diversity, optical properties and cellular microstructure in corals of the Great Barrier Reef with the aim of elucidating their photo-biological function/s as well as to identify novel proteins suitable for GFP-based technologies. We found numerous spectral variants, with emissions covering almost the full range of the visible spectrum. Many of these GFP-like proteins, especially in corals from the more extreme habitats, such as sun-exposed shallows or in deep water, showed a range of light-related spectral characteristics: high photostability, spectral tuning for energy transfer and dynamic photo-induced transformation properties. Intra-cellularly they were organized into spectral donor-acceptor pairs or even arrays, tuned for FRET. Coral color proteins thus offer an exciting potential to expand the use of the available GFPs in bio-imaging applications and as a basis for improved protein engineering.

  1. Preparation and biological properties of a novel composite scaffold of nano-hydroxyapatite/chitosan/carboxymethyl cellulose for bone tissue engineering

    Directory of Open Access Journals (Sweden)

    Chengdong Xiong

    2009-07-01

    Full Text Available Abstract In this study, we report the physico-chemical and biological properties of a novel biodegradable composite scaffold made of nano-hydroxyapatite and natural derived polymers of chitosan and carboxymethyl cellulose, namely, n-HA/CS/CMC, which was prepared by freeze-drying method. The physico-chemical properties of n-HA/CS/CMC scaffold were tested by infrared absorption spectra (IR, transmission electron microscope(TEM, scanning electron microscope(SEM, universal material testing machine and phosphate buffer solution (PBS soaking experiment. Besides, the biological properties were evaluated by MG63 cells and Mesenchymal stem cells (MSCs culture experiment in vitro and a short period implantation study in vivo. The results show that the composite scaffold is mainly formed through the ionic crossing-linking of the two polyions between CS and CMC, and n-HA is incorporated into the polyelectrolyte matrix of CS-CMC without agglomeration, which endows the scaffold with good physico-chemical properties such as highly interconnected porous structure, high compressive strength and good structural stability and degradation. More important, the results of cells attached, proliferated on the scaffold indicate that the scaffold is non-toxic and has good cell biocompatibility, and the results of implantation experiment in vivo further confirm that the scaffold has good tissue biocompatibility. All the above results suggest that the novel degradable n-HA/CS/CMC composite scaffold has a great potential to be used as bone tissue engineering material.

  2. Training mechanical engineering students to utilize biological inspiration during product development.

    Science.gov (United States)

    Bruck, Hugh A; Gershon, Alan L; Golden, Ira; Gupta, Satyandra K; Gyger, Lawrence S; Magrab, Edward B; Spranklin, Brent W

    2007-12-01

    The use of bio-inspiration for the development of new products and devices requires new educational tools for students consisting of appropriate design and manufacturing technologies, as well as curriculum. At the University of Maryland, new educational tools have been developed that introduce bio-inspired product realization to undergraduate mechanical engineering students. These tools include the development of a bio-inspired design repository, a concurrent fabrication and assembly manufacturing technology, a series of undergraduate curriculum modules and a new senior elective in the bio-inspired robotics area. This paper first presents an overview of the two new design and manufacturing technologies that enable students to realize bio-inspired products, and describes how these technologies are integrated into the undergraduate educational experience. Then, the undergraduate curriculum modules are presented, which provide students with the fundamental design and manufacturing principles needed to support bio-inspired product and device development. Finally, an elective bio-inspired robotics project course is present, which provides undergraduates with the opportunity to demonstrate the application of the knowledge acquired through the curriculum modules in their senior year using the new design and manufacturing technologies.

  3. Metabolic Engineering of Yeast and Plants for the Production of the Biologically Active Hydroxystilbene, Resveratrol

    Science.gov (United States)

    Jeandet, Philippe; Delaunois, Bertrand; Aziz, Aziz; Donnez, David; Vasserot, Yann; Cordelier, Sylvain; Courot, Eric

    2012-01-01

    Resveratrol, a stilbenic compound deriving from the phenyalanine/polymalonate route, being stilbene synthase the last and key enzyme of this pathway, recently has become the focus of a number of studies in medicine and plant physiology. Increased demand for this molecule for nutraceutical, cosmetic and possibly pharmaceutic uses, makes its production a necessity. In this context, the use of biotechnology through recombinant microorganisms and plants is particularly promising. Interesting results can indeed arise from the potential of genetically modified microorganisms as an alternative mechanism for producing resveratrol. Strategies used to tailoring yeast as they do not possess the genes that encode for the resveratrol pathway, will be described. On the other hand, most interest has centered in recent years, on STS gene transfer experiments from various origins to the genome of numerous plants. This work also presents a comprehensive review on plant molecular engineering with the STS gene, resulting in disease resistance against microorganisms and the enhancement of the antioxidant activities of several fruits in transgenic lines. PMID:22654481

  4. Characterization of mechanical and biological properties of 3-D scaffolds reinforced with zinc oxide for bone tissue engineering.

    Directory of Open Access Journals (Sweden)

    Pei Feng

    Full Text Available A scaffold for bone tissue engineering should have highly interconnected porous structure, appropriate mechanical and biological properties. In this work, we fabricated well-interconnected porous β-tricalcium phosphate (β-TCP scaffolds via selective laser sintering (SLS. We found that the mechanical and biological properties of the scaffolds were improved by doping of zinc oxide (ZnO. Our data showed that the fracture toughness increased from 1.09 to 1.40 MPam(1/2, and the compressive strength increased from 3.01 to 17.89 MPa when the content of ZnO increased from 0 to 2.5 wt%. It is hypothesized that the increase of ZnO would lead to a reduction in grain size and an increase in density of the strut. However, the fracture toughness and compressive strength decreased with further increasing of ZnO content, which may be due to the sharp increase in grain size. The biocompatibility of the scaffolds was investigated by analyzing the adhesion and the morphology of human osteoblast-like MG-63 cells cultured on the surfaces of the scaffolds. The scaffolds exhibited better and better ability to support cell attachment and proliferation when the content of ZnO increased from 0 to 2.5 wt%. Moreover, a bone like apatite layer formed on the surfaces of the scaffolds after incubation in simulated body fluid (SBF, indicating an ability of osteoinduction and osteoconduction. In summary, interconnected porous β-TCP scaffolds doped with ZnO were successfully fabricated and revealed good mechanical and biological properties, which may be used for bone repair and replacement potentially.

  5. Engineering catalyst microenvironments for metal-catalyzed hydrogenation of biologically derived platform chemicals.

    Science.gov (United States)

    Schwartz, Thomas J; Johnson, Robert L; Cardenas, Javier; Okerlund, Adam; Da Silva, Nancy A; Schmidt-Rohr, Klaus; Dumesic, James A

    2014-11-17

    It is shown that microenvironments formed around catalytically active sites mitigate catalyst deactivation by biogenic impurities that are present during the production of biorenewable chemicals from biologically derived species. Palladium and ruthenium catalysts are inhibited by the presence of sulfur-containing amino acids; however, these supported metal catalysts are stabilized by overcoating with poly(vinyl alcohol) (PVA), which creates a microenvironment unfavorable for biogenic impurities. Moreover, deactivation of Pd catalysts by carbon deposition from the decomposition of highly reactive species is suppressed by the formation of bimetallic PdAu nanoparticles. Thus, a PVA-overcoated PdAu catalyst was an order of magnitude more stable than a simple Pd catalyst in the hydrogenation of triacetic acid lactone, which is the first step in the production of biobased sorbic acid. A PVA-overcoated Ru catalyst showed a similar improvement in stability during lactic acid hydrogenation to propylene glycol in the presence of methionine. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Review: Metabolic engineering of unusual lipids in the synthetic biology era.

    Science.gov (United States)

    Aznar-Moreno, Jose A; Durrett, Timothy P

    2017-10-01

    The plant kingdom produces a variety of fatty acid structures, many of which possess functional groups useful for industrial applications. The species that produce these unusual fatty acids are often not suitable for large scale commercial production. The ability to create genetically modified plants, together with emerging synthetic biology approaches, offers the potential to develop alternative oil seed crops capable of producing high levels of modified lipids. In some cases, by combining genes from different species, non-natural lipids with a targeted structure can be conceived. However, the expression of the biosynthetic enzymes responsible for the synthesis of unusual fatty acids typically results in poor accumulation of the desired product. An improved understanding of fatty acid flux from synthesis to storage revealed that specialized enzymes are needed to traffic unusual fatty acids. Co-expression of some of these additional enzymes has incrementally increased the levels of unusual fatty acids in transgenic seeds. Understanding how the introduced pathways interact with the endogenous pathways will be important for further enhancing the levels of unusual fatty acids in transgenic plants. Eliminating endogenous activities, as well as segregating the different pathways, represent strategies to further increase accumulation of unusual lipids. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Frustrated bistability as a means to engineer oscillations in biological systems.

    Science.gov (United States)

    Krishna, S; Semsey, S; Jensen, M H

    2009-05-21

    Oscillations play an important physiological role in a variety of biological systems. For example, respiration and carbohydrate synthesis are coupled to the circadian clock in cyanobacteria (Ishiura et al 1998 Science 281 1519) and ultradian oscillations with time periods of a few hours have been observed in immune response (NF-kappaB, Hoffmann et al 2002 Science 298 1241, Neson et al 2004 Science 306 704), apoptosis (p53, Lahav et al 2004 Nat. Genet. 36 53), development (Hes, Hirata et al 2002 Science 298 840) and growth hormone secretion (Plotsky and Vale 1985 Science 230 461, Zeitler et al 1991 Proc. Natl. Acad. Sci. USA 88 8920). Here we discuss how any bistable system can be 'frustrated' to produce oscillations of a desired nature--we use the term frustration, in analogy to frustrated spins in antiferromagnets, to refer to the addition of a negative feedback loop that destabilizes the bistable system. We show that the molecular implementation can use a wide variety of methods ranging from translation regulation, using small non-coding RNAs, to targeted protein modification to transcriptional regulation. We also introduce a simple graphical method for determining whether a particular implementation will produce oscillations. The shape of the resulting oscillations can be readily tuned to produce spiky and asymmetric oscillations--quite different from the shapes produced by synthetic oscillators (Elowitz and Leibler 2000 Nature 403 335, Fung et al 2005 Nature 435 118). The time period and amplitude can also be manipulated and these oscillators are easy to reset or switch on and off using a tunable external input. The mechanism of frustrated bistability could thus prove to be an easily implementable way to synthesize flexible, designable oscillators.

  8. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    Science.gov (United States)

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  9. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions and novel technologies

    Directory of Open Access Journals (Sweden)

    Frank eSchreiber

    2012-10-01

    Full Text Available Nitrous oxide (N2O is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH or the reduction of nitrite (NO2- to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO2- to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria. In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO2-, NH2OH and nitroxyl (HNO. Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser based absorption spectroscopy. In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build-up.

  10. Doped tricalcium phosphate bone tissue engineering scaffolds using sucrose as template and microwave sintering: enhancement of mechanical and biological properties.

    Science.gov (United States)

    Ke, Dongxu; Bose, Susmita

    2017-09-01

    β-tricalcium phosphate (β-TCP) is a widely used biocompatible ceramic in orthopedic and dental applications. However, its osteoinductivity and mechanical properties still require improvements. In this study, porous β-TCP and MgO/ZnO-TCP scaffolds were prepared by the thermal decomposition of sucrose. Crack-free cylindrical scaffolds could only be prepared with the addition of MgO and ZnO due to their stabilization effects. Porous MgO/ZnO-TCP scaffolds with a density of 61.39±0.66%, an estimated pore size of 200μm and a compressive strength of 24.96±3.07MPa were prepared by using 25wt% sucrose after conventional sintering at 1250°C. Microwave sintering further increased the compressive strength to 37.94±6.70MPa, but it decreased the open interconnected porosity to 8.74±1.38%. In addition, the incorporation of polycaprolactone (PCL) increased 22.36±3.22% of toughness while maintaining its compressive strength at 25.45±2.21MPa. Human osteoblast cell line was seeded on scaffolds to evaluate the effects of MgO/ZnO and PCL on the biological property of β-TCP in vitro. Both MgO/ZnO and PCL improved osteoinductivity of β-TCP. PCL also decreased osteoblastic apoptosis due to its particular surface chemistry. This novel porous MgO/ZnO-TCP scaffold with PCL shows improved mechanical and biological properties, which has great potential in bone tissue engineering applications. Copyright © 2017. Published by Elsevier B.V.

  11. Design and validation of a dynamic cell-culture system for bone biology research and exogenous tissue-engineering applications.

    Science.gov (United States)

    Allori, Alexander C; Davidson, Edward H; Reformat, Derek D; Sailon, Alexander M; Freeman, James; Vaughan, Adam; Wootton, David; Clark, Elizabeth; Ricci, John L; Warren, Stephen M

    2016-10-01

    Bone lacunocanalicular fluid flow ensures chemotransportation and provides a mechanical stimulus to cells. Traditional static cell-culture methods are ill-suited to study the intricacies of bone biology because they ignore the three-dimensionality of meaningful cellular networks and the lacunocanalicular system; furthermore, reliance on diffusion alone for nutrient supply and waste product removal effectively limits scaffolds to 2-3 mm thickness. In this project, a flow-perfusion system was custom-designed to overcome these limitations: eight adaptable chambers housed cylindrical cell-seeded scaffolds measuring 12 or 24 mm in diameter and 1-10 mm in thickness. The porous scaffolds were manufactured using a three-dimensional (3D) periodic microprinting process and were composed of hydroxyapatite/tricalcium phosphate with variable thicknesses, strut sizes, pore sizes and structural configurations. A multi-channel peristaltic pump drew medium from parallel reservoirs and perfused it through each scaffold at a programmable rate. Hermetically sealed valves permitted sampling or replacement of medium. A gas-permeable membrane allowed for gas exchange. Tubing was selected to withstand continuous perfusion for > 2 months without leakage. Computational modelling was performed to assess the adequacy of oxygen supply and the range of fluid shear stress in the bioreactor-scaffold system, using 12 × 6 mm scaffolds, and these models suggested scaffold design modifications that improved oxygen delivery while enhancing physiological shear stress. This system may prove useful in studying complex 3D bone biology and in developing strategies for engineering thick 3D bone constructs. Copyright © 2013 John Wiley & Sons, Ltd. Copyright © 2013 John Wiley & Sons, Ltd.

  12. Enzyme engineering: A synthetic biology approach for more effective library generation and automated high-throughput screening

    Science.gov (United States)

    Ebert, Maximilian C. C. J. C.; Mugford, Paul F.; Pelletier, Joelle N.

    2017-01-01

    The Golden Gate strategy entails the use of type IIS restriction enzymes, which cut outside of their recognition sequence. It enables unrestricted design of unique DNA fragments that can be readily and seamlessly recombined. Successfully employed in other synthetic biology applications, we demonstrate its advantageous use to engineer a biocatalyst. Hot-spots for mutations were individuated in three distinct regions of Candida antarctica lipase A (Cal-A), the biocatalyst chosen as a target to demonstrate the versatility of this recombination method. The three corresponding gene segments were subjected to the most appropriate method of mutagenesis (targeted or random). Their straightforward reassembly allowed combining products of different mutagenesis methods in a single round for rapid production of a series of diverse libraries, thus facilitating directed evolution. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by development of a general, automated method for visual discrimination of the hydrolysis of varied substrates by whole cells. PMID:28178357

  13. Efficacy of genetically engineered biological agents in the treatment of uveitis associated with rheumatic diseases in children

    Directory of Open Access Journals (Sweden)

    V V Neroyev

    2012-01-01

    Full Text Available The efficiency of incorporating genetically engineered biological agents (GEBAs into a combination treatment regimen for rheumatic diseases (RD (juvenile idiopathic arthritis, Behcet's disease in relation to associated uveitis of varying severity was studied in 92 children aged 2 to 17 years. The follow-up lasted 1.5 to 49 months. Twenty-three patients took consecutively 2 to 5 GEBAs. When infliximab was used, remission of uveitis occurred in 21% of 38 children and the disease activity and/or recurrence rates reduced in an additional 21%. These were in 45 and 38.6% of 44 patients on adalimumab (ADA and in 27.8 and 27.8% of 18 patients on abatacept, respectively. There was an association of the efficiency of therapy with the severity of uveitis at the start of treatment. The use of ADA induced a steady remission of panuveitis resistant to therapy with glucocorticoids and cyclosporine in both patients with Behcet's disease. One of 4 rituximab-treated patients achieved a steady remission. Tocilizumab therapy caused an exacerbation of uveitis in 1 patient. The postoperative period showed no inflammatory complications in most cases (37 operations, 26 eyes, 20 patients. No local adverse reactions were seen; systemic reactions occurred in 14% of the patients, this caused GEBAs to be discontinued in 7%. There is evidence for a need for further investigations into the efficacy of GEBAs in RD-associated uveitis in children in order to define success criteria, differentiated indications, and therapy regimens.

  14. Enzyme engineering: A synthetic biology approach for more effective library generation and automated high-throughput screening.

    Directory of Open Access Journals (Sweden)

    Daniela Quaglia

    Full Text Available The Golden Gate strategy entails the use of type IIS restriction enzymes, which cut outside of their recognition sequence. It enables unrestricted design of unique DNA fragments that can be readily and seamlessly recombined. Successfully employed in other synthetic biology applications, we demonstrate its advantageous use to engineer a biocatalyst. Hot-spots for mutations were individuated in three distinct regions of Candida antarctica lipase A (Cal-A, the biocatalyst chosen as a target to demonstrate the versatility of this recombination method. The three corresponding gene segments were subjected to the most appropriate method of mutagenesis (targeted or random. Their straightforward reassembly allowed combining products of different mutagenesis methods in a single round for rapid production of a series of diverse libraries, thus facilitating directed evolution. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by development of a general, automated method for visual discrimination of the hydrolysis of varied substrates by whole cells.

  15. Mechanical, Biological and Electrochemical Investigations of Advanced Micro/Nano Materials for Tissue Engineering and Energy Storage

    Science.gov (United States)

    Pu, Juan

    Various micro/nano materials have been extensively studied for applications in tissue engineering and energy storage. Tissue engineering seeks to repair or replace damaged tissue by integrating approaches from cellular/molecular biology and material chemistry/engineering. A major challenge is the consistent design of three-dimensional (3D) scaffolds that mimic the structure and biological functions of extracellular matrix (ECM), guide cell migration, provide mechanical support, and regulate cell activity. Electrospun micro/nanofibers have been investigated as promising tissue engineering scaffolds because they resemble native ECM and possess tunable surface morphologies. Supercapacitors, one of the energy storage devices, bridge the performance gap between rechargeable batteries and conventional capacitors. Active electrode materials of supercapacitors must possess high specific surface area, high conductivity, and good electrochemical properties. Carbon-based micro/nano-particles, such as graphene, activated carbon (AC), and carbon nanotubes, are commonly used as active electrode materials for storing charge in supercapacitors by the electrical double layer mechanism due to their high specific surface area and excellent conductivity. In this thesis, the mechanical properties of electrospun bilayer microfibrous membranes were investigated for potential applications in tissue engineering. Bilayer microfibrous membranes of poly(l-lactic acid) (PLLA) were fabricated by electrospinning using a parallel-disk mandrel configuration, which resulted in the sequential deposition of a layer with aligned fibers (AFL) across the two parallel disks and a layer with random fibers (RFL), both deposited by a single process step. The membrane structure and fiber alignment were characterized by scanning electron microscopy and two-dimensional fast Fourier transform. Because of the intricacies of the generated electric field, the bilayer membranes exhibited higher porosity than the

  16. 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.

  17. Evaluation of Biological Toxicity of CdTe Quantum Dots with Different Coating Reagents according to Protein Expression of Engineering Escherichia coli

    Directory of Open Access Journals (Sweden)

    Wei Xu

    2015-01-01

    Full Text Available The results obtained from toxicity assessment of quantum dots (QDs can be used to establish guidelines for the application of QDs in bioimaging. This paper focused on the design of a novel method to evaluate the toxicity of CdTe QDs using engineering Escherichia coli as a model. The toxicity of mercaptoacetic acid (MPA, glutathione (GSH, and L-cysteine (Cys capped CdTe QDs was analyzed according to the heterologous protein expression in BL21/DE3, engineering Escherichia coli extensively used for protein expression. The results showed that the MPA-CdTe QDs had more serious toxicity than the other two kinds of CdTe QDs. The microscopic images and SEM micrographs further proved that both the proliferation and the protein expression of engineering Escherichia coli were inhibited after treatment with MPA-CdTe QDs. The proposed method is important to evaluate biological toxicity of both QDs and other nanoparticles.

  18. MORE: mixed optimization for reverse engineering--an application to modeling biological networks response via sparse systems of nonlinear differential equations.

    Science.gov (United States)

    Sambo, Francesco; de Oca, Marco A Montes; Di Camillo, Barbara; Toffolo, Gianna; Stützle, Thomas

    2012-01-01

    Reverse engineering is the problem of inferring the structure of a network of interactions between biological variables from a set of observations. In this paper, we propose an optimization algorithm, called MORE, for the reverse engineering of biological networks from time series data. The model inferred by MORE is a sparse system of nonlinear differential equations, complex enough to realistically describe the dynamics of a biological system. MORE tackles separately the discrete component of the problem, the determination of the biological network topology, and the continuous component of the problem, the strength of the interactions. This approach allows us both to enforce system sparsity, by globally constraining the number of edges, and to integrate a priori information about the structure of the underlying interaction network. Experimental results on simulated and real-world networks show that the mixed discrete/continuous optimization approach of MORE significantly outperforms standard continuous optimization and that MORE is competitive with the state of the art in terms of accuracy of the inferred networks.

  19. State-of-the-art protein engineering approaches using biological macromolecules: A review from immobilization to implementation view point.

    Science.gov (United States)

    Bilal, Muhammad; Iqbal, Hafiz M N; Guo, Shuqi; Hu, Hongbo; Wang, Wei; Zhang, Xuehong

    2018-03-01

    Over the past years, technological and scientific advances have proven biocatalysis as a sustainable alternative than traditional chemical catalysis including organo- or metallocatalysis. In this context, immobilization based approaches represent simple but effective routes for engineering enzyme catalysts with higher activities than wild-type derivatives. Many enzymes including oxidoreductases have been engineered by rational and directed evolution, to realize the catalytic activity, enantioselectivity, and stability attributes which are essential for their biotechnological exploitation. Induce yet stable activity in enzyme catalysis offer new insights and motivation to engineer efficient catalysts for practical and commercial purposes. It has now become possible to envisage substrate accessibility to the catalytic site of the enzyme by current computational capabilities that reduce the experimental work related to the enzyme selection, screening, and engineering. Herein, state-of-the-art protein engineering approaches for improving enzymatic activities including chemical modification, directed evolution, and rational design or their combination methods are discussed. The emphasis is also given to the applications of the resulting tailored catalysts ranging from fine chemicals to novel pharmaceutical compounds that use biocatalysts as a vital step. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Hybrid chitosan-ß-glycerol phosphate-gelatin nano-/micro fibrous scaffolds with suitable mechanical and biological properties for tissue engineering.

    Science.gov (United States)

    Lotfi, Marzieh; Bagherzadeh, Roohollah; Naderi-Meshkin, Hojjat; Mahdipour, Elahe; Mafinezhad, Asghar; Sadeghnia, Hamid Reza; Esmaily, Habibollah; Maleki, Masoud; Hasssanzadeh, Halimeh; Ghayaour-Mobarhan, Majid; Bidkhori, Hamid Reza; Bahrami, Ahmad Reza

    2016-03-01

    Scaffold-based tissue engineering is considered as a promising approach in the regenerative medicine. Graft instability of collagen, by causing poor mechanical properties and rapid degradation, and their hard handling remains major challenges to be addressed. In this research, a composite structured nano-/microfibrous scaffold, made from a mixture of chitosan-ß-glycerol phosphate-gelatin (chitosan-GP-gelatin) using a standard electrospinning set-up was developed. Gelatin-acid acetic and chitosan ß-glycerol phosphate-HCL solutions were prepared at ratios of 30/70, 50/50, 70/30 (w/w) and their mechanical and biological properties were engineered. Furthermore, the pore structure of the fabricated nanofibrous scaffolds was investigated and predicted using a theoretical model. Higher gelatin concentrations in the polymer blend resulted in significant increase in mean pore size and its distribution. Interaction between the scaffold and the contained cells was also monitored and compared in the test and control groups. Scaffolds with higher chitosan concentrations showed higher rate of cell attachment with better proliferation property, compared with gelatin-only scaffolds. The fabricated scaffolds, unlike many other natural polymers, also exhibit non-toxic and biodegradable properties in the grafted tissues. In conclusion, the data clearly showed that the fabricated biomaterial is a biologically compatible scaffold with potential to serve as a proper platform for retaining the cultured cells for further application in cell-based tissue engineering, especially in wound healing practices. These results suggested the potential of using mesoporous composite chitosan-GP-gelatin fibrous scaffolds for engineering three-dimensional tissues with different inherent cell characteristics. © 2015 Wiley Periodicals, Inc.

  1. Computer-aided biomedical imaging and graphics physiological measurement and control. Proceedings of the Biological Engineering Society, 6th Nordic meeting, Aberdeen, July 1984

    International Nuclear Information System (INIS)

    Jordan, M.; Perkins, W.J.; Upton, J.; Markham, J.

    1984-01-01

    The proceedings of the Sixth Nordic Meeting of the Biological Engineering Society held in Aberdeen in July 1984 on computer-aided biomedical imaging and graphics and physiological measurement and control are presented. The summaries of the papers presented cover the use of computer imaging and graphics in ultrasonic imaging, nuclear medicine, radiology, biomedical radiography, tomography and NMR imaging. The papers on the use of computers in physiological measurement and control cover subject headings including computer-based instrumentation, transducers, monitoring and control, assessment and therapy, clinical measurement, blood flow and signal processing and analysis. (U.K.)

  2. An ecologically-based method for selecting ecological indicators for assessing risks to biological diversity from genetically-engineered plants

    DEFF Research Database (Denmark)

    Andow, D. A.; Lövei, Gabor L; Arpaia, Salvatore

    2013-01-01

    The environmental risks associated with genetically-engineered (GE) organisms have been controversial, and so have the models for the assessment of these risks. We propose an ecologically-based environmental risk assessment (ERA) model that follows the 1998 USEPA guidelines, focusing on potential...

  3. Global Survey of Research and Capabilities in Genetically Engineered Organisms That Could be Used in Biological Warfare or Bioterrorism

    Science.gov (United States)

    2008-12-01

    information needed to carry out biological processes and construct other biomolecules, such as messenger RNA and proteins. The reader already familiar ...for Emerging Infectious Diseases and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong Cuba: Institute de Medicina ...Hospital de Bellvitge, Universidad de Barcelona • Unidad de Medicina Tropical, Servicio de Enfermedades Infecciosas, Hospital Ramon y Cajal, Madrid

  4. A new composite hydrogel combining the biological properties of collagen with the mechanical properties of a supramolecular scaffold for bone tissue engineering.

    Science.gov (United States)

    Maisani, Mathieu; Ziane, Sophia; Ehret, Camille; Levesque, Lucie; Siadous, Robin; Le Meins, Jean-François; Chevallier, Pascale; Barthélémy, Philippe; De Oliveira, Hugo; Amédée, Joëlle; Mantovani, Diego; Chassande, Olivier

    2018-03-01

    Tissue engineering is a promising alternative to autografts, allografts, or biomaterials to address the treatment of severe and large bone lesions. Classically, tissue engineering products associate a scaffold and cells and are implanted or injected into the lesion. These cells must be embedded in an appropriate biocompatible scaffold, which offers a favourable environment for their survival and differentiation. Here, we designed a composite hydrogel composed of collagen I, an extracellular matrix protein widely used in several therapeutic applications, which we associated with a physical hydrogel generated from a synthetic small amphiphilic molecule. This composite showed improved mechanical and biological characteristics as compared with gels obtained from each separate compound. Incorporation of the physical hydrogel prevented shrinkage of collagen and cell diffusion out of the gel and yielded a gel with a higher elastic modulus than those of gels obtained with each component alone. The composite hydrogel allowed cell adhesion and proliferation in vitro and long-term cell survival in vivo. Moreover, it promoted the differentiation of human adipose-derived stem cells in the absence of any osteogenic factors. In vivo, cells embedded in the composite gel and injected subcutaneously in immunodeficient mice produced lamellar osteoid tissue and differentiated into osteoblasts. This study points this new composite hydrogel as a promising scaffold for bone tissue engineering applications. Copyright © 2017 John Wiley & Sons, Ltd.

  5. Creating biological nanomaterials using synthetic biology.

    Science.gov (United States)

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  6. Creating biological nanomaterials using synthetic biology

    International Nuclear Information System (INIS)

    Rice, MaryJoe K; Ruder, Warren C

    2014-01-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

  7. Metabolic Engineering X Conference

    Energy Technology Data Exchange (ETDEWEB)

    Flach, Evan [American Institute of Chemical Engineers

    2015-05-07

    The International Metabolic Engineering Society (IMES) and the Society for Biological Engineering (SBE), both technological communities of the American Institute of Chemical Engineers (AIChE), hosted the Metabolic Engineering X Conference (ME-X) on June 15-19, 2014 at the Westin Bayshore in Vancouver, British Columbia. It attracted 395 metabolic engineers from academia, industry and government from around the globe.

  8. Manufacturing and Evaluation of a Biologically Inspired Engineered MAV Wing Compared to the Manduca Sexta Wing Under Simulated Flapping Conditions

    Science.gov (United States)

    2011-03-24

    thorax to the wings will continue for a short period of time, preserving the integrity of these wings. This small window was considered in order to...PromasterTM Digital XR EDO Aspherical LD (IF) 17-50 mm 1:2.8 Macro φ 67. Photomodeler provides the means to calibrate a camera via subroutine within...36. 20. DeLeón, N., O’Hara, R., and Palazotto, A., “Manufacturing of Engineering Bio- logically Inspired Flapping Wings,” 25th Annual US- Japan

  9. A proposal to establish an international network in molecular microbiology and genetic engineering for scientific cooperation and prevention of misuse of biological sciences in the framework of science for peace

    International Nuclear Information System (INIS)

    Becker, Y.

    1998-01-01

    The conference on 'Science and Technology for Construction of Peace' which was organized by the Landau Network Coordination Center and A. Volta Center for Scientific Culture dealt with conversion of military and technological capacities into sustainable civilian application. The ideas regarding the conversion of nuclear warheads into nuclear energy for civilian-use led to the idea that the extension of this trend of thought to molecular biology and genetic engineering, will be a useful contribution to Science for Peace. This idea of developing a Cooperation Network in Molecular Biology and Genetic Engineering that will function parallel to and with the Landau Network Coordination in the 'A. Volta' Center was discussed in the Second International Symposium on Science for Peace, Jerusalem, January 1997. It is the reason for the inclusion of the biological aspects in the deliberations of our Forum. It is hoped that the establishment of an international network in molecular biology and genetic engineering, similar to the Landau Network in physics, will support and achieve the decommissioning of biological weapons. Such a network in microbiology and genetic engineering will contribute to the elimination of biological weapons and to contributions to Science for Peace and to Culture of Peace activities of UNESCO. (author)

  10. Systems biology and metabolic modelling unveils limitations to polyhydroxybutyrate accumulation in sugarcane leaves; lessons for C4 engineering.

    Science.gov (United States)

    McQualter, Richard B; Bellasio, Chandra; Gebbie, Leigh K; Petrasovits, Lars A; Palfreyman, Robin W; Hodson, Mark P; Plan, Manuel R; Blackman, Deborah M; Brumbley, Stevens M; Nielsen, Lars K

    2016-02-01

    In planta production of the bioplastic polyhydroxybutyrate (PHB) is one important way in which plant biotechnology can address environmental problems and emerging issues related to peak oil. However, high biomass C4 plants such as maize, switch grass and sugarcane develop adverse phenotypes including stunting, chlorosis and reduced biomass as PHB levels in leaves increase. In this study, we explore limitations to PHB accumulation in sugarcane chloroplasts using a systems biology approach, coupled with a metabolic model of C4 photosynthesis. Decreased assimilation was evident in high PHB-producing sugarcane plants, which also showed a dramatic decrease in sucrose and starch content of leaves. A subtle decrease in the C/N ratio was found which was not associated with a decrease in total protein content. An increase in amino acids used for nitrogen recapture was also observed. Based on the accumulation of substrates of ATP-dependent reactions, we hypothesized ATP starvation in bundle sheath chloroplasts. This was supported by mRNA differential expression patterns. The disruption in ATP supply in bundle sheath cells appears to be linked to the physical presence of the PHB polymer which may disrupt photosynthesis by scattering photosynthetically active radiation and/or physically disrupting thylakoid membranes. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  11. How the biodiversity sciences may aid biological tools and ecological engineering to assess the impact of climatic changes.

    Science.gov (United States)

    Morand, S; Guégan, J-F

    2008-08-01

    This paper addresses how climate changes interact with other global changes caused by humans (habitat fragmentation, changes in land use, bioinvasions) to affect biodiversity. Changes in biodiversity at all levels (genetic, population and community) affect the functioning of ecosystems, in particular host-pathogen interactions, with major consequences in health ecology (emergence and re-emergence; the evolution of virulence and resistance). In this paper, the authors demonstrate that the biodiversity sciences, epidemiological theory and evolutionary ecology are indispensable in assessing the impact of climate changes, and also for modelling the evolution of host-pathogen interactions in a changing environment. The next step is to apply health ecology to the science of ecological engineering.

  12. Space Synthetic Biology (SSB)

    Data.gov (United States)

    National Aeronautics and Space Administration — This project focused on employing advanced biological engineering and bioelectrochemical reactor systems to increase life support loop closure and in situ resource...

  13. Mechanical and biological properties of the micro-/nano-grain functionally graded hydroxyapatite bioceramics for bone tissue engineering.

    Science.gov (United States)

    Zhou, Changchun; Deng, Congying; Chen, Xuening; Zhao, Xiufen; Chen, Ying; Fan, Yujiang; Zhang, Xingdong

    2015-08-01

    Functionally graded materials (FGM) open the promising approach for bone tissue repair. In this study, a novel functionally graded hydroxyapatite (HA) bioceramic with micrograin and nanograin structure was fabricated. Its mechanical properties were tailored by composition of micrograin and nanograin. The dynamic mechanical analysis (DMA) indicated that the graded HA ceramics had similar mechanical property compared to natural bones. Their cytocompatibility was evaluated via fluorescent microscopy and MTT colorimetric assay. The viability and proliferation of rabbit bone marrow mesenchymal stem cells (BMSCs) on ceramics indicated that this functionally graded HA ceramic had better cytocompatibility than conventional HA ceramic. This study demonstrated that functionally graded HA ceramics create suitable structures to satisfy both the mechanical and biological requirements of bone tissues. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. PHBV/PLLA-based composite scaffolds fabricated using an emulsion freezing/freeze-drying technique for bone tissue engineering: surface modification and in vitro biological evaluation

    International Nuclear Information System (INIS)

    Sultana, Naznin; Wang Min

    2012-01-01

    Tissue engineering combines living cells with biodegradable materials and/or bioactive components. Composite scaffolds containing biodegradable polymers and nanosized osteoconductive bioceramic with suitable properties are promising for bone tissue regeneration. In this paper, based on blending two biodegradable and biocompatible polymers, namely poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) and poly(l-lactic acid) (PLLA) with incorporated nano hydroxyapatite (HA), three-dimensional composite scaffolds with controlled microstructures and an interconnected porous structure, together with high porosity, were fabricated using an emulsion freezing/freeze-drying technique. The influence of various parameters involved in the emulsion freezing/freeze-drying technique was studied for the fabrication of good-quality polymer scaffolds based on PHBV polymers. The morphology, mechanical properties and crystallinity of PHBV/PLLA and HA in PHBV/PLLA composite scaffolds and PHBV polymer scaffolds were studied. The scaffolds were coated with collagen in order to improve wettability. During in vitro biological evaluation study, it was observed that SaOS-2 cells had high attachment on collagen-coated scaffolds. Significant improvement in cell proliferation and alkaline phosphatase activity for HA-incorporated composite scaffolds was observed due to the incorporation of HA. After 3 and 7 days of culture on all scaffolds, SaOS-2 cells also had normal morphology and growth. These results indicated that PHBV/PLLA-based scaffolds fabricated via an emulsion freezing/freeze-drying technique were favorable sites for osteoblastic cells and are promising for the applications of bone tissue engineering.

  15. A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.

    Science.gov (United States)

    Casini, Arturo; Chang, Fang-Yuan; Eluere, Raissa; King, Andrew M; Young, Eric M; Dudley, Quentin M; Karim, Ashty; Pratt, Katelin; Bristol, Cassandra; Forget, Anthony; Ghodasara, Amar; Warden-Rothman, Robert; Gan, Rui; Cristofaro, Alexander; Borujeni, Amin Espah; Ryu, Min-Hyung; Li, Jian; Kwon, Yong-Chan; Wang, He; Tatsis, Evangelos; Rodriguez-Lopez, Carlos; O'Connor, Sarah; Medema, Marnix H; Fischbach, Michael A; Jewett, Michael C; Voigt, Christopher; Gordon, D Benjamin

    2018-03-28

    Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species ( Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.

  16. Learning physical biology via modeling and simulation: A new course and textbook for science and engineering undergraduates

    Science.gov (United States)

    Nelson, Philip

    To a large extent, undergraduate physical-science curricula remain firmly rooted in pencil-and-paper calculation, despite the fact that most research is done with computers. To a large extent, undergraduate life-science curricula remain firmly rooted in descriptive approaches, despite the fact that much current research involves quantitative modeling. Not only does our pedagogy not reflect current reality; it also creates a spurious barrier between the fields, reinforcing the narrow silos that prevent students from connecting them. I'll describe an intermediate-level course on ``Physical Models of Living Systems.'' The prerequisite is first-year university physics and calculus. The course is a response to rapidly growing interest among undergraduates in a broad range of science and engineering majors. Students acquire several research skills that are often not addressed in traditional undergraduate courses: •Basic modeling skills; •Probabilistic modeling skills; •Data analysis methods; •Computer programming using a general-purpose platform like MATLAB or Python; •Pulling datasets from the Web for analysis; •Data visualization; •Dynamical systems, particularly feedback control. Partially supported by the NSF under Grants EF-0928048 and DMR-0832802.

  17. Radiochemistry at the University of Missouri-Columbia. A joint venture with chemistry, nuclear engineering, molecular biology, biochemistry, and the Missouri University Research Reactor (MURR)

    International Nuclear Information System (INIS)

    Miller, W.H.; Duval, P.; Jurisson, S.S.; Robertson, J.D.; Wall, J.D.; Quinn, T.P.; Volkert, W.A.; Neumeyer, G.M.

    2005-01-01

    Missouri University, a recipient of a U.S. Department of Energy Radiochemistry Education Award Program (REAP) grant in 1999, has significantly expanded its education and research mission in radiochemistry. While MU had a viable radiochemistry program through existing faculty expertise and the utilization of the Missouri University Research Reactor, the REAP award allowed MU to leverage its resources in significantly expanding capabilities in radiochemistry. Specifically, the grant enabled the: (1) hiring of a new faculty member in actinide radiochemistry (Dr. Paul Duval); (2) support of six graduate students in radiochemistry; (3) purchase of new radiochemistry laboratory equipment; (4) more extensive collaboration with DOE scientists through interactions with faculty and graduate students, and (5) revised radiochemical curriculum (joint courses across disciplines and new courses in actinide chemistry). The most significant impact of this award has been in encouraging interdisciplinary education and research. The proposal was initiated by a joint effort between Nuclear Engineering and Chemistry, but also included faculty in biochemistry, radiology, and molecular biology. Specific outcomes of the REAP grant thus far are: (1) increased educational and research capabilities in actinide chemistry (faculty hire and equipment acquisition); (2) increased integration of biochemistry and radiochemistry (e.g., radiochemical analysis of uranium speciation in biological systems); (3) stronger interdisciplinary integration of molecular biology and radiochemical sciences (alpha-emitters for treating cancer); (4) new and more extensive interactions with national laboratory facilities (e.g., student internships at LANL and LLBL, faculty and lab scientist exchange visits, analytical measurements and collaboration with the Advanced Photon Source), and (7) new research funding opportunities based on REAP partnership. (author)

  18. A Pseudomonas putida double mutant deficient in butanol assimilation: a promising step for engineering a biological biofuel production platform.

    Science.gov (United States)

    Cuenca, María Del Sol; Molina-Santiago, Carlos; Gómez-García, María R; Ramos, Juan L

    2016-03-01

    Biological production in heterologous hosts is of interest for the production of the C4 alcohol (butanol) and other chemicals. However, some hurdles need to be overcome in order to achieve an economically viable process; these include avoiding the consumption of butanol and maintaining tolerance to this solvent during production. Pseudomonas putida is a potential host for solvent production; in order to further adapt P. putida to this role, we generated mini-Tn5 mutant libraries in strain BIRD-1 that do not consume butanol. We analyzed the insertion site of the mini-Tn5 in a mutant that was deficient in assimilation of butanol using arbitrary PCR followed by Sanger sequencing and found that the transposon was inserted in the malate synthase B gene. Here, we show that in a second round of mutagenesis a double mutant unable to take up butanol had an insertion in a gene coding for a multisensor hybrid histidine kinase. The genetic context of the histidine kinase sensor revealed the presence of a set of genes potentially involved in butanol assimilation; qRT-PCR analysis showed induction of this set of genes in the wild type and the malate synthase mutant but not in the double mutant. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Layer-by-Layer Engineered Microbicide Drug Delivery System Targeting HIV-1 gp120: Physicochemical and Biological Properties.

    Science.gov (United States)

    Coulibaly, Fohona S; Ezoulin, Miezan J M; Purohit, Sudhaunshu S; Ayon, Navid J; Oyler, Nathan A; Youan, Bi-Botti C

    2017-10-02

    The purpose of this study was to engineer a model anti-HIV microbicide (tenofovir) drug delivery system targeting HIV-1 envelope glycoprotein gp120 (HIV-1 g120) for the prevention of HIV sexual transmission. HIV-1 g120 and mannose responsive particles (MRP) were prepared through the layer-by-layer coating of calcium carbonate (CaCO 3 ) with concanavalin A (Con A) and glycogen. MRP average particle size ranged from 881.7 ± 15.45 nm to 1130 ± 15.72 nm, depending on the number of Con A layers. Tenofovir encapsulation efficiency in CaCO 3 was 74.4% with drug loading of 16.3% (w/w). MRP was non-cytotoxic to Lactobacillus crispatus, human vaginal keratinocytes (VK2), and murine macrophage RAW 264.7 cells and did not induce any significant proinflammatory nitric oxide release. Overall, compared to control, no statistically significant increase in proinflammatory cytokine IL-1α, IL-1β, IL-6, MKC, IL-7, and interferon-γ-inducible protein 10 (IP10) levels was observed. Drug release profiles in the presence of methyl α-d-mannopyranoside and recombinant HIV-1 envelope glycoprotein gp120 followed Hixson-Crowell and Hopfenberg kinetic models, indicative of a surface-eroding system. The one Con A layer containing system was found to be the most sensitive (∼2-fold increase in drug release vs control SFS:VFS) at the lowest HIV gp120 concentration tested (25 μg/mL). Percent mucoadhesion, tested ex vivo on porcine vaginal tissue, ranged from 10% to 21%, depending on the number of Con A layers in the formulation. Collectively, these data suggested that the proposed HIV-1 g120 targeting, using MRP, potentially represent a safe and effective template for vaginal microbicide drug delivery, if future preclinical studies are conclusive.

  20. Implantation of a novel biologic and hybridized tissue engineered bioimplant in large tendon defect: an in vivo investigation.

    Science.gov (United States)

    Oryan, Ahmad; Moshiri, Ali; Parizi, Abdolhamid Meimandi; Maffulli, Nicola

    2014-02-01

    Surgical reconstruction of large Achilles tendon defects is technically demanding. There is no standard method, and tissue engineering may be a valuable option. We investigated the effects of 3D collagen and collagen-polydioxanone sheath (PDS) implants on a large tendon defect model in rabbits. Ninety rabbits were divided into three groups: control, collagen, and collagen-PDS. In all groups, 2 cm of the left Achilles tendon were excised and discarded. A modified Kessler suture was applied to all injured tendons to retain the gap length. The control group received no graft, the treated groups were repaired using the collagen only or the collagen-PDS prostheses. The bioelectrical characteristics of the injured areas were measured at weekly intervals. The animals were euthanized at 60 days after the procedure. Gross, histopathological and ultrastructural morphology and biophysical characteristics of the injured and intact tendons were investigated. Another 90 pilot animals were also used to investigate the inflammatory response and mechanism of graft incorporation during tendon healing. The control tendons showed severe hyperemia and peritendinous adhesion, and the gastrocnemius muscle of the control animals showed severe atrophy and fibrosis, with a loose areolar connective tissue filling the injured area. The tendons receiving either collagen or collagen-PDS implants showed lower amounts of peritendinous adhesion, hyperemia and muscle atrophy, and a dense tendon filled the defect area. Compared to the control tendons, application of collagen and collagen-PDS implants significantly improved water uptake, water delivery, direct transitional electrical current and tissue resistance to direct transitional electrical current. Compared to the control tendons, both prostheses showed significantly increased diameter, density and alignment of the collagen fibrils and maturity of the tenoblasts at ultrastructure level. Both prostheses influenced favorably tendon healing

  1. Bio Engineering Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry and biology laboratoriesThe Bio Engineering Laboratory (BeL) is theonly full spectrum biotechnology capability within the Department...

  2. Mechanical properties, biological activity and protein controlled release by poly(vinyl alcohol)–bioglass/chitosan–collagen composite scaffolds: A bone tissue engineering applications

    International Nuclear Information System (INIS)

    Pon-On, Weeraphat; Charoenphandhu, Narattaphol; Teerapornpuntakit, Jarinthorn; Thongbunchoo, Jirawan; Krishnamra, Nateetip; Tang, I-Ming

    2014-01-01

    In the present study, composite scaffolds made with different weight ratios (0.5:1, 1:1 and 2:1) of bioactive glass (15Ca:80Si:5P) (BG)/polyvinyl alcohol (PVA) (PVABG) and chitosan (Chi)/collagen (Col) (ChiCol) were prepared by three mechanical freeze–thaw followed by freeze-drying to obtain the porous scaffolds. The mechanical properties and the in vitro biocompatibility of the composite scaffolds to simulated body fluid (SBF) and to rat osteoblast-like UMR-106 cells were investigated. The results from the studies indicated that the porosity and compressive strength were controlled by the weight ratio of PVABG:ChiCol. The highest compressive modulus of the composites made was 214.64 MPa which was for the 1:1 weight ratio PVABG:ChiCol. Mineralization study in SBF showed the formation of apatite crystals on the PVABG:ChiCol surface after 7 days of incubation. In vitro cell availability and proliferation tests confirmed the osteoblast attachment and growth on the PVABG:ChiCol surface. MTT and ALP tests on the 1:1 weight ratio PVABG:ChiCol composite indicated that the UMR-106 cells were viable. Alkaline phosphatase activity was found to increase with increasing culturing time. In addition, we showed the potential of PVABG:ChiCol drug delivery through PBS solution studies. 81.14% of BSA loading had been achieved and controlled release for over four weeks was observed. Our results indicated that the PVABG:ChiCol composites, especially the 1:1 weight ratio composite exhibited significantly improved mechanical, mineral deposition, biological properties and controlled release. This made them potential candidates for bone tissue engineering applications. - Graphical abstract: Mechanical properties, biological activity and protein controlled release by poly(vinyl alcohol)–bioglass/chitosan–collagen composite scaffolds: A bone tissue engineering applications. - Highlights: • Preparation of PVABG:ChiCol hybrid composites and their bioactivities • Mechanical

  3. Mechanical properties, biological activity and protein controlled release by poly(vinyl alcohol)–bioglass/chitosan–collagen composite scaffolds: A bone tissue engineering applications

    Energy Technology Data Exchange (ETDEWEB)

    Pon-On, Weeraphat, E-mail: fsciwpp@ku.ac.th [Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Charoenphandhu, Narattaphol; Teerapornpuntakit, Jarinthorn; Thongbunchoo, Jirawan; Krishnamra, Nateetip [Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University (Thailand); Department of Physiology, Faculty of Science, Mahidol University (Thailand); Tang, I-Ming [ThEP Center, Commission of Higher Education, 328 Si Ayutthaya Rd. (Thailand); Department of Materials Science, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand)

    2014-05-01

    In the present study, composite scaffolds made with different weight ratios (0.5:1, 1:1 and 2:1) of bioactive glass (15Ca:80Si:5P) (BG)/polyvinyl alcohol (PVA) (PVABG) and chitosan (Chi)/collagen (Col) (ChiCol) were prepared by three mechanical freeze–thaw followed by freeze-drying to obtain the porous scaffolds. The mechanical properties and the in vitro biocompatibility of the composite scaffolds to simulated body fluid (SBF) and to rat osteoblast-like UMR-106 cells were investigated. The results from the studies indicated that the porosity and compressive strength were controlled by the weight ratio of PVABG:ChiCol. The highest compressive modulus of the composites made was 214.64 MPa which was for the 1:1 weight ratio PVABG:ChiCol. Mineralization study in SBF showed the formation of apatite crystals on the PVABG:ChiCol surface after 7 days of incubation. In vitro cell availability and proliferation tests confirmed the osteoblast attachment and growth on the PVABG:ChiCol surface. MTT and ALP tests on the 1:1 weight ratio PVABG:ChiCol composite indicated that the UMR-106 cells were viable. Alkaline phosphatase activity was found to increase with increasing culturing time. In addition, we showed the potential of PVABG:ChiCol drug delivery through PBS solution studies. 81.14% of BSA loading had been achieved and controlled release for over four weeks was observed. Our results indicated that the PVABG:ChiCol composites, especially the 1:1 weight ratio composite exhibited significantly improved mechanical, mineral deposition, biological properties and controlled release. This made them potential candidates for bone tissue engineering applications. - Graphical abstract: Mechanical properties, biological activity and protein controlled release by poly(vinyl alcohol)–bioglass/chitosan–collagen composite scaffolds: A bone tissue engineering applications. - Highlights: • Preparation of PVABG:ChiCol hybrid composites and their bioactivities • Mechanical

  4. Glycosylation Engineering

    DEFF Research Database (Denmark)

    Clausen, Henrik; Wandall, Hans H.; Steentoft, Catharina

    2017-01-01

    Knowledge of the cellular pathways of glycosylation across phylogeny provides opportunities for designing glycans via genetic engineering in a wide variety of cell types including bacteria, fungi, plant cells, and mammalian cells. The commercial demand for glycosylation engineering is broad......, including production of biological therapeutics with defined glycosylation (Chapter 57). This chapter describes how knowledge of glycan structures and their metabolism (Parts I–III of this book) has led to the current state of glycosylation engineering in different cell types. Perspectives for rapid...

  5. Mesenchymal stem cells: Identification, phenotypic characterization, biological properties and potential for regenerative medicine through biomaterial micro-engineering of their niche.

    Science.gov (United States)

    Kobolak, Julianna; Dinnyes, Andras; Memic, Adnan; Khademhosseini, Ali; Mobasheri, Ali

    2016-04-15

    Mesenchymal stem cells (MSCs) are multipotent stem cells. Although they were originally identified in bone marrow and described as 'marrow stromal cells', they have since been identified in many other anatomical locations in the body. MSCs can be isolated from bone marrow, adipose tissue, umbilical cord and other tissues but the richest tissue source of MSCs is fat. Since they are adherent to plastic, they may be expanded in vitro. MSCs have a distinct morphology and express a specific set of CD (cluster of differentiation) molecules. The phenotypic pattern for the identification of MSCs cells requires expression of CD73, CD90, and CD105 and lack of CD34, CD45, and HLA-DR antigens. Under appropriate micro-environmental conditions MSCs can proliferate and give rise to other cell types. Therefore, they are ideally suited for the treatment of systemic inflammatory and autoimmune conditions. They have also been implicated as key players in regenerating injured tissue following injury and trauma. MSC populations isolated from adipose tissue may also contain regulatory T (Treg) cells, which have the capacity for modulating the immune system. The immunoregulatory and regenerative properties of MSCs make them ideal for use as therapeutic agents in vivo. In this paper we review the literature on the identification, phenotypic characterization and biological properties of MSCs and discuss their potential for applications in cell therapy and regenerative medicine. We also discuss strategies for biomaterial micro-engineering of the stem cell niche. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Photonic engineering for biological study

    Science.gov (United States)

    Wu, Fei

    My dissertation focuses on designing and developing prototypes of optical tools in the laboratory that can facilitate practical medical therapies. More specifically, this dissertation examines two novel biophotonic techniques: (1) a frequency multiplexed confocal microscope with the potential to provide rational therapy of congestive heart failure (CHF), and (2) the "optical comb" with the potential to improve results of retina reattachment surgery and accelerate post surgical recovery. Next, I will discuss the background, design and initial experimental results of each study individually. Part I: The Frequency Multiplexed Confocal Microscope. To overcome the limitations of existing confocal microscope technology, this dissertation proposes a non-scanning, real-time, high resolution technique (a multi-point frequency multiplexed confocal microscope) to measure 3-D intracellular calcium ion concentration in a living cardiac myocyte. This method can be also applied to measure the intracellular sodium ion concentration, or other ions in which high quantum-yield fluorescent probes are available. The novelty of the proposed research lies in the introduction of carrier frequency multiplexing techniques which can differentiate fluorescence emitted at different spatial locations in cardiac myocyte by their modulated frequency. It therefore opens the possibility to visualize the transient dynamics of intracellular dynamics at multiple locations in cells simultaneously, which will shine a new light on our understanding of CHF. The procedure for frequency multiplexing proposed is described below. Multiple incident laser beams are focused onto different locations in an isolated rat cardiac myocyte with each beam modulated at a different carrier frequency. The fluorescence emission at each location therefore bears the same modulated frequency as the stimulation laser beam. Each fluorescence signal is sent to the photo multiplier tube (PMT) after being spatially filtered by a single mode fiber (functioning as a pinhole). Since each signal has a different carrier frequency, only one signal detector is required to collect multiple signal streams which eliminates the errors introduced by difference of multiple detectors. After taking the Fourier Transform of the collected data, multiple peaks can be found in the frequency domain. Each peak refers to a corresponding location in the sample. The temporal information of the fluorescence signal variation at each location can be obtained by demodulating the low frequency information from the carrier frequency, followed by an inverse Fourier transform. Part II: The "Optical Comb". Retinal detachment refers to separation of the inner layers of the retina from the underlying retinal pigment epithelium. It can cause degeneration of the retina and may lead to permanent vision loss if not promptly treated and hence is considered an ocular emergency. Currently, the only treatment available for retinal detachment is surgical reattachment. The idea of an "optical comb" is developed from the general working principle of the well known "optical tweezers" in the optical literature, which can pull micro-objects through the trapping force produced by a focused laser beam. If we can manage to incident the focused laser beam onto the misaligned photoreceptors and further scan it back and forth, trapping forces that produced may be able to "comb" the photoreceptors to be aligned, and thereby help with post surgery recovery. A series of experiments have been carried out to demonstrate the plausibility of this idea. First, several micro glass rods with size similar to human's photoreceptors (6 microns in diameter and 30 microns in length) were used. We observed that when the laser beam is focused close to one end of the micro rod originally laid on a glass coverslip, the rod is pulled to stand upright successfully, and we can manipulate the direction it faces by controlling its relative position to the laser beam. We are now experimenting with this combing technique with detached bovine retina samples to further verify its feasibility over live animal cells. (Abstract shortened by UMI.)

  7. Mechanical properties, biological activity and protein controlled release by poly(vinyl alcohol)-bioglass/chitosan-collagen composite scaffolds: a bone tissue engineering applications.

    Science.gov (United States)

    Pon-On, Weeraphat; Charoenphandhu, Narattaphol; Teerapornpuntakit, Jarinthorn; Thongbunchoo, Jirawan; Krishnamra, Nateetip; Tang, I-Ming

    2014-05-01

    In the present study, composite scaffolds made with different weight ratios (0.5:1, 1:1 and 2:1) of bioactive glass (15Ca:80Si:5P) (BG)/polyvinyl alcohol (PVA) (PVABG) and chitosan (Chi)/collagen (Col) (ChiCol) were prepared by three mechanical freeze-thaw followed by freeze-drying to obtain the porous scaffolds. The mechanical properties and the in vitro biocompatibility of the composite scaffolds to simulated body fluid (SBF) and to rat osteoblast-like UMR-106 cells were investigated. The results from the studies indicated that the porosity and compressive strength were controlled by the weight ratio of PVABG:ChiCol. The highest compressive modulus of the composites made was 214.64 MPa which was for the 1:1 weight ratio PVABG:ChiCol. Mineralization study in SBF showed the formation of apatite crystals on the PVABG:ChiCol surface after 7 days of incubation. In vitro cell availability and proliferation tests confirmed the osteoblast attachment and growth on the PVABG:ChiCol surface. MTT and ALP tests on the 1:1 weight ratio PVABG:ChiCol composite indicated that the UMR-106 cells were viable. Alkaline phosphatase activity was found to increase with increasing culturing time. In addition, we showed the potential of PVABG:ChiCol drug delivery through PBS solution studies. 81.14% of BSA loading had been achieved and controlled release for over four weeks was observed. Our results indicated that the PVABG:ChiCol composites, especially the 1:1 weight ratio composite exhibited significantly improved mechanical, mineral deposition, biological properties and controlled release. This made them potential candidates for bone tissue engineering applications. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Designing synthetic biology.

    Science.gov (United States)

    Agapakis, Christina M

    2014-03-21

    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

  9. 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.

  10. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  11. Engineer: The Professional Bulletin of Army Engineers

    Science.gov (United States)

    2009-12-01

    successful preparation was to assist the engineer platoons by requesting and coordinating route clearance, engineer dog teams, unmanned aerial vehicles...and has been indicated as a possible link to autism . Based on human biological monitoring conducted by the Center for Disease Control and

  12. Synthetic Biology in Health and Disease

    NARCIS (Netherlands)

    Passel, van M.W.J.; Lam, C.M.C.; Martins dos Santos, V.A.P.; Suarez Diez, M.

    2014-01-01

    Synthetic biology draws on the understanding from genetics, biology, chemistry, physics, engineering, and computational sciences to (re-)design and (re-)engineer biological functions. Here we address how synthetic biology can be possibly deployed to promote health and tackle disease. We discuss how

  13. Engineering of Secondary Metabolism.

    Science.gov (United States)

    O'Connor, Sarah E

    2015-01-01

    Secondary (specialized) metabolites, produced by bacteria, fungi, plants, and other organisms, exhibit enormous structural variation, and consequently display a wide range of biological activities. Secondary metabolism improves and modulates the phenotype of the host producer. Furthermore, these biological activities have resulted in the use of secondary metabolites in a variety of industrial and pharmaceutical applications. Metabolic engineering presents a powerful strategy to improve access to these valuable molecules. A critical overview of engineering approaches in secondary metabolism is presented, both in heterologous and native hosts. The recognition of the increasing role of compartmentalization in metabolic engineering is highlighted. Engineering approaches to modify the structure of key secondary metabolite classes are also critically evaluated.

  14. 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.

  15. 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)

  16. Chemical Engineering in the "BIO" world

    DEFF Research Database (Denmark)

    Chiarappa, Gianluca; Grassi, Mario; Abrami, Michela

    2017-01-01

    baptized Biomedical Engineering by Peppas and Langer and that now we can name Biological Engineering. Interestingly, although Biological Engineering focused on completely different topics from Chemical Engineering ones, it resorted to the same theoretical tools such as, for instance, mass, energy...

  17. 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.

  18. Genome scale engineering techniques for metabolic engineering.

    Science.gov (United States)

    Liu, Rongming; Bassalo, Marcelo C; Zeitoun, Ramsey I; Gill, Ryan T

    2015-11-01

    Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  19. Engineering assessment and feasibility study of Chattanooga Shale as a future source of uranium. [Preliminary mining; data on soils, meteorology, water resources, and biological resources

    Energy Technology Data Exchange (ETDEWEB)

    1978-06-01

    This volume contains five appendixes: Chattanooga Shale preliminary mining study, soils data, meteorologic data, water resources data, and biological resource data. The area around DeKalb County in Tennessee is the most likely site for commercial development for recovery of uranium. (DLC)

  20. Engineering Encounters: Engineering Adaptations

    Science.gov (United States)

    Gatling, Anne; Vaughn, Meredith Houle

    2015-01-01

    Engineering is not a subject that has historically been taught in elementary schools, but with the emphasis on engineering in the "Next Generation Science Standards," curricula are being developed to explicitly teach engineering content and design. However, many of the scientific investigations already conducted with students have…

  1. Systems Biology of Metabolism.

    Science.gov (United States)

    Nielsen, Jens

    2017-06-20

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.

  2. A glovebox with three levels of containment and clean room facilities for growing and handling biological material at physiologically correct gas compositions and with optimal quality assessment for tissue-engineering, ex vivo expansion, manipulation and gene therapy.

    Science.gov (United States)

    Villadsen, J A; Voeten, R G H M; Mosborg Peterson, P

    2002-07-01

    Traditional two levels of containment provide enclosure and underpressure in order to avoid hazardous material to flow towards e.g. a crewmember and thereby cause severe harm. The present-day demands for laboratory safety have revealed a paradox: In the laboratory overpressure is needed to prevent contamination of biological material and under pressure is needed to prevent the pollution of the environment. A new type of combined workbench/incubator has been constructed to meet future regulatory demands for handling and growing human biological cellular material at safe constant physiological conditions: A so-called three levels of containment glovebox/workbench. This new invention avoids the hazards of prior technology. It sets new standards for proper handling of biological materials and will meet the coming safety demands from the growing field of tissue engineering and ex vivo biotechnology. The invention is computer controlled, has a build in cleaning facility for assuring a particle free and aseptic working facility. We now have invented a solution to the above paradox concerning laboratory safety that seems to fulfil the need for safe biological experiments in microgravity. This concept has already been applied into ground-based research and is expected in a few years also to be applied similarly in the ISS environment. Furthermore, handling biological material mimicking in vivo conditions ex vivo requires precise and stabile monitoring and regulation of the isotherm and isobar conditions. Handling stem cells requires in addition low to very low oxygen tension to mimic the stem cells natural habitats. Besides that, the ex vivo gaseous atmosphere and temperature surrounding the cells has to be of same correct composition and temperature as found in the body in order to mimic in vivo situations in such way, that scientifically correct, reproducible and comparable results can be achieved. This fact is strengthened by forthcoming regulations as being prepared by

  3. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 6, is a collection of papers that discusses the role of integrated electronics in medical systems and the usage of biological mathematical models in biological systems. Other papers deal with the health care systems, the problems and methods of approach toward rehabilitation, as well as the future of biomedical engineering. One paper discusses the use of system identification as it applies to biological systems to estimate the values of a number of parameters (for example, resistance, diffusion coefficients) by indirect means. More particularly, the i

  4. The main features of electrical stimulation of biological tissues by implant electrodes: study from engineering perspective and equipment development to produce

    International Nuclear Information System (INIS)

    Suarez Bagnasco, D.; Alvarez Alonso, J.; Suarez Antola, R.

    2004-08-01

    The main features of electrical stimulation of biological tissues by implant electrodes are studied.These electrodes are applied in neural prostheses and cardiac pacing.Threshold phenomena are stressed and some aspects related with implant electrode design are discussed. A fairly through theoretical research about the optimal pulse shape for electrical stimulation of biological tissues is done.The excitation functional is introduced as a criterium to identify threshold pulses of electric current. We obtain the optimal pulse shapes that minimize the energy dissipated in tissues, or the energy taken by the load seen by the pulse generator, amongst other criteria.We show how these pulse shapes can be determined from experimentally measured strength-duration (S-D) curves using rectangular pulses of current. The development of a prototype of a new equipment is described.The equipment may be used to measure S-D curves and with this information it is able to syntetize the abovementioned optimal pulse shapes. The top-down design process is presented, involving both hardware and software.The construction and assembling of the prototype, as well as the implementation of software are described.Some testing and measures with the prototype, including test with biological tissues are described and assessed

  5. Mammalian Synthetic Biology

    OpenAIRE

    Martella, Andrea; Pollard, Steven M; Dai, Junbiao; Cai, Yizhi

    2016-01-01

    The enabling technologies of synthetic biology are opening up new opportunities for engineering and enhancement of mammalian cells. This will stimulate diverse applications in many life science sectors such as regenerative medicine, development of biosensing cell lines, therapeutic protein production, and generation of new synthetic genetic regulatory circuits. Harnessing the full potential of these new engineering-based approaches requires the design and assembly of large DNA constructs-pote...

  6. Cell and Tissue Engineering

    CERN Document Server

    2012-01-01

    “Cell and Tissue Engineering” introduces the principles and new approaches in cell and tissue engineering. It includes both the fundamentals and the current trends in cell and tissue engineering, in a way useful both to a novice and an expert in the field. The book is composed of 13 chapters all of which are written by the leading experts. It is organized to gradually assemble an insight in cell and tissue function starting form a molecular nano-level, extending to a cellular micro-level and finishing at the tissue macro-level. In specific, biological, physiological, biophysical, biochemical, medical, and engineering aspects are covered from the standpoint of the development of functional substitutes of biological tissues for potential clinical use. Topics in the area of cell engineering include cell membrane biophysics, structure and function of the cytoskeleton, cell-extracellular matrix interactions, and mechanotransduction. In the area of tissue engineering the focus is on the in vitro cultivation of ...

  7. Planetary engineering

    Science.gov (United States)

    Pollack, James B.; Sagan, Carl

    1991-01-01

    Assuming commercial fusion power, heavy lift vehicles and major advances in genetic engineering, the authors survey possible late-21st century methods of working major transformations in planetary environments. Much more Earthlike climates may be produced on Mars by generating low freezing point greenhouse gases from indigenous materials; on Venus by biological conversion of CO2 to graphite, by canceling the greenhouse effect with high-altitude absorbing fine particles, or by a sunshield at the first Lagrangian point; and on Titan by greenhouses and/or fusion warming. However, in our present state of ignorance we cannot guarantee a stable endstate or exclude unanticipated climatic feedbacks or other unintended consequences. Moreover, as the authors illustrate by several examples, many conceivable modes of planetary engineering are so wasteful of scarce solar system resources and so destructive of important scientific information as to raise profound ethical issues, even if they were economically feasible, which they are not. Global warming on Earth may lead to calls for mitigation by planetary engineering, e.g., emplacement and replenishment of anti-greenhouse layers at high altitudes, or sunshields in space. But here especially we must be concerned about precision, stability, and inadvertent side-effects. The safest and most cost-effective means of countering global warming - beyond, e.g., improved energy efficiency, CFC bans and alternative energy sources - is the continuing reforestation of approximately 2 times 107 sq km of the Earth's surface. This can be accomplished with present technology and probably at the least cost.

  8. Planetary engineering

    Science.gov (United States)

    Pollack, James B.; Sagan, Carl

    Assuming commercial fusion power, heavy lift vehicles and major advances in genetic engineering, the authors survey possible late-21st century methods of working major transformations in planetary environments. Much more Earthlike climates may be produced on Mars by generating low freezing point greenhouse gases from indigenous materials; on Venus by biological conversion of CO2 to graphite, by canceling the greenhouse effect with high-altitude absorbing fine particles, or by a sunshield at the first Lagrangian point; and on Titan by greenhouses and/or fusion warming. However, in our present state of ignorance we cannot guarantee a stable endstate or exclude unanticipated climatic feedbacks or other unintended consequences. Moreover, as the authors illustrate by several examples, many conceivable modes of planetary engineering are so wasteful of scarce solar system resources and so destructive of important scientific information as to raise profound ethical issues, even if they were economically feasible, which they are not. Global warming on Earth may lead to calls for mitigation by planetary engineering, e.g., emplacement and replenishment of anti-greenhouse layers at high altitudes, or sunshields in space. But here especially we must be concerned about precision, stability, and inadvertent side-effects. The safest and most cost-effective means of countering global warming - beyond, e.g., improved energy efficiency, CFC bans and alternative energy sources - is the continuing reforestation of approximately 2 times 107 sq km of the Earth's surface. This can be accomplished with present technology and probably at the least cost.

  9. Ship diesel emission aerosols: A comprehensive study on the chemical composition, the physical properties and the molecular biological and toxicological effects on human lung cells of aerosols from a ship diesel engine operated with heavy or light diesel fuel oil

    Science.gov (United States)

    Zimmermann, R.; Buters, J.; Öder, S.; Dietmar, G.; Kanashova, T.; Paur, H.; Dilger, M.; Mülhopt, S.; Harndorf, H.; Stengel, B.; Rabe, R.; Hirvonen, M.; Jokiniemi, J.; Hiller, K.; Sapcariu, S.; Berube, K.; Sippula, O.; Streibel, T.; Karg, E.; Schnelle-Kreis, J.; Lintelmann, J.; Sklorz, M.; Arteaga Salas, M.; Orasche, J.; Müller, L.; Reda, A.; Passig, J.; Radischat, C.; Gröger, T.; Weiss, C.

    2013-12-01

    The Virtual Helmholtz Institute-HICE (www.hice-vi.eu) addresses chemical & physical properties, transformation processes and health effects of anthropogenic combustion emissions. This is performed by thorough comprehensive chemical and physical characterization of combustion aerosols (including application of advantageous on-line methods) and studying of biological effects on human lung cell-cultures. A new ALI air-liquid-interface (ALI) exposition system and a mobile S2-biological laboratory were developed for the HICE-measurements. Human alveolar basal epithelial cells (A549 etc.) are ALI-exposed to fresh, diluted (1:40-1:100) combustion aerosols and subsequently were toxicologically and molecular-biologically characterized (e.g. proteomics). By using stable isotope labeling technologies (13C-Glucose/metabolomics; 2H-Lysine/SILAC-proteomics), high sensitivity and accuracy for detection of molecular-biological effects is achievable even at sub-toxic effect dose levels. Aerosols from wood combustion and ship diesel engine (heavy/light fuel oil) have been investigated. The effect of wood combustion and ship diesel PM e.g. on the protein expression of ALI-exposed A549 cells was compared. Filtered aerosol is used as gas-reference for the isotope labeling based method (SILAC). Therefore the effects of wood combustion- and shipping diesel-PM can be directly compared. Ship diesel aerosol causes a broader distribution in the observed fold changes (log2), i.e. more proteins are significantly up-/down-regulated in case of shipping diesel PM-exposure. This corresponds to a stronger biological reaction if compared to wood combustion-PM exposure. The chemical analysis results on wood combustion- and ship diesel-PM depict more polycyclic aromatic hydrocarbons (PAH)/oxidized-PAH but less of some transition metals (V, Fe) in the wood combustion case. Interestingly, alkylated PAH are considerably more abundant in shipping PM, suggesting that PAH/Oxy-PAH may be less relevant for

  10. Selection of nectar plants for use in ecological engineering to promote biological control of rice pests by the predatory bug, Cyrtorhinus lividipennis, (Heteroptera: Miridae.

    Directory of Open Access Journals (Sweden)

    Pingyang Zhu

    Full Text Available Ecological engineering for pest management involves the identification of optimal forms of botanical diversity to incorporate into a farming system to suppress pests, by promoting their natural enemies. Whilst this approach has been extensively researched in many temperate crop systems, much less has been done for rice. This paper reports the influence of various plant species on the performance of a key natural enemy of rice planthopper pests, the predatory mirid bug, Cyrtorhinus lividipennis. Survival of adult males and females was increased by the presence of flowering Tagetes erecta, Trida procumbens, Emilia sonchifolia (Compositae, and Sesamum indicum (Pedaliaceae compared with water or nil controls. All flower treatments resulted in increased consumption of brown plant hopper, Nilaparvata lugens, and for female C. lividipennis, S. indicum was the most favorable. A separate study with a wider range of plant species and varying densities of prey eggs showed that S. indicum most strongly promoted predation by C. lividipennis. Reflecting this, S. indicum gave a relatively high rate of prey search and low prey handling time. On this basis, S. indicum was selected for more detailed studies to check if its potential incorporation into the farming system would not inadvertently benefit Cnaphalocrocis medinalis and Marasmia patnalis, serious Lepidoptera pests of rice. Adult longevity and fecundity of both pests was comparable for S. indicum and water treatments and significantly lower than the honey solution treatment. Findings indicate that S. indicumis well suited for use as an ecological engineering plant in the margins of rice crops. Sesame indicum can be a valuable crop as well as providing benefits to C. lividipennis whilst denying benefit to key pests.

  11. Selection of Nectar Plants for Use in Ecological Engineering to Promote Biological Control of Rice Pests by the Predatory Bug, Cyrtorhinus lividipennis, (Heteroptera: Miridae)

    Science.gov (United States)

    Zhu, Pingyang; Lu, Zhongxian; Heong, Kongluen; Chen, Guihua; Zheng, Xusong; Xu, Hongxing; Yang, Yajun; Nicol, Helen I.; Gurr, Geoff M.

    2014-01-01

    Ecological engineering for pest management involves the identification of optimal forms of botanical diversity to incorporate into a farming system to suppress pests, by promoting their natural enemies. Whilst this approach has been extensively researched in many temperate crop systems, much less has been done for rice. This paper reports the influence of various plant species on the performance of a key natural enemy of rice planthopper pests, the predatory mirid bug, Cyrtorhinus lividipennis. Survival of adult males and females was increased by the presence of flowering Tagetes erecta, Trida procumbens, Emilia sonchifolia (Compositae), and Sesamum indicum (Pedaliaceae) compared with water or nil controls. All flower treatments resulted in increased consumption of brown plant hopper, Nilaparvata lugens, and for female C. lividipennis, S. indicum was the most favorable. A separate study with a wider range of plant species and varying densities of prey eggs showed that S. indicum most strongly promoted predation by C. lividipennis. Reflecting this, S. indicum gave a relatively high rate of prey search and low prey handling time. On this basis, S. indicum was selected for more detailed studies to check if its potential incorporation into the farming system would not inadvertently benefit Cnaphalocrocis medinalis and Marasmia patnalis, serious Lepidoptera pests of rice. Adult longevity and fecundity of both pests was comparable for S. indicum and water treatments and significantly lower than the honey solution treatment. Findings indicate that S. indicumis well suited for use as an ecological engineering plant in the margins of rice crops. Sesame indicum can be a valuable crop as well as providing benefits to C. lividipennis whilst denying benefit to key pests. PMID:25254377

  12. 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.

  13. Microscale technologies for cell engineering

    CERN Document Server

    Gaharwar, Akhilesh

    2016-01-01

    This book offers readers cutting-edge research at the interface of polymer science and engineering, biomedical engineering, materials science, and biology. State-of-the-art developments in microscale technologies for cell engineering applications are covered, including technologies relevant to both pluripotent and adult stem cells, the immune system, and somatic cells of the animal and human origin. This book bridges the gap in the understanding of engineering biology at multiple length scale, including microenvironmental control, bioprocessing, and tissue engineering in the areas of cardiac, cartilage, skeletal, and vascular tissues, among others. This book also discusses unique, emerging areas of micropatterning and three-dimensional printing models of cellular engineering, and contributes to the better understanding of the role of biophysical factors in determining the cell fate. Microscale Technologies for Cell Engineering is valuable for bioengineers, biomaterial scientists, tissue engineers, clinicians,...

  14. Progress Toward a Thermal-Hydrological-Mechanical-Chemical-Biological (THMCB) Experiment in the Homestake Mine Deep Underground Science and Engineering Laboratory

    Science.gov (United States)

    Sonnenthal, E. L.; Maher, K.; Elsworth, D.; Lowell, R. P.; Uzunlar, N.; Mailloux, B. J.; Conrad, M. E.; Olsen, N. J.; Jones, T. L.; Cruz, M. F.; Torchinsky, A.

    2011-12-01

    The purpose of performing a long-term hydrothermal experiment in a deep mine is to gain a scientific understanding of the coupled physical, chemical, and biological processes taking place in fractured rock under the influence of mechanical stress, thermal effects, and fluid flow. Only in a controlled experiment in a well-characterized rock mass, can a fractured rock be probed in 3-D through geophysical imaging, in situ measurements, geochemical/biological sampling, and numerical modeling. Our project is focused on the feasibility of a THMCB experiment in the Homestake Mine, South Dakota to study the long-term evolution (10+ years) of a perturbed heterogeneous rock mass. In addition to the experiment as a laboratory for studying crustal processes, it has direct application to Enhanced Geothermal Systems, carbon sequestration, and contaminant transport. Field activities have focused on fracture and feature mapping, flux measurements from flowing fractures, and collection of water and rock samples for geochemical, biological, and isotopic analyses. Fracture mapping and seepage measurements are being used to develop estimates of permeability and fluxes at different length scales and design the location and orientation of the heater array. Fluxes measured up to several liters/minute indicate localized regions of very high fracture permeability, likely in excess of 10-10 m2. Isotopic measurements indicate heterogeneity in the fracture network on the scale of tens of meters in addition to the large-scale geochemical heterogeneity observed in the mine. New methods for sampling and filtering water samples were developed and tested with the goal of performing radiocarbon analyses in DNA and phospholipid fatty acids. Analytical and numerical models of the thermal perturbation have been used to design the heater orientation and spacing. Reaction path and THC simulations were performed to assess geochemical and porosity/permeability changes as a function of the heat input

  15. Engineering Encounters: Reverse Engineering

    Science.gov (United States)

    McGowan, Veronica Cassone; Ventura, Marcia; Bell, Philip

    2017-01-01

    This column presents ideas and techniques to enhance your science teaching. This month's issue shares information on how students' everyday experiences can support science learning through engineering design. In this article, the authors outline a reverse-engineering model of instruction and describe one example of how it looked in our fifth-grade…

  16. Engineered phages for electronics.

    Science.gov (United States)

    Cui, Yue

    2016-11-15

    Phages are traditionally widely studied in biology and chemistry. In recent years, engineered phages have attracted significant attentions for functionalization or construction of electronic devices, due to their specific binding, catalytic, nucleating or electronic properties. To apply the engineered phages in electronics, these are a number of interesting questions: how to engineer phages for electronics? How are the engineered phages characterized? How to assemble materials with engineered phages? How are the engineered phages micro or nanopatterned? What are the strategies to construct electronics devices with engineered phages? This review will highlight the early attempts to address these questions and explore the fundamental and practical aspects of engineered phages in electronics, including the approaches for selection or expression of specific peptides on phage coat proteins, characterization of engineered phages in electronics, assembly of electronic materials, patterning of engineered phages, and construction of electronic devices. It provides the methodologies and opens up ex-cit-ing op-por-tu-ni-ties for the development of a variety of new electronic materials and devices based on engineered phages for future applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. In vitro generation of a scaffold-free tissue-engineered construct (TEC) derived from human synovial mesenchymal stem cells: biological and mechanical properties and further chondrogenic potential.

    Science.gov (United States)

    Ando, Wataru; Tateishi, Kosuke; Katakai, Daisuke; Hart, David A; Higuchi, Chikahisa; Nakata, Ken; Hashimoto, Jun; Fujie, Hiromichi; Shino, Konsei; Yoshikawa, Hideki; Nakamura, Norimasa

    2008-12-01

    The purpose of this study was to characterize a tissue-engineered construct (TEC) generated with human synovial mesenchymal stem cells (MSCs). MSCs were cultured in medium with ascorbic acid 2-phosphate (Asc-2P) and were subsequently detached from the substratum. The detached cell/matrix complex spontaneously contracted to develop a basic TEC. The volume of the TEC assessed by varying initial cell density showed that it was proportional to initial cell densities up to 4 x 10(5) cells/cm(2). Assessment of the mechanical properties of TEC using a custom device showed that the load at failure and stiffness of the constructs significantly increased with time of culture in the presence of Asc-2P, while in the absence of Asc-2P, the constructs were mechanically weak. Thus, the basic TEC possesses sufficiently self-supporting mechanical properties in spite of not containing artificial scaffolding. TEC further cultured in chondrogenic media exhibited positive alcian blue staining with elevated expression of chondrogenic marker genes. Based on these findings, such human TEC may be a promising method to promote cartilage repair for future clinical application.

  18. Branding the bio/biomedical engineering degree.

    Science.gov (United States)

    Voigt, Herbert F

    2011-01-01

    The future challenges to medical and biological engineering, sometimes referred to as biomedical engineering or simply bioengineering, are many. Some of these are identifiable now and others will emerge from time to time as new technologies are introduced and harnessed. There is a fundamental issue regarding "Branding the bio/biomedical engineering degree" that requires a common understanding of what is meant by a B.S. degree in Biomedical Engineering, Bioengineering, or Biological Engineering. In this paper we address some of the issues involved in branding the Bio/Biomedical Engineering degree, with the aim of clarifying the Bio/Biomedical Engineering brand.

  19. Regenerative engineering

    CERN Document Server

    Laurencin, Cato T

    2013-01-01

    Regenerative Engineering: The Future of Medicine Saadiq F. El-Amin III , MD , PhD; Joylene W.L. Thomas, MD ; Ugonna N. Ihekweazu, MD ; Mia D. Woods, MS; and Ashim Gupta, MSCell Biology Gloria Gronowicz, PhD and Karen Sagomonyants, DMDStem Cells and Tissue Regeneration Kristen Martins-Taylor, PhD; Xiaofang Wang, MD , PhD; Xue-Jun Li, PhD; and Ren-He Xu, MD , PhDIntroduction to Materials Science Sangamesh G. Kumbar, PhD and Cato T. Laurencin, MD , PhDBiomaterials A. Jon Goldberg, PhD and Liisa T. Kuhn, PhDIn Vitro Assessment of Cell-Biomaterial Interactions Yong Wang, PhDHost Response to Biomate

  20. Layered Systems Engineering Engines

    Science.gov (United States)

    Breidenthal, Julian C.; Overman, Marvin J.

    2009-01-01

    A notation is described for depicting the relationships between multiple, contemporaneous systems engineering efforts undertaken within a multi-layer system-of-systems hierarchy. We combined the concepts of remoteness of activity from the end customer, depiction of activity on a timeline, and data flow to create a new kind of diagram which we call a "Layered Vee Diagram." This notation is an advance over previous notations because it is able to be simultaneously precise about activity, level of granularity, product exchanges, and timing; these advances provide systems engineering managers a significantly improved ability to express and understand the relationships between many systems engineering efforts. Using the new notation, we obtain a key insight into the relationship between project duration and the strategy selected for chaining the systems engineering effort between layers, as well as insights into the costs, opportunities, and risks associated with alternate chaining strategies.

  1. Engineering Ecosystems and Synthetic Ecologies#

    Science.gov (United States)

    Mee, Michael T; Wang, Harris H

    2012-01-01

    Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here, we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. We highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of microbial ecosystem engineering. We argue that simply engineering individual microbes will lead to fragile homogenous populations that are difficult to sustain, especially in highly heterogeneous and unpredictable environments. Instead, engineered microbial ecosystems are likely to be more robust and able to achieve complex tasks at the spatial and temporal resolution needed for truly programmable biology. PMID:22722235

  2. Complex systems in metabolic engineering.

    Science.gov (United States)

    Winkler, James D; Erickson, Keesha; Choudhury, Alaksh; Halweg-Edwards, Andrea L; Gill, Ryan T

    2015-12-01

    Metabolic engineers manipulate intricate biological networks to build efficient biological machines. The inherent complexity of this task, derived from the extensive and often unknown interconnectivity between and within these networks, often prevents researchers from achieving desired performance. Other fields have developed methods to tackle the issue of complexity for their unique subset of engineering problems, but to date, there has not been extensive and comprehensive examination of how metabolic engineers use existing tools to ameliorate this effect on their own research projects. In this review, we examine how complexity affects engineering at the protein, pathway, and genome levels within an organism, and the tools for handling these issues to achieve high-performing strain designs. Quantitative complexity metrics and their applications to metabolic engineering versus traditional engineering fields are also discussed. We conclude by predicting how metabolic engineering practices may advance in light of an explicit consideration of design complexity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Engineer Ethics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dae Sik; Kim, Yeong Pil; Kim, Yeong Jin

    2003-03-15

    This book tells of engineer ethics such as basic understanding of engineer ethics with history of engineering as a occupation, definition of engineering and specialized job and engineering, engineer ethics as professional ethics, general principles of ethics and its limitation, ethical theory and application, technique to solve the ethical problems, responsibility, safety and danger, information engineer ethics, biotechnological ethics like artificial insemination, life reproduction, gene therapy and environmental ethics.

  4. Engineer Ethics

    International Nuclear Information System (INIS)

    Lee, Dae Sik; Kim, Yeong Pil; Kim, Yeong Jin

    2003-03-01

    This book tells of engineer ethics such as basic understanding of engineer ethics with history of engineering as a occupation, definition of engineering and specialized job and engineering, engineer ethics as professional ethics, general principles of ethics and its limitation, ethical theory and application, technique to solve the ethical problems, responsibility, safety and danger, information engineer ethics, biotechnological ethics like artificial insemination, life reproduction, gene therapy and environmental ethics.

  5. Towards paraconsistent engineering

    CERN Document Server

    2016-01-01

    This book presents a collection of contributions from related logics to applied paraconsistency. Moreover, all of them are dedicated to Jair Minoro Abe,on the occasion of his sixtieth birthday. He is one of the experts in Paraconsistent Engineering, who developed the so-called annotated logics. The book includes important contributions on foundations and applications of paraconsistent logics in connection with engineering, mathematical logic, philosophical logic, computer science, physics, economics, and biology. It will be of interest to students and researchers, who are working on engineering and logic. .

  6. Introduction to environmental engineering

    Science.gov (United States)

    Šalić, Anita; Zelić, Bruno

    2018-02-01

    Nowadays we can easily say that environmental engineering is truly an interdisciplinary science. Combining biology, ecology, geology, geography, mathematics, chemistry, agronomy, medicine, economy, etc. environmental engineering strives to use environmental understanding and advancements in technology to serve mankind by decreasing production of environmental hazards and the effects of those hazards already present in the soil, water, and air. Major activities of environmental engineer involve water supply, waste water and solid management, air and noise pollution control, environmental sustainability, environmental impact assessment, climate changes, etc. And all this with only one main goal - to prevent or reduce undesirable impacts of human activities on the environment. To ensure we all have tomorrow.

  7. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    Systems biology seeks to study biological systems as a whole, contrary to the reductionist approach that has dominated biology. Such a view of biological systems emanating from strong foundations of molecular level understanding of the individual components in terms of their form, function and interactions is promising to ...

  8. Biotechnology. Part 1: Historical aspects. Part 2: Microbiological engineering. Part 3: Enzymatic engineering. Part 4: Genetical engineering. Part 5: Quality control in biological industry. Part 6: Bio technologies in France and in the world; Biotechnologie. Partie 1: Historique. Partie 2: Le genie microbiologique. Partie 3: Le genie enzymatique. Partie 4: Le genie genetique. Partie 5: Controle qualite en bio-industrie. Partie 6: Les biotechnologies en France et dans le monde

    Energy Technology Data Exchange (ETDEWEB)

    Bouquet, J. [Lycee de Lille, 59 (France); Arnaud, A.; Galzy, P. [Ecole Nationale Superieure Agronomie de Montpellier, 34 (France); Guiraud, J.P. [Montpellier-2 Universite, 34 (France). Institut Superieur Ingenieurs de Montpellier; Leveau, J.Y.; Bouix, M.; Berset, C.; Goursaud, J.; Cuvelier, G.F. [Ecole Nationale Superieure des Industries Agricoles et Alimentaires, 91 - Massy (France); Engasser, J.M. [Institut Polytechnique de Lorraine, 54 - Vandoeuvre-les-Nancy (France); Cerisier, Y. [CNCM Institut Pasteur, 75 - Paris (France); Richard, H. [Ecole Nationale Superieure des Industries Agricoles et Alimentaires, 91 - Massy (France). Laboratoire de Chimie des Substances Naturelles; Scriban, R. [Ecole Nationale Superieure des Industries Alimentaires, 59 - Douai (France); Teoule, E. [Paris-6 Universite, 75 (France). Laboratoire Station de Genetique et d`Amelioration des Plantes; Martal, J. [INRA, 78 - Jouy-en-Josas (France); Mawas, C. [INSERM, Cancerologie et Therapeutique experimentales, 13 - Marseille (France); Pourquie, J. [Institut National Agronomique, 75 - Paris (France); Vandecasteele, J.P. [Institut Francais du Petrole, 92 - Rueil-Malmaison (France); Iwema, A. [Agence de l`eau Rhone-Mediterranee-Corse, 69 - Pierre-Benite (France); Lebeault, J.M. [Compiegne Universite, Centre de Recherche de Royalieu, 60 (France); Steenbrugge, H. [Gaz de France, 59 - Lille (France); Pierrard, S. [Veterinaire Inspecteur, 70 - Vesoul (France); Normand-Plessier, F. [Elf Sanofi, 94 - Gentilly (France); Raugel, P.J. [Economiste International, 94 - Ivry-sur-Seine (France); Guerrini, M.; Jupin, C. [Institut National de la Propriete Industrielle, 75 - Paris (France); Thomas, D. [Compiegne Universite Technologique, 60 (France)]|[Ecole Pratique des Hautes Etudes URA,CNRS, 60 - Compiegne (France); Nettancourt, D. de [Commission des Communautes Europeenes, Bruxelles (Belgium)

    1993-12-31

    The fourth edition of the book ``biotechnology`` has just been published. It keeps the general frame of the previous editions while adding the analysis of new areas such as the animal world, the environment, the question of patentability, the standards and regulations, the stake of research and formation in the CEE, the importance of the scientific research for the reciprocal understanding of bio technologies and environmental problems, the respect of the biological variety.. Among the treated subjects, those particularly interesting for the ETDE database are the waste waters and industrial wastes and the natural gas. Didactic guide particularly well documented by a valuable bibliography, this work is an indispensable tool for teacher-searcher, students and engineers. (O.M.) 1113 refs.

  9. Standardization in synthetic biology.

    Science.gov (United States)

    Müller, Kristian M; Arndt, Katja M

    2012-01-01

    Synthetic Biology is founded on the idea that complex biological systems are built most effectively when the task is divided in abstracted layers and all required components are readily available and well-described. This requires interdisciplinary collaboration at several levels and a common understanding of the functioning of each component. Standardization of the physical composition and the description of each part is required as well as a controlled vocabulary to aid design and ensure interoperability. Here, we describe standardization initiatives from several disciplines, which can contribute to Synthetic Biology. We provide examples of the concerted standardization efforts of the BioBricks Foundation comprising the request for comments (RFC) and the Registry of Standardized Biological parts as well as the international Genetically Engineered Machine (iGEM) competition.

  10. Introducing a dimensioning and simulation model useful for engineering practice for the modelling/optimization of enhanced biological P elimination.; Vorstellung eines in der Ingenieurpraxis nutzbaren Bemessungs- und Simulationsmodelles zur Abbildung/Optimierung der vermehrten biologischen P-Elimination

    Energy Technology Data Exchange (ETDEWEB)

    Wichern, M.; Rosenwinkel, K.H.; Binder, M.

    1999-07-01

    The paper describes in excerpts a stationary model, suitable for engineering practice, for assessing the efficiency of enhanced biological P elimination. Adapted to the latest state of knowledge and based on only a few measuring data, it can be used to dimension or optimize existing plant. It takes into account knowledge such as the following: growth of organisms with enhanced phosphorus accumulation (PAOs) in an anoxic environment, modelling of biomass die-back in an anaerobic environment, different yield and die-back rates of PAOs and non-bioP organisms, the share of denitrifying PAOs and degradation processes through hydrolysis/fermentation. (orig.) [German] Im Rahmen dieses Beitrages wird ein in der Ingenieurpraxis anwendbares stationaeres Modell zur Abschaetzung der Leistungsfaehigkeit der vermehrten biologischen P-Elimination in Auszuegen vorgestellt, das, angepasst an neueste Erkenntnisse, auf Basis weniger Messdaten zur Bemessung sowie Optimierung von bestehenden Anlagen eingesetzt werden kann. Erkenntnisse, wie z.B. das Wachsen der vermehrt phosphorspeichernden Organismen (PAO) im Anoxischen, die Abbildung des Biomassensterbens im Anaeroben, die unterschiedlichen Ertrags- und Sterberaten von PAOs und Nicht-BioP-Organismen, der Anteil der denitrifizierenden PAOs und Abbauprozesse durch Hydrolyse/Fermentation sind im Modell beruecksichtigt. (orig.)

  11. Biochemical engineering's grand adventure

    NARCIS (Netherlands)

    Noorman, H.J.; Heijnen, J.J.

    2017-01-01

    Building on the recent revolution in molecular biology, enabling a wealth of bio-product innovations made from renewable feedstocks, the biotechnology field is in a transition phase to bring the products to the market. This requires a shift from natural sciences to engineering sciences with first

  12. Engineering synergy in biotechnology

    DEFF Research Database (Denmark)

    Nielsen, Jens; Fussenegger, Martin; Keasling, Jay

    2014-01-01

    In this article, the author focuses on approaches in metabolic engineering and synthetic biology for the creation of efficient cell factories, which can be bused to convert biomass and other feedstocks for the generation of chemicals. Topics discussed include development of restriction enzymes, e...

  13. Anatomy for Biomedical Engineers

    Science.gov (United States)

    Carmichael, Stephen W.; Robb, Richard A.

    2008-01-01

    There is a perceived need for anatomy instruction for graduate students enrolled in a biomedical engineering program. This appeared especially important for students interested in and using medical images. These students typically did not have a strong background in biology. The authors arranged for students to dissect regions of the body that…

  14. Tissue engineered aortic valve

    OpenAIRE

    Dohmen, P M

    2012-01-01

    Several prostheses are available to replace degenerative diseased aortic valves with unique advantages and disadvantages. Bioprotheses show excellent hemodynamic behavior and low risk of thromboembolic complications, but are limited by tissue deterioration. Mechanical heart valves have extended durability, but permanent anticoagulation is mandatory. Tissue engineering created a new generation heart valve, which overcome limitations of biological and mechanical heart valves due to remodelling,...

  15. Computational Modeling in Tissue Engineering

    CERN Document Server

    2013-01-01

    One of the major challenges in tissue engineering is the translation of biological knowledge on complex cell and tissue behavior into a predictive and robust engineering process. Mastering this complexity is an essential step towards clinical applications of tissue engineering. This volume discusses computational modeling tools that allow studying the biological complexity in a more quantitative way. More specifically, computational tools can help in:  (i) quantifying and optimizing the tissue engineering product, e.g. by adapting scaffold design to optimize micro-environmental signals or by adapting selection criteria to improve homogeneity of the selected cell population; (ii) quantifying and optimizing the tissue engineering process, e.g. by adapting bioreactor design to improve quality and quantity of the final product; and (iii) assessing the influence of the in vivo environment on the behavior of the tissue engineering product, e.g. by investigating vascular ingrowth. The book presents examples of each...

  16. Biological computation

    CERN Document Server

    Lamm, Ehud

    2011-01-01

    Introduction and Biological BackgroundBiological ComputationThe Influence of Biology on Mathematics-Historical ExamplesBiological IntroductionModels and Simulations Cellular Automata Biological BackgroundThe Game of Life General Definition of Cellular Automata One-Dimensional AutomataExamples of Cellular AutomataComparison with a Continuous Mathematical Model Computational UniversalitySelf-Replication Pseudo Code Evolutionary ComputationEvolutionary Biology and Evolutionary ComputationGenetic AlgorithmsExample ApplicationsAnalysis of the Behavior of Genetic AlgorithmsLamarckian Evolution Genet

  17. The Physics behind Systems Biology

    Directory of Open Access Journals (Sweden)

    Radde Nicole E.

    2016-12-01

    Full Text Available Systems Biology is a young and rapidly evolving research field, which combines experimental techniques and mathematical modeling in order to achieve a mechanistic understanding of processes underlying the regulation and evolution of living systems. Systems Biology is often associated with an Engineering approach: The purpose is to formulate a data-rich, detailed simulation model that allows to perform numerical (‘in silico’ experiments and then draw conclusions about the biological system. While methods from Engineering may be an appropriate approach to extending the scope of biological investigations to experimentally inaccessible realms and to supporting data-rich experimental work, it may not be the best strategy in a search for design principles of biological systems and the fundamental laws underlying Biology. Physics has a long tradition of characterizing and understanding emergent collective behaviors in systems of interacting units and searching for universal laws. Therefore, it is natural that many concepts used in Systems Biology have their roots in Physics. With an emphasis on Theoretical Physics, we will here review the ‘Physics core’ of Systems Biology, show how some success stories in Systems Biology can be traced back to concepts developed in Physics, and discuss how Systems Biology can further benefit from its Theoretical Physics foundation.

  18. Micromechanics of engineered and biological systems

    Indian Academy of Sciences (India)

    Here, the structural deforma- tion interacts nonlinearly with the static electric field ensuing between electrical conductors and dielectrics. As has been argued well in the litera- ture, electrostatic force scales vary favourably at the microscale and therefore numerous micro- systems devices use this. Many such devices are.

  19. Gene engineering biological therapy for juvenile arthritis

    Directory of Open Access Journals (Sweden)

    Kh Mikhel's

    2011-01-01

    However, GEBA therapy cannot completely cure the disease as before despite the progress achieved. GEBAs have potentially a number of serious side effects, among which there are severe infections and there is a risk of developing malignancies and autoimmune processes. Their administration requires careful monitoring to reveal the early development of serious adverse reactions, thus preventing a poor outcome.

  20. Lectures in Physics, Biology and Engineering

    Indian Academy of Sciences (India)

    admin

    2017-06-29

    Jun 29, 2017 ... A popular misconception about scienti ic breakthroughs is that they are predicated on brilliant schemes whose dazzling provenance is the exclusive preserve of quirky masterminds. This talk attempts to debunk the myth by demonstrating, to the contrary, that absurd and preposterous ideas, neglected and ...

  1. Lectures in Physics, Biology and Engineering

    Indian Academy of Sciences (India)

    admin

    2017-06-29

    Story-Sunspots/dp/0199674752/. A popular misconception about scienti ic breakthroughs is that they are predicated on brilliant schemes whose dazzling provenance is the exclusive preserve of quirky masterminds. This talk ...

  2. Synthetic biology: from mainstream to counterculture.

    Science.gov (United States)

    Sleator, Roy D

    2016-09-01

    Existing at the interface of science and engineering, synthetic biology represents a new and emerging field of mainstream biology. However, there also exists a counterculture of Do-It-Yourself biologists, citizen scientists, who have made significant inroads, particularly in the design and development of new tools and techniques. Herein, I review the development and convergence of synthetic biology's mainstream and countercultures.

  3. Mechanical engineering

    CERN Document Server

    Darbyshire, Alan

    2010-01-01

    Alan Darbyshire's best-selling text book provides five-star high quality content to a potential audience of 13,000 engineering students. It explains the most popular specialist units of the Mechanical Engineering, Manufacturing Engineering and Operations & Maintenance Engineering pathways of the new 2010 BTEC National Engineering syllabus. This challenging textbook also features contributions from specialist lecturers, ensuring that no stone is left unturned.

  4. Reevaluating synthesis by biology.

    Science.gov (United States)

    Yadav, Vikramaditya G; Stephanopoulos, Gregory

    2010-06-01

    The two cornerstones of synthetic biology are the introduction of the new technology of chemical DNA synthesis and its subsequent emphasis on the use of standardized biological parts in the construction of genetic systems aimed at eliciting of desired cellular behavior. A number of high-impact applications have been proposed for this technology, notable among them being the biological synthesis of valuable compounds for chemical or pharmaceutical use. To this end, synthetic biologists propose assembling metabolic pathways in toto by combining genes isolated from a variety of sources. While pathway construction is similar to approaches established long ago by Metabolic Engineering, the two methods deviate significantly when it comes to pathway optimization. Synthetic biologists opt for gene-combinatorial methods whereby large numbers of pathways, comprising several combinations of genes from different sources, and their mutants, are evaluated in search for an optimal pathway configuration. Metabolic engineering, on the contrary, aims to optimize pathways by tuning the activity of the intermediate reaction steps. Both, rational methods based on kinetics and regulation, as well as combinatorial methods, typically in this order, are used to this end. We argue that a systematic approach consisting of fine-tuning the properties of individual pathway components, prominently enzymes, is a superior strategy to searches spanning large genetic spaces in engineering optimal microbes for the production of chemical and pharmaceutical products. Copyright 2010 Elsevier Ltd. All rights reserved.

  5. Molecular, cellular, and tissue engineering

    CERN Document Server

    Bronzino, Joseph D

    2015-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering. Molecular, Cellular, and Tissue Engineering, the fourth volume of the handbook, presents material from respected scientists with diverse backgrounds in molecular biology, transport phenomena, physiological modeling, tissue engineering, stem cells, drug delivery systems, artificial organs, and personalized medicine. More than three dozen specific topics are examined, including DNA vaccines, biomimetic systems, cardiovascular dynamics, biomaterial scaffolds, cell mechanobiology, synthetic biomaterials, pluripotent stem cells, hematopoietic stem cells, mesenchymal stem cells, nanobiomaterials for tissue engineering, biomedical imaging of engineered tissues, gene therapy, noninvasive targeted protein and peptide drug deliver...

  6. Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Wiley, H S.

    2006-06-01

    The biology revolution over the last 50 years has been driven by the ascendancy of molecular biology. This was enthusiastically embraced by most biologists because it took us into increasingly familiar territory. It took mysterious processes, such as the replication of genetic material and assigned them parts that could be readily understood by the human mind. When we think of ''molecular machines'' as being the underlying basis of life, we are using a paradigm derived from everyday experience. However, the price that we paid was a relentless drive towards reductionism and the attendant balkanization of biology. Now along comes ''systems biology'' that promises us a solution to the problem of ''knowing more and more about less and less''. Unlike molecular biology, systems biology appears to be taking us into unfamiliar intellectual territory, such as statistics, mathematics and computer modeling. Not surprisingly, systems biology has met with widespread skepticism and resistance. Why do we need systems biology anyway and how does this new area of research promise to change the face of biology in the next couple of decades?

  7. Biological therapeutics

    National Research Council Canada - National Science Library

    Greenstein, Ben; Brook, Daniel A

    2011-01-01

    This introductory textbook covers all the main categories of biological medicines, including vaccines, hormonal preparations, drugs for rheumatoid arthritis and other connective tissue diseases, drugs...

  8. Systems Biology of Industrial Microorganisms

    Science.gov (United States)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  9. Industrial Engineering

    DEFF Research Database (Denmark)

    Karlsson, Christer

    2015-01-01

    Industrial engineering is a discipline that is concerned with increasing the effectiveness of (primarily) manufacturing and (occasionally).......Industrial engineering is a discipline that is concerned with increasing the effectiveness of (primarily) manufacturing and (occasionally)....

  10. Governing Engineering

    DEFF Research Database (Denmark)

    Buch, Anders

    2012-01-01

    Most people agree that our world face daunting problems and, correctly or not, technological solutions are seen as an integral part of an overall solution. But what exactly are the problems and how does the engineering ‘mind set’ frame these problems? This chapter sets out to unravel dominant...... perspectives in challenge per-ception in engineering in the US and Denmark. Challenge perception and response strategies are closely linked through discursive practices. Challenge perceptions within the engineering community and the surrounding society are thus critical for the shaping of engineering education...... and the engineering profession. Through an analysis of influential reports and position papers on engineering and engineering education the chapter sets out to identify how engineering is problematized and eventually governed. Drawing on insights from governmentality studies the chapter strives to elicit the bodies...

  11. Governing Engineering

    DEFF Research Database (Denmark)

    Buch, Anders

    2011-01-01

    Abstract: Most people agree that our world faces daunting problems and, correctly or not, technological solutions are seen as an integral part of an overall solution. But what exactly are the problems and how does the engineering ‘mind set’ frame these problems? This chapter sets out to unravel...... dominant perspectives in challenge perception in engineering in the US and Denmark. Challenge perception and response strategies are closely linked through discursive practices. Challenge perceptions within the engineering community and the surrounding society are thus critical for the shaping...... of engineering education and the engineering profession. Through an analysis of influential reports and position papers on engineering and engineering education the chapter sets out to identify how engineering is problematized and eventually governed. Drawing on insights from governmentality studies the chapter...

  12. Engineering _ litteraturliste

    DEFF Research Database (Denmark)

    Sillasen, Martin Krabbe; Daugbjerg, Peer; Nielsen, Keld

    2017-01-01

    Litteraturliste udarbejdet som grundlag for artiklen ”Engineering – svaret på naturfagenes udfordringer?”......Litteraturliste udarbejdet som grundlag for artiklen ”Engineering – svaret på naturfagenes udfordringer?”...

  13. Refinement and standardization of synthetic biological parts and devices.

    Science.gov (United States)

    Canton, Barry; Labno, Anna; Endy, Drew

    2008-07-01

    The ability to quickly and reliably engineer many-component systems from libraries of standard interchangeable parts is one hallmark of modern technologies. Whether the apparent complexity of living systems will permit biological engineers to develop similar capabilities is a pressing research question. We propose to adapt existing frameworks for describing engineered devices to biological objects in order to (i) direct the refinement and use of biological 'parts' and 'devices', (ii) support research on enabling reliable composition of standard biological parts and (iii) facilitate the development of abstraction hierarchies that simplify biological engineering. We use the resulting framework to describe one engineered biological device, a genetically encoded cell-cell communication receiver named BBa_F2620. The description of the receiver is summarized via a 'datasheet' similar to those widely used in engineering. The process of refinement and characterization leading to the BBa_F2620 datasheet may serve as a starting template for producing many standardized genetically encoded objects.

  14. Molecular biomimetics: nanotechnology through biology

    Science.gov (United States)

    Sarikaya, Mehmet; Tamerler, Candan; Jen, Alex K.-Y.; Schulten, Klaus; Baneyx, François

    2003-09-01

    Proteins, through their unique and specific interactions with other macromolecules and inorganics, control structures and functions of all biological hard and soft tissues in organisms. Molecular biomimetics is an emerging field in which hybrid technologies are developed by using the tools of molecular biology and nanotechnology. Taking lessons from biology, polypeptides can now be genetically engineered to specifically bind to selected inorganic compounds for applications in nano- and biotechnology. This review discusses combinatorial biological protocols, that is, bacterial cell surface and phage-display technologies, in the selection of short sequences that have affinity to (noble) metals, semiconducting oxides and other technological compounds. These genetically engineered proteins for inorganics (GEPIs) can be used in the assembly of functional nanostructures. Based on the three fundamental principles of molecular recognition, self-assembly and DNA manipulation, we highlight successful uses of GEPI in nanotechnology.

  15. 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.

  16. Engineering Motion

    Science.gov (United States)

    Tuttle, Nicole; Stanley, Wendy; Bieniek, Tracy

    2016-01-01

    For many teachers, engineering can be intimidating; teachers receive little training in engineering, particularly those teaching early elementary students. In addition, the necessity of differentiating for students with special needs can make engineering more challenging to teach. This article describes a professional development program…

  17. Biomodel Engineering - From Structure to Behavior

    NARCIS (Netherlands)

    Breitling, Rainer; Donaldson, Robin A.; Gilbert, David R.; Heiner, Monika; Priami, C; Breitling, R; Gilbert, D; Heiner, M; Uhrmacher, AM

    2010-01-01

    Biomodel engineering is the science of designing, constructing and analyzing computational models of biological systems. It forms a systematic and powerful extension of earlier mathematical modeling approaches and has recently gained popularity in systems biology and synthetic biology. In this brief

  18. Tissue engineering in dentistry.

    Science.gov (United States)

    Abou Neel, Ensanya Ali; Chrzanowski, Wojciech; Salih, Vehid M; Kim, Hae-Won; Knowles, Jonathan C

    2014-08-01

    of this review is to inform practitioners with the most updated information on tissue engineering and its potential applications in dentistry. The authors used "PUBMED" to find relevant literature written in English and published from the beginning of tissue engineering until today. A combination of keywords was used as the search terms e.g., "tissue engineering", "approaches", "strategies" "dentistry", "dental stem cells", "dentino-pulp complex", "guided tissue regeneration", "whole tooth", "TMJ", "condyle", "salivary glands", and "oral mucosa". Abstracts and full text articles were used to identify causes of craniofacial tissue loss, different approaches for craniofacial reconstructions, how the tissue engineering emerges, different strategies of tissue engineering, biomaterials employed for this purpose, the major attempts to engineer different dental structures, finally challenges and future of tissue engineering in dentistry. Only those articles that dealt with the tissue engineering in dentistry were selected. There have been a recent surge in guided tissue engineering methods to manage periodontal diseases beyond the traditional approaches. However, the predictable reconstruction of the innate organisation and function of whole teeth as well as their periodontal structures remains challenging. Despite some limited progress and minor successes, there remain distinct and important challenges in the development of reproducible and clinically safe approaches for oral tissue repair and regeneration. Clearly, there is a convincing body of evidence which confirms the need for this type of treatment, and public health data worldwide indicates a more than adequate patient resource. The future of these therapies involving more biological approaches and the use of dental tissue stem cells is promising and advancing. Also there may be a significant interest of their application and wider potential to treat disorders beyond the craniofacial region. Considering the

  19. Mesoscopic biology

    Indian Academy of Sciences (India)

    Abstract. In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. ... National Center for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bangalore 560 065, India ...

  20. Computational biology

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

  1. Mesoscopic biology

    Indian Academy of Sciences (India)

    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological ...

  2. Immune engineering: from systems immunology to engineering immunity.

    Science.gov (United States)

    Jiang, Ning

    2017-03-01

    The smallpox vaccine represents the earliest attempt in engineering immunity. The recent success of chimeric antigen receptor T cells (CAR-T cells) in cancer once again demonstrates the clinical potential of immune engineering. Inspired by this success, diverse approaches have been used to boost various aspects of immunity: engineering dendritic cells (DCs), natural killer (NK) cells, T cells, antibodies, cytokines, small peptides, and others. With recent development of various high-throughput technologies (of which engineers, especially biomedical engineers/bioengineers contributed significantly), such as immune repertoire sequencing, and analytical methods, a systems level of understanding immunity (or the lack of it) beyond model animals has provided critical insights into the human immune system. This review focuses on recent progressed made in systems biology and the engineering of adaptive immunity.

  3. Computational engineering

    CERN Document Server

    2014-01-01

    The book presents state-of-the-art works in computational engineering. Focus is on mathematical modeling, numerical simulation, experimental validation and visualization in engineering sciences. In particular, the following topics are presented: constitutive models and their implementation into finite element codes, numerical models in nonlinear elasto-dynamics including seismic excitations, multiphase models in structural engineering and multiscale models of materials systems, sensitivity and reliability analysis of engineering structures, the application of scientific computing in urban water management and hydraulic engineering, and the application of genetic algorithms for the registration of laser scanner point clouds.

  4. Grand challenges in space synthetic biology.

    Science.gov (United States)

    Menezes, Amor A; Montague, Michael G; Cumbers, John; Hogan, John A; Arkin, Adam P

    2015-12-06

    Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth. © 2015 The Authors.

  5. Architectural Engineers

    DEFF Research Database (Denmark)

    Petersen, Rikke Premer

    engineering is addresses from two perspectives – as an educational response and an occupational constellation. Architecture and engineering are two of the traditional design professions and they frequently meet in the occupational setting, but at educational institutions they remain largely estranged....... The paper builds on a multi-sited study of an architectural engineering program at the Technical University of Denmark and an architectural engineering team within an international engineering consultancy based on Denmark. They are both responding to new tendencies within the building industry where...... the role of engineers and architects increasingly overlap during the design process, but their approaches reflect different perceptions of the consequences. The paper discusses some of the challenges that design education, not only within engineering, is facing today: young designers must be equipped...

  6. Tissue engineering

    CERN Document Server

    Fisher, John P; Bronzino, Joseph D

    2007-01-01

    Increasingly viewed as the future of medicine, the field of tissue engineering is still in its infancy. As evidenced in both the scientific and popular press, there exists considerable excitement surrounding the strategy of regenerative medicine. To achieve its highest potential, a series of technological advances must be made. Putting the numerous breakthroughs made in this field into a broad context, Tissue Engineering disseminates current thinking on the development of engineered tissues. Divided into three sections, the book covers the fundamentals of tissue engineering, enabling technologies, and tissue engineering applications. It examines the properties of stem cells, primary cells, growth factors, and extracellular matrix as well as their impact on the development of tissue engineered devices. Contributions focus on those strategies typically incorporated into tissue engineered devices or utilized in their development, including scaffolds, nanocomposites, bioreactors, drug delivery systems, and gene t...

  7. Performance of machinery in potato production in one growing season

    Directory of Open Access Journals (Sweden)

    Kun Zhou

    2015-12-01

    Full Text Available Statistics on the machinery performance are essential for farm managers to make better decisions. In this paper, the performance of all machineries in five sequential operations, namely bed forming, stone separation, planting, spraying and harvesting in the potato production system, were investigated during one growing season. In order to analyse and decompose the recorded GPS data into various time and distance elements for estimation of the machinery performance, an automatic GPS analysis tool was developed. The field efficiency and field capacity were estimated for each operation. Specifically, the measured average field efficiency was 71.3% for bed forming, 68.5% for stone separation, 40.3% for planting, 69.7% for spraying, and 67.4% for harvesting. The measured average field capacities were 1.46 ha/h, 0.53 ha/h, 0.47 ha/h, 10.21 ha/h, 0.51 ha/h, for the bed forming, stone separation, planting, spraying, and harvesting operations, respectively. These results deviate from the corresponding estimations calculated based on norm data from the American Society of Agricultural and Biological Engineers (ASABE. The deviations indicate that norms provided by ASABE cannot be used directly for the prediction of performance of the machinery used in this work. Moreover, the measured data of bed forming and stone separation could be used as supplementary data for the ASABE which does not provide performance norms for these two operations. The gained results can help farm managers to make better management and operational decisions that result in potential improvement in productivity and profitability as well as in potential environmental benefits.

  8. Performance of machinery in potato production in one growing season

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, K.; Jensen, A.L.; Bochtis, D.D.; Sørensen, C.G.

    2015-07-01

    Statistics on the machinery performance are essential for farm managers to make better decisions. In this paper, the performance of all machineries in five sequential operations, namely bed forming, stone separation, planting, spraying and harvesting in the potato production system, were investigated during one growing season. In order to analyse and decompose the recorded GPS data into various time and distance elements for estimation of the machinery performance, an automatic GPS analysis tool was developed. The field efficiency and field capacity were estimated for each operation. Specifically, the measured average field efficiency was 71.3% for bed forming, 68.5% for stone separation, 40.3% for planting, 69.7% for spraying, and 67.4% for harvesting. The measured average field capacities were 1.46 ha/h, 0.53 ha/h, 0.47 ha/h, 10.21 ha/h, 0.51 ha/h, for the bed forming, stone separation, planting, spraying, and harvesting operations, respectively. These results deviate from the corresponding estimations calculated based on norm data from the American Society of Agricultural and Biological Engineers (ASABE). The deviations indicate that norms provided by ASABE cannot be used directly for the prediction of performance of the machinery used in this work. Moreover, the measured data of bed forming and stone separation could be used as supplementary data for the ASABE which does not provide performance norms for these two operations. The gained results can help farm managers to make better management and operational decisions that result in potential improvement in productivity and profitability as well as in potential environmental benefits. (Author)

  9. Computational and Genomic Analysis of Mycobacteriophage: A Longitudinal Study of Technology Engineered Biology Courses That Implemented an Inquiry Based Laboratory Practice Designed to Enhance, Encourage, and Empower Student Learning

    Science.gov (United States)

    Hollowell, Gail P.; Osler, James E.; Hester, April L.

    2015-01-01

    This paper provides an applied research rational for a longitudinal investigation that involved teaching a "Technology Engineered Science Education Course" via an Interactive Laboratory Based Genomics Curriculum. The Technology st Engineering [TE] methodology was first introduced at the SAPES: South Atlantic Philosophy of Education…

  10. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  11. Biological Oceanography

    Science.gov (United States)

    Dyhrman, Sonya

    2004-10-01

    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  12. VI Latin American Congress on Biomedical Engineering

    CERN Document Server

    Hadad, Alejandro

    2015-01-01

    This volume presents the proceedings of the CLAIB 2014, held in Paraná, Entre Ríos, Argentina 29, 30 & 31 October 2014. The proceedings, presented by the Regional Council of Biomedical Engineering for Latin America (CORAL) offer research findings, experiences and activities between institutions and universities to develop Bioengineering, Biomedical Engineering and related sciences. The conferences of the American Congress of Biomedical Engineering are sponsored by the International Federation for Medical and Biological Engineering (IFMBE), Society for Engineering in Biology and Medicine (EMBS) and the Pan American Health Organization (PAHO), among other organizations and international agencies and bringing together scientists, academics and biomedical engineers in Latin America and other continents in an environment conducive to exchange and professional growth. The Topics include: - Bioinformatics and Computational Biology - Bioinstrumentation; Sensors, Micro and Nano Technologies - Biomaterials, Tissu...

  13. Biological process linkage networks.

    Directory of Open Access Journals (Sweden)

    Dikla Dotan-Cohen

    Full Text Available The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning patterns of interactions between biological processes by analyzing protein-protein interactions, transcriptional co-expression and genetic interactions. At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN.We construct, catalogue, and analyze different types of PLNs derived from different data sources and different species. When applied to the Gene Ontology, many of the resulting links connect processes that are distant from each other in the hierarchy, even though the connection makes eminent sense biologically. Some others, however, carry an element of surprise and may reflect mechanisms that are unique to the organism under investigation. In this aspect our method complements the link structure between processes inherent in the Gene Ontology, which by its very nature is species-independent. As a practical application of the linkage of processes we demonstrate that it can be effectively used in protein function prediction, having the power to increase both the coverage and the accuracy of predictions, when carefully integrated into prediction methods.Our approach constitutes a promising new direction towards understanding the higher levels of organization of the cell as a system which should help current efforts to re-engineer ontologies and improve our ability to predict which proteins are involved in specific biological processes.

  14. CRISPR and the Rebirth of Synthetic Biology

    NARCIS (Netherlands)

    Heidari, Raheleh; Shaw, David Martin; Elger, Bernice Simone

    Emergence of novel genome engineering technologies such as clustered regularly interspaced short palindromic repeat (CRISPR) has refocused attention on unresolved ethical complications of synthetic biology. Biosecurity concerns, deontological issues and human right aspects of genome editing have

  15. Artificially Engineered Protein Polymers.

    Science.gov (United States)

    Yang, Yun Jung; Holmberg, Angela L; Olsen, Bradley D

    2017-06-07

    Modern polymer science increasingly requires precise control over macromolecular structure and properties for engineering advanced materials and biomedical systems. The application of biological processes to design and synthesize artificial protein polymers offers a means for furthering macromolecular tunability, enabling polymers with dispersities of ∼1.0 and monomer-level sequence control. Taking inspiration from materials evolved in nature, scientists have created modular building blocks with simplified monomer sequences that replicate the function of natural systems. The corresponding protein engineering toolbox has enabled the systematic development of complex functional polymeric materials across areas as diverse as adhesives, responsive polymers, and medical materials. This review discusses the natural proteins that have inspired the development of key building blocks for protein polymer engineering and the function of these elements in material design. The prospects and progress for scalable commercialization of protein polymers are reviewed, discussing both technology needs and opportunities.

  16. 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.

  17. Engineering functional bladder tissues.

    Science.gov (United States)

    Horst, Maya; Madduri, Srinivas; Gobet, Rita; Sulser, Tullio; Milleret, Vinzent; Hall, Heike; Atala, Anthony; Eberli, Daniel

    2013-07-01

    End stage bladder disease can seriously affect patient quality of life and often requires surgical reconstruction with bowel tissue, which is associated with numerous complications. Bioengineering of functional bladder tissue using tissue-engineering techniques could provide new functional tissues for reconstruction. In this review, we discuss the current state of this field and address different approaches to enable physiologic voiding in engineered bladder tissues in the near future. In a collaborative effort, we gathered researchers from four institutions to discuss the current state of functional bladder engineering. A MEDLINE® and PubMed® search was conducted for articles related to tissue engineering of the bladder, with special focus on the cells and biomaterials employed as well as the microenvironment, vascularisation and innervation strategies used. Over the last decade, advances in tissue engineering technology have laid the groundwork for the development of a biological substitute for bladder tissue that can support storage of urine and restore physiologic voiding. Although many researchers have been able to demonstrate the formation of engineered tissue with a structure similar to that of native bladder tissue, restoration of physiologic voiding using these constructs has never been demonstrated. The main issues hindering the development of larger contractile tissues that allow physiologic voiding include the development of correct muscle alignment, proper innervation and vascularization. Tissue engineering of a construct that will support the contractile properties that allow physiologic voiding is a complex process. The combination of smart scaffolds with controlled topography, the ability to deliver multiple trophic factors and an optimal cell source will allow for the engineering of functional bladder tissues in the near future. Copyright © 2012 John Wiley & Sons, Ltd.

  18. Biological Pathways

    Science.gov (United States)

    Skip to main content Biological Pathways Fact Sheet Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features ...

  19. Opportunities in Biological Sciences; [VGM Career Horizons Series].

    Science.gov (United States)

    Winter, Charles A.

    This book provides job descriptions and discusses career opportunities in various fields of the biological sciences. These fields include: (1) biotechnology, genetics, biomedical engineering, microbiology, mycology, systematic biology, marine and aquatic biology, botany, plant physiology, plant pathology, ecology, and wildlife biology; (2) the…

  20. Invisible Engineers

    Science.gov (United States)

    Ohashi, Hideo

    Questionnaire to ask “mention three names of scientists you know” and “three names of engineers you know” was conducted and the answers from 140 adults were analyzed. The results indicated that the image of scientists is represented by Nobel laureates and that of engineers by great inventors like Thomas Edison and industry founders like Soichiro Honda. In order to reveal the image of engineers among young generation, questionnaire was conducted for pupils in middle and high schools. Answers from 1,230 pupils were analyzed and 226 names mentioned as engineers were classified. White votes reached 60%. Engineers who are neither big inventors nor company founders collected less than 1% of named votes. Engineers are astonishingly invisible from young generation. Countermeasures are proposed.

  1. Engineering mechanics

    CERN Document Server

    Gross, Dietmar; Schröder, Jörg; Wall, Wolfgang A; Rajapakse, Nimal

    Statics is the first volume of a three-volume textbook on Engineering Mechanics. The authors, using a time-honoured straightforward and flexible approach, present the basic concepts and principles of mechanics in the clearest and simplest form possible to advanced undergraduate engineering students of various disciplines and different educational backgrounds. An important objective of this book is to develop problem solving skills in a systematic manner. Another aim of this volume is to provide engineering students as well as practising engineers with a solid foundation to help them bridge the gap between undergraduate studies on the one hand and advanced courses on mechanics and/or practical engineering problems on the other. The book contains numerous examples, along with their complete solutions. Emphasis is placed upon student participation in problem solving. The contents of the book correspond to the topics normally covered in courses on basic engineering mechanics at universities and colleges. Now in i...

  2. Human engineering

    International Nuclear Information System (INIS)

    Yang, Seong Hwan; Park, Bum; Gang, Yeong Sik; Gal, Won Mo; Baek, Seung Ryeol; Choe, Jeong Hwa; Kim, Dae Sung

    2006-07-01

    This book mentions human engineering, which deals with introduction of human engineering, Man-Machine system like system design, and analysis and evaluation of Man-Machine system, data processing and data input, display, system control of man, human mistake and reliability, human measurement and design of working place, human working, hand tool and manual material handling, condition of working circumstance, working management, working analysis, motion analysis working measurement, and working improvement and design in human engineering.

  3. Software engineering

    CERN Document Server

    Sommerville, Ian

    2010-01-01

    The ninth edition of Software Engineering presents a broad perspective of software engineering, focusing on the processes and techniques fundamental to the creation of reliable, software systems. Increased coverage of agile methods and software reuse, along with coverage of 'traditional' plan-driven software engineering, gives readers the most up-to-date view of the field currently available. Practical case studies, a full set of easy-to-access supplements, and extensive web resources make teaching the course easier than ever.

  4. Information engineering

    Energy Technology Data Exchange (ETDEWEB)

    Hunt, D.N.

    1997-02-01

    The Information Engineering thrust area develops information technology to support the programmatic needs of Lawrence Livermore National Laboratory`s Engineering Directorate. Progress in five programmatic areas are described in separate reports contained herein. These are entitled Three-dimensional Object Creation, Manipulation, and Transport, Zephyr:A Secure Internet-Based Process to Streamline Engineering Procurements, Subcarrier Multiplexing: Optical Network Demonstrations, Parallel Optical Interconnect Technology Demonstration, and Intelligent Automation Architecture.

  5. Engineering Electromagnetics

    International Nuclear Information System (INIS)

    Kim, Se Yun

    2009-01-01

    This book deals with engineering electromagnetics. It contains seven chapters, which treats understanding of engineering electromagnetics such as magnet and electron spin, current and a magnetic field and an electromagnetic wave, Essential tool for engineering electromagnetics on rector and scalar, rectangular coordinate system and curl vector, electrostatic field with coulomb rule and method of electric images, Biot-Savart law, Ampere law and magnetic force, Maxwell equation and an electromagnetic wave and reflection and penetration of electromagnetic plane wave.

  6. Neural engineering

    CERN Document Server

    2013-01-01

    Neural Engineering, 2nd Edition, contains reviews and discussions of contemporary and relevant topics by leading investigators in the field. It is intended to serve as a textbook at the graduate and advanced undergraduate level in a bioengineering curriculum. This principles and applications approach to neural engineering is essential reading for all academics, biomedical engineers, neuroscientists, neurophysiologists, and industry professionals wishing to take advantage of the latest and greatest in this emerging field.

  7. Concise Review: Organ Engineering: Design, Technology, and Integration

    NARCIS (Netherlands)

    Kaushik, G.; Leijten, Jeroen Christianus Hermanus; Khademhosseini, A.

    Engineering complex tissues and whole organs has the potential to dramatically impact translational medicine in several avenues. Organ engineering is a discipline that integrates biological knowledge of embryological development, anatomy, physiology, and cellular interactions with enabling

  8. EDITORIAL: Physical Biology

    Science.gov (United States)

    Roscoe, Jane

    2004-06-01

    Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure and dynamics of a single molecule to cellular networks and organisms. The journal encourages the development of a new biology-driven physics based on the extraordinary and increasingly rich data arising in biology, and provides research directions for those involved in the creation of novel bio-engineered systems. Physical Biology will publish a stimulating combination of full length research articles, communications, perspectives, reviews and tutorials from a wide range of disciplines covering topics such as: Single-molecule studies and nanobiotechnology Molecular interactions and protein folding Charge transfer and photobiology Ion channels; structure, function and ion regulation Molecular motors and force generation Subcellular processes Biological networks and neural systems Modeling aspects of molecular and cell biology Cell-cell signaling and interaction Biological patterns and development Evolutionary processes Novel tools and methods in physical biology Experts in the areas encompassed by the journal's scope have been appointed to the Editorial Scientific Committee and the composition of the Committee will be updated regularly to reflect the developments in this new and exciting field. Physical Biology is free online to everyone in 2004; you are invited to take advantage of this offer by visiting the journal homepage at http://physbio.iop.org This special print edition of Physical Biology is a combination of issues 1 and 2 of this electronic-only journal and it brings together an impressive range of articles in the fields covered, including a popular

  9. Quantum biology of the retina.

    Science.gov (United States)

    Sia, Paul Ikgan; Luiten, André N; Stace, Thomas M; Wood, John Pm; Casson, Robert J

    2014-08-01

    The emerging field of quantum biology has led to a greater understanding of biological processes at the microscopic level. There is recent evidence to suggest that non-trivial quantum features such as entanglement, tunnelling and coherence have evolved in living systems. These quantum features are particularly evident in supersensitive light-harvesting systems such as in photosynthesis and photoreceptors. A biomimetic strategy utilizing biological quantum phenomena might allow new advances in the field of quantum engineering, particularly in quantum information systems. In addition, a better understanding of quantum biological features may lead to novel medical diagnostic and therapeutic developments. In the present review, we discuss the role of quantum physics in biological systems with an emphasis on the retina. © 2014 Royal Australian and New Zealand College of Ophthalmologists.

  10. Engineering tribology

    CERN Document Server

    Stachowiak, Gwidon; Batchelor, A W; Batchelor, Andrew W

    2005-01-01

    As with the previous edition, the third edition of Engineering Tribology provides a thorough understanding of friction and wear using technologies such as lubrication and special materials. Tribology is a complex topic with its own terminology and specialized concepts, yet is vitally important throughout all engineering disciplines, including mechanical design, aerodynamics, fluid dynamics and biomedical engineering. This edition includes updated material on the hydrodynamic aspects of tribology as well as new advances in the field of biotribology, with a focus throughout on the engineering ap

  11. Systems metabolic engineering strategies for the production of amino acids.

    Science.gov (United States)

    Ma, Qian; Zhang, Quanwei; Xu, Qingyang; Zhang, Chenglin; Li, Yanjun; Fan, Xiaoguang; Xie, Xixian; Chen, Ning

    2017-06-01

    Systems metabolic engineering is a multidisciplinary area that integrates systems biology, synthetic biology and evolutionary engineering. It is an efficient approach for strain improvement and process optimization, and has been successfully applied in the microbial production of various chemicals including amino acids. In this review, systems metabolic engineering strategies including pathway-focused approaches, systems biology-based approaches, evolutionary approaches and their applications in two major amino acid producing microorganisms: Corynebacterium glutamicum and Escherichia coli, are summarized.

  12. Space Synthetic Biology Project

    Science.gov (United States)

    Howard, David; Roman, Monsi; Mansell, James (Matt)

    2015-01-01

    Synthetic biology is an effort to make genetic engineering more useful by standardizing sections of genetic code. By standardizing genetic components, biological engineering will become much more similar to traditional fields of engineering, in which well-defined components and subsystems are readily available in markets. Specifications of the behavior of those components and subsystems can be used to model a system which incorporates them. Then, the behavior of the novel system can be simulated and optimized. Finally, the components and subsystems can be purchased and assembled to create the optimized system, which most often will exhibit behavior similar to that indicated by the model. The Space Synthetic Biology project began in 2012 as a multi-Center effort. The purpose of this project was to harness Synthetic Biology principals to enable NASA's missions. A central target for application was to Environmental Control & Life Support (ECLS). Engineers from NASA Marshall Space Flight Center's (MSFC's) ECLS Systems Development Branch (ES62) were brought into the project to contribute expertise in operational ECLS systems. Project lead scientists chose to pursue the development of bioelectrochemical technologies to spacecraft life support. Therefore, the ECLS element of the project became essentially an effort to develop a bioelectrochemical ECLS subsystem. Bioelectrochemical systems exploit the ability of many microorganisms to drive their metabolisms by direct or indirect utilization of electrical potential gradients. Whereas many microorganisms are capable of deriving the energy required for the processes of interest (such as carbon dioxide (CO2) fixation) from sunlight, it is believed that subsystems utilizing electrotrophs will exhibit smaller mass, volume, and power requirements than those that derive their energy from sunlight. In the first 2 years of the project, MSFC personnel conducted modeling, simulation, and conceptual design efforts to assist the

  13. Standardization for natural product synthetic biology

    NARCIS (Netherlands)

    Zhao, Huimin; Medema, Marnix H.

    2016-01-01

    Standardization is one of the foundational features of modern-day engineering, and the use of standardized parts and processes is a key element that distinguishes bona fide synthetic biology from traditional genetic engineering. Here, we discuss the role of standardization in natural product

  14. Proceedings of the 1. National Forum of Science and Technology on Health; 13. Brazilian Congress on Biomedical Engineering; 4. Brazilian Congress of Physicists on Medicine; Brazilian Meeting on Biology and Nuclear Medicine; Brazilian Meeting on Radiological Protection

    International Nuclear Information System (INIS)

    Costa, E.T.; Martins, H.L.; Muehlen, S.S.; Rockman, T.M.B.

    1992-01-01

    This 1. National Forum of Science and Technology on Health presents works of several scientific institutions, including topics on bioengineering; modelling and simulation; sensors and transducers; ultrasonic on medicine; instrumentation processing of signs and medical images; biomedical informatics and clinical software; engineering of rehabilitation; bio-materials and bio-mechanical; clinical engineering; in vivo and in vitro nuclear medicine; radioisotope production and utilization; radiology; radiology protection and dosimetry; radiotherapy; evaluation of technology on health and education. (C.G.C.)

  15. Genetically Engineering Entomopathogenic Fungi.

    Science.gov (United States)

    Zhao, H; Lovett, B; Fang, W

    2016-01-01

    Entomopathogenic fungi have been developed as environmentally friendly alternatives to chemical insecticides in biocontrol programs for agricultural pests and vectors of disease. However, mycoinsecticides currently have a small market share due to low virulence and inconsistencies in their performance. Genetic engineering has made it possible to significantly improve the virulence of fungi and their tolerance to adverse conditions. Virulence enhancement has been achieved by engineering fungi to express insect proteins and insecticidal proteins/peptides from insect predators and other insect pathogens, or by overexpressing the pathogen's own genes. Importantly, protein engineering can be used to mix and match functional domains from diverse genes sourced from entomopathogenic fungi and other organisms, producing insecticidal proteins with novel characteristics. Fungal tolerance to abiotic stresses, especially UV radiation, has been greatly improved by introducing into entomopathogens a photoreactivation system from an archaean and pigment synthesis pathways from nonentomopathogenic fungi. Conversely, gene knockout strategies have produced strains with reduced ecological fitness as recipients for genetic engineering to improve virulence; the resulting strains are hypervirulent, but will not persist in the environment. Coupled with their natural insect specificity, safety concerns can also be mitigated by using safe effector proteins with selection marker genes removed after transformation. With the increasing public concern over the continued use of synthetic chemical insecticides and growing public acceptance of genetically modified organisms, new types of biological insecticides produced by genetic engineering offer a range of environmentally friendly options for cost-effective control of insect pests. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Radiological Engineering: A graduate engineering - based curriculum for radiation protection

    International Nuclear Information System (INIS)

    Kearfott, K.J.; Wepfer, W.J.

    1994-01-01

    Several U.S. universities maintain formal graduate health physics curricula within their Colleges of Engineering. The term radiological engineering was coined to describe the discipline of applying engineering principles to the radiation protection aspects of nuclear technology. Radiological engineering programmes may require a specific core group of courses such as radiation biology, radiation protection practice, nuclear physics, radiation detectors, and radiation dosimetry. Students then might specialist in environmental, nuclear facilities or medical applications areas by selecting advanced courses and graduate design or research projects. In some instances the master's degree may be completed through remotely-delivered lectures. Such programmes promise to assist in educating a new group of engineering professionals dedicated to the safe utilisation of nuclear technology. The Georgis Institute of Technology's programme will serve as the specific example for this report. 8 refs., 1 fig

  17. Genetic Engineering

    Science.gov (United States)

    Phillips, John

    1973-01-01

    Presents a review of genetic engineering, in which the genotypes of plants and animals (including human genotypes) may be manipulated for the benefit of the human species. Discusses associated problems and solutions and provides an extensive bibliography of literature relating to genetic engineering. (JR)

  18. Corrosion Engineering.

    Science.gov (United States)

    White, Charles V.

    A description is provided for a Corrosion and Corrosion Control course offered in the Continuing Engineering Education Program at the General Motors Institute (GMI). GMI is a small cooperative engineering school of approximately 2,000 students who alternate between six-week periods of academic study and six weeks of related work experience in…

  19. Systems Engineering

    Science.gov (United States)

    Pellerano, Fernando

    2015-01-01

    This short course provides information on what systems engineering is and how the systems engineer guides requirements, interfaces with the discipline leads, and resolves technical issues. There are many system-wide issues that either impact or are impacted by the thermal subsystem. This course will introduce these issues and illustrate them with real life examples.

  20. Fluids engineering

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    Fluids engineering has played an important role in many applications, from ancient flood control to the design of high-speed compact turbomachinery. New applications of fluids engineering, such as in high-technology materials processing, biotechnology, and advanced combustion systems, have kept up unwaining interest in the subject. More accurate and sophisticated computational and measurement techniques are also constantly being developed and refined. On a more fundamental level, nonlinear dynamics and chaotic behavior of fluid flow are no longer an intellectual curiosity and fluid engineers are increasingly interested in finding practical applications for these emerging sciences. Applications of fluid technology to new areas, as well as the need to improve the design and to enhance the flexibility and reliability of flow-related machines and devices will continue to spur interest in fluids engineering. The objectives of the present seminar were: to exchange current information on arts, science, and technology of fluids engineering; to promote scientific cooperation between the fluids engineering communities of both nations, and to provide an opportunity for the participants and their colleagues to explore possible joint research programs in topics of high priority and mutual interest to both countries. The Seminar provided an excellent forum for reviewing the current state and future needs of fluids engineering for the two nations. With the Seminar ear-marking the first formal scientific exchange between Korea and the United States in the area of fluids engineering, the scope was deliberately left broad and general

  1. Food Engineering

    NARCIS (Netherlands)

    Boom, R.M.; Janssen, A.E.M.

    2014-01-01

    Food engineering is a rapidly changing discipline. Traditionally, the main focus was on food preservation and stabilization, whereas trends now are on diversity, health, taste, and sustainable production. Next to a general introduction of the definition of food engineering, this article gives a

  2. Biomedical Engineering

    CERN Document Server

    Suh, Sang C; Tanik, Murat M

    2011-01-01

    Biomedical Engineering: Health Care Systems, Technology and Techniques is an edited volume with contributions from world experts. It provides readers with unique contributions related to current research and future healthcare systems. Practitioners and researchers focused on computer science, bioinformatics, engineering and medicine will find this book a valuable reference.

  3. International Genetically Engineered Machine (iGEM) Competition

    CSIR Research Space (South Africa)

    Sparrow, RW

    2010-07-01

    Full Text Available iGEM, the International Genetically Engineered Machine competition, is an initiative from MIT and has become the premiere undergraduate synthetic biology competition. The competing teams consist of students who work on a synthetic biology project...

  4. Biological preconcentrator

    Science.gov (United States)

    Manginell, Ronald P [Albuquerque, NM; Bunker, Bruce C [Albuquerque, NM; Huber, Dale L [Albuquerque, NM

    2008-09-09

    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  5. Emotional engineering

    CERN Document Server

    In an age of increasing complexity, diversification and change, customers expect services that cater to their needs and to their tastes. Emotional Engineering vol 2. describes how their expectations can be satisfied and managed throughout the product life cycle, if producers focus their attention more on emotion. Emotional engineering provides the means to integrate products to create a new social framework and develops services beyond product realization to create of value across a full lifetime.  14 chapters cover a wide range of topics that can be applied to product, process and industry development, with special attention paid to the increasing importance of sensing in the age of extensive and frequent changes, including: • Multisensory stimulation and user experience  • Physiological measurement • Tactile sensation • Emotional quality management • Mental model • Kansei engineering.   Emotional Engineering vol 2 builds on Dr Fukuda’s previous book, Emotional Engineering, and provides read...

  6. Computational Intelligence for Engineering Systems

    CERN Document Server

    Madureira, A; Vale, Zita

    2011-01-01

    "Computational Intelligence for Engineering Systems" provides an overview and original analysis of new developments and advances in several areas of computational intelligence. Computational Intelligence have become the road-map for engineers to develop and analyze novel techniques to solve problems in basic sciences (such as physics, chemistry and biology) and engineering, environmental, life and social sciences. The contributions are written by international experts, who provide up-to-date aspects of the topics discussed and present recent, original insights into their own experien

  7. News: Synthetic biology leading to specialty chemicals

    Science.gov (United States)

    Synthetic biology can combine the disciplines of biology, engineering, and chemistry productively to form molecules of great scientific and commercial value. Recent advances in the new field are explored for their connection to new tools that have been used to elucidate productio...

  8. Meeting Report: Synthetic Biology Jamboree for Undergraduates

    Science.gov (United States)

    Campbell, A. Malcolm

    2005-01-01

    The field of synthetic biology (the name is derived from an analogy to synthetic chemistry) has recognized itself as a "field" only since about 2002. Synthetic biology has gotten some high-profile attention recently, but most people are not aware the field even exists. Synthetic biologists apply engineering principles to genomic circuits to…

  9. Biological rhythms

    Science.gov (United States)

    Halberg, F.

    1975-01-01

    An overview is given of basic features of biological rhythms. The classification of periodic behavior of physical and psychological characteristics as circadian, circannual, diurnal, and ultradian is discussed, and the notion of relativistic time as it applies in biology is examined. Special attention is given to circadian rhythms which are dependent on the adrenocortical cycle. The need for adequate understanding of circadian variations in the basic physiological indicators of an individual (heart rate, body temperature, systolic and diastolic blood pressure, etc.) to ensure the effectiveness of prophylactic and therapeutic measures is stressed.

  10. Expanding the scope of the IEEE Transactions on Rehabilitation Engineering to explicitly include Neural Engineering.

    Science.gov (United States)

    Robinson, C J

    2000-09-01

    The original scope of this Transactions implicitly gave it wide latitude to include all aspects of biologically based Neural Engineering. The Transactions now has an additional explicit charter to target Neural Engineering and its links to rehabilitation, from the very basic science to the highly engineered design application. This Transactions will become a prime repository for the emerging field of Neural Engineering, without losing its rehabilitation roots.

  11. Integrating biological redesign: where synthetic biology came from and where it needs to go.

    Science.gov (United States)

    Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

    2014-03-27

    Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Tissue engineering of cartilages using biomatrices

    DEFF Research Database (Denmark)

    Melrose, J.; Chuang, C.; Whitelock, J.

    2008-01-01

    Tissue engineering is an exciting new cross-disciplinary methodology which applies the principles of engineering and structure-function relationships between normal and pathological tissues to develop biological substitute to restore, maintain or improve tissue function. Tissue engineering...... therefore involves a melange of approaches encompassing developmental biology, tissue mechanics, medicine, cell differentiation and survival biology, mechanostransduction and nano-fabrication technology. The central tissue of interest in this review is cartilage. Traumatic injuries, congenital abnormalities...... engineering approaches and many of these are discussed and their in vitro and in vivo applications covered in this review. Tissue engineering is entering an exciting era; significant advances have been made; however, many technical challenges remain to be solved before this technology becomes widely...

  13. Marine Biology

    Science.gov (United States)

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  14. Mesoscopic biology

    Indian Academy of Sciences (India)

    Abstract. In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in ...

  15. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  16. Biological digestion

    International Nuclear Information System (INIS)

    Rosevear, A.

    1988-01-01

    This paper discusses the biological degradation of non-radioactive organic material occurring in radioactive wastes. The biochemical steps are often performed using microbes or isolated enzymes in combination with chemical steps and the aim is to oxidise the carbon, hydrogen, nitrogen and sulphur to their respective oxides. (U.K.)

  17. Biology Notes.

    Science.gov (United States)

    School Science Review, 1981

    1981-01-01

    Outlines a variety of laboratory procedures, techniques, and materials including construction of a survey frame for field biology, a simple tidal system, isolation and applications of plant protoplasts, tropisms, teaching lung structure, and a key to statistical methods for biologists. (DS)

  18. Systems Metabolic Engineering of Escherichia coli.

    Science.gov (United States)

    Choi, Kyeong Rok; Shin, Jae Ho; Cho, Jae Sung; Yang, Dongsoo; Lee, Sang Yup

    2016-05-01

    Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.

  19. Synthetic Biology: Knowledge Accessed by Everyone (Open Sources)

    Science.gov (United States)

    Sánchez Reyes, Patricia Margarita

    2016-01-01

    Using the principles of biology, along with engineering and with the help of computer, scientists manage to copy. DNA sequences from nature and use them to create new organisms. DNA is created through engineering and computer science managing to create life inside a laboratory. We cannot dismiss the role that synthetic biology could lead in…

  20. Biomolecular engineering for nanobio/bionanotechnology

    Science.gov (United States)

    Nagamune, Teruyuki

    2017-04-01

    Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.

  1. Requirements Engineering

    CERN Document Server

    Hull, Elizabeth; Dick, Jeremy

    2011-01-01

    Written for those who want to develop their knowledge of requirements engineering process, whether practitioners or students.Using the latest research and driven by practical experience from industry, Requirements Engineering gives useful hints to practitioners on how to write and structure requirements. It explains the importance of Systems Engineering and the creation of effective solutions to problems. It describes the underlying representations used in system modeling and introduces the UML2, and considers the relationship between requirements and modeling. Covering a generic multi-layer r

  2. Engineering mathematics

    CERN Document Server

    Bird, John

    2014-01-01

    A practical introduction to the core mathematics required for engineering study and practiceNow in its seventh edition, Engineering Mathematics is an established textbook that has helped thousands of students to succeed in their exams.John Bird's approach is based on worked examples and interactive problems. This makes it ideal for students from a wide range of academic backgrounds as the student can work through the material at their own pace. Mathematical theories are explained in a straightforward manner, being supported by practical engineering examples and applications in order to ensure

  3. Cost Methodology for Biomass Feedstocks: Herbaceous Crops and Agricultural Residues

    Energy Technology Data Exchange (ETDEWEB)

    Turhollow Jr, Anthony F [ORNL; Webb, Erin [ORNL; Sokhansanj, Shahabaddine [ORNL

    2009-12-01

    This report describes a set of procedures and assumptions used to estimate production and logistics costs of bioenergy feedstocks from herbaceous crops and agricultural residues. The engineering-economic analysis discussed here is based on methodologies developed by the American Society of Agricultural and Biological Engineers (ASABE) and the American Agricultural Economics Association (AAEA). An engineering-economic analysis approach was chosen due to lack of historical cost data for bioenergy feedstocks. Instead, costs are calculated using assumptions for equipment performance, input prices, and yield data derived from equipment manufacturers, research literature, and/or standards. Cost estimates account for fixed and variable costs. Several examples of this costing methodology used to estimate feedstock logistics costs are included at the end of this report.

  4. 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

  5. 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.

  6. Modularization of genetic elements promotes synthetic metabolic engineering.

    Science.gov (United States)

    Qi, Hao; Li, Bing-Zhi; Zhang, Wen-Qian; Liu, Duo; Yuan, Ying-Jin

    2015-11-15

    In the context of emerging synthetic biology, metabolic engineering is moving to the next stage powered by new technologies. Systematical modularization of genetic elements makes it more convenient to engineer biological systems for chemical production or other desired purposes. In the past few years, progresses were made in engineering metabolic pathway using synthetic biology tools. Here, we spotlighted the topic of implementation of modularized genetic elements in metabolic engineering. First, we overviewed the principle developed for modularizing genetic elements and then discussed how the genetic modules advanced metabolic engineering studies. Next, we picked up some milestones of engineered metabolic pathway achieved in the past few years. Last, we discussed the rapid raised synthetic biology field of "building a genome" and the potential in metabolic engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. All India Seminar on Biomedical Engineering 2012

    CERN Document Server

    Bhatele, Mukta

    2013-01-01

    This book is a collection of articles presented by researchers and practitioners, including engineers, biologists, health professionals and informatics/computer scientists, interested in both theoretical advances and applications of information systems, artificial intelligence, signal processing, electronics and other engineering tools in areas related to biology and medicine in the All India Seminar on Biomedical Engineering 2012 (AISOBE 2012), organized by The Institution of Engineers (India), Jabalpur Local Centre, Jabalpur, India during November 3-4, 2012. The content of the book is useful to doctors, engineers, researchers and academicians as well as industry professionals.

  8. Coastal Engineering

    NARCIS (Netherlands)

    Van der Velden, E.T.J.M.

    1989-01-01

    Introduction, waves, sediment transport, littoral transport, lonshore sediment transport, onshore-offshore sediment transport, coastal changes, dune erosion and storm surges, sedimentation in channels and trenches, coastal engineering in practice.

  9. Software engineering

    CERN Document Server

    Sommerville, Ian

    2016-01-01

    For courses in computer science and software engineering The Fundamental Practice of Software Engineering Software Engineering introduces readers to the overwhelmingly important subject of software programming and development. In the past few years, computer systems have come to dominate not just our technological growth, but the foundations of our world's major industries. This text seeks to lay out the fundamental concepts of this huge and continually growing subject area in a clear and comprehensive manner. The Tenth Edition contains new information that highlights various technological updates of recent years, providing readers with highly relevant and current information. Sommerville's experience in system dependability and systems engineering guides the text through a traditional plan-based approach that incorporates some novel agile methods. The text strives to teach the innovators of tomorrow how to create software that will make our world a better, safer, and more advanced place to live.

  10. Nuclear Engineering

    International Nuclear Information System (INIS)

    Anon.

    1977-01-01

    The Nuclear Engineering Division is engaged in both teaching and research. Staff members teach both graduate and undergraduate courses at the UPR Mayaguez Campus and direct the thesis work of nuclear engineering students. They do research on their own projects and assist the staff of other PRNC divisions as the need arises. The scientists on the Division's staff all hold joint appointments at PRNC and UPR, and they make up the faculty of the UPR Nuclear Engineering Department, the Head of the PRNC Division being also the Chairman of the UPR Department. The Division provides the classrooms, offices, laboratories and equipment, and most of the administrative personnel required for the education and training of the graduate students at the UPR Nuclear Engineering Department

  11. Harmonic engine

    Science.gov (United States)

    Bennett, Charles L [Livermore, CA

    2009-10-20

    A high efficiency harmonic engine based on a resonantly reciprocating piston expander that extracts work from heat and pressurizes working fluid in a reciprocating piston compressor. The engine preferably includes harmonic oscillator valves capable of oscillating at a resonant frequency for controlling the flow of working fluid into and out of the expander, and also preferably includes a shunt line connecting an expansion chamber of the expander to a buffer chamber of the expander for minimizing pressure variations in the fluidic circuit of the engine. The engine is especially designed to operate with very high temperature input to the expander and very low temperature input to the compressor, to produce very high thermal conversion efficiency.

  12. Green Engineering

    Science.gov (United States)

    Green Engineering is the design, commercialization and use of processes and products that are feasible and economical while reducing the generation of pollution at the source and minimizing the risk to human health and the environment.

  13. Engineering personnel

    International Nuclear Information System (INIS)

    Paskievici, W.

    The expansion of nuclear power is taxing human, material, and capital resources in developed and developing countries. This paper explores the human resources as represented by employment, graduation statistics, and educational curricula for nuclear engineers. (E.C.B.)

  14. Crystal Engineering

    Indian Academy of Sciences (India)

    Nangia (2002). “Today, research areas under the wide umbrella of crystal engineering include: supramolecular synthesis; nanotechnology; separation science and catalysis; supramolecular materials and devices; polymorphism; cocrystals, crystal structure prediction; drug design and ligand–protein binding.”

  15. Geoenvironmental engineering

    International Nuclear Information System (INIS)

    Shin, Eun Cheol; Park, Jeong Jun

    2009-08-01

    This book deals with definition of soil and scope of clean-up of soil, trend of geoenvironmental engineering at home and foreign countries, main concern of geoenvironmental engineering in domestic and abroad, design and building of landfills such as summary, trend of landfill policy in Korea, post management of landfill facilities, stabilizing and stability of landfill, research method and soil pollution source, restoration technology of soil pollution like restoration technique of oil pollution with thermal processing.

  16. Reliability Engineering

    International Nuclear Information System (INIS)

    Lee, Sang Yong

    1992-07-01

    This book is about reliability engineering, which describes definition and importance of reliability, development of reliability engineering, failure rate and failure probability density function about types of it, CFR and index distribution, IFR and normal distribution and Weibull distribution, maintainability and movability, reliability test and reliability assumption in index distribution type, normal distribution type and Weibull distribution type, reliability sampling test, reliability of system, design of reliability and functionality failure analysis by FTA.

  17. Microwave engineering

    CERN Document Server

    Pozar, David M

    2012-01-01

    The 4th edition of this classic text provides a thorough coverage of RF and microwave engineering concepts, starting from fundamental principles of electrical engineering, with applications to microwave circuits and devices of practical importance.  Coverage includes microwave network analysis, impedance matching, directional couplers and hybrids, microwave filters, ferrite devices, noise, nonlinear effects, and the design of microwave oscillators, amplifiers, and mixers. Material on microwave and RF systems includes wireless communications, radar, radiometry, and radiation hazards. A large

  18. Systems metabolic engineering for chemicals and materials.

    Science.gov (United States)

    Lee, Jeong Wook; Kim, Tae Yong; Jang, Yu-Sin; Choi, Sol; Lee, Sang Yup

    2011-08-01

    Metabolic engineering has contributed significantly to the enhanced production of various value-added and commodity chemicals and materials from renewable resources in the past two decades. Recently, metabolic engineering has been upgraded to the systems level (thus, systems metabolic engineering) by the integrated use of global technologies of systems biology, fine design capabilities of synthetic biology, and rational-random mutagenesis through evolutionary engineering. By systems metabolic engineering, production of natural and unnatural chemicals and materials can be better optimized in a multiplexed way on a genome scale, with reduced time and effort. Here, we review the recent trends in systems metabolic engineering for the production of chemicals and materials by presenting general strategies and showcasing representative examples. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. VII Latin American Congress on Biomedical Engineering

    CERN Document Server

    Bustamante, John; Sierra, Daniel

    2017-01-01

    This volume presents the proceedings of the CLAIB 2016, held in Bucaramanga, Santander, Colombia, 26, 27 & 28 October 2016. The proceedings, presented by the Regional Council of Biomedical Engineering for Latin America (CORAL), offer research findings, experiences and activities between institutions and universities to develop Bioengineering, Biomedical Engineering and related sciences. The conferences of the American Congress of Biomedical Engineering are sponsored by the International Federation for Medical and Biological Engineering (IFMBE), Society for Engineering in Biology and Medicine (EMBS) and the Pan American Health Organization (PAHO), among other organizations and international agencies to bring together scientists, academics and biomedical engineers in Latin America and other continents in an environment conducive to exchange and professional growth.

  20. Biologic Scaffolds.

    Science.gov (United States)

    Costa, Alessandra; Naranjo, Juan Diego; Londono, Ricardo; Badylak, Stephen F

    2017-09-01

    Biologic scaffold materials composed of allogeneic or xenogeneic extracellular matrix are commonly used for the repair and functional reconstruction of injured and missing tissues. These naturally occurring bioscaffolds are manufactured by the removal of the cellular content from source tissues while preserving the structural and functional molecular units of the remaining extracellular matrix (ECM). The mechanisms by which these bioscaffolds facilitate constructive remodeling and favorable clinical outcomes include release or creation of effector molecules that recruit endogenous stem/progenitor cells to the site of scaffold placement and modulation of the innate immune response, specifically the activation of an anti-inflammatory macrophage phenotype. The methods by which ECM biologic scaffolds are prepared, the current understanding of in vivo scaffold remodeling, and the associated clinical outcomes are discussed in this article. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  1. Improvement of Synthetic Biology Tools for DNA Editing

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda

    The unpredictability and complexity of biological systems limit the development of economically efficient bio-based production processes that rely on renewable carbon sources and are essential for biosustainability and environmental protection. Synthetic biology (synbio) aims at making biology...... easier to engineer and addresses these challenges.The ability to systematically construct, modify and tune biological systems from fully characterized biological components, or parts, is crucial to the success of synbio projects. This thesis aims at contributing to standardization and part sharing...

  2. Pathway analysis and optimization in metabolic engineering

    National Research Council Canada - National Science Library

    Torres, Néstor V; Voit, Eberhard O

    2002-01-01

    ... Engineering introduces researchers and advanced students in biology and engineering to methods of optimizing biochemical systems of biotechnological relevance. It examines the development of strategies for manipulating metabolic pathways, demonstrates the need for effective systems models, and discusses their design and analysis, while placing special emp...

  3. Metabolic engineering of terpenoid biosynthesis in plants

    NARCIS (Netherlands)

    Aharoni, A.; Jongsma, M.A.; Kim, T.Y.; Ri, M.B.; Giri, A.P.; Verstappen, F.W.A.; Schwab, W.; Bouwmeester, H.J.

    2006-01-01

    Metabolic engineering of terpenoids in plants is a fascinating research topic from two main perspectives. On the one hand, the various biological activities of these compounds make their engineering a new tool for improving a considerable number of traits in crops. These include for example enhanced

  4. Biological radioprotector

    International Nuclear Information System (INIS)

    Stefanescu, Ioan; Titescu, Gheorghe; Tamaian, Radu; Haulica, Ion; Bild, Walther

    2002-01-01

    According to the patent description, the biological radioprotector is deuterium depleted water, DDW, produced by vacuum distillation with an isotopic content lower than natural value. It appears as such or in a mixture with natural water and carbon dioxide. It can be used for preventing and reducing the ionizing radiation effects upon humans or animal organisms, exposed therapeutically, professionally or accidentally to radiation. The most significant advantage of using DDW as biological radioprotector results from its way of administration. Indeed no one of the radioprotectors currently used today can be orally administrated, what reduces the patients' compliance to prophylactic administrations. The biological radioprotector is an unnoxious product obtained from natural water, which can be administrated as food additive instead of drinking water. Dose modification factor is according to initial estimates around 1.9, what is a remarkable feature when one takes into account that the product is toxicity-free and side effect-free and can be administrated prophylactically as a food additive. A net radioprotective action of the deuterium depletion was evidenced experimentally in laboratory animals (rats) hydrated with DDW of 30 ppm D/(D+H) concentration as compared with normally hydrated control animals. Knowing the effects of irradiation and mechanisms of the acute radiation disease as well as the effects of administration of radiomimetic chemicals upon cellular lines of fast cell division, it appears that the effects of administrating DDW result from stimulation of the immunity system. In conclusion, the biological radioprotector DDW presents the following advantages: - it is obtained from natural products without toxicity; - it is easy to be administrated as a food additive, replacing the drinking water; - besides radioprotective effects, the product has also immunostimulative and antitumoral effects

  5. Crusts: biological

    Science.gov (United States)

    Belnap, Jayne; Elias, Scott A.

    2013-01-01

    Biological soil crusts, a community of cyanobacteria, lichens, mosses, and fungi, are an essential part of dryland ecosystems. They are critical in the stabilization of soils, protecting them from wind and water erosion. Similarly, these soil surface communities also stabilized soils on early Earth, allowing vascular plants to establish. They contribute nitrogen and carbon to otherwise relatively infertile dryland soils, and have a strong influence on hydrologic cycles. Their presence can also influence vascular plant establishment and nutrition.

  6. Synthetic Biology Guides Biofuel Production

    Directory of Open Access Journals (Sweden)

    Michael R. Connor

    2010-01-01

    Full Text Available The advancement of microbial processes for the production of renewable liquid fuels has increased with concerns about the current fuel economy. The development of advanced biofuels in particular has risen to address some of the shortcomings of ethanol. These advanced fuels have chemical properties similar to petroleum-based liquid fuels, thus removing the need for engine modification or infrastructure redesign. While the productivity and titers of each of these processes remains to be improved, progress in synthetic biology has provided tools to guide the engineering of these processes through present and future challenges.

  7. Synthetic Biology Guides Biofuel Production

    Science.gov (United States)

    Connor, Michael R.; Atsumi, Shota

    2010-01-01

    The advancement of microbial processes for the production of renewable liquid fuels has increased with concerns about the current fuel economy. The development of advanced biofuels in particular has risen to address some of the shortcomings of ethanol. These advanced fuels have chemical properties similar to petroleum-based liquid fuels, thus removing the need for engine modification or infrastructure redesign. While the productivity and titers of each of these processes remains to be improved, progress in synthetic biology has provided tools to guide the engineering of these processes through present and future challenges. PMID:20827393

  8. Marine biology

    International Nuclear Information System (INIS)

    Thurman, H.V.; Webber, H.H.

    1984-01-01

    This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the nature of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index

  9. Biological heart valves.

    Science.gov (United States)

    Ciubotaru, Anatol; Cebotari, Serghei; Tudorache, Igor; Beckmann, Erik; Hilfiker, Andres; Haverich, Axel

    2013-10-01

    Cardiac valvular pathologies are often caused by rheumatic fever in young adults, atherosclerosis in elderly patients, or by congenital malformation of the heart in children, in effect affecting almost all population ages. Almost 300,000 heart valve operations are performed worldwide annually. Tissue valve prostheses have certain advantages over mechanical valves such as biocompatibility, more physiological hemodynamics, and no need for life-long systemic anticoagulation. However, the major disadvantage of biological valves is related to their durability. Nevertheless, during the last decade, the number of patients undergoing biological, rather than mechanical, valve replacement has increased from half to more than three-quarters for biological implants. Continuous improvement in valve fabrication includes development of new models and shapes, novel methods of tissue treatment, and preservation and implantation techniques. These efforts are focused not only on the improvement of morbidity and mortality of the patients but also on the improvement of their quality of life. Heart valve tissue engineering aims to provide durable, "autologous" valve prostheses. These valves demonstrate adaptive growth, which may avoid the need of repeated operations in growing patients.

  10. Framework to investigate emergence in system engineering

    CSIR Research Space (South Africa)

    Oosthuizen, R

    2011-09-01

    Full Text Available to Fromm [7] this is achieved through the application of established scientific knowledge. Natural sciences such as physics, chemistry and biology use experiments to gather data to validate or prove hypotheses and theories, being the basis... look at how to approach real life and complex problems. 2.2 Complex System Engineering Fromm [7] reiterated that when engineering complex systems, science is used to explain and to understand complexity while engineering attempts to hide...

  11. Advanced computational approaches to biomedical engineering

    CERN Document Server

    Saha, Punam K; Basu, Subhadip

    2014-01-01

    There has been rapid growth in biomedical engineering in recent decades, given advancements in medical imaging and physiological modelling and sensing systems, coupled with immense growth in computational and network technology, analytic approaches, visualization and virtual-reality, man-machine interaction and automation. Biomedical engineering involves applying engineering principles to the medical and biological sciences and it comprises several topics including biomedicine, medical imaging, physiological modelling and sensing, instrumentation, real-time systems, automation and control, sig

  12. Engineering Airway Epithelium

    Directory of Open Access Journals (Sweden)

    John P. Soleas

    2012-01-01

    Full Text Available Airway epithelium is constantly presented with injurious signals, yet under healthy circumstances, the epithelium maintains its innate immune barrier and mucociliary elevator function. This suggests that airway epithelium has regenerative potential (I. R. Telford and C. F. Bridgman, 1990. In practice, however, airway regeneration is problematic because of slow turnover and dedifferentiation of epithelium thereby hindering regeneration and increasing time necessary for full maturation and function. Based on the anatomy and biology of the airway epithelium, a variety of tissue engineering tools available could be utilized to overcome the barriers currently seen in airway epithelial generation. This paper describes the structure, function, and repair mechanisms in native epithelium and highlights specific and manipulatable tissue engineering signals that could be of great use in the creation of artificial airway epithelium.

  13. J. Maynard Smith: From Engineering to Evolution

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 11. J. Maynard Smith: From Engineering to Evolution. Amitabh Joshi ... Author Affiliations. Amitabh Joshi1. Evolutionary Biology Laboratory, Evolutionary and Organismal Biology Unit, JNCSAR, Jakkur P.O., Bangalore 560064, India.

  14. Synthetic biology of antimicrobial discovery

    Science.gov (United States)

    Zakeri, Bijan; Lu, Timothy K.

    2012-01-01

    Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore, used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery. PMID:23654251

  15. Engineering Optics

    CERN Document Server

    Iizuka, Keigo

    2008-01-01

    Engineering Optics is a book for students who want to apply their knowledge of optics to engineering problems, as well as for engineering students who want to acquire the basic principles of optics. It covers such important topics as optical signal processing, holography, tomography, holographic radars, fiber optical communication, electro- and acousto-optic devices, and integrated optics (including optical bistability). As a basis for understanding these topics, the first few chapters give easy-to-follow explanations of diffraction theory, Fourier transforms, and geometrical optics. Practical examples, such as the video disk, the Fresnel zone plate, and many more, appear throughout the text, together with numerous solved exercises. There is an entirely new section in this updated edition on 3-D imaging.

  16. Engineering physics

    CERN Document Server

    Mukherji, Uma

    2015-01-01

    ENGINEERING PHYSICS is designed as a textbook for first year engineering students of a two semester course in Applied Physics according to new revised syllabus. However the scope of this book is not only limited to undergraduate engineering students and science students, it can also serve as a reference book for practicing scientists.Advanced technological topics like LCD, Squid, Maglev system, Electron microscopes, MRI, Photonics - Photonic fibre, Nano-particles, CNT, Quantum computing etc., are explained with basic underlying principles of Physics.This text explained following topics with numerous solved, unsolved problems and questions from different angles. Part-I contains crystal structure, Liquid crystal, Thermo-electric effect, Thermionic emission, Ultrasonic, Acoustics, semiconductor and magnetic materials. Whereas Part-2 contains Optics, X-rays, Electron optics, Dielectric materials, Quantum Physics and Schrodinger wave equation, Laser, Fibre-optics and Holography, Radio-activity, Super-conductivity,...

  17. Engineering surveying

    CERN Document Server

    Schofield, W

    2007-01-01

    Engineering surveying involves determining the position of natural and man-made features on or beneath the Earth's surface and utilizing these features in the planning, design and construction of works. It is a critical part of any engineering project. Without an accurate understanding of the size, shape and nature of the site the project risks expensive and time-consuming errors or even catastrophic failure.Engineering Surveying 6th edition covers all the basic principles and practice of this complex subject and the authors bring expertise and clarity. Previous editions of this classic text have given readers a clear understanding of fundamentals such as vertical control, distance, angles and position right through to the most modern technologies, and this fully updated edition continues that tradition.This sixth edition includes:* An introduction to geodesy to facilitate greater understanding of satellite systems* A fully updated chapter on GPS, GLONASS and GALILEO for satellite positioning in surveying* Al...

  18. Synthetic biology: Emerging bioengineering in Indonesia

    Science.gov (United States)

    Suhandono, Sony

    2017-05-01

    The development of synthetic biology will shape the new era of science and technology. It is an emerging bioengineering technique involving genetic engineering which can alter the phenotype and behavior of the cell or the new product. Synthetic biology may produce biomaterials, drugs, vaccines, biosensors, and even a recombinant secondary metabolite used in herbal and complementary medicine, such as artemisinin, a malaria drug which is usually extracted from the plant Artemisia annua. The power of synthetic biology has encouraged scientists in Indonesia, and is still in early development. This paper also covers some research from an Indonesian research institute in synthetic biology such as observing the production of bio surfactants and the enhanced production of artemisinin using a transient expression system. Synthetic biology development in Indonesia may also be related to the iGEM competition, a large synthetic biology research competition which was attended by several universities in Indonesia. The application of synthetic biology for drug discovery will be discussed.

  19. Micro Engineering

    DEFF Research Database (Denmark)

    Alting, Leo; Kimura, F.; Hansen, Hans Nørgaard

    2003-01-01

    The paper addresses the questions of how micro products are designed and how they are manufactured. Definitions of micro products and micro engineering are discussed and the presentation is aimed at describing typical issues, possibilities and tools regarding design of micro products. The implica......The paper addresses the questions of how micro products are designed and how they are manufactured. Definitions of micro products and micro engineering are discussed and the presentation is aimed at describing typical issues, possibilities and tools regarding design of micro products...

  20. Biochemistry engineering

    International Nuclear Information System (INIS)

    Jang, Ho Nam

    1993-01-01

    This deals with biochemistry engineering with nine chapters. It explains bionics on development and prospect, basics of life science on classification and structure, enzyme and metabolism, fundamentals of chemical engineering on viscosity, shear rate, PFR, CSTR, mixing, dispersion, measurement and response, Enzyme kinetics, competitive inhibition, pH profile, temperature profile, stoichiometry and fermentation kinetics, bio-reactor on Enzyme-reactor and microorganism-reactor, measurement and processing on data acquisition and data processing, separation and purification, waste water treatment and economics of bionics process.

  1. Software engineering

    CERN Document Server

    Thorin, Marc

    1985-01-01

    Software Engineering describes the conceptual bases as well as the main methods and rules on computer programming. This book presents software engineering as a coherent and logically built synthesis and makes it possible to properly carry out an application of small or medium difficulty that can later be developed and adapted to more complex cases. This text is comprised of six chapters and begins by introducing the reader to the fundamental notions of entities, actions, and programming. The next two chapters elaborate on the concepts of information and consistency domains and show that a proc

  2. Engineering tribology

    CERN Document Server

    Stachowiak, Gwidon

    2014-01-01

    Engineering Tribology, 4th Edition is an established introductory reference focusing on the key concepts and engineering implications of tribology. Taking an interdisciplinary view, the book brings together the relevant knowledge from different fields needed to achieve effective analysis and control of friction and wear. Updated to cover recent advances in tribology, this new edition includes new sections on ionic and mesogenic lubricants, surface texturing, and multiscale characterization of 3D surfaces and coatings. Current trends in nanotribology are discussed, such as those relating to

  3. Biological biomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Jorge-Herrero, E. [Servicio de Cirugia Experimental. Clinica Puerta de Hierro, Madrid (Spain)

    1997-05-01

    There are a number of situations in which substances of biological origin are employed as biomaterials. Most of them are macromolecules derived from isolated connective tissue or the connective tissue itself in membrane form, in both cases, the tissue can be used in its natural form or be chemically treated. In other cases, certain blood vessels can be chemically pretreated and used as vascular prostheses. Proteins such as albumin, collagen and fibrinogen are employed to coat vascular prostheses. Certain polysaccharides have also been tested for use in controlled drug release systems. Likewise, a number of tissues, such as dura mater, bovine pericardium, procine valves and human valves, are used in the preparation of cardiac prostheses. We also use veins from animals or humans in arterial replacement. In none of these cases are the tissues employed dissimilar to the native tissues as they have been chemically modified, becoming a new bio material with different physical and biochemical properties. In short, we find that natural products are being utilized as biomaterials and must be considered as such; thus, it is necessary to study both their chemicobiological and physicomechanical properties. In the present report, we review the current applications, problems and future prospects of some of these biological biomaterials. (Author) 84 refs.

  4. World Congress on Engineering and Computer Science 2012

    CERN Document Server

    Ao, Sio-Iong; Amouzegar, Mahyar; Rieger, Burghard

    2014-01-01

    IAENG Transactions on Engineering Technologies contains forty-nine revised and extended research articles, written by prominent researchers participating in the conference. Topics covered include circuits, engineering mathematics, control theory, communications systems, systems engineering, manufacture engineering, computational biology, chemical engineering, and industrial applications. This book offers the state of art of tremendous advances in engineering technologies and physical science and applications, and also serves as an excellent source of reference for researchers and graduate students working with/on engineering technologies and physical science and applications.

  5. Programming Biology for Health and Sustainability

    Science.gov (United States)

    Silver, Pamela

    2015-03-01

    Biology presents us with an array of design principles. From studies of both simple and more complex systems, we understand some of the fundamentals of how Nature works. We are interested in using the foundations of biology to engineer cells in a logical and predictable way to perform certain functions. By necessity, the predictable engineering of biology requires knowledge of quantitative behavior of individual cells and communities. By building and analyzing synthetic systems, we learn more about the fundamentals of biological design as well as engineer useful living devices with myriad applications. For example, we are interested in building cells that can perform specific tasks, such as remembering past events and thus acting as biological computers. Moreover, we design cells with predictable biological properties that serve as cell-based sensors, factories for generating useful commodities and improved centers for carbon fixation. We have recently engineered natural gut bacteria that can non-invasively report on the dynamics of the animal gut. In doing so, we have made new findings about how cells interact with and impact on their environment. These principles can be applied to problems of all natural environments.

  6. Combustion engineering

    CERN Document Server

    Ragland, Kenneth W

    2011-01-01

    Introduction to Combustion Engineering The Nature of Combustion Combustion Emissions Global Climate Change Sustainability World Energy Production Structure of the Book   Section I: Basic Concepts Fuels Gaseous Fuels Liquid Fuels Solid Fuels Problems Thermodynamics of Combustion Review of First Law Concepts Properties of Mixtures Combustion StoichiometryChemical EnergyChemical EquilibriumAdiabatic Flame TemperatureChemical Kinetics of CombustionElementary ReactionsChain ReactionsGlobal ReactionsNitric Oxide KineticsReactions at a Solid SurfaceProblemsReferences  Section II: Combustion of Gaseous and Vaporized FuelsFlamesLaminar Premixed FlamesLaminar Flame TheoryTurbulent Premixed FlamesExplosion LimitsDiffusion FlamesGas-Fired Furnaces and BoilersEnergy Balance and EfficiencyFuel SubstitutionResidential Gas BurnersIndustrial Gas BurnersUtility Gas BurnersLow Swirl Gas BurnersPremixed-Charge Engine CombustionIntroduction to the Spark Ignition EngineEngine EfficiencyOne-Zone Model of Combustion in a Piston-...

  7. Metabolic Engineering

    Indian Academy of Sciences (India)

    IAS Admin

    and in vitro to be able to alter properties of the encoded enzyme, and (6) assemble an array of genes for their expression inside the host cell. Although bacteria and yeast are the pioneering hosts for metabolic engineering, other organisms such as fungi, animal as well as plant cells are also used nowadays for similar experi ...

  8. Metabolic Engineering

    Indian Academy of Sciences (India)

    IAS Admin

    Metabolic engineering is a process for modulating the me- tabolism of the organisms so as to produce the required amounts of the desired metabolite through genetic manipula- tions. Considering its advantages over the other chemical synthesis routes, this area of biotechnology is likely to revolu- tionize the way in which ...

  9. Sound engineer

    CERN Document Server

    Mara, Wil

    2015-01-01

    "Readers will learn what it takes to succeed as a sound engineer. The book also explains the necessary educational steps, useful character traits, potential hazards, and daily job tasks related to this career. Sidebars include thought-provoking trivia. Questions in the backmatter ask for text-dependent analysis. Photos, a glossary, and additional resources are included."-- Provided by publisher.

  10. Gene therapy for cartilage and bone tissue engineering

    CERN Document Server

    Hu, Yu-Chen

    2014-01-01

    "Gene Therapy for Cartilage and Bone Tissue Engineering" outlines the tissue engineering and possible applications of gene therapy in the field of biomedical engineering as well as basic principles of gene therapy, vectors and gene delivery, specifically for cartilage and bone engineering. It is intended for tissue engineers, cell therapists, regenerative medicine scientists and engineers, gene therapist and virologists. Dr. Yu-Chen Hu is a Distinguished Professor at the Department of Chemical Engineering, National Tsing Hua University and has received the Outstanding Research Award (National Science Council), Asia Research Award (Society of Chemical Engineers, Japan) and Professor Tsai-Teh Lai Award (Taiwan Institute of Chemical Engineers). He is also a fellow of the American Institute for Medical and Biological Engineering (AIMBE) and a member of the Tissue Engineering International & Regenerative Medicine Society (TERMIS)-Asia Pacific Council.

  11. Engineering Lubrication in Articular Cartilage

    Science.gov (United States)

    McNary, Sean M.; Athanasiou, Kyriacos A.

    2012-01-01

    Despite continuous progress toward tissue engineering of functional articular cartilage, significant challenges still remain. Advances in morphogens, stem cells, and scaffolds have resulted in enhancement of the bulk mechanical properties of engineered constructs, but little attention has been paid to the surface mechanical properties. In the near future, engineered tissues will be able to withstand and support the physiological compressive and tensile forces in weight-bearing synovial joints such as the knee. However, there is an increasing realization that these tissue-engineered cartilage constructs will fail without the optimal frictional and wear properties present in native articular cartilage. These characteristics are critical to smooth, pain-free joint articulation and a long-lasting, durable cartilage surface. To achieve optimal tribological properties, engineered cartilage therapies will need to incorporate approaches and methods for functional lubrication. Steady progress in cartilage lubrication in native tissues has pushed the pendulum and warranted a shift in the articular cartilage tissue-engineering paradigm. Engineered tissues should be designed and developed to possess both tribological and mechanical properties mirroring natural cartilage. In this article, an overview of the biology and engineering of articular cartilage structure and cartilage lubrication will be presented. Salient progress in lubrication treatments such as tribosupplementation, pharmacological, and cell-based therapies will be covered. Finally, frictional assays such as the pin-on-disk tribometer will be addressed. Knowledge related to the elements of cartilage lubrication has progressed and, thus, an opportune moment is provided to leverage these advances at a critical step in the development of mechanically and tribologically robust, biomimetic tissue-engineered cartilage. This article is intended to serve as the first stepping stone toward future studies in functional

  12. Biocommodity Engineering.

    Science.gov (United States)

    Lynd; Wyman; Gerngross

    1999-10-01

    The application of biotechnology to the production of commodity products (fuels, chemicals, and materials) offering benefits in terms of sustainable resource supply and environmental quality is an emergent area of intellectual endeavor and industrial practice with great promise. Such "biocommodity engineering" is distinct from biotechnology motivated by health care at multiple levels, including economic driving forces, the importance of feedstocks and cost-motivated process engineering, and the scale of application. Plant biomass represents both the dominant foreseeable source of feedstocks for biotechnological processes as well as the only foreseeable sustainable source of organic fuels, chemicals, and materials. A variety of forms of biomass, notably many cellulosic feedstocks, are potentially available at a large scale and are cost-competitive with low-cost petroleum whether considered on a mass or energy basis, and in terms of price defined on a purchase or net basis for both current and projected mature technology, and on a transfer basis for mature technology. Thus the central, and we believe surmountable, impediment to more widespread application of biocommodity engineering is the general absence of low-cost processing technology. Technological and research challenges associated with converting plant biomass into commodity products are considered relative to overcoming the recalcitrance of cellulosic biomass (converting cellulosic biomass into reactive intermediates) and product diversification (converting reactive intermediates into useful products). Advances are needed in pretreatment technology to make cellulosic materials accessible to enzymatic hydrolysis, with increased attention to the fundamental chemistry operative in pretreatment processes likely to accelerate progress. Important biotechnological challenges related to the utilization of cellulosic biomass include developing cellulase enzymes and microorganisms to produce them, fermentation of

  13. Biological effects

    International Nuclear Information System (INIS)

    Trott, K.R.

    1973-01-01

    Following an introduction into the field of cellular radiation effect considering the most important experimental results, the biological significance of the colony formation ability is brought out. The inactivation concept of stem cells does not only prove to be good, according to the present results, in the interpretation of the pathogenesis of acute radiation effects on moult tissue, it also enables chronicle radiation injuries to be interpreted through changes in the fibrous part of the organs. Radiation therapy of tumours can also be explained to a large extent by the radiation effect on the unlimited reproductiveness of tumour cells. The more or less similar dose effect curves for healthy and tumour tissue in practice lead to intermittent irradiation. The dependence of the intermittent doses and intervals on factors such as Elkind recovery, synchronisation, redistribution, reoxygenation, repopulation and regeneration are reviewed. (ORU/LH) [de

  14. Bioinspired Hydrogels to Engineer Cancer Microenvironments.

    Science.gov (United States)

    Park, Kyung Min; Lewis, Daniel; Gerecht, Sharon

    2017-06-21

    Recent research has demonstrated that tumor microenvironments play pivotal roles in tumor development and metastasis through various physical, chemical, and biological factors, including extracellular matrix (ECM) composition, matrix remodeling, oxygen tension, pH, cytokines, and matrix stiffness. An emerging trend in cancer research involves the creation of engineered three-dimensional tumor models using bioinspired hydrogels that accurately recapitulate the native tumor microenvironment. With recent advances in materials engineering, many researchers are developing engineered tumor models, which are promising platforms for the study of cancer biology and for screening of therapeutic agents for better clinical outcomes. In this review, we discuss the development and use of polymeric hydrogel materials to engineer native tumor ECMs for cancer research, focusing on emerging technologies in cancer engineering that aim to accelerate clinical outcomes.

  15. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  16. Toward scalable parts families for predictable design of biological circuits.

    Science.gov (United States)

    Lucks, Julius B; Qi, Lei; Whitaker, Weston R; Arkin, Adam P

    2008-12-01

    Our current ability to engineer biological circuits is hindered by design cycles that are costly in terms of time and money, with constructs failing to operate as desired, or evolving away from the desired function once deployed. Synthetic biologists seek to understand biological design principles and use them to create technologies that increase the efficiency of the genetic engineering design cycle. Central to the approach is the creation of biological parts--encapsulated functions that can be composited together to create new pathways with predictable behaviors. We define five desirable characteristics of biological parts--independence, reliability, tunability, orthogonality and composability, and review studies of small natural and synthetic biological circuits that provide insights into each of these characteristics. We propose that the creation of appropriate sets of families of parts with these properties is a prerequisite for efficient, predictable engineering of new function in cells and will enable a large increase in the sophistication of genetic engineering applications.

  17. Opportunities for Merging Chemical and Biological Synthesis

    Science.gov (United States)

    Wallace, Stephen; Balskus, Emily P.

    2014-01-01

    Organic chemists and metabolic engineers use largely orthogonal technologies to access small molecules like pharmaceuticals and commodity chemicals. As the use of biological catalysts and engineered organisms for chemical production grows, it is becoming increasingly evident that future efforts for chemical manufacture will benefit from the integration and unified expansion of these two fields. This review will discuss approaches that combine chemical and biological synthesis for small molecule production. We highlight recent advances in combining enzymatic and non-enzymatic catalysis in vitro, discuss the application of design principles from organic chemistry for engineering non-biological reactivity into enzymes, and describe the development of biocompatible chemistry that can be interfaced with microbial metabolism. PMID:24747284

  18. 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

  19. Structural Interfaces and Attachments in Biology

    CERN Document Server

    Birman, Victor; Genin, Guy

    2013-01-01

    Attachment of dissimilar materials in engineering and surgical practice is a perennial challenge. Bimaterial attachment sites are common locations for injury, repeated injury, and mechanical failure. Nature presents several highly effective solutions to the challenge of bimaterial attachment that differ from those found in engineering practice. Structural Interfaces and Attachments in Biology describes the attachment of dissimilar materials from multiple perspectives. The text will simultaneously elucidate natural bimaterial attachments and outline engineering principles underlying successful attachments to the communities of tissue engineers and surgeons. Included an in-depth analysis of the biology of attachments in the body and mechanisms by which robust attachments are formed, a review of current concepts of attaching dissimilar materials in surgical practice and a discussion of bioengineering approaches that are currently being developed. This book also: Provides the first comprehensive treatment of phys...

  20. Air pollution engineering

    Science.gov (United States)

    Maduna, Karolina; Tomašić, Vesna

    2017-11-01

    Air pollution is an environmental and a social problem which leads to a multitude of adverse effects on human health and standard of human life, state of the ecosystems and global change of climate. Air pollutants are emitted from natural, but mostly from anthropogenic sources and may be transported over long distances. Some air pollutants are extremely stable in the atmosphere and may accumulate in the environment and in the food chain, affecting human beings, animals and natural biodiversity. Obviously, air pollution is a complex problem that poses multiple challenges in terms of management and abatements of the pollutants emission. Effective approach to the problems of air pollution requires a good understanding of the sources that cause it, knowledge of air quality status and future trends as well as its impact on humans and ecosystems. This chapter deals with the complexities of the air pollution and presents an overview of different technical processes and equipment for air pollution control, as well as basic principles of their work. The problems of air protection as well as protection of other ecosystems can be solved only by the coordinated endeavors of various scientific and engineering disciplines, such as chemistry, physics, biology, medicine, chemical engineering and social sciences. The most important engineering contribution is mostly focused on development, design and operation of equipment for the abatement of harmful emissions into environment.

  1. Engineering Review Information System

    Science.gov (United States)

    Grems, III, Edward G. (Inventor); Henze, James E. (Inventor); Bixby, Jonathan A. (Inventor); Roberts, Mark (Inventor); Mann, Thomas (Inventor)

    2015-01-01

    A disciplinal engineering review computer information system and method by defining a database of disciplinal engineering review process entities for an enterprise engineering program, opening a computer supported engineering item based upon the defined disciplinal engineering review process entities, managing a review of the opened engineering item according to the defined disciplinal engineering review process entities, and closing the opened engineering item according to the opened engineering item review.

  2. NASA, Engineering, and Swarming Robots

    Science.gov (United States)

    Leucht, Kurt

    2015-01-01

    This presentation is an introduction to NASA, to science and engineering, to biologically inspired robotics, and to the Swarmie ant-inspired robot project at KSC. This presentation is geared towards elementary school students, middle school students, and also high school students. This presentation is suitable for use in STEM (science, technology, engineering, and math) outreach events. The first use of this presentation will be on Oct 28, 2015 at Madison Middle School in Titusville, Florida where the author has been asked by the NASA-KSC Speakers Bureau to speak to the students about the Swarmie robots.

  3. Engine Handling.

    Science.gov (United States)

    1983-02-01

    air seal for long life turbine engine. AIAA - 81 - 1440 4.- STEWART P.A.E., BRASNETT K.A., The contribution of dynamic x - ray to gas turbine air...trio exigeant A ce nivoau. Los calculo 4’int~gration du syotime adjoint sont trio p~nalisanto en tempo de calcul. LuA vatu g.aeh d & apt~If adjoint

  4. Robot engineering

    International Nuclear Information System (INIS)

    Jung, Seul

    2006-02-01

    This book deals with robot engineering, giving descriptions of robot's history, current tendency of robot field, work and characteristic of industrial robot, essential merit and vector, application of matrix, analysis of basic vector, expression of Denavit-Hartenberg, robot kinematics such as forward kinematics, inverse kinematics, cases of MATLAB program, and motion kinematics, robot kinetics like moment of inertia, centrifugal force and coriolis power, and Euler-Lagrangian equation course plan, SIMULINK position control of robots.

  5. News: Synthetic biology leading to specialty chemicals ...

    Science.gov (United States)

    Synthetic biology can combine the disciplines of biology, engineering, and chemistry productively to form molecules of great scientific and commercial value. Recent advances in the new field are explored for their connection to new tools that have been used to elucidate production pathways to a wide variety of chemicals generated by microorganisms. The selection and enhancement of microbiological strains through the practice of strain engineering enables targets of design, construction, and optimization. This news column aspires to cover recent literature relating to the development and understanding of clean technology.

  6. Web Engineering

    Energy Technology Data Exchange (ETDEWEB)

    White, Bebo

    2003-06-23

    Web Engineering is the application of systematic, disciplined and quantifiable approaches to development, operation, and maintenance of Web-based applications. It is both a pro-active approach and a growing collection of theoretical and empirical research in Web application development. This paper gives an overview of Web Engineering by addressing the questions: (a) why is it needed? (b) what is its domain of operation? (c) how does it help and what should it do to improve Web application development? and (d) how should it be incorporated in education and training? The paper discusses the significant differences that exist between Web applications and conventional software, the taxonomy of Web applications, the progress made so far and the research issues and experience of creating a specialization at the master's level. The paper reaches a conclusion that Web Engineering at this stage is a moving target since Web technologies are constantly evolving, making new types of applications possible, which in turn may require innovations in how they are built, deployed and maintained.

  7. Synthetic biology platform technologies for antimicrobial applications.

    Science.gov (United States)

    Braff, Dana; Shis, David; Collins, James J

    2016-10-01

    The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Tuning the dials of Synthetic Biology

    Science.gov (United States)

    Arpino, James A. J.; Hancock, Edward J.; Anderson, James; Barahona, Mauricio; Stan, Guy-Bart V.; Polizzi, Karen

    2013-01-01

    Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others. PMID:23704788

  9. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology......, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed....

  10. US Competitiveness in Synthetic Biology.

    Science.gov (United States)

    Gronvall, Gigi Kwik

    2015-01-01

    Synthetic biology is an emerging technical field that aims to make biology easier to engineer; the field has applications in strategically important sectors for the US economy. While the United States currently leads in synthetic biology R&D, other nations are heavily investing in order to boost their economies, which will inevitably diminish the US leadership position. This outcome is not entirely negative--additional investments will expand markets--but it is critical that the US government take steps to remain competitive: There are applications from which the US population and economy may benefit; there are specific applications with importance for national defense; and US technical leadership will ensure that US experts have a leading role in synthetic biology governance, regulation, and oversight. Measures to increase competitiveness in S&T generally are broadly applicable for synthetic biology and should be pursued. However, the US government will also need to take action on fundamental issues that will affect the field's development, such as countering anti-GMO (genetically modified organism) sentiments and anti-GMO legislation. The United States should maintain its regulatory approach so that it is the product that is regulated, not the method used to create a product. At the same time, the United States needs to ensure that the regulatory framework is updated so that synthetic biology products do not fall into regulatory gaps. Finally, the United States needs to pay close attention to how synthetic biology applications may be governed internationally, such as through the Nagoya Protocol of the Convention on Biological Diversity, so that beneficial applications may be realized.

  11. Bullying Prevention: a Summary of the Report of the National Academies of Sciences, Engineering, and Medicine : Committee on the Biological and Psychosocial Effects of Peer Victimization: Lessons for Bullying Prevention.

    Science.gov (United States)

    Flannery, Daniel J; Todres, Jonathan; Bradshaw, Catherine P; Amar, Angela Frederick; Graham, Sandra; Hatzenbuehler, Mark; Masiello, Matthew; Moreno, Megan; Sullivan, Regina; Vaillancourt, Tracy; Le Menestrel, Suzanne M; Rivara, Frederick

    2016-11-01

    Long tolerated as a rite of passage into adulthood, bullying is now recognized as a major and preventable public health problem. The consequences of bullying-for those who are bullied, the perpetrators of bullying, and the witnesses-include poor physical health, anxiety, depression, increased risk for suicide, poor school performance, and future delinquent and aggressive behavior. Despite ongoing efforts to address bullying at the law, policy, and programmatic levels, there is still much to learn about the consequences of bullying and the effectiveness of various responses. In 2016, the National Academies of Sciences, Engineering, and Medicine published a report entitled Preventing Bullying Through Science, Policy and Practice, which examined the evidence on bullying, its impact, and responses to date. This article summarizes the report's key findings and recommendations related to bullying prevention.

  12. 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

  13. Tracking the emergence of synthetic biology.

    Science.gov (United States)

    Shapira, Philip; Kwon, Seokbeom; Youtie, Jan

    2017-01-01

    Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years. This paper contributes to efforts to delineate this emerging domain by presenting a newly constructed bibliometric definition of synthetic biology. Our approach is dimensioned from a core set of papers in synthetic biology, using procedures to obtain benchmark synthetic biology publication records, extract keywords from these benchmark records, and refine the keywords, supplemented with articles published in dedicated synthetic biology journals. We compare our search strategy with other recent bibliometric approaches to define synthetic biology, using a common source of publication data for the period from 2000 to 2015. The paper details the rapid growth and international spread of research in synthetic biology in recent years, demonstrates that diverse research disciplines are contributing to the multidisciplinary development of synthetic biology research, and visualizes this by profiling synthetic biology research on the map of science. We further show the roles of a relatively concentrated set of research sponsors in funding the growth and trajectories of synthetic biology. In addition to discussing these analyses, the paper notes limitations and suggests lines for further work.

  14. 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.

  15. Engineering justice transforming engineering education and practice

    CERN Document Server

    Leydens, Jon A

    2018-01-01

    Using social justice as a catalyst for curricular transformation, Engineering Justice presents an examination of how politics, culture, and other social issues are inherent in the practice of engineering. It aims to align engineering curricula with socially just outcomes, increase enrollment among underrepresented groups, and lessen lingering gender, class, and ethnicity gaps by showing how the power of engineering knowledge can be explicitly harnessed to serve the underserved and address social inequalities. This book is meant to transform the way educators think about engineering curricula through creating or transforming existing courses to attract, retain, and motivate engineering students to become professionals who enact engineering for social justice. Engineering Justice offers thought-provoking chapters on: why social justice is inherent yet often invisible in engineering education and practice; engineering design for social justice; social justice in the engineering sciences; social justice in human...

  16. Toward design-based engineering of industrial microbes.

    Science.gov (United States)

    Tyo, Keith E J; Kocharin, Kanokarn; Nielsen, Jens

    2010-06-01

    Engineering industrial microbes has been hampered by incomplete knowledge of cell biology. Thus an iterative engineering cycle of modeling, implementation, and analysis has been used to increase knowledge of the underlying biology while achieving engineering goals. Recent advances in Systems Biology technologies have drastically improved the amount of information that can be collected in each iteration. As well, Synthetic Biology tools are melding modeling and molecular implementation. These advances promise to move microbial engineering from the iterative approach to a design-oriented paradigm, similar to electrical circuits and architectural design. Genome-scale metabolic models, new tools for controlling expression, and integrated -omics analysis are described as key contributors in moving the field toward Design-based Engineering. Copyright 2010 Elsevier Ltd. All rights reserved.

  17. 15th International Conference on Biomedical Engineering

    CERN Document Server

    2014-01-01

    This volume presents the proceedings of the 15th ICMBE held from 4th to 7th December 2013, Singapore. Biomedical engineering is applied in most aspects of our healthcare ecosystem. From electronic health records to diagnostic tools to therapeutic, rehabilitative and regenerative treatments, the work of biomedical engineers is evident. Biomedical engineers work at the intersection of engineering, life sciences and healthcare. The engineers would use principles from applied science including mechanical, electrical, chemical and computer engineering together with physical sciences including physics, chemistry and mathematics to apply them to biology and medicine. Applying such concepts to the human body is very much the same concepts that go into building and programming a machine. The goal is to better understand, replace or fix a target system to ultimately improve the quality of healthcare. With this understanding, the conference proceedings offer a single platform for individuals and organisations working i...

  18. Gentic engineering for practical application.

    Science.gov (United States)

    Klingmüller, W

    1979-04-01

    Genetic engineering has ushered in a new era in biology. Although many problems are still to be solved, there are examples that point to a possible later application for the benefit of mankind: Bacteria can be manipulated to degrade crude-oil spillages, to produce human insulin and to bind nitrogen from the air. If all the bacteria that are indigenous to agricultural soils could be made to bind nitrogen, an increase in soil fertility might well result.

  19. Gentic engineering for practical application

    Energy Technology Data Exchange (ETDEWEB)

    Klingmuller, W.

    1979-04-01

    Genetic engineering has ushered in a new era in biology. Although many problems are still to be solved, there are examples that point to a possible later application for the benefit of mankind: Bacteria can be manipulated to degrade crude-oil spillages, to produce human insulin and to bind nitrogen from the air. If all the bacteria that are indigenous to agricultural soils could be made to bind nitrogen, and increase in soil fertility might well result.

  20. Microprocessor engineering

    CERN Document Server

    Holdsworth, B

    2013-01-01

    Microprocessor Engineering provides an insight in the structures and operating techniques of a small computer. The book is comprised of 10 chapters that deal with the various aspects of computing. The first two chapters tackle the basic arithmetic and logic processes. The third chapter covers the various memory devices, both ROM and RWM. Next, the book deals with the general architecture of microprocessor. The succeeding three chapters discuss the software aspects of machine operation, while the last remaining three chapters talk about the relationship of the microprocessor with the outside wo

  1. Inverse problems in systems biology

    International Nuclear Information System (INIS)

    Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

    2009-01-01

    Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

  2. Internet Search Engines

    OpenAIRE

    Fatmaa El Zahraa Mohamed Abdou

    2004-01-01

    A general study about the internet search engines, the study deals main 7 points; the differance between search engines and search directories, components of search engines, the percentage of sites covered by search engines, cataloging of sites, the needed time for sites appearance in search engines, search capabilities, and types of search engines.

  3. Metabolic engineering in methanotrophic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Kalyuzhnaya, MG; Puri, AW; Lidstrom, ME

    2015-05-01

    Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems. (C) 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  4. A Synthetic Biology Architecture to Detoxify and Enrich Mars Soil for Agriculture

    Data.gov (United States)

    National Aeronautics and Space Administration — Although the theoretical case for space biological engineering is convincing, since recent studies on the use of biology in space showed substantial payload...

  5. Protein engineering for metabolic engineering: current and next-generation tools

    Science.gov (United States)

    Marcheschi, Ryan J.; Gronenberg, Luisa S.; Liao, James C.

    2014-01-01

    Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically-produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. This article reviews advances of selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use, produce non-natural amino acids, alcohols, and carboxylic acids, and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes. PMID:23589443

  6. Synthetic biology as red herring.

    Science.gov (United States)

    Preston, Beth

    2013-12-01

    It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice-agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...

  8. Synthetic Biology: game changer in intelectual property

    Directory of Open Access Journals (Sweden)

    Laurens Landeweerd

    2016-12-01

    Full Text Available Synthetic biology can be considered a game changer that plays an important role in the current NBIC, or BINC convergence of nano-, bio-, info and cognitive sciences. Although most synthetic biology experts are unaware of it, the field appeals to the imagination in its adherence to targets that were usually associated with premodern alchemist science. This paper elaborates several aspects of synthetic biology as well as its consequences for long held notions of intellectual property and the ontological categories of scientific discovery on the one hand and engineering on the other, the distinction between natural and artificial, the grown and the made.

  9. Genetic engineering and sustainable production of ornamentals

    DEFF Research Database (Denmark)

    Lütken, Henrik Vlk; Clarke, Jihong Liu; Müller, Renate

    2012-01-01

    Abstract Through the last decades, environmentally and health-friendly production methods and conscientious use of resources have become crucial for reaching the goal of a more sustainable plant production. Protection of the environment requires careful consumption of limited resources and reduct....... In conclusion, molecular breeding approaches are dealt with in a way allowing a critical biological assessment and enabling the scientific community and public to put genetic engineering of ornamental plants into a perspective regarding their usefulness in plant breeding........ This review presents the more recent progress of genetic engineering in ornamental breeding, delivers an overview of the biological background of the used technologies and critically evaluates the usefulness of the strategies to obtain improved ornamental plants. First, genetic engineering is addressed......, compactness can be accomplished by using a natural transformation approach without recombinant DNA technology. Secondly, metabolic engineering approaches targeting elements of the ethylene signal transduction pathway are summarized as a possible alternative to avoid the use of chemical ethylene inhibitors...

  10. Teacher-to-Teacher: An Annotated Bibliography on DNA and Genetic Engineering.

    Science.gov (United States)

    Mertens, Thomas R., Comp.

    1984-01-01

    Presented is an annotated bibliography of 24 books on DNA and genetic engineering. Areas considered in these books include: basic biological concepts to help understand advances in genetic engineering; applications of genetic engineering; social, legal, and moral issues of genetic engineering; and historical aspects leading to advances in…

  11. The History of Chemical Engineering and Pedagogy: The Paradox of Tradition and Innovation

    Science.gov (United States)

    Wankat, Phillip C.

    2009-01-01

    The Massachusetts Institute of Technology started the first US chemical engineering program six score years ago. Since that time, the chemical engineering curriculum has evolved. The latest versions of the curriculum are attempts to broaden chemical engineering to add product engineering, biology and nanotechnology to the traditional process…

  12. Establishing the need for an engineering standard for agricultural hitch pins.

    Science.gov (United States)

    Deboy, G R; Knapp, W M; Field, W E; Krutz, G W; Corum, C L

    2012-04-01

    pin engineering standard that would reflect current agricultural applications and practices and that would be promoted to both original equipment manufacturers and manufacturers and suppliers of replacement hitch pins. The standard should address the design of composite pins, heat treating, surface hardening, loading capacity and labeling of such, incorporation of unintentional disengagement prevention devices, indicators of the need for replacement due to wear, and safety information that should be included in operator instructions. ASABE is the most appropriate organization to develop such a standard. It was also concluded that agricultural safety and health programs and professionals need to raise the awareness of farmers concerning the appropriate selection and use of agricultural hitch pins, including the need to replace non-standard pins with pins less likely to fail or disengage during use, the need to replace hitch pins with indications of potential failure, and the importance of using appropriate safety chains, especially during transport of equipment behind tractors and trucks on public roads.

  13. An engineering context for software engineering

    OpenAIRE

    Riehle, Richard D.

    2008-01-01

    New engineering disciplines are emerging in the late Twentieth and early Twenty-first Century. One such emerging discipline is software engineering. The engineering community at large has long harbored a sense of skepticism about the validity of the term software engineering. During most of the fifty-plus years of software practice, that skepticism was probably justified. Professional education of software developers often fell short of the standard expected for conventional engineers; so...

  14. Biological effects of radiation

    International Nuclear Information System (INIS)

    2013-01-01

    This fourth chapter presents: cell structure and metabolism; radiation interaction with biological tissues; steps of the production of biological effect of radiation; radiosensitivity of tissues; classification of biological effects; reversibility, transmissivity and influence factors; pre-natal biological effects; biological effects in therapy and syndrome of acute irradiation

  15. Towards evolution-guided microbial engineering - tools development and applications

    DEFF Research Database (Denmark)

    Genee, Hans Jasper

    microbial vitamin uptake systems, ii)directed protein evolution to elucidate sequence-function relationships ofbacterial small molecule transport systems, and iii) perform sequencephenotypicanalysis of combinatorially engineered metabolic pathwaysresulting in significant productivity improvements......-performing microorganisms.However, an insufficient understanding of biological complexity currentlyrenders strict forward engineering approaches inadequate. Our success forthe development of useful biological systems is therefore largelydetermined by our abilities to generate microbial diversity and evaluate itsphenotypic...... of an early-stagethiamine cell factory. Additionally, this thesis presents two advancedgenetic engineering methods that enable rapid combinatorial engineering ofboth plasmid and chromosomal DNA.Overall, the results of this thesis illustrate the benefits of advancing theconstruction and screening toolbox...

  16. Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

    Science.gov (United States)

    Jalili, Mahdi

    2018-03-01

    I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

  17. Application of computational intelligence to biology

    CERN Document Server

    Sekhar, Akula

    2016-01-01

    This book is a contribution of translational and allied research to the proceedings of the International Conference on Computational Intelligence and Soft Computing. It explains how various computational intelligence techniques can be applied to investigate various biological problems. It is a good read for Research Scholars, Engineers, Medical Doctors and Bioinformatics researchers.

  18. Biological Art of Producing Useful Chemicals

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 3. Metabolic Engineering: Biological Art of Producing Useful Chemicals. Ram Kulkarni. General Article Volume 21 Issue 3 March 2016 pp 233-237. Fulltext. Click here to view fulltext PDF. Permanent link:

  19. Synthetic biology advances for pharmaceutical production

    Science.gov (United States)

    Breitling, Rainer; Takano, Eriko

    2015-01-01

    Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems. PMID:25744872

  20. Engineering electromagnetics

    CERN Document Server

    Thomas, David T; Hartnett, James P; Hughes, William F

    1973-01-01

    The applications involving electromagnetic fields are so pervasive that it is difficult to estimate their contribution to the industrial output: generation of electricity, power transmission lines, electric motors, actuators, relays, radio, TV and microwave transmission and reception, magnetic storage, and even the mundane little magnet used to hold a paper note on the refrigerator are all electromagnetic in nature. One would be hard pressed to find a device that works without relaying on any electromagnetic principle or effect. This text provides a good theoretical understanding of the electromagnetic field equations but also treats a large number of applications. In fact, no topic is presented unless it is directly applicable to engineering design or unless it is needed for the understanding of another topic. In electrostatics, for example, the text includes discussions of photocopying, ink-jet printing, electrostatic separation and deposition, sandpaper production, paint spraying, and powder coating. In ma...