WorldWideScience

Sample records for bottom-up synthetic biology

  1. Social and ethical checkpoints for bottom-up synthetic biology, or protocells.

    Science.gov (United States)

    Bedau, Mark A; Parke, Emily C; Tangen, Uwe; Hantsche-Tangen, Brigitte

    2009-12-01

    An alternative to creating novel organisms through the traditional "top-down" approach to synthetic biology involves creating them from the "bottom up" by assembling them from non-living components; the products of this approach are called "protocells." In this paper we describe how bottom-up and top-down synthetic biology differ, review the current state of protocell research and development, and examine the unique ethical, social, and regulatory issues raised by bottom-up synthetic biology. Protocells have not yet been developed, but many expect this to happen within the next five to ten years. Accordingly, we identify six key checkpoints in protocell development at which particular attention should be given to specific ethical, social and regulatory issues concerning bottom-up synthetic biology, and make ten recommendations for responsible protocell science that are tied to the achievement of these checkpoints. PMID:19816801

  2. Social and ethical checkpoints for bottom-up synthetic biology, or protocells

    OpenAIRE

    Bedau M.A.; Parke E.C.; Tangen U.; Hantsche-Tangen B.

    2009-01-01

    An alternative to creating novel organisms through the traditional “top-down” approach to synthetic biology involves creating them from the “bottom up” by assembling them from non-living components; the products of this approach are called “protocells.” In this paper we describe how bottom-up and top-down synthetic biology differ, review the current state of protocell research and development, and examine the unique ethical, social, and regulatory issues raised by bottom-up synthetic biology....

  3. A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology

    OpenAIRE

    Carbonell-Ballestero, M.; Duran-Nebreda, S.; Montanez, R.; Sole, R.; Macia, J.; Rodriguez-Caso, C.

    2014-01-01

    Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses—the so-called transfer function—and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the in...

  4. A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology.

    Science.gov (United States)

    Carbonell-Ballestero, Max; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard; Macía, Javier; Rodríguez-Caso, Carlos

    2014-12-16

    Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses-the so-called transfer function-and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined. PMID:25404136

  5. Construction of membrane-bound artificial cells using microfluidics: a new frontier in bottom-up synthetic biology

    Science.gov (United States)

    Elani, Yuval

    2016-01-01

    The quest to construct artificial cells from the bottom-up using simple building blocks has received much attention over recent decades and is one of the grand challenges in synthetic biology. Cell mimics that are encapsulated by lipid membranes are a particularly powerful class of artificial cells due to their biocompatibility and the ability to reconstitute biological machinery within them. One of the key obstacles in the field centres on the following: how can membrane-based artificial cells be generated in a controlled way and in high-throughput? In particular, how can they be constructed to have precisely defined parameters including size, biomolecular composition and spatial organization? Microfluidic generation strategies have proved instrumental in addressing these questions. This article will outline some of the major principles underpinning membrane-based artificial cells and their construction using microfluidics, and will detail some recent landmarks that have been achieved. PMID:27284034

  6. Nanomaterial processing using self-assembly-bottom-up chemical and biological approaches

    International Nuclear Information System (INIS)

    Nanotechnology is touted as the next logical sequence in technological evolution. This has led to a substantial surge in research activities pertaining to the development and fundamental understanding of processes and assembly at the nanoscale. Both top-down and bottom-up fabrication approaches may be used to realize a range of well-defined nanostructured materials with desirable physical and chemical attributes. Among these, the bottom-up self-assembly process offers the most realistic solution toward the fabrication of next-generation functional materials and devices. Here, we present a comprehensive review on the physical basis behind self-assembly and the processes reported in recent years to direct the assembly of nanoscale functional blocks into hierarchically ordered structures. This paper emphasizes assembly in the synthetic domain as well in the biological domain, underscoring the importance of biomimetic approaches toward novel materials. In particular, two important classes of directed self-assembly, namely, (i) self-assembly among nanoparticle–polymer systems and (ii) external field-guided assembly are highlighted. The spontaneous self-assembling behavior observed in nature that leads to complex, multifunctional, hierarchical structures within biological systems is also discussed in this review. Recent research undertaken to synthesize hierarchically assembled functional materials have underscored the need as well as the benefits harvested in synergistically combining top-down fabrication methods with bottom-up self-assembly. (review article)

  7. Emulating biology: Building nanostructures from the bottom up

    OpenAIRE

    Seeman, Nadrian C.; Belcher, Angela M.

    2002-01-01

    The biological approach to nanotechnology has produced self-assembled objects, arrays and devices; likewise, it has achieved the recognition of inorganic systems and the control of their growth. Can these approaches now be integrated to produce useful systems?

  8. Synthetic biology, inspired by synthetic chemistry

    OpenAIRE

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

    2012-01-01

    The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology -about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal an...

  9. Mineralization of Synthetic Polymer Scaffolds: A Bottom-upApproach for the Development of Artificial Bone

    Energy Technology Data Exchange (ETDEWEB)

    Song, Jie; Viengkham, Malathong; Bertozzi, Carolyn R.

    2004-09-27

    The controlled integration of organic and inorganic components confers natural bone with superior mechanical properties. Bone biogenesis is thought to occur by templated mineralization of hard apatite crystals by an elastic protein scaffold, a process we sought to emulate with synthetic biomimetic hydrogel polymers. Crosslinked polymethacrylamide and polymethacrylate hydrogels were functionalized with mineral-binding ligands and used to template the formation of hydroxyapatite. Strong adhesion between the organic and inorganic materials was achieved for hydrogels functionalized with either carboxylate or hydroxy ligands. The mineral-nucleating potential of hydroxyl groups identified here broadens the design parameters for synthetic bone-like composites and suggests a potential role for hydroxylated collagen proteins in bone mineralization.

  10. 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

  11. Synthetic Biology: Integrated Gene Circuits

    OpenAIRE

    Nandagopal, Nagarajan; Michael B Elowitz

    2011-01-01

    A major goal of synthetic biology is to develop a deeper understanding of biological design principles from the bottom up, by building circuits and studying their behavior in cells. Investigators initially sought to design circuits “from scratch” that functioned as independently as possible from the underlying cellular system. More recently, researchers have begun to develop a new generation of synthetic circuits that integrate more closely with endogenous cellular processes. These approaches...

  12. Synthetic biology: A foundation for multi-scale molecular biology

    OpenAIRE

    Bower, Adam G; McClintock, Maria K; Stephen S. Fong

    2010-01-01

    The field of synthetic biology has made rapid progress in a number of areas including method development, novel applications and community building. In seeking to make biology “engineerable,” synthetic biology is increasing the accessibility of biological research to researchers of all experience levels and backgrounds. One of the underlying strengths of synthetic biology is that it may establish the framework for a rigorous bottom-up approach to studying biology starting at the DNA level. Bu...

  13. Parallel- and serial-contact electrochemical metallization of monolayer nanopatterns: A versatile synthetic tool en route to bottom-up assembly of electric nanocircuits

    Directory of Open Access Journals (Sweden)

    Jonathan Berson

    2012-02-01

    Full Text Available Contact electrochemical transfer of silver from a metal-film stamp (parallel process or a metal-coated scanning probe (serial process is demonstrated to allow site-selective metallization of monolayer template patterns of any desired shape and size created by constructive nanolithography. The precise nanoscale control of metal delivery to predefined surface sites, achieved as a result of the selective affinity of the monolayer template for electrochemically generated metal ions, provides a versatile synthetic tool en route to the bottom-up assembly of electric nanocircuits. These findings offer direct experimental support to the view that, in electrochemical metal deposition, charge is carried across the electrode–solution interface by ion migration to the electrode rather than by electron transfer to hydrated ions in solution.

  14. Pictures of Synthetic Biology

    OpenAIRE

    Cserer, Amelie; Seiringer, Alexandra

    2009-01-01

    This article is concerned with the representation of Synthetic Biology in the media and by biotechnology experts. An analysis was made of German-language media articles published between 2004 and 2008, and interviews with biotechnology-experts at the Synthetic Biology conference SB 3.0 in Zurich 2007. The results have been reflected in terms of the definition of Synthetic Biology, applications of Synthetic Biology and the perspectives of opportunities and risks. In the media, Synthetic Biolog...

  15. 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. PMID:24156739

  16. Synthetic biological networks

    International Nuclear Information System (INIS)

    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)

  17. Synthetic biology and biosecurity.

    Science.gov (United States)

    Robienski, Jürgen; Simon, Jürgen

    2014-01-01

    This article discusses the conflict fields and legal questions of synthetic biology, esp. concerning biosecurity. A respective jurisprudential discussion has not taken place yet in Germany apart from few statements and recommendations. But in Germany, Europe and the USA, it is generally accepted that a broad discussion is necessary. This is esp. true for the question of biosecurity and the possible dangers arising from Synthetic Biology. PMID:25845204

  18. Culture from the Bottom Up

    Science.gov (United States)

    Atkinson, Dwight; Sohn, Jija

    2013-01-01

    The culture concept has been severely criticized for its top-down nature in TESOL, leading arguably to its falling out of favor in the field. But what of the fact that people do "live culturally" (Ingold, 1994)? This article describes a case study of culture from the bottom up--culture as understood and enacted by its individual users.…

  19. Creating biological nanomaterials using synthetic biology

    International Nuclear Information System (INIS)

    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)

  20. Creating biological nanomaterials using synthetic biology

    Directory of Open Access Journals (Sweden)

    MaryJoe K Rice

    2014-01-01

    Full Text Available 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.

  1. Creating biological nanomaterials using synthetic biology

    OpenAIRE

    MaryJoe K Rice; 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 bi...

  2. Synthetic biology: Understanding biological design from synthetic circuits

    OpenAIRE

    Mukherji, Shankar; van Oudenaarden, Alexander

    2009-01-01

    An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems — from synthetic promoters to the control of cell–cell interactions — has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple...

  3. A computational study of liposome logic: towards cellular computing from the bottom up

    OpenAIRE

    Smaldon, James; Romero-Campero, Francisco J.; Fernández Trillo, Francisco; Gheorghe, Marian; Alexander, Cameron; Krasnogor, Natalio

    2010-01-01

    In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This “liposome logic” approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in “top-down” synthetic biology, particularly in the specification, design and impl...

  4. Synthetic Biology for Therapeutic Applications

    OpenAIRE

    Abil, Zhanar; Xiong, Xiong; Zhao, Huimin

    2014-01-01

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug d...

  5. Analog synthetic biology.

    Science.gov (United States)

    Sarpeshkar, R

    2014-03-28

    We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations. PMID:24567476

  6. Synthetic biology: advancing biological frontiers by building synthetic systems

    OpenAIRE

    Chen, Yvonne Yu-Hsuan; Galloway, Kate E.; Smolke, Christina D.

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  7. Implementation Alternatives for Bottom-Up Evaluation

    OpenAIRE

    Brass, Stefan

    2010-01-01

    Bottom-up evaluation is a central part of query evaluation / program execution in deductive databases. It is used after a source code optimization like magic sets or SLDmagic that ensures that only facts relevant for the query can be derived. Then bottom-up evaluation simply performs the iteration of the standard TP -operator to compute the minimal model. However, there are different ways to implement bottom-up evaluation efficiently. Since this is most critical for the performance of a deduc...

  8. Microfluidic Technologies for Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Sung Kuk Lee

    2011-06-01

    Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

  9. 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. PMID:26690379

  10. Synthetic Genomics and Synthetic Biology Applications Between Hopes and Concerns

    OpenAIRE

    König, Harald; Frank, Daniel; Heil, Reinhard; Coenen, Christopher

    2013-01-01

    New organisms and biological systems designed to satisfy human needs are among the aims of synthetic genomics and synthetic biology. Synthetic biology seeks to model and construct biological components, functions and organisms that do not exist in nature or to redesign existing biological systems to perform new functions. Synthetic genomics, on the other hand, encompasses technologies for the generation of chemically-synthesized whole genomes or larger parts of genomes, allowing to simultaneo...

  11. Synthetic biology: insights into biological computation.

    Science.gov (United States)

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  12. Where Synthetic Biology Meets ET

    Science.gov (United States)

    Rothschild, Lynn J.

    2016-01-01

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

  13. Ethical Issues in Synthetic Biology

    OpenAIRE

    Heavey, Patrick Joseph

    2013-01-01

    Synthetic biology has been defined as: “the design and construction of new biological parts, devices, and systems, and the re-design of existing, natural biological systems for useful purposes” (syntheticbiology.org). The convergence of scientific fields such as molecular biology, computer science and others have rendered it a natural progression, based on existing knowledge.The fact that humanity has reached a stage of development where it seems feasible to “create” life, or design it to a h...

  14. Bottom-up approach to silicon nanoelectronics

    OpenAIRE

    Mizumita, Hiroshi; Oda, S

    2005-01-01

    Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920) International audience This paper presents a brief review of our recent work investigating a novel bottom-up approach to realize silicon based nanoelectronics. We discuss fabrication technique, electronic properties and device applications of silicon nanodots as a building block for nanoscale silicon devices.

  15. Engineering life through Synthetic Biology.

    Science.gov (United States)

    Chopra, Paras; Kamma, Akhil

    2006-01-01

    Synthetic Biology is a field involving synthesis of novel biological systems which are not generally found in nature. It has brought a new paradigm in science as it has enabled scientists to create life from the scratch, hence helping better understand the principles of biology. The viability of living organisms that use unnatural molecules is also being explored. Unconventional projects such as DNA playing tic-tac-toe, bacterial photographic film, etc. are taking biology to its extremes. The field holds a promise for mass production of cheap drugs and programming bacteria to seek-and-destroy tumors in the body. However, the complexity of biological systems make the field a challenging one. In addition to this, there are other major technical and ethical challenges which need to be addressed before the field realizes its true potential. PMID:17274769

  16. Bottom-up organic integrated circuits

    OpenAIRE

    Smits, Edsger C. P; Mathijssen, Simon G. J.; van Hal, Paul A.; Setayesh, Sepas; Geuns, Thomas C. T.; Mutsaers, Kees A. H. A.; Cantatore, Eugenio; Wondergem, Harry J.; Werzer, Oliver; Resel, Roland; Kemerink, Martijn; Kirchmeyer, Stephan; Muzafarov, Aziz M.; Ponomarenko, Sergei A.; de Boer, Bert

    2008-01-01

    Self- assembly - the autonomous organization of components into patterns and structures(1) - is a promising technology for the mass production of organic electronics. Making integrated circuits using a bottom- up approach involving self- assembling molecules was proposed(2) in the 1970s. The basic building block of such an integrated circuit is the self- assembled- monolayer field- effect transistor ( SAMFET), where the semiconductor is a monolayer spontaneously formed on the gate dielectric....

  17. Synthetic biology character and impact

    CERN Document Server

    Pade, Christian; Wigger, Henning; Gleich, Arnim

    2015-01-01

    Synthetic Biology is already an object of intensive debate. However, to a great extent the discussion to date has been concerned with fundamental ethical, religious and philosophical questions. By contrast, based on an investigation of the field’s scientific and technological character, this book focuses on new functionalities provided by synthetic biology and explores the associated opportunities and risks. Following an introduction to the subject and a discussion of the most central paradigms and methodologies, the book provides an overview of the structure of this field of science and technology. It informs the reader about the current stage of development, as well as topical problems and potential opportunities in important fields of application. But not only the science itself is in focus. In order to investigate its broader impact, ecological as well as ethical implications will be considered, paving the way for a discussion of responsibilities in the context of a field at a transitional crossroads be...

  18. 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…

  19. Word selection affects perceptions of synthetic biology

    OpenAIRE

    Tonidandel Scott; Bye-Nagel Kyri; Snell Sam; Pearson Brianna; Heyer Laurie J; Campbell A Malcolm

    2011-01-01

    Abstract Members of the synthetic biology community have discussed the significance of word selection when describing synthetic biology to the general public. In particular, many leaders proposed the word "create" was laden with negative connotations. We found that word choice and framing does affect public perception of synthetic biology. In a controlled experiment, participants perceived synthetic biology more negatively when "create" was used to describe the field compared to "construct" (...

  20. Bottom-up holographic approach to QCD

    Energy Technology Data Exchange (ETDEWEB)

    Afonin, S. S. [V. A. Fock Department of Theoretical Physics, Saint Petersburg State University, 1 ul. Ulyanovskaya, 198504 (Russian Federation)

    2016-01-22

    One of the most known result of the string theory consists in the idea that some strongly coupled gauge theories may have a dual description in terms of a higher dimensional weakly coupled gravitational theory — the so-called AdS/CFT correspondence or gauge/gravity correspondence. The attempts to apply this idea to the real QCD are often referred to as “holographic QCD” or “AdS/QCD approach”. One of directions in this field is to start from the real QCD and guess a tentative dual higher dimensional weakly coupled field model following the principles of gauge/gravity correspondence. The ensuing phenomenology can be then developed and compared with experimental data and with various theoretical results. Such a bottom-up holographic approach turned out to be unexpectedly successful in many cases. In the given short review, the technical aspects of the bottom-up holographic approach to QCD are explained placing the main emphasis on the soft wall model.

  1. Bottom-up holographic approach to QCD

    International Nuclear Information System (INIS)

    One of the most known result of the string theory consists in the idea that some strongly coupled gauge theories may have a dual description in terms of a higher dimensional weakly coupled gravitational theory — the so-called AdS/CFT correspondence or gauge/gravity correspondence. The attempts to apply this idea to the real QCD are often referred to as “holographic QCD” or “AdS/QCD approach”. One of directions in this field is to start from the real QCD and guess a tentative dual higher dimensional weakly coupled field model following the principles of gauge/gravity correspondence. The ensuing phenomenology can be then developed and compared with experimental data and with various theoretical results. Such a bottom-up holographic approach turned out to be unexpectedly successful in many cases. In the given short review, the technical aspects of the bottom-up holographic approach to QCD are explained placing the main emphasis on the soft wall model

  2. 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.

  3. Microbial synthetic biology for human therapeutics

    OpenAIRE

    Jain, Aastha; Bhatia, Pooja; Chugh, Archana

    2012-01-01

    The emerging field of synthetic biology holds tremendous potential for developing novel drugs to treat various human conditions. The current study discusses the scope of synthetic biology for human therapeutics via microbial approach. In this context, synthetic biology aims at designing, engineering and building new microbial synthetic cells that do not pre-exist in nature as well as re-engineer existing microbes for synthesis of therapeutic products. It is expected that the construction of n...

  4. 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

  5. Towards developing algal synthetic biology.

    Science.gov (United States)

    Scaife, Mark Aden; Smith, Alison Gail

    2016-06-15

    The genetic, physiological and metabolic diversity of microalgae has driven fundamental research into photosynthesis, flagella structure and function, and eukaryotic evolution. Within the last 10 years these organisms have also been investigated as potential biotechnology platforms, for example to produce high value compounds such as long chain polyunsaturated fatty acids, pigments and antioxidants, and for biodiesel precursors, in particular triacylglycerols (TAGs). Transformation protocols, molecular tools and genome sequences are available for a number of model species including the green alga Chlamydomonas reinhardtii and the diatom Phaeodactylum tricornutum, although for both species there are bottlenecks to be overcome to allow rapid and predictable genetic manipulation. One approach to do this would be to apply the principles of synthetic biology to microalgae, namely the cycle of Design-Build-Test, which requires more robust, predictable and high throughput methods. In this mini-review we highlight recent progress in the areas of improving transgene expression, genome editing, identification and design of standard genetic elements (parts), and the use of microfluidics to increase throughput. We suggest that combining these approaches will provide the means to establish algal synthetic biology, and that application of standard parts and workflows will avoid parallel development and capitalize on lessons learned from other systems. PMID:27284033

  6. Synergistic Synthetic Biology: Units in Concert

    OpenAIRE

    PabloCarbonell; Jean-YvesTrosset

    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 experimen...

  7. A computational study of liposome logic: towards cellular computing from the bottom up.

    Science.gov (United States)

    Smaldon, James; Romero-Campero, Francisco J; Fernández Trillo, Francisco; Gheorghe, Marian; Alexander, Cameron; Krasnogor, Natalio

    2010-09-01

    In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This "liposome logic" approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in "top-down" synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of "bottom-up" liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie's stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up. PMID:21886681

  8. Microbial synthetic biology for human therapeutics.

    Science.gov (United States)

    Jain, Aastha; Bhatia, Pooja; Chugh, Archana

    2012-06-01

    The emerging field of synthetic biology holds tremendous potential for developing novel drugs to treat various human conditions. The current study discusses the scope of synthetic biology for human therapeutics via microbial approach. In this context, synthetic biology aims at designing, engineering and building new microbial synthetic cells that do not pre-exist in nature as well as re-engineer existing microbes for synthesis of therapeutic products. It is expected that the construction of novel microbial genetic circuitry for human therapeutics will greatly benefit from the data generated by 'omics' approaches and multidisciplinary nature of synthetic biology. Development of novel antimicrobial drugs and vaccines by engineering microbial systems are a promising area of research in the field of synthetic biology for human theragnostics. Expression of plant based medicinal compounds in the microbial system using synthetic biology tools is another avenue dealt in the present study. Additionally, the study suggest that the traditional medicinal knowledge can do value addition for developing novel drugs in the microbial systems using synthetic biology tools. The presented work envisions the success of synthetic biology for human therapeutics via microbial approach in a holistic manner. Keeping this in view, various legal and socio-ethical concerns emerging from the use of synthetic biology via microbial approach such as patenting, biosafety and biosecurity issues have been touched upon in the later sections. PMID:23730360

  9. A Critical Perspective on Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Michel Morange

    2009-07-01

    Full Text Available Synthetic biology emerged around 2000 as a new biological discipline. It shares with systems biology the same modular vision of organisms, but is more concerned with applications than with a better understanding of the functioning of organisms. A herald of this new discipline is Craig Venter who aims to create an artificial microorganism with the minimal genome compatible with life and to implement into it different 'functional modules' to generate new micro-organisms adapted to specific tasks. Synthetic biology is based on the possibilities raised by genetic engineering, but it aims to engineer organisms, and not simply to modify them, mimicking the practice of computer engineers. Three points will be discussed: In what regard does synthetic biology represent a new epistemology of the life sciences? What are the relations between synthetic biology and evolutionary biology? What is the raison d'être of synthetic biology as a discipline independent of nanotechnologies?

  10. Synthetic biology: a utilitarian perspective.

    Science.gov (United States)

    Smith, Kevin

    2013-10-01

    I examine the positive and negative features of synthetic biology ('SynBio') from a utilitarian ethical perspective. The potential beneficial outcomes from SynBio in the context of medicine are substantial; however it is not presently possible to predict precise outcomes due to the nascent state of the field. Potential negative outcomes from SynBio also exist, including iatrogenesis and bioterrorism; however it is not yet possible to quantify these risks. I argue that the application of a 'precautionary' approach to SynBio is ethically fraught, as is the notion that SynBio-associated knowledge ought to be restricted. I conclude that utilitarians ought to support a broadly laissez-faire stance in respect of SynBio. PMID:24010857

  11. Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering.

    Science.gov (United States)

    Vijayachandran, Lakshmi S; Thimiri Govinda Raj, Deepak B; Edelweiss, Evelina; Gupta, Kapil; Maier, Josef; Gordeliy, Valentin; Fitzgerald, Daniel J; Berger, Imre

    2013-01-01

    Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach. PMID:23328086

  12. Bottom-up assembly of metallic germanium

    Science.gov (United States)

    Scappucci, Giordano; Klesse, Wolfgang M.; Yeoh, Lareine A.; Carter, Damien J.; Warschkow, Oliver; Marks, Nigel A.; Jaeger, David L.; Capellini, Giovanni; Simmons, Michelle Y.; Hamilton, Alexander R.

    2015-08-01

    Extending chip performance beyond current limits of miniaturisation requires new materials and functionalities that integrate well with the silicon platform. Germanium fits these requirements and has been proposed as a high-mobility channel material, a light emitting medium in silicon-integrated lasers, and a plasmonic conductor for bio-sensing. Common to these diverse applications is the need for homogeneous, high electron densities in three-dimensions (3D). Here we use a bottom-up approach to demonstrate the 3D assembly of atomically sharp doping profiles in germanium by a repeated stacking of two-dimensional (2D) high-density phosphorus layers. This produces high-density (1019 to 1020 cm-3) low-resistivity (10-4Ω · cm) metallic germanium of precisely defined thickness, beyond the capabilities of diffusion-based doping technologies. We demonstrate that free electrons from distinct 2D dopant layers coalesce into a homogeneous 3D conductor using anisotropic quantum interference measurements, atom probe tomography, and density functional theory.

  13. Synthetic biology: programming cells for biomedical applications.

    Science.gov (United States)

    Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

    2012-01-01

    The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry. PMID:23502560

  14. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    Directory of Open Access Journals (Sweden)

    Giordano Emanuele

    2010-11-01

    Full Text Available Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. Conclusions This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.

  15. Word selection affects perceptions of synthetic biology

    Directory of Open Access Journals (Sweden)

    Tonidandel Scott

    2011-07-01

    Full Text Available Abstract Members of the synthetic biology community have discussed the significance of word selection when describing synthetic biology to the general public. In particular, many leaders proposed the word "create" was laden with negative connotations. We found that word choice and framing does affect public perception of synthetic biology. In a controlled experiment, participants perceived synthetic biology more negatively when "create" was used to describe the field compared to "construct" (p = 0.008. Contrary to popular opinion among synthetic biologists, however, low religiosity individuals were more influenced negatively by the framing manipulation than high religiosity people. Our results suggest that synthetic biologists directly influence public perception of their field through avoidance of the word "create".

  16. Opportunities for microfluidic technologies in synthetic biology

    OpenAIRE

    Gulati, Shelly; Rouilly, Vincent; Niu, Xize; Chappell, James; Kitney, Richard I.; Edel, Joshua B.; Paul S Freemont; deMello, Andrew J.

    2009-01-01

    We introduce microfluidics technologies as a key foundational technology for synthetic biology experimentation. Recent advances in the field of microfluidics are reviewed and the potential of such a technological platform to support the rapid development of synthetic biology solutions is discussed.

  17. Mammalian synthetic biology: emerging medical applications

    OpenAIRE

    Kis, Zoltán; Pereira, Hugo Sant'Ana; Homma, Takayuki; Pedrigi, Ryan M.; Krams, Rob

    2015-01-01

    In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON–OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and tog...

  18. Grand challenges in space synthetic biology.

    Science.gov (United States)

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

    2015-12-01

    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. PMID:26631337

  19. Synthetic biology: mapping the scientific landscape.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves.

  20. Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry

    OpenAIRE

    Harris, D. Calvin; Jewett, Michael C.

    2012-01-01

    Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology ...

  1. Grand challenges in space synthetic biology

    OpenAIRE

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

    2015-01-01

    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...

  2. Bridging the gap between systems biology and synthetic biology

    OpenAIRE

    Liu, Di; Hoynes-O’Connor, Allison; Zhang, Fuzhong

    2013-01-01

    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, syst...

  3. The 'atom-splitting' moment of synthetic biology: Nuclear physics and synthetic biology share common features

    OpenAIRE

    Valentine, Alex J; Kleinert, Aleysia; Verdier, Jerome

    2012-01-01

    Synthetic biology and nuclear physics share many commonalities in terms of public perception and funding. Synthetic biologists could learn valuable lessons from the history of the atomic bomb and nuclear power.

  4. Upgrading protein synthesis for synthetic biology

    OpenAIRE

    O’Donoghue, Patrick; Ling, Jiqiang; Wang, Yane-Shih; Söll, Dieter

    2013-01-01

    Genetic code expansion for synthesis of proteins containing noncanonical amino acids is a rapidly growing field in synthetic biology. Creating optimal orthogonal translation systems will require re-engineering central components of the protein synthesis machinery on the basis of a solid mechanistic biochemical understanding of the synthetic process.

  5. Standardization for natural product synthetic biology.

    Science.gov (United States)

    Zhao, Huimin; Medema, Marnix H

    2016-08-27

    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 synthetic biology, focusing on standardization of data on biosynthetic pathways and gene clusters, as well as the role of standardization in the process of biosynthetic gene cluster engineering. PMID:27313083

  6. Standardization for natural product synthetic biology

    OpenAIRE

    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 synthetic biology, focusing on standardization of data on biosynthetic pathways and gene clusters, as well as the role of standardization in the process of biosynthetic gene cluster engineering.

  7. Informing Biological Design by Integration of Systems and Synthetic Biology

    OpenAIRE

    Smolke, Christina D.; Silver, Pamela A.

    2011-01-01

    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.

  8. Bottom-up Attention Orienting in Young Children with Autism

    Science.gov (United States)

    Amso, Dima; Haas, Sara; Tenenbaum, Elena; Markant, Julie; Sheinkopf, Stephen J.

    2014-01-01

    We examined the impact of simultaneous bottom-up visual influences and meaningful social stimuli on attention orienting in young children with autism spectrum disorders (ASDs). Relative to typically-developing age and sex matched participants, children with ASDs were more influenced by bottom-up visual scene information regardless of whether…

  9. Bridging the gap between systems biology and synthetic biology

    Directory of Open Access Journals (Sweden)

    FuzhongZhang

    2013-07-01

    Full Text Available Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics and metabolomics, aiming to fill the gap between systems and synthetic biology.

  10. Synthetic biology and biosecurity: challenging the "myths".

    Science.gov (United States)

    Jefferson, Catherine; Lentzos, Filippa; Marris, Claire

    2014-01-01

    Synthetic biology, a field that aims to "make biology easier to engineer," is routinely described as leading to an increase in the "dual-use" threat, i.e., the potential for the same scientific research to be "used" for peaceful purposes or "misused" for warfare or terrorism. Fears have been expressed that the "de-skilling" of biology, combined with online access to the genomic DNA sequences of pathogenic organisms and the reduction in price for DNA synthesis, will make biology increasingly accessible to people operating outside well-equipped professional research laboratories, including people with malevolent intentions. The emergence of do-it-yourself (DIY) biology communities and of the student iGEM competition has come to epitomize this supposed trend toward greater ease of access and the associated potential threat from rogue actors. In this article, we identify five "myths" that permeate discussions about synthetic biology and biosecurity, and argue that they embody misleading assumptions about both synthetic biology and bioterrorism. We demonstrate how these myths are challenged by more realistic understandings of the scientific research currently being conducted in both professional and DIY laboratories, and by an analysis of historical cases of bioterrorism. We show that the importance of tacit knowledge is commonly overlooked in the dominant narrative: the focus is on access to biological materials and digital information, rather than on human practices and institutional dimensions. As a result, public discourse on synthetic biology and biosecurity tends to portray speculative scenarios about the future as realities in the present or the near future, when this is not warranted. We suggest that these "myths" play an important role in defining synthetic biology as a "promissory" field of research and as an "emerging technology" in need of governance. PMID:25191649

  11. Bottom-up Initiatives for Photovoltaic: Incentives and Barriers

    Directory of Open Access Journals (Sweden)

    Kathrin Reinsberger

    2014-06-01

    Full Text Available When facing the challenge of restructuring the energy system, bottom-up initiatives can aid the diffusion of decentralized and clean energy technologies. We focused here on a bottom-up initiative of citizen-funded and citizen-operated photovoltaic power plants. The project follows a case study-based approach and examines two different community initiatives. The aim is to investigate the potential incentives and barriers relating to participation or non-participation in predefined community PV projects. Qualitative, as well as quantitative empirical research was used to examine the key factors in the further development of bottom-up initiatives as contributors to a general energy transition.

  12. WISB: Warwick Integrative Synthetic Biology Centre.

    Science.gov (United States)

    McCarthy, John

    2016-06-15

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. PMID:27284024

  13. Nanoelectronics: Thermoelectric Phenomena in «Bottom-Up» Approach

    OpenAIRE

    Yu.A. Kruglyak; P.A. Kondratenko; Yu.М. Lopatkin

    2014-01-01

    Thermoelectric phenomena of Seebeck and Peltier, quality indicators and thermoelectric optimization, ballistic and diffusive phonon heat current are discussed in the frame of the «bottom-up» approach of modern nanoelectronics.

  14. Nanoelectronics: Thermoelectric Phenomena in «Bottom-Up» Approach

    Directory of Open Access Journals (Sweden)

    Yu.A. Kruglyak

    2014-04-01

    Full Text Available Thermoelectric phenomena of Seebeck and Peltier, quality indicators and thermoelectric optimization, ballistic and diffusive phonon heat current are discussed in the frame of the «bottom-up» approach of modern nanoelectronics.

  15. Synthetic Tools for Molecular Biology

    OpenAIRE

    Dervan, Peter B.

    1988-01-01

    Chemistry has made tremendous advances over the past four decades in the broad fields of synthesis and understanding chemical reactivity. In that same time span, a series of revolutionary events occurred in biology. First came the discovery of the double helical structure of DNA in the 1950s by Watson and Crick. This discovery allowed the elucidation of the mechanisms of DNA replication -- how DNA makes copies of itself -- and DNA transcription and translation -- the processes that allow the ...

  16. Build to understand: synthetic approaches to biology.

    Science.gov (United States)

    Wang, Le-Zhi; Wu, Fuqing; Flores, Kevin; Lai, Ying-Cheng; Wang, Xiao

    2016-04-18

    In this review we discuss how synthetic biology facilitates the task of investigating genetic circuits that are observed in naturally occurring biological systems. Specifically, we give examples where experimentation with synthetic gene circuits has been used to understand four fundamental mechanisms intrinsic to development and disease: multistability, stochastic gene expression, oscillations, and cell-cell communication. Within each area, we also discuss how mathematical modeling has been employed as an essential tool to guide the design of novel gene circuits and as a theoretical basis for exploring circuit topologies exhibiting robust behaviors in the presence of noise. PMID:26686885

  17. Synthetic Biology: Applications in the Food Sector.

    Science.gov (United States)

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

    2016-08-17

    Synthetic biology also termed as "genomic alchemy" represents a powerful area of science that is based on the convergence of biological sciences with systems engineering. It has been fittingly described as "moving from reading the genetic code to writing it" as it focuses on building, modeling, designing and fabricating novel biological systems using customized gene components that result in artificially created genetic circuitry. The scientifically compelling idea of the technological manipulation of life has been advocated since long time. Realization of this idea has gained momentum with development of high speed automation and the falling cost of gene sequencing and synthesis following the completion of the human genome project. Synthetic biology will certainly be instrumental in shaping the development of varying areas ranging from biomedicine, biopharmaceuticals, chemical production, food and dairy quality monitoring, packaging, and storage of food and dairy products, bioremediation and bioenergy production, etc. However, potential dangers of using synthetic life forms have to be acknowledged and adoption of policies by the scientific community to ensure safe practice while making important advancements in the ever expanding field of synthetic biology is to be fully supported and implemented. PMID:25365334

  18. Bottom-Up Synthesis and Sensor Applications of Biomimetic Nanostructures

    Directory of Open Access Journals (Sweden)

    Li Wang

    2016-01-01

    Full Text Available The combination of nanotechnology, biology, and bioengineering greatly improved the developments of nanomaterials with unique functions and properties. Biomolecules as the nanoscale building blocks play very important roles for the final formation of functional nanostructures. Many kinds of novel nanostructures have been created by using the bioinspired self-assembly and subsequent binding with various nanoparticles. In this review, we summarized the studies on the fabrications and sensor applications of biomimetic nanostructures. The strategies for creating different bottom-up nanostructures by using biomolecules like DNA, protein, peptide, and virus, as well as microorganisms like bacteria and plant leaf are introduced. In addition, the potential applications of the synthesized biomimetic nanostructures for colorimetry, fluorescence, surface plasmon resonance, surface-enhanced Raman scattering, electrical resistance, electrochemistry, and quartz crystal microbalance sensors are presented. This review will promote the understanding of relationships between biomolecules/microorganisms and functional nanomaterials in one way, and in another way it will guide the design and synthesis of biomimetic nanomaterials with unique properties in the future.

  19. Synthetic biology and biosecurity: challenging the "myths"

    OpenAIRE

    Jefferson, C.; Lentzos, F.; Marris, C.

    2014-01-01

    Synthetic biology, a field that aims to "make biology easier to engineer," is routinely described as leading to an increase in the "dual-use" threat, i.e., the potential for the same scientific research to be "used" for peaceful purposes or "misused" for warfare or terrorism. Fears have been expressed that the "de-skilling" of biology, combined with online access to the genomic DNA sequences of pathogenic organisms and the reduction in price for DNA synthesis, will make biology increasingly a...

  20. A Personalist Ontological Approach to Synthetic Biology.

    Science.gov (United States)

    Gómez-Tatay, Lucía; Hernández-Andreu, José Miguel; Aznar, Justo

    2016-07-01

    Although synthetic biology is a promising discipline, it also raises serious ethical questions that must be addressed in order to prevent unwanted consequences and to ensure that its progress leads toward the good of all. Questions arise about the role of this discipline in a possible redefinition of the concept of life and its creation. With regard to the products of synthetic biology, the moral status that they should be given as well as the ethically correct way to behave towards them are not clear. Moreover, risks that could result from a misuse of this technology or from an accidental release of synthetic organisms into the environment cannot be ignored; concerns about biosecurity and biosafety appear. Here we discuss these and other questions from a personalist ontological framework, which defends human life as an essential value and proposes a set of principles to ensure the safeguarding of this and other values that are based on it. PMID:26644292

  1. Synthetic biology advances for pharmaceutical production

    OpenAIRE

    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.

  2. 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 synt

  3. Preparing Synthetic Biology for the World

    Directory of Open Access Journals (Sweden)

    Gerd H.G. Moe-Behrens

    2013-01-01

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

  4. Synthetic biology and microdevices: a powerful combination

    OpenAIRE

    Venken, Lyn; Marchal, Kathleen; Vanderleyden, Jos

    2013-01-01

    Recent developments demonstrate that the combination of microbiology with micro-and nanoelectronics is a successful approach to develop new miniaturized sensing devices and other technologies. In the last decade, there has been a shift from the optimization of the abiotic components, for example, the chip, to the improvement of the processing capabilities of cells through genetic engineering. The synthetic biology approach will not only give rise to systems with new functionalities, but will ...

  5. Infobiotics : computer-aided synthetic systems biology

    OpenAIRE

    Blakes, Jonathan

    2013-01-01

    Until very recently Systems Biology has, despite its stated goals, been too reductive in terms of the models being constructed and the methods used have been, on the one hand, unsuited for large scale adoption or integration of knowledge across scales, and on the other hand, too fragmented. The thesis of this dissertation is that better computational languages and seamlessly integrated tools are required by systems and synthetic biologists to enable them to meet the significant challenges inv...

  6. Biologic and synthetic skin substitutes: An overview

    Directory of Open Access Journals (Sweden)

    Halim Ahmad

    2010-10-01

    Full Text Available The current trend of burn wound care has shifted to more holistic approach of improvement in the long-term form and function of the healed burn wounds and quality of life. This has demanded the emergence of various skin substitutes in the management of acute burn injury as well as post burn reconstructions. Skin substitutes have important roles in the treatment of deep dermal and full thickness wounds of various aetiologies. At present, there is no ideal substitute in the market. Skin substitutes can be divided into two main classes, namely, biological and synthetic substitutes. The biological skin substitutes have a more intact extracellular matrix structure, while the synthetic skin substitutes can be synthesised on demand and can be modulated for specific purposes. Each class has its advantages and disadvantages. The biological skin substitutes may allow the construction of a more natural new dermis and allow excellent re-epithelialisation characteristics due to the presence of a basement membrane. Synthetic skin substitutes demonstrate the advantages of increase control over scaffold composition. The ultimate goal is to achieve an ideal skin substitute that provides an effective and scar-free wound healing.

  7. An integrated top-down and bottom-up strategy for characterization protein isoforms and modifications

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Si; Tolic, Nikola; Tian, Zhixin; Robinson, Errol W.; Pasa-Tolic, Ljiljana

    2011-04-15

    Bottom-up and top-down strategies are two commonly used methods for mass spectrometry (MS) based protein identification; each method has its own advantages and disadvantages. In this chapter, we describe an integrated top-down and bottom-up approach facilitated by concurrent liquid chromatography-mass spectrometry (LC-MS) analysis and fraction collection for comprehensive high-throughput intact protein profiling. The approach employs a high resolution reversed phase (RP) LC separation coupled with LC eluent fraction collection and concurrent on-line MS with a high field (12 Tesla) Fourier-transform ion cyclotron resonance (FTICR) mass spectrometer. Protein elusion profiles and tentative modified protein identification are made using detected intact protein mass in conjunction with bottom-up protein identifications from the enzymatic digestion and analysis of corresponding LC fractions. Specific proteins of biological interest are incorporated into a target ion list for subsequent off-line gas-phase fragmentation that uses an aliquot of the original collected LC fraction, an aliquot of which was also used for bottom-up analysis.

  8. Two Dimensional Polymerization of Graphene Oxide: Bottom-up Approach

    OpenAIRE

    Atanasov, Victor; Russev, Stoyan; Lyutov, Lyudmil; Zagranyarski, Yulian; Dimitrova, Iglika; Avdeev, Georgy; Avramova, Ivalina; Vulcheva, Evgenia; Kirilov, Kiril; Tzonev, Atanas; Abrashev, Miroslav; Tsutsumanova, Gichka

    2012-01-01

    We demonstrate a bottom-up synthesis of structures similar to graphene oxide via a two dimensional polymerization. Experimental evidence and discussion are conveyed as well as a general framework for this two dimensional polymerization. The proposed morphologies and lattice structures of these graphene oxides are derived from aldol condensation of alternating three nucleophilic and three electrophilic centers of benzenetriol.

  9. Diffusion of synthetic biology: a challenge to biosafety

    OpenAIRE

    Schmidt, Markus

    2008-01-01

    One of the main aims of synthetic biology is to make biology easier to engineer. Major efforts in synthetic biology are made to develop a toolbox to design biological systems without having to go through a massive research and technology process. With this “de-skilling” agenda, synthetic biology might finally unleash the full potential of biotechnology and spark a wave of innovation, as more and more people have the necessary skills to engineer biology. But this ultimate domestication of biol...

  10. Synthetic biology for pharmaceutical drug discovery

    Directory of Open Access Journals (Sweden)

    Trosset JY

    2015-12-01

    Full Text Available Jean-Yves Trosset,1 Pablo Carbonell2,3 1Bioinformation Research Laboratory, Sup’Biotech, Villejuif, France; 2Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK; 3Department of Experimental and Health Sciences (DCEXS, Research Programme on Biomedical Informatics (GRIB, Hospital del Mar Medical Research Institute (IMIM, Universitat Pompeu Fabra (UPF, Barcelona, Spain Abstract: Synthetic biology (SB is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell–cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity. Keywords: metabolic engineering, plant synthetic biology, natural products, synthetic quorum sensing, drug resistance

  11. Synthetic biology and its regulation in the European Union.

    Science.gov (United States)

    Buhk, Hans-Jörg

    2014-12-25

    The term synthetic biology is used increasingly, but without a clear definition. Most of the recent research carried out in this field is genetic engineering, as defined by current GMO-legislation in the EU. Synthetic biology has developed its own language. In vitro synthesis of DNA also carries the label synthetic biology. It is important to analyze whether present and future activities of synthetic biology are within the scope of existing EU-legislation. PMID:24572655

  12. Synthetic biology: An emerging research field in China

    OpenAIRE

    Pei, Lei; Schmidt, Markus; Wei, Wei

    2011-01-01

    Synthetic biology is considered as an emerging research field that will bring new opportunities to biotechnology. There is an expectation that synthetic biology will not only enhance knowledge in basic science, but will also have great potential for practical applications. Synthetic biology is still in an early developmental stage in China. We provide here a review of current Chinese research activities in synthetic biology and its different subfields, such as research on genetic circuits, mi...

  13. 75 FR 52752 - Request for Comments on Synthetic Biology

    Science.gov (United States)

    2010-08-27

    ... HUMAN SERVICES Request for Comments on Synthetic Biology AGENCY: Department of Health and Human Services... public comment on the emerging science of synthetic biology, including its potential applications and... synthetic biology. The President asked the Commission to address this topic on May 20, 2010, following...

  14. Synthetic biology, patenting, health and global justice

    OpenAIRE

    Belt, van den, H.

    2011-01-01

    The legal and moral issues that synthetic biology (SB) and its medical applications are likely to raise with regard to intellectual property (IP) and patenting are best approached through the lens of a theoretical framework highlighting the “co-construction” or “co-evolution” of patent law and technology. The current situation is characterized by a major contest between the so-called IP frame and the access-to-knowledge frame. In SB this contest is found in the contrasting approaches of Craig...

  15. Assessment and management of biosafety in synthetic biology

    OpenAIRE

    Zhengjun Guan; Lei Pei; Markus Schmidt; Wei Wei

    2012-01-01

    While having developed into one of the most dynamic fields of the life sciences, synthetic biology may pose potential risks to the environment and human health. Based on current national and international risk assessment methods and current regulation of synthetic biology, we reviewed risk assessment in relation to synthetic biology’s research subfields (such as DNA-based biocircuits, minimal genome, protocells and chemical synthetic biology), its relation with biosafety engineering, its effe...

  16. Bottom-up effects on attention capture and choice

    DEFF Research Database (Denmark)

    Peschel, Anne; Orquin, Jacob Lund; Mueller Loose, Simone

    information available to form a decision. Does changing one visual cue in the stimulus set affect attention towards this cue and what does that mean for the choice outcome? To address this, we conducted a combined eye tracking and choice experiment in a consumer choice setting with visual shelf simulations of......Attention processes and decision making are accepted to be closely linked together because only information that is attended to can be incorporated in the decision process. Little is known however, to which extent bottom-up processes of attention affect stimulus selection and therefore the...... different product categories. Surface size and visual saliency of a product label were manipulated to determine bottom-up effects on attention and choice. Results show a strong and significant increase in attention in terms of fixation likelihood towards product labels which are larger and more visually...

  17. Bottom-up approaches for defining future climate mitigation commitments

    Energy Technology Data Exchange (ETDEWEB)

    Den Elzen, M.G.J.; Berk, M.M.

    2004-07-01

    This report analyses a number of alternative, bottom-up approaches, i.e. technology and performance standards; technology Research and Development agreements, sectoral targets (national /transnational), sector based Clean Development Mechanism (CDM), and sustainable development policies and measures (SD-PAMs). Included are technology and performance standards; technology, research and development agreements, sectoral targets (national /transnational), and sector-based (CDM), and sustainable development policies and measures (SD-PAMs). A more bottom-up approach for defining national emission targets, the so-called Triptych approach is also explored and compared with more top-down types of approaches (Multi-Stage and Contraction and Convergence) based on a quantitative and qualitative analysis. While bottom-up approaches are concluded as being valuable components of a future climate regime, they, in themselves, do not seem to offer a real alternative to emission reduction and limitation targets, as they provide little certainty about the overall environmental effectiveness of climate policies. In comparison with Multi-stage and the C and C approaches, the global Triptych approach offers the opportunity of early participation by developing countries' without the risk of creating large amounts of surplus emissions as in C and C; in using the approach we also avoid the need for dividing up the non-Annex I countries as in Multi-Stage. However, there will be substantial implementation problems related to the institutional and technical capabilities required. Thus it would seem better to exclude the least developing countries and have them first participate in some of the alternative bottom-up approaches.

  18. Magic for Filter Optimization in Dynamic Bottom-up Processing

    CERN Document Server

    Minnen, G

    1996-01-01

    Off-line compilation of logic grammars using Magic allows an incorporation of filtering into the logic underlying the grammar. The explicit definite clause characterization of filtering resulting from Magic compilation allows processor independent and logically clean optimizations of dynamic bottom-up processing with respect to goal-directedness. Two filter optimizations based on the program transformation technique of Unfolding are discussed which are of practical and theoretical interest.

  19. Bottom-up Budgeting FY 2015 Assessment: Camarines Sur

    OpenAIRE

    Maramot, Joyce Anne; Yasay, Donald B.; de Guzman, Reinier

    2015-01-01

    Bottom-up budgeting (BUB) is an adaptation of the participatory budgeting model in identifying and providing solutions to poverty at the municipal/city level. Leaders of civil society organizations engage with LGU officials in formulating a poverty alleviation plan to be considered in preparing the budget of national agencies the following fiscal year. This paper reports on how the guideline was implemented in three municipalities in Camarines Sur. The study then presents suggestions and reco...

  20. Mapping the Emergence of Synthetic Biology.

    Science.gov (United States)

    Raimbault, Benjamin; Cointet, Jean-Philippe; Joly, Pierre-Benoît

    2016-01-01

    In this paper, we apply an original scientometric analyses to a corpus comprising synthetic biology (SynBio) publications in Thomson Reuters Web of Science to characterize the emergence of this new scientific field. Three results were drawn from this empirical investigation. First, despite the exponential growth of publications, the study of population level statistics (newcomers proportion, collaboration network structure) shows that SynBio has entered a stabilization process since 2010. Second, the mapping of textual and citational networks shows that SynBio is characterized by high heterogeneity and four different approaches: the central approach, where biobrick engineering is the most widespread; genome engineering; protocell creation; and metabolic engineering. We suggest that synthetic biology acts as an umbrella term allowing for the mobilization of resources, and also serves to relate scientific content and promises of applications. Third, we observed a strong intertwinement between epistemic and socio-economic dynamics. Measuring scientific production and impact and using structural analysis data, we identified a core set of mostly American scientists. Biographical analysis shows that these central and influential scientists act as "boundary spanners," meaning that their importance to the field lies not only in their academic contributions, but also in their capacity to interact with other social spaces that are outside the academic sphere. PMID:27611324

  1. Synthetic biology analysed tools for discussion and evaluation

    CERN Document Server

    2016-01-01

    Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic bi...

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

    Science.gov (United States)

    Rodríguez López, Blanca

    2014-01-01

    Synthetic biology is a new discipline that is twofold: firstly it offers the promise to pay benefits that can alleviate some of the ills that plague mankind; On the other hand, like all technologies, holds risks. Given these, the most critical and concerned about the risks, invoke the application of the precautionary principle, common in cases where an activity or new technology creates risks to the environment and/or human health, but far from universally accepted happens to be currently one of the most controversial principles. In this paper the question of the risks and benefits of synthetic biology and the relevance of applying the precautionary principle are analyzed. To do this we proceed as follows. The first part focuses on synthetic biology. At first, this discipline is characterized, with special attention to what is novel compared to the known as "genetic engineering". In the second stage both the benefits and the risks associated with it are discussed. The first part concludes with a review of the efforts currently being made to control or minimize the risks. The second part aims to analyze the precautionary principle and its possible relevance to the case of Synthetic Biology. At first, the different versions and interpretations of the principle and the various criticisms of which has been the subject are reviewed. Finally, after discarding the Precautionary Principle as an useful tool, it is seen as more appropriate some recent proposals to treat technologies that take into account not only risks but also their benefits. PMID:25845210

  3. 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...

  4. A Bottom-Up Approach to SUSY Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Horn, Claus; /SLAC

    2011-11-11

    This paper proposes a new way to do event generation and analysis in searches for new physics at the LHC. An abstract notation is used to describe the new particles on a level which better corresponds to detector resolution of LHC experiments. In this way the SUSY discovery space can be decomposed into a small number of eigenmodes each with only a few parameters, which allows to investigate the SUSY parameter space in a model-independent way. By focusing on the experimental observables for each process investigated the Bottom-Up Approach allows to systematically study the boarders of the experimental efficiencies and thus to extend the sensitivity for new physics.

  5. Recent progress in backreacted bottom-up holographic QCD

    Energy Technology Data Exchange (ETDEWEB)

    Järvinen, Matti [Laboratoire de Physique Théorique, École Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05 (France)

    2016-01-22

    Recent progress in constructing holographic models for QCD is discussed, concentrating on the bottom-up models which implement holographically the renormalization group flow of QCD. The dynamics of gluons can be modeled by using a string-inspired model termed improved holographic QCD, and flavor can be added by introducing space filling branes in this model. The flavor fully backreacts to the glue in the Veneziano limit, giving rise to a class of models which are called V-QCD. The phase diagrams and spectra of V-QCD are in good agreement with results for QCD obtained by other methods.

  6. Wikipedia: organisation from a bottom-up approach

    OpenAIRE

    Spek, Sander; Postma, Eric; Herik, H. Jaap van den

    2006-01-01

    Wikipedia can be considered as an extreme form of a self-managing team, as a means of labour division. One could expect that this bottom-up approach, with the absense of top-down organisational control, would lead to a chaos, but our analysis shows that this is not the case. In the Dutch Wikipedia, an integrated and coherent data structure is created, while at the same time users succeed in distributing roles by self-selection. Some users focus on an area of expertise, while others edit over ...

  7. The Interplay of Top-Down and Bottom-Up

    DEFF Research Database (Denmark)

    Winkler, Till; Brown, Carol V.; Ozturk, Pinar

    2014-01-01

    The exchange of patient health information across different organizations involved in healthcare delivery has potential benefits for a wide range of stakeholders. However, many governments in Europe and in the U.S. have, despite both top-down and bottom-up initiatives, experienced major barriers in...... achieving sustainable models for implementing health information exchange (HIE) throughout their healthcare systems. In the case of the U.S., three years after stimulus funding allocated as part of the 2009 HITECH Act, the extent to which government funding will be needed to sustain health information...

  8. Distinguishing Top-Down From Bottom-Up Effects

    OpenAIRE

    Shea, Nicholas

    2015-01-01

    The distinction between top-down and bottom-up effects is widely relied on in experimental psychology. However, there is an important problem with the way it is normally defined. Top-down effects are effects of previously-stored information on processing the current input. But on the face of it that includes the information that is implicit in the operation of any psychological process – in its dispositions to transition from some types of representational state to others. This paper suggests...

  9. Bottom-up graphene nanoribbon field-effect transistors

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, Patrick B. [Applied Science and Technology, University of California, Berkeley, California 94720 (United States); Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720 (United States); Pedramrazi, Zahra [Department of Physics, University of California, Berkeley, California 94720 (United States); Madani, Ali [Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720 (United States); Chen, Yen-Chia; Crommie, Michael F. [Department of Physics, University of California, Berkeley, California 94720 (United States); Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720 (United States); Oteyza, Dimas G. de [Department of Physics, University of California, Berkeley, California 94720 (United States); Centro de Física de Materiales CSIC/UPV-EHU-Materials Physics Center, San Sebastián E-20018 (Spain); Chen, Chen [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Fischer, Felix R. [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720 (United States); Bokor, Jeffrey, E-mail: jbokor@eecs.berkeley.edu [Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720 (United States); Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720 (United States)

    2013-12-16

    Recently developed processes have enabled bottom-up chemical synthesis of graphene nanoribbons (GNRs) with precise atomic structure. These GNRs are ideal candidates for electronic devices because of their uniformity, extremely narrow width below 1 nm, atomically perfect edge structure, and desirable electronic properties. Here, we demonstrate nano-scale chemically synthesized GNR field-effect transistors, made possible by development of a reliable layer transfer process. We observe strong environmental sensitivity and unique transport behavior characteristic of sub-1 nm width GNRs.

  10. Synthetic biology as a source of global health innovation

    OpenAIRE

    Rooke, Jenny

    2013-01-01

    Synthetic biology has the potential to contribute breakthrough innovations to the pursuit of new global health solutions. Wishing to harness the emerging tools of synthetic biology for the goals of global health, in 2011 the Bill & Melinda Gates Foundation put out a call for grant applications to “Apply Synthetic Biology to Global Health Challenges” under its “Grand Challenges Explorations” program. A highly diverse pool of over 700 applications was received. Proposed applications of syntheti...

  11. Eukaryotic Systems Broaden the Scope of Synthetic Biology

    OpenAIRE

    Haynes, Karmella A.; Silver, Pamela A.

    2009-01-01

    Synthetic biology aims to engineer novel cellular functions by assembling well-characterized molecular parts (i.e., nucleic acids and proteins) into biological “devices” that exhibit predictable behavior. Recently, efforts in eukaryotic synthetic biology have sprung from foundational work in bacteria. Designing synthetic circuits to operate reliably in the context of differentiating and morphologically complex cells presents unique challenges and opportunities for progress in the field. This ...

  12. The Ethics of Synthetic Biology: Outlining the Agenda

    OpenAIRE

    Deplazes, A.; Ganguli-Mitra, A; Biller-Andorno, N

    2009-01-01

    The projects and aims of synthetic biology raise various ethical questions, challenging some of our basic moral concepts. This chapter addresses these issues in three steps. First, we present an overview of different types of ethical issues related to synthetic biology by assigning them to three main categories: method-related, application-related, and distribution-related issues. The first category concerns the procedure and aims of synthetic biology, the second deals with certain planned ap...

  13. Robust synthetic biology design: stochastic game theory approach

    OpenAIRE

    Chen, Bor-Sen; Chang, Chia-Hung; Lee, Hsiao-Ching

    2009-01-01

    Motivation: Synthetic biology is to engineer artificial biological systems to investigate natural biological phenomena and for a variety of applications. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to uncertain initial conditions and disturbances of extra-cellular environments on the host cell. At present, how to design a robust synthetic gene network to work properly under these uncertain factors is the m...

  14. Athena: Modular CAM/CAD Software for Synthetic Biology

    OpenAIRE

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

    2009-01-01

    Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling techniques in conjunction with molecular biology techniques have been successful in constructing biological devices such as switches, oscillators, and gates. The ambition of synthetic biology is to construct complex systems from such fundamental devices, much in the same way electronic circuits are bu...

  15. Inverse Magnetic Catalysis in Bottom-Up Holographic QCD

    CERN Document Server

    Evans, Nick; Scott, Marc

    2016-01-01

    We explore the effect of magnetic field on chiral condensation in QCD via a simple bottom up holographic model which inputs QCD dynamics through the running of the anomalous dimension of the quark bilinear. Bottom up holography is a form of effective field theory and we use it to explore the dependence on the coefficients of the two lowest order terms linking the magnetic field and the quark condensate. In the massless theory, we identify a region of parameter space where magnetic catalysis occurs at zero temperature but inverse magnetic catalysis at temperatures of order the thermal phase transition. The model shows similar non-monotonic behaviour in the condensate with B at intermediate T as the lattice data. This behaviour is due to the separation of the meson melting and chiral transitions in the holographic framework. The introduction of quark mass raises the scale of B where inverse catalysis takes over from catalysis until the inverse catalysis lies outside the regime of validity of the effective descr...

  16. 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.

  17. Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Ferrer, Daniel; Petritis, Konstantinos; Robinson, Errol W.; Hixson, Kim K.; Tian, Zhixin; Lee, Jung Hwa; Lee, Sang-Won; Tolic, Nikola; Weitz, Karl K.; Belov, Mikhail E.; Smith, Richard D.; Pasa-Tolic, Ljiljana

    2011-02-01

    Integrated top-down bottom-up proteomics combined with online digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to highthroughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications (PTMs). Herein, we describe recent efforts towards efficient integration of bottom-up and top-down LCMS based proteomic strategies. Since most proteomic platforms (i.e. LC systems) operate in acidic environments, we exploited the compatibility of the pepsin (i.e. the enzyme’s natural acidic activity) for the integration of bottom-up and top-down proteomics. Pressure enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an offline mode using a Barocycler or an online mode using a modified high pressure LC system referred to as a fast online digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultra-rapid integrated bottom-up top-down proteomic strategy employing a standard mixture of proteins and a monkey pox virus proteome.

  18. From bottom-up approaches to levels of organization and extended critical transitions

    Directory of Open Access Journals (Sweden)

    Giuseppe eLongo

    2012-07-01

    Full Text Available Biological thinking is structured by the notion of level of organization. We will show that this notion acquires a precise meaning in critical phenomena: they disrupt, by the appearance of infinite quantities, the mathematical (possibly equational determination at a given level, when moving at an ``higher'' one. As a result, their analysis cannot be called genuinely bottom-up, even though it remains upward in a restricted sense.At the same time, criticality and related phenomena are very common in biology. Because of this, we claim that bottom-up approaches are not sufficient, in principle, to capture biological phenomena. In the second part of this paper, following the work of Francis Bailly, we discuss a strong criterium of level transition. The core idea of the criterium is to start from the breaking of the symmetries and determination at a ``first'' level in order to ``move'' at the others. If biological phenomena have multiple, emph{sustained} levels of organization in this sense, then they should be interpreted as emph{extended} critical transitions.

  19. Directed Evolution: An Evolving and Enabling Synthetic Biology Tool

    OpenAIRE

    Cobb, Ryan E.; Si, Tong; Zhao, Huimin

    2012-01-01

    Synthetic biology, with its goal of designing biological entities for wide-ranging purposes, remains a field of intensive research interest. However, the vast complexity of biological systems has heretofore rendered rational design prohibitively difficult. As a result, directed evolution remains a valuable tool for synthetic biology, enabling the identification of desired functionalities from large libraries of variants. This review highlights the most recent advances in the use of directed e...

  20. Challenges and opportunities in synthetic biology for chemical engineers

    OpenAIRE

    Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

    2012-01-01

    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 opportunitie...

  1. Making the results of bottom-up energy savings comparable

    Directory of Open Access Journals (Sweden)

    Moser Simon

    2012-01-01

    Full Text Available The Energy Service Directive (ESD has pushed forward the issue of energy savings calculations without clarifying the methodological basis. Savings achieved in the Member States are calculated with rather non-transparent and hardly comparable Bottom-up (BU methods. This paper develops the idea of parallel evaluation tracks separating the Member States’ issue of ESD verification and comparable savings calculations. Comparability is ensured by developing a standardised BU calculation kernel for different energy efficiency improvement (EEI actions which simultaneously depicts the different calculation options in a structured way (e.g. baseline definition, system boundaries, double counting. Due to the heterogeneity of BU calculations the approach requires a central database where Member States feed in input data on BU actions according to a predefined structure. The paper demonstrates the proposed approach including a concrete example of application.

  2. Bottom-Up Discrete Symmetries for Cabibbo Mixing

    CERN Document Server

    Varzielas, Ivo de Medeiros; Talbert, Jim

    2016-01-01

    We perform a bottom-up search for discrete non-Abelian symmetries capable of quantizing the Cabibbo angle that parameterizes CKM mixing. Given a particular Abelian symmetry structure in the up and down sectors, we construct representations of the associated residual generators which explicitly depend on the degrees of freedom present in our effective mixing matrix. We then discretize those degrees of freedom and utilize the Groups, Algorithms, Programming (GAP) package to close the associated finite groups. This short study is performed in the context of recent results indicating that, without resorting to special model-dependent corrections, no small-order finite group can simultaneously predict all four parameters of the three-generation CKM matrix and that only groups of $\\mathcal{O}(10^{2})$ can predict the analogous parameters of the leptonic PMNS matrix, regardless of whether neutrinos are Dirac or Majorana particles. Therefore a natural model of flavour might instead incorporate small(er) finite groups...

  3. Scientific Opinion on Risk Assessment of Synthetic Biology.

    Science.gov (United States)

    Epstein, Michelle M; Vermeire, Theo

    2016-08-01

    In 2013, three Scientific Committees of the European Commission (EC) drafted Scientific Opinions on synthetic biology that provide an operational definition and address risk assessment methodology, safety aspects, environmental risks, knowledge gaps, and research priorities. These Opinions contribute to the international discussions on the risk governance for synthetic biology developments. PMID:27234301

  4. Next generation tools to accelerate the synthetic biology process.

    Science.gov (United States)

    Shih, Steve C C; Moraes, Christopher

    2016-05-16

    Synthetic biology follows the traditional engineering paradigm of designing, building, testing and learning to create new biological systems. While such approaches have enormous potential, major challenges still exist in this field including increasing the speed at which this workflow can be performed. Here, we present recently developed microfluidic tools that can be used to automate the synthetic biology workflow with the goal of advancing the likelihood of producing desired functionalities. With the potential for programmability, automation, and robustness, the integration of microfluidics and synthetic biology has the potential to accelerate advances in areas such as bioenergy, health, and biomaterials. PMID:27146265

  5. Cooperativity to increase Turing pattern space for synthetic biology

    OpenAIRE

    Diambra, Luis; Senthivel, Vivek Raj; Menendez, Diego Barcena; Isalan, Mark

    2015-01-01

    It is hard to bridge the gap between mathematical formulations and biological implementations of Turing patterns, yet this is necessary for both understanding and engineering these networks with synthetic biology approaches. Here, we model a reaction–diffusion system with two morphogens in a monostable regime, inspired by components that we recently described in a synthetic biology study in mammalian cells.1 The model employs a single promoter to express both the activator and inhibitor genes...

  6. BUEES:a bottom-up event extraction system

    Institute of Scientific and Technical Information of China (English)

    Xiao DING; Bing QIN; Ting LIU

    2015-01-01

    Traditional event extraction systems focus mainly on event type identifi cation and event participant extraction based on pre-specifi ed event type paradigms and manually annotated corpora. However, different domains have different event type paradigms. When transferring to a new domain, we have to build a new event type paradigm and annotate a new corpus from scratch. This kind of conventional event extraction system requires massive human effort, and hence prevents event extraction from being widely applicable. In this paper, we present BUEES, a bottom-up event extraction system, which extracts events from the web in a completely unsupervised way. The system automatically builds an event type paradigm in the input corpus, and then proceeds to extract a large number of instance patterns of these events. Subsequently, the system extracts event arguments according to these patterns. By conducting a series of experiments, we demonstrate the good performance of BUEES and compare it to a state-of-the-art Chinese event extraction system, i.e., a supervised event extraction system. Experimental results show that BUEES performs comparably (5% higher F-measure in event type identifi cation and 3% higher F-measure in event argument extraction), but without any human effort.

  7. Nonplanar conductive surfaces via "bottom-up" nanostructured gold coating.

    Science.gov (United States)

    Vinod, T P; Jelinek, Raz

    2014-03-12

    Development of technologies for the construction of bent, curved, and flexible conductive surfaces is among the most important albeit challenging goals in the promising field of "flexible electronics". We present a generic solution-based "bottom-up" approach for assembling conductive gold nanostructured layers on nonplanar polymer surfaces. The simple two-step experimental scheme is based upon incubation of an amine-displaying polymer [the abundantly used poly(dimethylsiloxane) (PDMS), selected here as a proof of concept] with Au(SCN)4(-), followed by a brief treatment with a conductive polymer [poly(3,4-thylenedioxythiophene)/poly(styrenesulfonate)] solution. Importantly, no reducing agent is co-added to the gold complex solution. The resultant surfaces are conductive and exhibit a unique "nanoribbon" gold morphology. The scheme yields conductive layers upon PDMS in varied configurations: planar, "wrinkled", and mechanically bent surfaces. The technology is simple, inexpensive, and easy to implement for varied polymer surfaces (and other substances), opening the way for practical applications in flexible electronics and related fields. PMID:24548243

  8. Bottom-up Visual Integration in the Medial Parietal Lobe.

    Science.gov (United States)

    Pflugshaupt, Tobias; Nösberger, Myriam; Gutbrod, Klemens; Weber, Konrad P; Linnebank, Michael; Brugger, Peter

    2016-03-01

    Largely based on findings from functional neuroimaging studies, the medial parietal lobe is known to contribute to internally directed cognitive processes such as visual imagery or episodic memory. Here, we present 2 patients with behavioral impairments that extend this view. Both had chronic unilateral lesions of nearly the entire medial parietal lobe, but in opposite hemispheres. Routine neuropsychological examination conducted >4 years after the onset of brain damage showed little deficits of minor severity. In contrast, both patients reported persistent unusual visual impairment. A comprehensive series of tachistoscopic experiments with lateralized stimulus presentation and comparison with healthy participants revealed partial visual hemiagnosia for stimuli presented to their contralesional hemifield, applying inferential single-case statistics to evaluate deficits and dissociations. Double dissociations were found in 4 experiments during which participants had to integrate more than one visual element, either through comparison or formation of a global gestalt. Against the background of recent neuroimaging findings, we conclude that of all medial parietal structures, the precuneus is the most likely candidate for a crucial involvement in such bottom-up visual integration. PMID:25331599

  9. Systems Approaches for Synthetic Biology: A Pathway Toward Mammalian Design

    Directory of Open Access Journals (Sweden)

    RahulRekhi

    2013-10-01

    Full Text Available We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches—stochasticity, complexity, and scale—with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility towards synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications.

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

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Keasling, Jay

    2015-01-01

    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....

  11. Bottom-up formation of endohedral mono-metallofullerenes is directed by charge transfer

    Science.gov (United States)

    Dunk, Paul W.; Mulet-Gas, Marc; Nakanishi, Yusuke; Kaiser, Nathan K.; Rodríguez-Fortea, Antonio; Shinohara, Hisanori; Poblet, Josep M.; Marshall, Alan G.; Kroto, Harold W.

    2014-12-01

    An understanding of chemical formation mechanisms is essential to achieve effective yields and targeted products. One of the most challenging endeavors is synthesis of molecular nanocarbon. Endohedral metallofullerenes are of particular interest because of their unique properties that offer promise in a variety of applications. Nevertheless, the mechanism of formation from metal-doped graphite has largely eluded experimental study, because harsh synthetic methods are required to obtain them. Here we report bottom-up formation of mono-metallofullerenes under core synthesis conditions. Charge transfer is a principal factor that guides formation, discovered by study of metallofullerene formation with virtually all available elements of the periodic table. These results could enable production strategies that overcome long-standing problems that hinder current and future applications of metallofullerenes.

  12. Bottom-Up Colloidal Crystal Assembly with a Twist.

    Science.gov (United States)

    Mahynski, Nathan A; Rovigatti, Lorenzo; Likos, Christos N; Panagiotopoulos, Athanassios Z

    2016-05-24

    Globally ordered colloidal crystal lattices have broad utility in a wide range of optical and catalytic devices, for example, as photonic band gap materials. However, the self-assembly of stereospecific structures is often confounded by polymorphism. Small free-energy differences often characterize ensembles of different structures, making it difficult to produce a single morphology at will. Current techniques to handle this problem adopt one of two approaches: that of the "top-down" or "bottom-up" methodology, whereby structures are engineered starting from the largest or smallest relevant length scales, respectively. However, recently, a third approach for directing high fidelity assembly of colloidal crystals has been suggested which relies on the introduction of polymer cosolutes into the crystal phase [Mahynski, N.; Panagiotopoulos, A. Z.; Meng, D.; Kumar, S. K. Nat. Commun. 2014, 5, 4472]. By tuning the polymer's morphology to interact uniquely with the void symmetry of a single desired crystal, the entropy loss associated with polymer confinement has been shown to strongly bias the formation of that phase. However, previously, this approach has only been demonstrated in the limiting case of close-packed crystals. Here, we show how this approach may be generalized and extended to complex open crystals, illustrating the utility of this "structure-directing agent" paradigm in engineering the nanoscale structure of ordered colloidal materials. The high degree of transferability of this paradigm's basic principles between relatively simple crystals and more complex ones suggests that this represents a valuable addition to presently known self-assembly techniques. PMID:27124487

  13. Synthetic biology approach to reconstituting the ubiquitylation cascade in bacteria

    OpenAIRE

    Keren-Kaplan, Tal; Attali, Ilan; Motamedchaboki, Khatereh; Davis, Brian A.; Tanner, Neta; Reshef, Yael; Laudon, Einat; Kolot, Mikhail; Levin-Kravets, Olga; Kleifeld, Oded; Glickman, Michael; Horazdovsky, Bruce F.; Wolf, Dieter A; Prag, Gali

    2012-01-01

    A new system to achieve bona fide ubiquitin conjugation in E. coli circumvents specificity problems associated with previous in-vitro approaches, adding to the synthetic biology toolbox aimed at addressing the complexity of cellular ubiquitin modification.

  14. Synthetic Biology and the Argument from Continuity with Established Technologies

    DEFF Research Database (Denmark)

    Christiansen, Andreas

    2015-01-01

    ignores the distinction between what reasons we have and what we should do all things considered. I then illustrate the Continuity Argument and its problems in the case where human manipulation of organisms’ genetic makeup is a suggested reason for finding synthetic biology problematic. Finally, I suggest......Defenders of synthetic biology commonly make reference to the fact that established technologies, such as domestication or selective breeding, share some of the features of synthetic biology that critics argue make it ethically problematic. In this chapter, I reconstruct such references as...... instances of a type of argument which I dub the Continuity Argument. Roughly, the Continuity Argument seeks to show that if we are not disposed to reject the established technology, then features that this technology share with synthetic biology cannot provide reasons to find it ethically problematic. I...

  15. Non-natural Nucleic Acids for Synthetic Biology

    OpenAIRE

    Appella, Daniel H.

    2009-01-01

    Genetic manipulation is an important facet of synthetic biology but can be complicated by undesired nuclease degradation. Incorporating non-natural nucleic acids into a gene could convey resistance to nucleases and promote expression. The compatibility of non-natural nucleosides with polymerases is reviewed with a focus on results from the past two years. Details are provided about how the different systems could be useful in synthetic biology.

  16. Building Enhancers From the Ground Up: A Synthetic Biology Approach

    OpenAIRE

    Amit, Roee; Garcia, Hernan G.; Phillips, Rob; Fraser, Scott E.

    2011-01-01

    A challenge of the synthetic biology approach is to use our understanding of a system to recreate a biological function with specific properties. We have applied this framework to bacterial enhancers, combining a driver, transcription factor binding sites, and a poised polymerase to create synthetic modular enhancers. Our findings suggest that enhancer-based transcriptional control depends critically and quantitatively on DNA looping, leading to complex regulatory effects when the enhancer ca...

  17. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

  18. Using synthetic biology to make cells tomorrow's test tubes.

    Science.gov (United States)

    Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

    2016-04-18

    The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting. PMID:26952708

  19. Ecological perspectives on synthetic biology: insights from microbial population biology

    OpenAIRE

    Ana E. Escalante; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent member...

  20. Aspects of the political economy of development and synthetic biology.

    Science.gov (United States)

    Wellhausen, Rachel; Mukunda, Gautam

    2009-12-01

    What implications might synthetic biology's potential as a wholly new method of production have for the world economy, particularly developing countries? Theories of political economy predict that synthetic biology can shift terms of trade and displace producers in developing countries. Governments, however, retain the ability to mitigate negative changes through social safety nets and to foster adaptation to some changes through research, education and investment. We consider the effects the synthetic production of otherwise naturally derived molecules are likely to have on trade and investment, particularly in developing countries. Both rubber in Malaysia and indigo dyes in India provide historical examples of natural molecules that faced market dislocations from synthetic competitors. Natural rubber was able to maintain significant market share, while natural indigo vanished from world markets. These cases demonstrate the two extremes of the impact synthetic biology might have on naturally derived products. If developing countries can cushion the pain of technological changes by providing producers support as they retool or exit, the harmful effects of synthetic biology can be mitigated while its benefits can still be captured. PMID:19816807

  1. Synthetic Biology and Biosecurity: Challenging the “Myths”

    Science.gov (United States)

    Jefferson, Catherine; Lentzos, Filippa; Marris, Claire

    2014-01-01

    Synthetic biology, a field that aims to “make biology easier to engineer,” is routinely described as leading to an increase in the “dual-use” threat, i.e., the potential for the same scientific research to be “used” for peaceful purposes or “misused” for warfare or terrorism. Fears have been expressed that the “de-skilling” of biology, combined with online access to the genomic DNA sequences of pathogenic organisms and the reduction in price for DNA synthesis, will make biology increasingly accessible to people operating outside well-equipped professional research laboratories, including people with malevolent intentions. The emergence of do-it-yourself (DIY) biology communities and of the student iGEM competition has come to epitomize this supposed trend toward greater ease of access and the associated potential threat from rogue actors. In this article, we identify five “myths” that permeate discussions about synthetic biology and biosecurity, and argue that they embody misleading assumptions about both synthetic biology and bioterrorism. We demonstrate how these myths are challenged by more realistic understandings of the scientific research currently being conducted in both professional and DIY laboratories, and by an analysis of historical cases of bioterrorism. We show that the importance of tacit knowledge is commonly overlooked in the dominant narrative: the focus is on access to biological materials and digital information, rather than on human practices and institutional dimensions. As a result, public discourse on synthetic biology and biosecurity tends to portray speculative scenarios about the future as realities in the present or the near future, when this is not warranted. We suggest that these “myths” play an important role in defining synthetic biology as a “promissory” field of research and as an “emerging technology” in need of governance. PMID:25191649

  2. Synthetic Biology of Cyanobacteria: Unique Challenges and Opportunities

    Directory of Open Access Journals (Sweden)

    Bertram M Berla

    2013-08-01

    Full Text Available Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria’s potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as ‘chassis’ strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a ‘green E. coli’. In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

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

    Science.gov (United States)

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

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function. PMID:26696234

  4. Aspects of the political economy of development and synthetic biology

    OpenAIRE

    Wellhausen, Rachel; Mukunda, Gautam

    2009-01-01

    What implications might synthetic biology’s potential as a wholly new method of production have for the world economy, particularly developing countries? Theories of political economy predict that synthetic biology can shift terms of trade and displace producers in developing countries. Governments, however, retain the ability to mitigate negative changes through social safety nets and to foster adaptation to some changes through research, education and investment. We consider the effects the...

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

    Directory of Open Access Journals (Sweden)

    Eric Young

    2010-01-01

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

  6. Synthetic biology: enormous possibility, exaggerated perils

    Directory of Open Access Journals (Sweden)

    Russ Zachary N

    2008-04-01

    Full Text Available Abstract The following essay was written by a freshman undergraduate student majoring in Bioengineering at the University of Maryland, Mr. Zachary Russ. Mr. Russ was one of 94 students who submitted a 1000 to 1200 word essay to the 3rd Annual Bioethics Essay Contest sponsored by the Institute of Biological Engineering (IBE. A group of professionals in Biological Engineering assessed and ranked the essays in a blinded process. Five semi-finalists were invited to present their essays at a session at the annual meeting of IBE in Chapel Hill, NC on March 8, 2008. Five judges scored the presentations at the annual meeting and selected Mr. Russ's contribution as the overall winner (1st Place. Below is his essay.

  7. How synthetic biology will reconsider natural bioluminescence and its applications.

    Science.gov (United States)

    Reeve, Benjamin; Sanderson, Theo; Ellis, Tom; Freemont, Paul

    2014-01-01

    As our understanding of natural biological systems grows, so too does our ability to alter and rebuild them. Synthetic biology is the application of engineering principles to biology in order to design and construct novel biological systems for specific applications. Bioluminescent organisms offer a treasure trove of light-emitting enzymes that may have applications in many areas of bioengineering, from biosensors to lighting. A few select bioluminescent organisms have been well researched and the molecular and genetic basis of their luminescent abilities elucidated, with work underway to understand the basis of luminescence in many others. Synthetic biology will aim to package these light-emitting systems as self-contained biological modules, characterize their properties, and then optimize them for use in other chassis organisms. As this catalog of biological parts grows, synthetic biologists will be able to engineer complex biological systems with the ability to emit light. These may use luminescence for an array of disparate functions, from providing illumination to conveying information or allowing communication between organisms. PMID:25216951

  8. Selection platforms for directed evolution in synthetic biology.

    Science.gov (United States)

    Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

    2016-08-15

    Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. PMID:27528765

  9. Synthetic biology for microbial production of lipid-based biofuels.

    Science.gov (United States)

    d'Espaux, Leo; Mendez-Perez, Daniel; Li, Rachel; Keasling, Jay D

    2015-12-01

    The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing. PMID:26479184

  10. Scaling up self-assembly: bottom-up approaches to macroscopic particle organization.

    Science.gov (United States)

    Lash, M H; Fedorchak, M V; McCarthy, J J; Little, S R

    2015-07-28

    This review presents an overview of recent work in the field of non-Brownian particle self-assembly. Compared to nanoparticles that naturally self-assemble due to Brownian motion, larger, non-Brownian particles (d > 6 μm) are less prone to autonomously organize into crystalline arrays. The tendency for particle systems to experience immobilization and kinetic arrest grows with particle radius. In order to overcome this kinetic limitation, some type of external driver must be applied to act as an artificial "thermalizing force" upon non-Brownian particles, inducing particle motion and subsequent crystallization. Many groups have explored the use of various agitation methods to overcome the natural barriers preventing self-assembly to which non-Brownian particles are susceptible. The ability to create materials from a bottom-up approach with these characteristics would allow for precise control over their pore structure (size and distribution) and surface properties (topography, functionalization and area), resulting in improved regulation of key characteristics such as mechanical strength, diffusive properties, and possibly even photonic properties. This review will highlight these approaches, as well as discuss the potential impact of bottom-up macroscale particle assembly. The applications of such technology range from customizable and autonomously self-assembled niche microenvironments for drug delivery and tissue engineering to new acoustic dampening, battery, and filtration materials, among others. Additionally, crystals made from non-Brownian particles resemble naturally derived materials such as opals, zeolites, and biological tissue (i.e. bone, cartilage and lung), due to their high surface area, pore distribution, and tunable (multilevel) hierarchy. PMID:25947543

  11. Regenesis how synthetic biology will reinvent nature and ourselves

    CERN Document Server

    Church, George M

    2012-01-01

    Imagine a future in which human beings have become immune to all viruses, in which bacteria can custom-produce everyday items, like a drinking cup, or generate enough electricity to end oil dependency. Building a house would entail no more work than planting a seed in the ground. These scenarios may seem far-fetched, but pioneering geneticist George Church and science writer Ed Regis show that synthetic biology is bringing us ever closer to making such visions a reality. In "Regenesis," Church and Regis explorethe possibilities--and perils--of the emerging field of synthetic biology. Synthetic biology, in which living organisms are selectively altered by modifying substantial portions of their genomes, allows for the creation of entirely new species of organisms. Until now, nature has been the exclusive arbiter of life, death, and evolution; with synthetic biology, we now have the potential to write our own biological future. Indeed, as Church and Regis show, it even enables us to revisit crucial points in th...

  12. Synthetic Nanopores: Biological Analogues and Nanofluidic Devices

    Science.gov (United States)

    Davenport, Matthew W.

    Nanoscopic pores in biological systems -- cells, for example -- are responsible for regulating the transport of ionic and molecular species between physiologically distinct compartments maintained by thin plasma membranes. These biological pores are proteinaceous structures: long, contorted chains of chemical building blocks called amino acids. Protein pores have evolved to span a staggering range of shapes, sizes and chemical properties, each crucial to a pore's unique functionality. Protein pores have extremely well-defined jobs. For instance, pores called ion channels only transport ions. Within this family, there are pores designated to selectively transport specific ions, such as sodium channels for sodium, chloride channels for chloride and so on. Further subdivisions exist within each type of ion channel, resulting in a pantheon of specialized proteins pores. Specificity and selectivity are bestowed upon a pore through its unique incorporation and arrangement of its amino acids, which in turn have their own unique chemical and physical properties. With hundreds of task-specific pores, deciphering the precise relationship between form and function in these protein channels is a critical, but daunting task. In this thesis, we examine an alternative for probing the fundamental mechanisms responsible for transport on the nanoscale. Solid-state membranes offer well-defined structural surrogates to directly address the science underlying pore functionality. Numerous protein pores rely on electronic interactions, size exclusion principles and hydrophobic effects to fulfill their duties, regardless of their amino acid sequence. Substituting an engineered and well-characterized pore, we strive to achieve and, thus, understand the hallmarks of biological pore function: analyte recognition and selective transport. While we restrict our study to only two readily available membrane materials -- one a polymer and the other a ceramic -- nanofabrication techniques give us

  13. Directed evolution and synthetic biology applications to microbial systems.

    Science.gov (United States)

    Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

    2016-06-01

    Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. PMID:27054950

  14. TinkerCell: modular CAD tool for synthetic biology

    Directory of Open Access Journals (Sweden)

    Bergmann Frank T

    2009-10-01

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

  15. DNA Synthesis, Assembly and Applications in Synthetic Biology

    OpenAIRE

    Ma, Siying; Tang, Nicholas; Tian, Jingdong

    2012-01-01

    The past couple of years saw exciting new developments in microchip-based gene synthesis technologies. Such technologies hold the potential for significantly increasing the throughput and decreasing the cost of gene synthesis. Together with more efficient enzymatic error correction and genome assembly methods, these new technologies are pushing the field of synthetic biology to a higher level.

  16. Plant synthetic biology: a new platform for industrial biotechnology.

    Science.gov (United States)

    Fesenko, Elena; Edwards, Robert

    2014-05-01

    Thirty years after the production of the first generation of genetically modified plants we are now set to move into a new era of recombinant crop technology through the application of synthetic biology to engineer new and complex input and output traits. The use of synthetic biology technologies will represent more than incremental additions of transgenes, but rather the directed design of completely new metabolic pathways, physiological traits, and developmental control strategies. The need to enhance our ability to improve crops through new engineering capability is now increasingly pressing as we turn to plants not just for food, but as a source of renewable feedstocks for industry. These accelerating and diversifying demands for new output traits coincide with a need to reduce inputs and improve agricultural sustainability. Faced with such challenges, existing technologies will need to be supplemented with new and far-more-directed approaches to turn valuable resources more efficiently into usable agricultural products. While these objectives are challenging enough, the use of synthetic biology in crop improvement will face public acceptance issues as a legacy of genetically modified technologies in many countries. Here we review some of the potential benefits of adopting synthetic biology approaches in improving plant input and output traits for their use as industrial chemical feedstocks, as linked to the rapidly developing biorefining industry. Several promising technologies and biotechnological targets are identified along with some of the key regulatory and societal challenges in the safe and acceptable introduction of such technology. PMID:24638901

  17. Toward the First Data Acquisition Standard in Synthetic Biology.

    Science.gov (United States)

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

    2016-08-19

    This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London. PMID:26854090

  18. Synthetic Biology Provides a Toehold in the Fight against Zika.

    Science.gov (United States)

    Hall, Roy A; Macdonald, Joanne

    2016-06-01

    The World Health Organization has identified the development of a rapid point-of-care diagnostic test for Zika virus as a top research priority. In a recent Cell paper, Pardee et al. (2016) have exploited recent advances in synthetic biology and molecular engineering to deliver a sensitive, affordable, and field-ready Zika test. PMID:27281566

  19. Synthetic Self-Assembled Materials in Biological Environments.

    Science.gov (United States)

    Versluis, Frank; van Esch, Jan H; Eelkema, Rienk

    2016-06-01

    Synthetic self-assembly has long been recognized as an excellent approach for the formation of ordered structures on the nanoscale. Although the development of synthetic self-assembling materials has often been inspired by principles observed in nature (e.g., the assembly of lipids, DNA, proteins), until recently the self-assembly of synthetic molecules has mainly been investigated ex vivo. The past few years however, have witnessed the emergence of a research field in which synthetic, self-assembling systems are used that are capable of operating as bioactive materials in biological environments. Here, this up-and-coming field, which has the potential of becoming a key area in chemical biology and medicine, is reviewed. Two main categories of applications of self-assembly in biological environments are identified and discussed, namely therapeutic and imaging agents. Within these categories key concepts, such as triggers and molecular constraints for in vitro/in vivo self-assembly and the mode of interaction between the assemblies and the biological materials will be discussed. PMID:27042774

  20. Cooperativity To Increase Turing Pattern Space for Synthetic Biology

    Science.gov (United States)

    2014-01-01

    It is hard to bridge the gap between mathematical formulations and biological implementations of Turing patterns, yet this is necessary for both understanding and engineering these networks with synthetic biology approaches. Here, we model a reaction–diffusion system with two morphogens in a monostable regime, inspired by components that we recently described in a synthetic biology study in mammalian cells.1 The model employs a single promoter to express both the activator and inhibitor genes and produces Turing patterns over large regions of parameter space, using biologically interpretable Hill function reactions. We applied a stability analysis and identified rules for choosing biologically tunable parameter relationships to increase the likelihood of successful patterning. We show how to control Turing pattern sizes and time evolution by manipulating the values for production and degradation relationships. More importantly, our analysis predicts that steep dose–response functions arising from cooperativity are mandatory for Turing patterns. Greater steepness increases parameter space and even reduces the requirement for differential diffusion between activator and inhibitor. These results demonstrate some of the limitations of linear scenarios for reaction–diffusion systems and will help to guide projects to engineer synthetic Turing patterns. PMID:25122550

  1. Synthetic Biology and Human Health: Potential Applications for Spaceflight

    Science.gov (United States)

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

    2011-01-01

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

  2. Mapping practices of project management – merging top-down and bottom-up perspectives

    DEFF Research Database (Denmark)

    Thuesen, Christian

    2015-01-01

    This paper presents a new methodology for studying different accounts of project management practices based on network mapping and analysis. Drawing upon network mapping and visualization as an analytical strategy top-down and bottom-up accounts of project management practice are analysed and...... promising strategy for visualizing and analysing different accounts of project management practices....... compared. The analysis initially reveals a substantial difference between the top-down and bottom-up accounts of practice. Furthermore it identifies a soft side of project management that is central in the bottom-up account but absent from the top-down. Finally, the study shows that network mapping is a...

  3. Cooperation between Top-Down and Bottom-Up Theorem Provers by Subgoal Clause Transfer

    OpenAIRE

    Fuchs, Dirk

    1999-01-01

    Top-down and bottom-up theorem proving approaches have each specific ad-vantages and disadvantages. Bottom-up provers profit from strong redundancycontrol and suffer from the lack of goal-orientation, whereas top-down provers aregoal-oriented but have weak calculi when their proof lengths are considered. Inorder to integrate both approaches our method is to achieve cooperation betweena top-down and a bottom-up prover: The top-down prover generates subgoalclauses, then they are processed by a ...

  4. Vasculogenic potential evaluation of bottom-up, PCL scaffolds guiding early angiogenesis in tissue regeneration.

    Science.gov (United States)

    Rossi, L; Attanasio, C; Vilardi, E; De Gregorio, M; Netti, P A

    2016-06-01

    Vascularization is a key factor in the successful integration of tissue engineered (TE) grafts inside the host body. Biological functions of the newly formed tissue depend, in fact, on a reliable and fast spread of the vascular network inside the scaffold. In this study, we propose a technique for evaluating vascularization in TE constructs assembled by a bottom-up approach. The rational, ordered assembly of building blocks (BBs) into a 3D scaffold can improve vessel penetration, and-unlike most current technologies-is compatible with the insertion of different elements that can be designed independently (e.g. structural units, growth factor depots etc.). Poly(ε-caprolactone) scaffolds composed of orderly and randomly assembled sintered microspheres were used to assess the degree of vascularization in a pilot in vivo study. Scaffolds were implanted in a rat subcutaneous pocket model, and retrieved after 7 days. We introduce three quantitative factors as a measure of vascularization: the total percentage of vascularization, the vessels diameter distribution and the vascular penetration depth. These parameters were derived by image analysis of microcomputed tomographic scans of biological specimens perfused with a radiopaque polymer. The outcome of this study suggests that the rational assembly of BBs helps the onset and organization of a fully functional vascular network. PMID:27117793

  5. A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data

    Energy Technology Data Exchange (ETDEWEB)

    Du, Xiuxia; Callister, Stephen J.; Manes, Nathan P.; Adkins, Joshua N.; Alexandridis, Roxana A.; Zeng, Xiaohua; Roh, Jung Hyeob; Smith, William E.; Donohue, Timothy J.; Kaplan, Samuel; Smith, Richard D.; Lipton, Mary S.

    2008-07-01

    Motivation: Biological systems are in a continual state of flux, which necessitates an understanding of the dynamic nature of protein abundances. The study of protein abundance dynamics has become feasible with recent improvements in mass spectrometry-based quantitative proteomics. However, a number of challenges still re-main related to how best to extract biological information from dy-namic proteomics data; for example, challenges related to extrane-ous variability, missing abundance values, and the identification of significant temporal patterns. Results: This article describes a strategy that addresses the afore-mentioned issues for the analysis of temporal bottom-up proteomics data. The core strategy for the data analysis algorithms and subse-quent data interpretation was formulated to take advantage of the temporal properties of the data. The analysis procedure presented herein was applied to data from a Rhodobacter sphaeroides 2.4.1 time-course study. The results were in close agreement with existing knowledge about R. sphaeroides, therefore demonstrating the utility of this analytical strategy.

  6. Synthetic toxicology: where engineering meets biology and toxicology.

    Science.gov (United States)

    Schmidt, Markus; Pei, Lei

    2011-03-01

    This article examines the implications of synthetic biology (SB) for toxicological sciences. Starting with a working definition of SB, we describe its current subfields, namely, DNA synthesis, the engineering of DNA-based biological circuits, minimal genome research, attempts to construct protocells and synthetic cells, and efforts to diversify the biochemistry of life through xenobiology. Based on the most important techniques, tools, and expected applications in SB, we describe the ramifications of SB for toxicology under the label of synthetic toxicology. We differentiate between cases where SB offers opportunities for toxicology and where SB poses challenges for toxicology. Among the opportunities, we identified the assistance of SB to construct novel toxicity testing platforms, define new toxicity-pathway assays, explore the potential of SB to improve in vivo biotransformation of toxins, present novel biosensors developed by SB for environmental toxicology, discuss cell-free protein synthesis of toxins, reflect on the contribution to toxic use reduction, and the democratization of toxicology through do-it-yourself biology. Among the identified challenges for toxicology, we identify synthetic toxins and novel xenobiotics, biosecurity and dual-use considerations, the potential bridging of toxic substances and infectious agents, and do-it-yourself toxin production. PMID:21068213

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

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, micro...

  8. The updated bottom up solution applied to atmospheric pressure photoionization and electrospray ionization mass spectrometry

    Science.gov (United States)

    The Updated Bottom Up Solution (UBUS) was recently applied to atmospheric pressure chemical ionization (APCI) mass spectrometry (MS) of triacylglycerols (TAGs). This report demonstrates that the UBUS applies equally well to atmospheric pressure photoionization (APPI) MS and to electrospray ionizatio...

  9. A Bottom up Initiative: Meditation & Mindfulness 'Eastern' Practices in the "Western" Academia

    DEFF Research Database (Denmark)

    Singla, Rashmi

    case of bottom up initiative, where the students themselves have demanded inclusion of non- conventional psychosocial interventions illustrated by meditation and mindfulness as Eastern psychological practices, thus filling the gap related to the existential, spiritual approaches. The western...

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

    OpenAIRE

    Bor-Sen Chen; Chia-Chou Wu

    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...

  11. Identifying robust clusters and multi-community nodes by combining top-down and bottom-up approaches to clustering

    CERN Document Server

    Gaiteri, Chris; Szymanski, Boleslaw; Kuzmin, Konstantin; Xie, Jierui; Lee, Changkyu; Blanche, Timothy; Neto, Elias Chaibub; Huang, Su-Chun; Grabowski, Thomas; Madhyastha, Tara; Komashko, Vitalina

    2015-01-01

    Biological functions are often realized by groups of interacting molecules or cells. Membership in these groups may overlap when molecules or cells are reused in multiple functions. Traditional clustering methods assign each component to one group. Noisy measurements are common in high-throughput biological datasets. These two limitations reduce our ability to accurately define clusters in biological datasets and to interpret their biological functions. To address these limitations, we designed an algorithm called SpeakEasy, which detects overlapping or non-overlapping communities in biological networks. Input to SpeakEasy can be physical networks, such as molecular interactions, or inferred networks, such as gene coexpression networks. The networks can be directed or undirected, and may contain negative links. SpeakEasy combines traditional bottom-up and top-down approaches to clustering, by creating competition between clusters. Nodes that oscillate between multiple clusters in this competition are classifi...

  12. The Chicago Fire of 1871: A Bottom Up Approach to Disaster Relief

    OpenAIRE

    Emily C. Skarbek

    2014-01-01

    Can bottom-up relief efforts lead to recovery after disasters? Conventional wisdom and contemporary public policy suggest that major crises require centralized authority to provide disaster relief goods. Using a novel set of comprehensive donation and expenditure data collected from archival records, this paper examines a bottom-up relief effort following one of the most devastating natural disasters of the nineteenth century: the Chicago Fire of 1871. Findings show that while there was no ce...

  13. A Critique of 'Bottom-up' Peacebuilding: Do Peaceful Individuals Make Peaceful Societies?

    OpenAIRE

    Lefranc, Sandrine

    2011-01-01

    This chapter is concerned with dialogue-based post-conflict practices currently being promoted vigorously by certain international organizations. On the one hand, there is "transitional justice" with its cornerstone forums, deemed truth and reconciliation commissions. On the other hand, there are various "bottom-up" peacebuilding techniques (local dialogues, coexistence programs, conflict resolution training, and so on). Generally speaking, these "bottom-up" approaches work to transform indiv...

  14. Mapping practices of project management – merging top-down and bottom-up perspectives

    OpenAIRE

    Thuesen, Christian

    2015-01-01

    This paper presents a new methodology for studying different accounts of project management practices based on network mapping and analysis. Drawing upon network mapping and visualization as an analytical strategy top-down and bottom-up accounts of project management practice are analysed and compared. The analysis initially reveals a substantial difference between the top-down and bottom-up accounts of practice. Furthermore it identifies a soft side of project management that is central in t...

  15. Methane and ethane from global oil and gas production: bottom-up simulations over three decades

    OpenAIRE

    Höglund-Isaksson, L.

    2016-01-01

    Existing bottom-up emission inventories of historical methane and ethane emissions from global oil and gas systems do not well explain year-on-year variations estimated by top-down models from atmospheric measurements. This paper develops a bottom-up methodology which allows for country- and year specific source attribution of methane and ethane emissions from global oil and natural gas production for the period 1980 to 2012. The analysis rests on country-specific simulations of associated ga...

  16. Application of synthetic biology in cyanobacteria and algae

    Directory of Open Access Journals (Sweden)

    Bo eWang

    2012-09-01

    Full Text Available Cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and CO2 and their relatively simple genetic background for genetic manipulation. Increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. In the article, we critically review recent progresses in developing genetic tools for characterizing or manipulating cyanobacteria and algae, the applications of genetically modified strains for synthesizing renewable products such as biofuels and chemicals. In addition, the emergent challenges in the development and application of synthetic biology for cyanobacteria and algae are also discussed.

  17. Synthetic glycopeptides and glycoproteins with applications in biological research

    Directory of Open Access Journals (Sweden)

    Ulrika Westerlind

    2012-05-01

    Full Text Available Over the past few years, synthetic methods for the preparation of complex glycopeptides have been drastically improved. The need for homogenous glycopeptides and glycoproteins with defined chemical structures to study diverse biological phenomena further enhances the development of methodologies. Selected recent advances in synthesis and applications, in which glycopeptides or glycoproteins serve as tools for biological studies, are reviewed. The importance of specific antibodies directed to the glycan part, as well as the peptide backbone has been realized during the development of synthetic glycopeptide-based anti-tumor vaccines. The fine-tuning of native chemical ligation (NCL, expressed protein ligation (EPL, and chemoenzymatic glycosylation techniques have all together enabled the synthesis of functional glycoproteins. The synthesis of structurally defined, complex glycopeptides or glyco-clusters presented on natural peptide backbones, or mimics thereof, offer further possibilities to study protein-binding events.

  18. 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).

  19. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments.

    Science.gov (United States)

    Lebert, Dorothée; Louwagie, Mathilde; Goetze, Sandra; Picard, Guillaume; Ossola, Reto; Duquesne, Caroline; Basler, Konrad; Ferro, Myriam; Rinner, Oliver; Aebersold, Ruedi; Garin, Jérôme; Mouz, Nicolas; Brunner, Erich; Brun, Virginie

    2015-02-01

    In bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy, and precision of peptide detection and quantification. Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS proteomic data obtained under different experimental conditions. Here, we describe the design, synthesis, and validation of a universal protein standard, called DIGESTIF, that can be added to any biological sample. The DIGESTIF standard consists of a soluble recombinant protein scaffold to which a set of 11 artificial peptides (iRT peptides) with good ionization properties has been incorporated. In the protein scaffold, the amino acids flanking iRT peptide cleavage sites were selected either to favor or hinder protease cleavage. After sample processing, the retention time and relative intensity pattern of the released iRT peptides can be used to assess the quality of sample workup, the extent of digestion, and the performance of the LC-MS system. Thus, DIGESTIF can be used to standardize a broad spectrum of applications, ranging from simple replicate measurements to large-scale biomarker screening in biomedical applications. PMID:25495225

  20. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes

    Science.gov (United States)

    Poirel, Christopher L.; Rodrigues, Richard R.; Chen, Katherine C.; Tyson, John J.

    2013-01-01

    Abstract Top-down analyses in systems biology can automatically find correlations among genes and proteins in large-scale datasets. However, it is often difficult to design experiments from these results. In contrast, bottom-up approaches painstakingly craft detailed models that can be simulated computationally to suggest wet lab experiments. However, developing the models is a manual process that can take many years. These approaches have largely been developed independently. We present Linker, an efficient and automated data-driven method that can analyze molecular interactomes to propose extensions to models that can be simulated. Linker combines teleporting random walks and k-shortest path computations to discover connections from a source protein to a set of proteins collectively involved in a particular cellular process. We evaluate the efficacy of Linker by applying it to a well-known dynamic model of the cell division cycle in Saccharomyces cerevisiae. Compared to other state-of-the-art methods, subnetworks computed by Linker are heavily enriched in Gene Ontology (GO) terms relevant to the cell cycle. Finally, we highlight how networks computed by Linker elucidate the role of a protein kinase (Cdc5) in the mitotic exit network of a dynamic model of the cell cycle. PMID:23641868

  1. Modeling Visual Exploration in Rhesus Macaques with Bottom-Up Salience and Oculomotor Statistics

    Science.gov (United States)

    König, Seth D.; Buffalo, Elizabeth A.

    2016-01-01

    There is a growing interest in studying biological systems in natural settings, in which experimental stimuli are less artificial and behavior is less controlled. In primate vision research, free viewing of complex images has elucidated novel neural responses, and free viewing in humans has helped discover attentional and behavioral impairments in patients with neurological disorders. In order to fully interpret data collected from free viewing of complex scenes, it is critical to better understand what aspects of the stimuli guide viewing behavior. To this end, we have developed a novel viewing behavior model called a Biased Correlated Random Walk (BCRW) to describe free viewing behavior during the exploration of complex scenes in monkeys. The BCRW can predict fixation locations better than bottom-up salience. Additionally, we show that the BCRW can be used to test hypotheses regarding specific attentional mechanisms. For example, we used the BCRW to examine the source of the central bias in fixation locations. Our analyses suggest that the central bias may be caused by a natural tendency to reorient the eyes toward the center of the stimulus, rather than a photographer's bias to center salient items in a scene. Taken together these data suggest that the BCRW can be used to further our understanding of viewing behavior and attention, and could be useful in optimizing stimulus and task design.

  2. Bottoms Up

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    China’s high-end liquor is becoming a luxury item and a favorite among collectors spring Festival, the most important festival for the Chinese, is a time for celebration—and what would a celebration be without bottles of holi-

  3. pClone: Synthetic Biology Tool Makes Promoter Research Accessible to Beginning Biology Students

    Science.gov (United States)

    Campbell, A. Malcolm; Eckdahl, Todd; Cronk, Brian; Andresen, Corinne; Frederick, Paul; Huckuntod, Samantha; Shinneman, Claire; Wacker, Annie; Yuan, Jason

    2014-01-01

    The "Vision and Change" report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area…

  4. From DNA to Targeted Therapeutics: Bringing Synthetic Biology to the Clinic

    OpenAIRE

    Chen, Yvonne Y; Smolke, Christina D.

    2011-01-01

    Synthetic biology aims to make biological engineering more scalable and predictable, lowering the cost and facilitating the translation of synthetic biological systems to practical applications. Increasingly sophisticated, rationally designed synthetic systems that are capable of complex functions pave the way to translational applications, including disease diagnostics and targeted therapeutics. Here, we provide an overview of recent developments in synthetic biology in the context of transl...

  5. 合成生物学发展现状与前景%Progress and perspective of synthetic biology

    Institute of Scientific and Technical Information of China (English)

    熊燕; 陈大明; 杨琛; 赵国屏

    2011-01-01

    合成生物学是综合了科学与工程的一个崭新的生物学研究领域,为生命现象及其运动规律的解析提供了一种采用“自下而上”合成策略的正向工程学的研究思路和方法手段,在经济和社会发展中具有巨大的应用开发潜力.近年来,DNA合成与系统生物学技术的发展使生命系统复杂基因回路的设计、合成与组装逐步成为可能,并应用于生物基化学品、生物燃料、医药中间体、保健产品的生产和环境保护等领域.但是,合成生物学的研究仍然面临科学、技术和伦理的挑战,只有积极地应对这些问题,在加大研究开发支持力度的同时,做好必要的风险监管,才能真正把握合成生物学发展带来的历史机遇.%Synthetic biology is an emerging field of biological research that combines science and engineering to study the mechanism of life and for a variety of technological applications. Research in synthetic biology has primarily focused on developing an engineering dogma for bottom-up design and synthesis of biological circuits from standardized parts and modules followed by optimizing their operation on well-characterized chassis, in vivo or in vitro. Recent progress in synthetic biology, such as significant improvements in efficient DNA/gene synthesis and ever increasing knowledge of biological systems via genomic and functional genomic analysis enables scientists to design and construct increasingly complex genetic devices and circuits, to synthesize and assembly bacterial genomes, and to develop artificially modified biological systems to produce renewable chemicals, biofuels, pharmaceutical intermediates, health care products and new tools for environment protection. However, neither the scientific complexity nor the technological uncertainty of the research has been thoroughly studied. In addition, the legal and ethical concerns of its social and humanitarian impact is largely yet to be addressed. Proper

  6. Metabolomics methods for the synthetic biology of secondary metabolism.

    Science.gov (United States)

    Nguyen, Quoc-Thai; Merlo, Maria E; Medema, Marnix H; Jankevics, Andris; Breitling, Rainer; Takano, Eriko

    2012-07-16

    Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or "awakening" of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent advances in DNA sequencing and synthesis to achieve unprecedented control over metabolic pathways. One of the indispensable tools in the synthetic biology toolbox is metabolomics, the global quantification of small biomolecules. This review illustrates the pivotal role of metabolomics for the synthetic microbiology of secondary metabolism, including its crucial role in novel compound discovery in microbes, the examination of side products of engineered metabolic pathways, as well as the identification of major bottlenecks for the overproduction of compounds of interest, especially in combination with metabolic modeling. We conclude by highlighting remaining challenges and recent technological advances that will drive metabolomics towards fulfilling its potential as a cornerstone technology of synthetic microbiology. PMID:22710183

  7. Materials Manufactured from 3D Printed Synthetic Biology Arrays

    Science.gov (United States)

    Gentry, Diana; Micks, Ashley

    2013-01-01

    Many complex, biologically-derived materials have extremely useful properties (think wood or silk), but are unsuitable for space-related applications due to production, manufacturing, or processing limitations. Large-scale ecosystem-based production, such as raising and harvesting trees for wood, is impractical in a self-contained habitat such as a space station or potential Mars colony. Manufacturing requirements, such as the specialized equipment needed to harvest and process cotton, add too much upmass for current launch technology. Cells in nature are already highly specialized for making complex biological materials on a micro scale. We envision combining these strengths with the recently emergent technologies of synthetic biology and 3D printing to create 3D-structured arrays of cells that are bioengineered to secrete different materials in a specified three-dimensional pattern.

  8. Engineered Protein Machines: Emergent Tools for Synthetic Biology.

    Science.gov (United States)

    Glasscock, Cameron J; Lucks, Julius B; DeLisa, Matthew P

    2016-01-21

    Nature has evolved an array of intricate protein assemblies that work together to perform the chemistry that maintains life. These protein machines function with exquisite specificity and coordination to accomplish their tasks, from DNA and RNA synthesis to protein folding and post-translational modifications. Despite their complexity, synthetic biologists have succeeded in redesigning many aspects of these molecular machines. For example, natural DNA polymerases have now been engineered to catalyze the synthesis of alternative genetic polymers called XNAs, orthogonal RNA polymerases and ribosomes have been engineered to enable the construction of genetic logic gates, and protein biogenesis machinery such as chaperonins and protein translocons have been repurposed to improve folding and expression of recombinant proteins. In this Review, we highlight the progress made in understanding, engineering, and repurposing bacterial protein machines for use in synthetic biology and biotechnology. PMID:26933735

  9. Bottom-up learning of hierarchical models in a class of deterministic POMDP environments

    Directory of Open Access Journals (Sweden)

    Itoh Hideaki

    2015-09-01

    Full Text Available The theory of partially observable Markov decision processes (POMDPs is a useful tool for developing various intelligent agents, and learning hierarchical POMDP models is one of the key approaches for building such agents when the environments of the agents are unknown and large. To learn hierarchical models, bottom-up learning methods in which learning takes place in a layer-by-layer manner from the lowest to the highest layer are already extensively used in some research fields such as hidden Markov models and neural networks. However, little attention has been paid to bottom-up approaches for learning POMDP models. In this paper, we present a novel bottom-up learning algorithm for hierarchical POMDP models and prove that, by using this algorithm, a perfect model (i.e., a model that can perfectly predict future observations can be learned at least in a class of deterministic POMDP environments

  10. Rigid Biological Systems as Models for Synthetic Composites

    Science.gov (United States)

    Mayer, George

    2005-11-01

    Advances that have been made in understanding the mechanisms underlying the mechanical behavior of a number of biological materials (namely mollusk shells and sponge spicules) are discussed here. Attempts at biomimicry of the structure of a nacreous layer of a mollusk shell have shown reasonable success. However, they have revealed additional issues that must be addressed if new synthetic composite materials that are based on natural systems are to be constructed. Some of the important advantages and limitations of copying from nature are also described here.

  11. Integrated Assessment of Energy Policies: A Decomposition of Top-Down and Bottom-Up

    Energy Technology Data Exchange (ETDEWEB)

    Boehringer, Christoph (Univ. of Oldenburg (Germany)); Rutherford, Thomas F. (ETH Zuerich (Switzerland))

    2008-01-15

    The formulation of market equilibrium problems as mixed complementarity problems (MCP) permits integration of bottom-up programming models of the energy system into top-down general equilibrium models of the overall economy. Yet, in practise the MCP approach loses analytical tractability of income effects, when the energy system includes upper and lowrbounds on many decision variables . We therefore advocate the use of complementarity methods to solve only the top-down economic equilibrium model and employ quadratic programming to solve the underlying bottom-up energy supply model. A simple iterative procedure reconciles the equilibrium prices and quantities between both models.

  12. Increased performance in a bottom-up designed robot by experimentally guided redesign

    DEFF Research Database (Denmark)

    Larsen, Jørgen Christian

    2013-01-01

    Purpose – Using a bottom-up, model-free approach when building robots is often seen as a less scientific way, compared to a top-down model-based approach, because the results are not easily generalizable to other systems. The authors, however, hypothesize that this problem may be addressed by using...... solid experimental methods. The purpose of this paper is to show how well-known experimental methods from bio-mechanics are used to measure and locate weaknesses in a bottom-up, model-free implementation of a quadruped walker and come up with a better solution. Design/methodology/approach – To study the...

  13. Fast and bottom-up object detection, segmentation, and evaluation using gestalt principles

    OpenAIRE

    Kootstra G.; Kragic D.

    2011-01-01

    In many scenarios, domestic robot will regularly encounter unknown objects. In such cases, top-down knowledge about the object for detection, recognition, and classification cannot be used. To learn about the object, or to be able to grasp it, bottom-up object segmentation is an important competence for the robot. Also when there is top-down knowledge, prior segmentation of the object can improve recognition and classification. In this paper, we focus on the problem of bottom-up detection and...

  14. TMS-induced theta phase synchrony reveals a bottom-up network in working memory.

    Science.gov (United States)

    Miyauchi, Eri; Kitajo, Keiichi; Kawasaki, Masahiro

    2016-05-27

    Global theta phase synchronization between the frontal and sensory areas has been suggested to connect the relevant areas for executive processes of working memory (WM). However, little is known regarding network directionality (i.e. top-down or bottom-up) of this interaction. To address the issue, the present study conducted transcranial magnetic stimulation (TMS)-electroencephalography (EEG) experiment during WM tasks. Results showed that TMS-induced increases in theta phase synchronization were observed only when TMS was delivered to the sensory areas but not the frontal area. These findings suggest that network directionality represented in WM is bottom-up rather than top-down. PMID:27063284

  15. A bottom-up model to describe consumers’ preferences towards late season peaches

    OpenAIRE

    Etiénne Groot; Luis M. Albisu

    2015-01-01

    Peaches are consumed in Mediterranean countries since ancient times. Nowadays there are few areas in Europe that produce peaches with Protected Designation of Origin (PDO), and the Calanda area is one of them. The aim of this work is to describe consumers’ preferences towards late season PDO Calanda peaches in the city of Zaragoza, Spain, by a bottom-up model. The bottom-up model proves greater amount of information than top-down models. In this approach it is estimated one utility function p...

  16. Recent insight into the biological activities of synthetic xanthone derivatives.

    Science.gov (United States)

    Shagufta; Ahmad, Irshad

    2016-06-30

    Xanthones are a class of oxygen containing heterocyclic compounds with a broad range of biological activities, and they have prominent significance in the field of medicinal chemistry. Xanthone is an attractive scaffold for the design and development of new drugs due to its promising biological activities, primarily as anticancer, antimalarial, antimicrobial, anti-HIV, anticonvulsant, anticholinesterase, antioxidant, anti-inflammatory, and as inhibitors of several enzymes like α-glycosidase, topoisomerase, protein kinase, aromatase, etc. In this review, we have compiled and discussed recent developments on the pharmacological profile of synthetic xanthone derivatives for different therapeutic targets. The review highlights the therapeutic significance of xanthones and offers support in the development of new xanthone derivatives as therapeutic agents. PMID:27111599

  17. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    OpenAIRE

    Giordano Emanuele; Furini Simone; Ceroni Francesca; Cavalcanti Silvio

    2010-01-01

    Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR) and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel syntheti...

  18. Bottom-up or top-down in dream neuroscience? A top-down critique of two bottom-up studies.

    Science.gov (United States)

    Foulkes, David; Domhoff, G William

    2014-07-01

    Recent neuroscientific studies of dreaming, specifically those in relation to waking sensory-motor impairments, but also more generally, betray a faulty understanding of the sort of process that dreaming is. They adhere to the belief that dreaming is a bottom-up phenomenon, whose form and content is dictated by sensory-motor brain stem activity, rather than a top-down process initiated and controlled by higher-level cognitive systems. But empirical data strongly support the latter alternative, and refute the conceptualization and interpretation of recent studies of dreaming in sensory-motor impairment in particular and of recent dream neuroscience in general. PMID:24905546

  19. pClone: Synthetic Biology Tool Makes Promoter Research Accessible to Beginning Biology Students

    OpenAIRE

    Campbell, A. Malcolm; Eckdahl, Todd; Cronk, Brian; Andresen, Corinne; Frederick, Paul; Huckuntod, Samantha; Shinneman, Claire; Wacker, Annie; Yuan, Jason

    2014-01-01

    The Vision and Change report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area of science. We developed a laboratory module called pClone that empowers students to use advances in molecular cloning methods to discover new promoters for use...

  20. Bacterial microcompartments as metabolic modules for plant synthetic biology.

    Science.gov (United States)

    Gonzalez-Esquer, C Raul; Newnham, Sarah E; Kerfeld, Cheryl A

    2016-07-01

    Bacterial microcompartments (BMCs) are megadalton-sized protein assemblies that enclose segments of metabolic pathways within cells. They increase the catalytic efficiency of the encapsulated enzymes while sequestering volatile or toxic intermediates from the bulk cytosol. The first BMCs discovered were the carboxysomes of cyanobacteria. Carboxysomes compartmentalize the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) with carbonic anhydrase. They enhance the carboxylase activity of RuBisCO by increasing the local concentration of CO2 in the vicinity of the enzyme's active site. As a metabolic module for carbon fixation, carboxysomes could be transferred to eukaryotic organisms (e.g. plants) to increase photosynthetic efficiency. Within the scope of synthetic biology, carboxysomes and other BMCs hold even greater potential when considered a source of building blocks for the development of nanoreactors or three-dimensional scaffolds to increase the efficiency of either native or heterologously expressed enzymes. The carboxysome serves as an ideal model system for testing approaches to engineering BMCs because their expression in cyanobacteria provides a sensitive screen for form (appearance of polyhedral bodies) and function (ability to grow on air). We recount recent progress in the re-engineering of the carboxysome shell and core to offer a conceptual framework for the development of BMC-based architectures for applications in plant synthetic biology. PMID:26991644

  1. Characterizing seamless ligation cloning extract for synthetic biological applications.

    Science.gov (United States)

    Messerschmidt, Katrin; Hochrein, Lena; Dehm, Daniel; Schulz, Karina; Mueller-Roeber, Bernd

    2016-09-15

    Synthetic biology aims at designing and engineering organisms. The engineering process typically requires the establishment of suitable DNA constructs generated through fusion of multiple protein coding and regulatory sequences. Conventional cloning techniques, including those involving restriction enzymes and ligases, are often of limited scope, in particular when many DNA fragments must be joined or scar-free fusions are mandatory. Overlap-based-cloning methods have the potential to overcome such limitations. One such method uses seamless ligation cloning extract (SLiCE) prepared from Escherichia coli cells for straightforward and efficient in vitro fusion of DNA fragments. Here, we systematically characterized extracts prepared from the unmodified E. coli strain DH10B for SLiCE-mediated cloning and determined DNA sequence-associated parameters that affect cloning efficiency. Our data revealed the virtual absence of length restrictions for vector backbone (up to 13.5 kbp) and insert (90 bp to 1.6 kbp). Furthermore, differences in GC content in homology regions are easily tolerated and the deletion of unwanted vector sequences concomitant with targeted fragment insertion is straightforward. Thus, SLiCE represents a highly versatile DNA fusion method suitable for cloning projects in virtually all molecular and synthetic biology projects. PMID:27311554

  2. Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition

    Science.gov (United States)

    Cegelski, Lynette

    2015-04-01

    The genomics and proteomics revolutions have been enormously successful in providing crucial "parts lists" for biological systems. Yet, formidable challenges exist in generating complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell assemblies. Bacterial biofilms are complex multicellular bacterial communities protected by a slime-like extracellular matrix that confers protection to environmental stress and enhances resistance to antibiotics and host defenses. As a non-crystalline, insoluble, heterogeneous assembly, the biofilm extracellular matrix poses a challenge to compositional analysis by conventional methods. In this perspective, bottom-up and top-down solid-state NMR approaches are described for defining chemical composition in complex macrosystems. The "sum-of-the-parts" bottom-up approach was introduced to examine the amyloid-integrated biofilms formed by Escherichia coli and permitted the first determination of the composition of the intact extracellular matrix from a bacterial biofilm. An alternative top-down approach was developed to define composition in Vibrio cholerae biofilms and relied on an extensive panel of NMR measurements to tease out specific carbon pools from a single sample of the intact extracellular matrix. These two approaches are widely applicable to other heterogeneous assemblies. For bacterial biofilms, quantitative parameters of matrix composition are needed to understand how biofilms are assembled, to improve the development of biofilm inhibitors, and to dissect inhibitor modes of action. Solid-state NMR approaches will also be invaluable in obtaining parameters of matrix architecture.

  3. Optimal Environmental Conditions and Anomalous Ecosystem Responses: Constraining Bottom-up Controls of Phytoplankton Biomass in the California Current System

    Science.gov (United States)

    Jacox, Michael G.; Hazen, Elliott L.; Bograd, Steven J.

    2016-06-01

    In Eastern Boundary Current systems, wind-driven upwelling drives nutrient-rich water to the ocean surface, making these regions among the most productive on Earth. Regulation of productivity by changing wind and/or nutrient conditions can dramatically impact ecosystem functioning, though the mechanisms are not well understood beyond broad-scale relationships. Here, we explore bottom-up controls during the California Current System (CCS) upwelling season by quantifying the dependence of phytoplankton biomass (as indicated by satellite chlorophyll estimates) on two key environmental parameters: subsurface nitrate concentration and surface wind stress. In general, moderate winds and high nitrate concentrations yield maximal biomass near shore, while offshore biomass is positively correlated with subsurface nitrate concentration. However, due to nonlinear interactions between the influences of wind and nitrate, bottom-up control of phytoplankton cannot be described by either one alone, nor by a combined metric such as nitrate flux. We quantify optimal environmental conditions for phytoplankton, defined as the wind/nitrate space that maximizes chlorophyll concentration, and present a framework for evaluating ecosystem change relative to environmental drivers. The utility of this framework is demonstrated by (i) elucidating anomalous CCS responses in 1998–1999, 2002, and 2005, and (ii) providing a basis for assessing potential biological impacts of projected climate change.

  4. Beyond directed evolution: Darwinian selection as a tool for synthetic biology

    OpenAIRE

    Porcar, Manuel

    2009-01-01

    Synthetic biology is an engineering approach that seeks to design and construct new biological parts, devices and systems, as well as to re-design existing components. However, rationally designed synthetic circuits may not work as expected due to the context-dependence of biological parts. Darwinian selection, the main mechanism through which evolution works, is a major force in creating biodiversity and may be a powerful tool for synthetic biology. This article reviews selection-based techn...

  5. Real-Time Biological Annotation of Synthetic Compounds.

    Science.gov (United States)

    Gerry, Christopher J; Hua, Bruce K; Wawer, Mathias J; Knowles, Jonathan P; Nelson, Shawn D; Verho, Oscar; Dandapani, Sivaraman; Wagner, Bridget K; Clemons, Paul A; Booker-Milburn, Kevin I; Boskovic, Zarko V; Schreiber, Stuart L

    2016-07-20

    Organic chemists are able to synthesize molecules in greater number and chemical complexity than ever before. Yet, a majority of these compounds go untested in biological systems, and those that do are often tested long after the chemist can incorporate the results into synthetic planning. We propose the use of high-dimensional "multiplex" assays, which are capable of measuring thousands of cellular features in one experiment, to annotate rapidly and inexpensively the biological activities of newly synthesized compounds. This readily accessible and inexpensive "real-time" profiling method can be used in a prospective manner to facilitate, for example, the efficient construction of performance-diverse small-molecule libraries that are enriched in bioactives. Here, we demonstrate this concept by synthesizing ten triads of constitutionally isomeric compounds via complexity-generating photochemical and thermal rearrangements and measuring compound-induced changes in cellular morphology via an imaging-based "cell painting" assay. Our results indicate that real-time biological annotation can inform optimization efforts and library syntheses by illuminating trends relating to biological activity that would be difficult to predict if only chemical structure were considered. We anticipate that probe and drug discovery will benefit from the use of optimization efforts and libraries that implement this approach. PMID:27398798

  6. Bottom-Up Molecular Tunneling Junctions Formed by Self-Assembly

    NARCIS (Netherlands)

    Zhang, Yanxi; Zhao, Zhiyuan; Fracasso, Davide; Chiechi, Ryan C

    2014-01-01

    This Minireview focuses on bottom-up molecular tunneling junctions - a fundamental component of molecular electronics - that are formed by self-assembly. These junctions are part of devices that, in part, fabricate themselves, and therefore, are particularly dependent on the chemistry of the molecul

  7. Ways toward a European Vocational Education and Training Space: A "Bottom-Up" Approach

    Science.gov (United States)

    Blings, Jessica; Spottl, Georg

    2008-01-01

    Purpose: This paper seeks to concentrate on bottom-up approaches in order to promote a European vocational education and training (VET) concept. The overall aim of this article is to demonstrate that sophisticated approaches still have a chance of becoming common practice in European countries. Design/methodology/approach: The centre of the…

  8. Top-Down or Bottom-Up? Coping with Territorial Fragmentation in the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Illner, Michal

    Houndmills, Basingstoke: PALGRAVE MACMILLAN, 2010 - (Baldersheim, H.; Lawrence, E.), s. 214-233 ISBN 978-0-230-23333-1 R&D Projects: GA MŠk 2D06006 Institutional research plan: CEZ:AV0Z70280505 Keywords : Czech Republic * municipalities * bottom-up consolidation Subject RIV: AO - Sociology, Demography

  9. Conciliating TOP-DOWN and BOTTOM-UP approaches in Websites quality evaluation

    OpenAIRE

    Biscoglio, Isabella; Trentanni, Gianluca

    2007-01-01

    Websites are the most important media of our times. Consequently a method which allows us to better evaluate websites quality is priceless. In this paper two websites evaluation opposite approaches, namely "bottom-up" and "top-down", are compared and an hypothesis of their meeting in the middle is shown.

  10. Bottom-up control of water hyacinth weevil populations: Do the plants regulate the insects?

    Science.gov (United States)

    A key measure of dietary sufficiency relates to an insect’s reproductive ability so oögenesis, a nutrient-limited process, can be subject to bottom-up regulation. We hypothesized that aquatic nutrient flux seasonally affects ovarian development thereby controlling population growth of two specialis...

  11. Nanoelectronics: the Hall Effect and Measurement of Electrochemical Potentials by «Bottom-Up» Approach

    OpenAIRE

    Yu.A. Kruglyak; P.A. Kondratenko; Yu.М. Lopatkin

    2015-01-01

    Classical and quantum Hall effects, measurement of electrochemical potentials, the Landauer formulas and Buttiker formula, measurement of Hall potential, an account of magnetic field in the NEGF method, quantum Hall effect, Landau method, and edge states in graphene are discussed in the frame of the «bottom-up» approach of modern nanoelectronics.

  12. Oriented bottom-up growth of armchair graphene nanoribbons on germanium

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, Michael Scott; Jacobberger, Robert Michael

    2016-03-15

    Graphene nanoribbon arrays, methods of growing graphene nanoribbon arrays and electronic and photonic devices incorporating the graphene nanoribbon arrays are provided. The graphene nanoribbons in the arrays are formed using a scalable, bottom-up, chemical vapor deposition (CVD) technique in which the (001) facet of the germanium is used to orient the graphene nanoribbon crystals along the [110] directions of the germanium.

  13. Nanoelectronics: the Hall Effect and Measurement of Electrochemical Potentials by «Bottom-Up» Approach

    Directory of Open Access Journals (Sweden)

    Yu.A. Kruglyak

    2015-06-01

    Full Text Available Classical and quantum Hall effects, measurement of electrochemical potentials, the Landauer formulas and Buttiker formula, measurement of Hall potential, an account of magnetic field in the NEGF method, quantum Hall effect, Landau method, and edge states in graphene are discussed in the frame of the «bottom-up» approach of modern nanoelectronics.

  14. How Adolescents Comprehend Unfamiliar Proverbs: The Role of Top-Down and Bottom-Up Processes.

    Science.gov (United States)

    Nippold, Marilyn A.; Allen, Melissa M.; Kirsch, Dixon I.

    2000-01-01

    Relationships between word knowledge and proverb comprehension was examined in 150 typically achieving adolescents (ages 12, 15, and 18). Word knowledge was associated with proverb comprehension in all groups, particularly in the case of abstract proverbs. Results support a model of proverb comprehension in adolescents that includes bottom-up in…

  15. Co-financing of bottom-up approaches towards Broadband Infrastructure Development

    DEFF Research Database (Denmark)

    Williams, Idongesit

    2016-01-01

    networks –leading to the demise of some of these initiatives. This paper proposes co-financing of these networks as a means of sustaining the bottom-up Broadband network. The argument of this paper is anchored on two of developing country cases. One in India and the other in Ghana. One survived with...

  16. Learning affects top down and bottom up modulation of eye movements in decision making

    DEFF Research Database (Denmark)

    Orquin, Jacob Lund; Bagger, Martin; Mueller Loose, Simone

    2013-01-01

    different information presentation formats. We thereby operationalized top down and bottom up control as the effect of individual utility levels and presentation formats on attention capture on a trial-by-trial basis. The experiment revealed an increase in top down control of eye movements over time...

  17. Learning affects top down and bottom up modulation of eye movements in decision making

    Directory of Open Access Journals (Sweden)

    Jacob L. Orquin

    2013-11-01

    Full Text Available Repeated decision making is subject to changes over time such as decreases in decision time and information use and increases in decision accuracy. We show that a traditional strategy selection view of decision making cannot account for these temporal dynamics without relaxing main assumptions about what defines a decision strategy. As an alternative view we suggest that temporal dynamics in decision making are driven by attentional and perceptual processes and that this view has been expressed in the information reduction hypothesis. We test the information reduction hypothesis by integrating it in a broader framework of top down and bottom up processes and derive the predictions that repeated decisions increase top down control of attention capture which in turn leads to a reduction in bottom up attention capture. To test our hypotheses we conducted a repeated discrete choice experiment with three different information presentation formats. We thereby operationalized top down and bottom up control as the effect of individual utility levels and presentation formats on attention capture on a trial-by-trial basis. The experiment revealed an increase in top down control of eye movements over time and that decision makers learn to attend to high utility stimuli and ignore low utility stimuli. We furthermore find that the influence of presentation format on attention capture reduces over time indicating diminishing bottom up control.

  18. A photofunctional bottom-up bis(dipyrrinato)zinc(II) complex nanosheet

    Science.gov (United States)

    Sakamoto, Ryota; Hoshiko, Ken; Liu, Qian; Yagi, Toshiki; Nagayama, Tatsuhiro; Kusaka, Shinpei; Tsuchiya, Mizuho; Kitagawa, Yasutaka; Wong, Wai-Yeung; Nishihara, Hiroshi

    2015-04-01

    Two-dimensional polymeric nanosheets have recently gained much attention, particularly top-down nanosheets such as graphene and metal chalcogenides originating from bulk-layered mother materials. Although molecule-based bottom-up nanosheets manufactured directly from molecular components can exhibit greater structural diversity than top-down nanosheets, the bottom-up nanosheets reported thus far lack useful functionalities. Here we show the design and synthesis of a bottom-up nanosheet featuring a photoactive bis(dipyrrinato)zinc(II) complex motif. A liquid/liquid interfacial synthesis between a three-way dipyrrin ligand and zinc(II) ions results in a multi-layer nanosheet, whereas an air/liquid interfacial reaction produces a single-layer or few-layer nanosheet with domain sizes of >10 μm on one side. The bis(dipyrrinato)zinc(II) metal complex nanosheet is easy to deposit on various substrates using the Langmuir-Schäfer process. The nanosheet deposited on a transparent SnO2 electrode functions as a photoanode in a photoelectric conversion system, and is thus the first photofunctional bottom-up nanosheet.

  19. Oral bioavailability and pharmacodynamic activity of hesperetin nanocrystals generated using a novel bottom-up technology

    DEFF Research Database (Denmark)

    Shete, Ganesh; Pawar, Yogesh B; Thanki, Kaushik; Jain, Sanyog; Bansal, Arvind Kumar

    2015-01-01

    In the present study, nanocrystalline solid dispersion (NSD) was developed to enhance the release rate and oral bioavailability of hesperetin (HRN). NSD of HRN was prepared using a novel bottom-up technology platform. It is a spray drying based technology to generate solid particles, containing...

  20. Integration of top-down and bottom-up information for audio organization and retrieval

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand

    sources based on latent Dirichlet allocation (LDA). The model is used to integrate bottom-up features (reflecting timbre, loudness, tempo and chroma), meta-data aspects (lyrics) and top-down aspects, namely user generated open vocabulary tags. The model and representation is evaluated on the auxiliary...

  1. Top-down model estimates, bottom-up inventories, and future projections of global natural and anthropogenic emissions of nitrous oxide

    Science.gov (United States)

    Davidson, E. A.; Kanter, D.

    2013-12-01

    Nitrous oxide (N2O) is the third most abundantly emitted greenhouse gas and the largest remaining emitted ozone depleting substance. It is a product of nitrifying and denitrifying bacteria in soils, sediments and water bodies. Humans began to disrupt the N cycle in the preindustrial era as they expanded agricultural land, used fire for land clearing and management, and cultivated leguminous crops that carry out biological N fixation. This disruption accelerated after the industrial revolution, especially as the use of synthetic N fertilizers became common after 1950. Here we present findings from a new United Nations Environment Programme report, in which we constrain estimates of the anthropogenic and natural emissions of N2O and consider scenarios for future emissions. Inventory-based estimates of natural emissions from terrestrial, marine and atmospheric sources range from 10 to 12 Tg N2O-N/yr. Similar values can be derived for global N2O emissions that were predominantly natural before the industrial revolution. While there was inter-decadal variability, there was little or no consistent trend in atmospheric N2O concentrations between 1730 and 1850, allowing us to assume near steady state. Assuming an atmospheric lifetime of 120 years, the 'top-down' estimate of pre-industrial emissions of 11 Tg N2O-N/yr is consistent with the bottom-up inventories for natural emissions, although the former includes some modest pre-industrial anthropogenic effects (probably top-down methodology yields an estimate of 5.3 Tg N2O-N/yr (range 5.2 - 5.5) net anthropogenic emissions for the period 2000-2007. Based on a review of bottom-up inventories, we estimate total net anthropogenic N2O emissions of 6.0 Tg N2O-N/yr (5.4-8.4 Tg N2O-N/yr). Estimates (and ranges) by sector (in Tg N2O-N/yr) are: agriculture 4.1 Tg (3.8-6.8); biomass burning 0.7 (0.5-1.7); energy and transport 0.7 (0.5-1.2); industry 0.7 (0.3-1.1); and other 0.5 (0.2 - 0.8). Tropical deforestation has reduced

  2. Carnosic acid biosynthesis elucidated by a synthetic biology platform.

    Science.gov (United States)

    Ignea, Codruta; Athanasakoglou, Anastasia; Ioannou, Efstathia; Georgantea, Panagiota; Trikka, Fotini A; Loupassaki, Sofia; Roussis, Vassilios; Makris, Antonios M; Kampranis, Sotirios C

    2016-03-29

    Synthetic biology approaches achieving the reconstruction of specific plant natural product biosynthetic pathways in dedicated microbial "chassis" have provided access to important industrial compounds (e.g., artemisinin, resveratrol, vanillin). However, the potential of such production systems to facilitate elucidation of plant biosynthetic pathways has been underexplored. Here we report on the application of a modular terpene production platform in the characterization of the biosynthetic pathway leading to the potent antioxidant carnosic acid and related diterpenes in Salvia pomifera and Rosmarinus officinalis.Four cytochrome P450 enzymes are identified (CYP76AH24, CYP71BE52, CYP76AK6, and CYP76AK8), the combined activities of which account for all of the oxidation events leading to the biosynthesis of the major diterpenes produced in these plants. This approach develops yeast as an efficient tool to harness the biotechnological potential of the numerous sequencing datasets that are increasingly becoming available through transcriptomic or genomic studies. PMID:26976595

  3. Testing of Synthetic Biological Membranes for Forward Osmosis Applications

    Science.gov (United States)

    Parodi, Jurek; Mangado, Jaione Romero; Stefanson, Ofir; Flynn, Michael; Mancinelli, Rocco; Kawashima, Brian; Trieu, Serena; Brozell, Adrian; Rosenberg, Kevan

    2016-01-01

    Commercially available forward osmosis membranes have been extensively tested for human space flight wastewater treatment. Despite the improvements achieved in the last decades, there is still a challenge to produce reliable membranes with anti-fouling properties, chemical resistance, and high flux and selectivity. Synthetic biological membranes that mimic the ones present in nature, which underwent millions of years of evolution, represent a potential solution for further development and progress in membrane technology. Biomimetic forward osmosis membranes based on a polymeric support filter and coated with surfactant multilayers have been engineered to investigate how different manufacturing processes impact the performance and structure of the membrane. However, initial results of the first generation prototype membranes tests reveal a high scatter in the data, due to the current testing apparatus set up. The testing apparatus has been upgraded to improve data collection, reduce errors, and to allow higher control of the testing process.

  4. Can the natural diversity of quorum sensing advance synthetic biology?

    Directory of Open Access Journals (Sweden)

    Rene Michele Davis

    2015-03-01

    Full Text Available Quorum-sensing networks enable bacteria to sense and respond to chemical signals produced by neighboring bacteria. They are widespread: over one hundred morphologically and genetically distinct species of eubacteria are known to use quorum sensing to control gene expression. This diversity suggests the potential to use natural protein variants to engineer parallel, input-specific, cell-cell communication pathways. However, only three distinct signaling pathways, Lux, Las, and Rhl, have been adapted for and broadly used in engineered systems. The paucity of unique quorum-sensing systems and their propensity for crosstalk limits the usefulness of our current quorum-sensing toolkit. This review discusses the need for more signaling pathways, roadblocks to using multiple pathways in parallel, and strategies for expanding the quorum-sensing toolbox for synthetic biology.

  5. The appeasement of Doug: a synthetic approach to enhancer biology.

    Science.gov (United States)

    Vincent, Ben J; Estrada, Javier; DePace, Angela H

    2016-04-18

    Genetic approaches have been instrumental in dissecting developmental enhancers by characterizing their transcription factor binding sites. Though some enhancers have been well-studied in this regard, we cannot currently build developmental enhancers from scratch. Reconstitution experiments can provide important complementary tests of our understanding of enhancer function, but these experiments are exceedingly rare in the literature, possibly due to the difficulty of publishing negative results. In this perspective, we argue that the time is right for a synthetic approach to enhancer biology. Focusing primarily on Drosophila enhancers as examples, we review classic and modern methods for dissecting enhancer function as well as computational tools for enhancer design. We include our own negative results from attempts to reconstitute the stripe 2 enhancer from the even-skipped locus and discuss possible ways forward. We believe that with a communal effort in open data sharing, we can make substantial progress toward a complete understanding of enhancer function. PMID:26936291

  6. 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.

  7. The construction of imaginaries of the public as a threat to synthetic biology

    OpenAIRE

    Marris, C.

    2015-01-01

    Scientific institutions and innovation-focused government bodies have identified public attitudes to synthetic biology as an obstruction to the field. This view is based on a perception that the public is (or will likely become) fearful of synthetic biology and that a ‘public scare’ would impede development of the field. Fear of the public's fear of synthetic biology, which I characterise as ‘synbiophobia-phobia’, has been the driving force behind the promotion of public engagement and other ...

  8. The life cycle of bottom-up ideas : case studies of the companies where the simulation game method was applied

    OpenAIRE

    Forssén, Minna

    2002-01-01

    The main aim of this thesis is to study the life cycle of the incremental "bottom-up" ideas, which concern process and organizational matters. According to earlier studies, bottom-up ideas are not always successfully used and managed and as well there exists need for more study on organizational and process innovations. It is therefore useful to study this phenomenon more and gain more information about how organizations manage the development and implementation of these bottom-up ideas. ...

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

    Science.gov (United States)

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

    2016-01-01

    BrisSynBio is the Bristol-based Biotechnology and Biological Sciences Research Council (BBSRC)/Engineering and Physical Sciences Research Council (EPSRC)-funded Synthetic Biology Research Centre. It is one of six such Centres in the U.K. BrisSynBio's emphasis is on rational and predictive bimolecular modelling, design and engineering in the context of synthetic biology. It trains the next generation of synthetic biologists in these approaches, to facilitate translation of fundamental synthetic biology research to industry and the clinic, and to do this within an innovative and responsible research framework. PMID:27284028

  10. Metabolic modelling in the development of cell factories by synthetic biology

    Directory of Open Access Journals (Sweden)

    Paula Tuulia Jouhten

    2012-10-01

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

  11. Synthetic Biology as an Enabling Technology for Space Exploration

    Science.gov (United States)

    Rothschild, Lynn J.

    2016-01-01

    Human exploration off planet is severely limited by the cost of launching materials into space and by re-supply. Thus materials brought from Earth must be light, stable and reliable at destination. Using traditional approaches, a lunar or Mars base would require either transporting a hefty store of metals or heavy manufacturing equipment and construction materials for in situ extraction; both would severely limit any other mission objectives. Long-term human space presence requires periodic replenishment, adding a massive cost overhead. Even robotic missions often sacrifice science goals for heavy radiation and thermal protection. Biology has the potential to solve these problems because life can replicate and repair itself, and perform a wide variety of chemical reactions including making food, fuel and materials. Synthetic biology enhances and expands life's evolved repertoire. Using organisms as feedstock, additive manufacturing through bioprinting will make possible the dream of producing bespoke tools, food, smart fabrics and even replacement organs on demand. This new approach and the resulting novel products will enable human exploration and settlement on Mars, while providing new manufacturing approaches for life on Earth.

  12. Synthetic Biology and the Search for Extraterrestrial Life

    Science.gov (United States)

    Rothschild, L. J.; Fujishima, K.

    2014-03-01

    "Are we alone?" is one of the primary questions of astrobiology, and whose answer defines our significance in the universe. Unfortunately, this quest is hindered by the fact that we have only one confirmed example of life, that of earth. While this is enormously helpful in helping to define the minimum envelope for life, it strains credulity to imagine that life, if it arose multiple times, has not taken other routes. To help fill this gap, our lab has begun using synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - as an enabling technology. One theme, the "Hell Cell" project, focuses on creating artificial extremophiles in order to push the limits for Earth life, and to understand how difficult it is for life to evolve into extreme niches. In another project, we are reevolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids. This should lead to a more universal theory of the origin of life based on materials found commonly in meteorites and other pre-biotic settings.

  13. The generation of myricetin-nicotinamide nanococrystals by top down and bottom up technologies.

    Science.gov (United States)

    Liu, Mingyu; Hong, Chao; Li, Guowen; Ma, Ping; Xie, Yan

    2016-09-30

    Myricetin-nicotinamide (MYR-NIC) nanococrystal preparation methods were developed and optimized using both top down and bottom up approaches. The grinding (top down) method successfully achieved nanococrystals, but there were some micrometer range particles and aggregation. The key consideration of the grinding technology was to control the milling time to determine a balance between the particle size and distribution. In contrast, a modified bottom up approach based on a solution method in conjunction with sonochemistry resulted in a uniform MYR-NIC nanococrystal that was confirmed by powder x-ray diffraction, scanning electron microscopy, dynamic light scattering, and differential scanning calorimeter, and the particle dissolution rate and amount were significantly greater than that of MYR-NIC cocrystal. Notably, this was a simple method without the addition of any non-solvent. We anticipate our findings will provide some guidance for future nanococrystal preparation as well as its application in both chemical and pharmaceutical area. PMID:27535365

  14. Cognitive Functions of the Posterior Parietal Cortex: Top-down and bottom-up attentional control

    Directory of Open Access Journals (Sweden)

    Sarah Shomstein

    2012-07-01

    Full Text Available Although much less is known about human parietal cortex than that of homologous monkey cortex, recent studies, employing neuroimaging and neuropsychological methods, have begun to elucidate increasingly fine-grained functional and structural distinctions.\tThis review is focused on recent neuroimaging and neuropsychological studies elucidating the cognitive roles of dorsal and ventral regions of parietal cortex in top-down and bottom-up attentional orienting, and on the interaction between the two attentional allocation mechanisms. Evidence is reviewed arguing that regions along the dorsal areas of the parietal cortex, including the superior parietal lobule (SPL are involved in top-down attentional orienting, while ventral regions including the temporo-parietal junction (TPJ are involved in bottom-up attentional orienting.

  15. Hybrid Top-Down/Bottom-Up Strategy Using Superwettability for the Fabrication of Patterned Colloidal Assembly.

    Science.gov (United States)

    Wang, Yuezhong; Wei, Cong; Cong, Hailin; Yang, Qiang; Wu, Yuchen; Su, Bin; Zhao, Yongsheng; Wang, Jingxia; Jiang, Lei

    2016-02-24

    Superwettability of substrates has had a profound influence on the production of novel and advanced colloidal assemblies in recent decades owing to its effect on the spreading area, evaporation rate, and the resultant assembly structure. In this paper, we investigated in detail the influence of the superwettability of a transfer/template substrate on the colloidal assembly from a hybrid top-down/bottom-up strategy. By taking advantage of a superhydrophilic flat transfer substrate and a superhydrophobic groove-structured silicon template, the patterned colloidal microsphere assembly was formed including linear and mesh-, cyclic-, and multistopband assembly arrays of microspheres, and the optic-waveguide of a circular colloidal structure was demonstrated. We believed this liquid top-down/bottom-up strategy would open an efficient avenue for assembling/integrating microspheres building blocks into device applications in a low-cost manner. PMID:26824430

  16. Co-financing of bottom-up approaches towards Broadband Infrastructure Development:

    DEFF Research Database (Denmark)

    Williams, Idongesit

    2016-01-01

    Bottom – up Broadband infrastructure development facilitated by the civil societies and social enterprises are on the increase. However, the problem plaguing the development of these bottom-up approaches in developing countries is the financial capacity to expand their small networks into larger...... networks –leading to the demise of some of these initiatives. This paper proposes co-financing of these networks as a means of sustaining the bottom-up Broadband network. The argument of this paper is anchored on two of developing country cases. One in India and the other in Ghana. One survived with...... financial injection and the other did not due to low revenue. This paper, based on these cases, proposes the utilization and the reintroduction of Universal Service funds in developing countries to aid these small networks. This is a qualitative study, the Grounded Theory approach was used adopted gather...

  17. A balance of bottom-up and top-down in linking climate policies

    Science.gov (United States)

    Green, Jessica F.; Sterner, Thomas; Wagner, Gernot

    2014-12-01

    Top-down climate negotiations embodied by the Kyoto Protocol have all but stalled, chiefly because of disagreements over targets and objections to financial transfers. To avoid those problems, many have shifted their focus to linkage of bottom-up climate policies such as regional carbon markets. This approach is appealing, but we identify four obstacles to successful linkage: different levels of ambition; competing domestic policy objectives; objections to financial transfers; and the difficulty of close regulatory coordination. Even with a more decentralized approach, overcoming the 'global warming gridlock' of the intergovernmental negotiations will require close international coordination. We demonstrate how a balance of bottom-up and top-down elements can create a path toward an effective global climate architecture.

  18. Transition UGent: a bottom-up initiative towards a more sustainable university

    OpenAIRE

    Block, Thomas; Van de Velde, Riet

    2016-01-01

    The vibrant think-tank ‘Transition UGent’ engaged over 250 academics, students and people from the university management in suggesting objectives and actions for the Sustainability Policy of Ghent University (Belgium). Founded in 2012, this bottom-up initiative succeeded to place sustainability high on the policy agenda of our university. Through discussions within 9 working groups and using the transition management method, Transition UGent developed system analyses, sustainability visions a...

  19. Integrating top down policies and bottom up practices in Urban and Periurban Agriculture: an Italian dilemma

    OpenAIRE

    Cinà, Giuseppe; Di Iacovo, Francesco

    2015-01-01

    The paper deals with some relevant and contradictory aspects of urban and peri-urban agriculture in Italy: the traditional exclusion of agricultural areas from the goals of territorial planning; the separation between top-down policies and bottom-up practices; the lack of agricultural policies at local scale. In the first part the paper summarises the weak relation between urban planning and agriculture, showing how in Italy this gap has been only partially overcome by new laws and plans. Mor...

  20. Reforming the taxation of multijurisdictional enterprises in Europe: coopetition in a bottom-up federation

    OpenAIRE

    Gérard, Marcel

    2006-01-01

    This paper investigates replacing separate taxation by consolidation and formulary apportionment in a Bottom-up Federation, when a multijurisdictional firm is mobile in various respects. The reform is decided cooperatively by all the jurisdictions or by some of them, while tax rates remain within the competence of each jurisdiction. The paper sets forth the conditions for the reform to be social welfare enhancing, while not increasing tax competition. Among them, the formula should emphasize ...

  1. Bottom-up effects of soil quality on a coffee arthropod interaction web

    OpenAIRE

    Gonthier, DJ; Dominguez, GM; Witter, JD; Spongberg, AL; Philpott, SM

    2013-01-01

    Nutrient availability and soil quality influence herbivores through changes in plant traits and can have cascading effects on herbivore interactions. In complex systems, with many positive and negative interactions, the consequences of these bottom-up effects are still not well established. We carried out a set of studies to determine the impact of soil quality (organic compost amendments) on a hemipteran herbivore (Coccus viridis), two ant mutualists, predators, pathogens, parasitoids of C. ...

  2. Self-assembled nanostructured resistive switching memory devices fabricated by templated bottom-up growth

    OpenAIRE

    Ji-Min Song; Jang-Sik Lee

    2016-01-01

    Metal-oxide-based resistive switching memory device has been studied intensively due to its potential to satisfy the requirements of next-generation memory devices. Active research has been done on the materials and device structures of resistive switching memory devices that meet the requirements of high density, fast switching speed, and reliable data storage. In this study, resistive switching memory devices were fabricated with nano-template-assisted bottom up growth. The electrochemical ...

  3. Public participation GIS to support a bottom-up approach in forest landscape planning

    OpenAIRE

    Paletto A; Lora C; Frattegiani M; De Meo I; Ferretti F

    2013-01-01

    Forest landscape planning analyses all forest aspects (economic, ecological and social) and defines long-term forest management guidelines. Various actors are involved in landscape planning; therefore the analysis needs to take into account goals and targets of the different stakeholders. The participatory process can strongly support the development of a bottom-up forest plan definition when stakeholders are involved throughout the decision-making process. In this way, management guidelines ...

  4. Environmental Sustainability and Regulation: To-Down Versus Bottom-Up Regulation

    OpenAIRE

    Mariam, Yohannes

    2001-01-01

    Environmental regulation can be broadly divided into those that follow the top-down and bottom-up approaches. The two approaches have similar objective with respect to environmental protection and sustainability. However, the success with which each approach achieves goals of environmental protection and sustainability may vary. Moreover, the costs and benefits of each approach differ. The present study will explore the implication of environmental regulation to sustainability, costs associat...

  5. New bottom-up algorithm for assembly plan generation : opportunities for micro-factory design.

    OpenAIRE

    Perrard, Christophe; Lutz, Philippe; Salgueiro, Paulo

    2007-01-01

    This paper discusses a new approach dedicated to assembly plan generation, called "bottom-up algorithm". It is compared to the traditional "top-down approach", usually used to perform this stage of the design process of the assembly systems for "macro-products". We explore why this new algorithm is better adapted for designing a microassembly system. The case of watch assembly plans generation is described through the both approaches and the obtained results are compared.

  6. Bottom-Up Dependent Gating of Frontal Signals in Early Visual Cortex

    OpenAIRE

    Ekstrom, L. B.; P. R. Roelfsema; Arsenault, J.T.; Bonmassar, G.; Vanduffel, W.

    2008-01-01

    The frontal eye field (FEF) is one of several cortical regions thought to modulate sensory inputs. Moreover, several hypotheses suggest that the FEF can only modulate early visual areas in the presence of a visual stimulus. To test for bottom-up gating of frontal signals, we microstimulated subregions in the FEF of two monkeys and measured the effects throughout the brain with functional magnetic resonance imaging. The activity of higher-order visual areas was strongly modulated by FEF stimul...

  7. Combining shape and color: a bottom-up approach to evaluate object similarities

    OpenAIRE

    PASCUCCI, ALESSIO

    2011-01-01

    The objective of the present work is to develop a bottom-up approach to estimate the similarity between two unknown objects. Given a set of digital images, we want to identify the main objects and to determine whether they are similar or not. In the last decades many object recognition and classification strategies, driven by higher-level activities, have been successfully developed. The peculiarity of this work, instead, is the attempt to work without any training phase nor a priori knowledg...

  8. The Application of Bottom-up and Top-down Processing in L2 Listening Comprehension

    Institute of Scientific and Technical Information of China (English)

    温颖茜

    2008-01-01

    Listening comprehension is one of the four basic skills for language learning and is also one of the most difficult tasks L2 learners ever experienced.L2 listening comprehemion is a cognitvive process,in which listeners use both bottom-up andtop-downprocessing to comprehend the auraltext.Thepaper focmes on the applicationof the two approaches in L2 lis-tening comprehemiom

  9. A VHDL-AMS Modeling Methodology for Top-Down/Bottom-Up Design of RF Systems

    OpenAIRE

    Maehne, Torsten; Vachoux, Alain; Giroud, Frédéric; Contaldo, Matteo

    2009-01-01

    This paper presents a modelling methodology for the top-down/bottom-up design of RF systems based on systematic use of VHDL-AMS models. The model interfaces are parameterizable and pin-accurate. The designer can choose to parameterize the models using performance specifications or device parameters back-annotated from the transistor-level implementation. The abstraction level used for the description of the respective analog/digital component behavior has been chosen to achieve a good t...

  10. Can bottom-up ocean CO2 fluxes be reconciled with atmospheric 13C observations?

    OpenAIRE

    Alden, Caroline B.; Miller, John B.; White, James W.C.

    2011-01-01

    The rare stable carbon isotope, 13C, has been used previously to partition CO2 fluxes into land and ocean components. Net ocean and land fluxes impose distinctive and predictable fractionation patterns upon the stable isotope ratio, making it an excellent tool for distinguishing between them. Historically, isotope constrained inverse methods for calculating CO2 surface fluxes—the ‘double deconvolution’—have disagreed with bottom-up ocean flux estimates. In this study, we use the double deconv...

  11. Bottom-Up Cost Analysis of a High Concentration PV Module

    Energy Technology Data Exchange (ETDEWEB)

    Horowitz, Kelsey A. W.; Woodhouse, Michael; Lee, Hohyun; Smestad, Greg P.

    2016-03-31

    We present a bottom-up model of III-V multi-junction cells, as well as a high concentration PV (HCPV) module. We calculate $0.59/W(DC) manufacturing costs for our model HCPV module design with today's capabilities, and find that reducing cell costs and increasing module efficiency offer the most promising paths for future cost reductions. Cell costs could be significantly reduced via substrate reuse and improved manufacturing yields.

  12. Plasma-surface interactions for top-down and bottom-up nanofabrication

    Science.gov (United States)

    Ono, Kouichi

    2015-09-01

    Plasma processing is now widely employed for the fabrication of nanostructures in diverse fields of micro/nanoelectronic, optoelectronic, energy conversion, and sensing devices. The top-down plasma processes are indispensable in today's microelectronics industry, relying on the use of primarily anisotropic plasma etching following the lithography to define mask patterns; in some cases, self-assembled masks are served for the subsequent etching. The bottom-up ones are often employed to synthesize nanostructures such as nanotubes and nanowires, relying on the use of plasma enhanced chemical vapor deposition and plasma sputtering on self-assembled as well as lithographically formed patterns of metal catalysts. Moreover, the mask-less top-down approaches have recently been demonstrated to form nanopillars and periodic nanoripples, and the catalyst-free bottom-up approaches have been demonstrated to form nanowires. This talk is concerned with the current understanding and future prospects for plasma-surface interactions responsible for these top-down and bottom-up plasma nanofabrication processes, with attention placed on the fabrication of nanoscale fins and gates and also nanowires of silicon. On nanometer scale, ions and neutrals incident on surfaces are few in number during processing; thus, the nanoscale plasma-surface interactions concerned are stochastic, owing to the temporal as well as spatial uniformity of the incident flux and angle of them on surfaces being processed at nanoscale.

  13. Top-down and bottom-up definitions of human failure events in human reliability analysis

    International Nuclear Information System (INIS)

    In the probabilistic risk assessments (PRAs) used in the nuclear industry, human failure events (HFEs) are determined as a subset of hardware failures, namely those hardware failures that could be triggered by human action or inaction. This approach is top-down, starting with hardware faults and deducing human contributions to those faults. Elsewhere, more traditionally human factors driven approaches would tend to look at opportunities for human errors first in a task analysis and then identify which of those errors is risk significant. The intersection of top-down and bottom-up approaches to defining HFEs has not been carefully studied. Ideally, both approaches should arrive at the same set of HFEs. This question is crucial, however, as human reliability analysis (HRA) methods are generalized to new domains like oil and gas. The HFEs used in nuclear PRAs tend to be top-down - defined as a subset of the PRA - whereas the HFEs used in petroleum quantitative risk assessments (QRAs) often tend to be bottom-up - derived from a task analysis conducted by human factors experts. The marriage of these approaches is necessary in order to ensure that HRA methods developed for top-down HFEs are also sufficient for bottom-up applications.

  14. A Bottom-up Trend in Research of Management of Technology

    Directory of Open Access Journals (Sweden)

    Yoko Ishino

    2014-12-01

    Full Text Available Management of Technology (MOT is defined as an academic discipline of management that enables organizations to manage their technological fundamentals to create competitive advantage. MOT covers a wide range of contents including administrative strategy, R&D management, manufacturing management, technology transfer, production control, marketing, accounting, finance, business ethics, and others. For each topic, researchers have conducted their MOT research at various levels. However, a practical and pragmatic side of MOT surely affects its research trends. Finding changes of MOT research trends, or the chronological transitions of principal subjects, can help understand the key concepts of current MOT. This paper studied a bottom-up trend in research fields in MOT by applying a text-mining method to the conference proceedings of IAMOT (International Association for Management of Technology. First, focusing on only nouns found several keywords, which more frequently emerge over time in the IAMOT proceedings. Then, expanding the scope into other parts of speech viewed the keywords in a natural context. Finally, it was found that the use of an important keyword has qualitatively and quantitatively extended over time. In conclusion, a bottom-up trend in MOT research was detected and the effects of the social situation on the trend were discussed.Keywords: Management of Technology; Text Mining; Research Trend; Bottom-up Trend; Patent

  15. Top-down and bottom-up modulation in processing bimodal face/voice stimuli

    Directory of Open Access Journals (Sweden)

    VanRullen Rufin

    2010-03-01

    Full Text Available Abstract Background Processing of multimodal information is a critical capacity of the human brain, with classic studies showing bimodal stimulation either facilitating or interfering in perceptual processing. Comparing activity to congruent and incongruent bimodal stimuli can reveal sensory dominance in particular cognitive tasks. Results We investigated audiovisual interactions driven by stimulus properties (bottom-up influences or by task (top-down influences on congruent and incongruent simultaneously presented faces and voices while ERPs were recorded. Subjects performed gender categorisation, directing attention either to faces or to voices and also judged whether the face/voice stimuli were congruent in terms of gender. Behaviourally, the unattended modality affected processing in the attended modality: the disruption was greater for attended voices. ERPs revealed top-down modulations of early brain processing (30-100 ms over unisensory cortices. No effects were found on N170 or VPP, but from 180-230 ms larger right frontal activity was seen for incongruent than congruent stimuli. Conclusions Our data demonstrates that in a gender categorisation task the processing of faces dominate over the processing of voices. Brain activity showed different modulation by top-down and bottom-up information. Top-down influences modulated early brain activity whereas bottom-up interactions occurred relatively late.

  16. Top-down or bottom-up modelling. An application to CO2 abatement

    International Nuclear Information System (INIS)

    In four articles a comparison is made of bottom-up, or engineers'' models, and top-down models, which comprise macro-econometric models, computable general equilibrium models and also models in the system dynamics tradition. In the first article the history of economic modelling is outlined. In the second article the multi-sector macro-economic Computable General Equilibrium model for the Netherlands is described. It can be used to study the long-term effects of fiscal policy measures on economic and environmental indicators, in particular the effects on the level of CO2-emissions. The aim of article 3 is to describe the structure of the electricity supply industry in the UK and how it can be represented in a bottom-up sub-model within a more general E3 sectoral model of the UK economy. The objective of the last paper (4) is mainly a methodological discussion about integrating top-down and bottom-up models which can be used to assess CO2 abatement policies impacts on economic activity

  17. Enabling a next generation of synthetic biology community organization and leadership.

    Science.gov (United States)

    Palmer, Megan J; Jewett, Michael C

    2014-03-21

    Synthetic biology seeks to make engineering of complex biological functions more efficient, reliable, and predictable. Advancing the process of engineering biology requires community organization and leadership. As synthetic biology matures into a globally significant enterprise, the community needs to enable a next generation of leaders to organize the field's responsible advancement. We discuss key points raised at a community meeting on these issues at SB6.0--the Sixth International Meeting on Synthetic Biology--and highlight opportunities to carry forward the conversation. PMID:24617412

  18. Zooplankton and forage fish species off Peru: Large-scale bottom-up forcing and local-scale depletion

    Science.gov (United States)

    Ayón, Patricia; Swartzman, Gordon; Bertrand, Arnaud; Gutiérrez, Mariano; Bertrand, Sophie

    2008-10-01

    The Humboldt Current System, like all upwelling systems, has dramatic quantities of plankton-feeding fish, which suggested that their population dynamics may ‘drive’ or ‘control’ ecosystem dynamics. With this in mind we analysed the relationship between forage fish populations and their main prey, zooplankton populations. Our study combined a zooplankton sampling program (1961-2005) with simultaneous acoustic observations on fish from 40 pelagic surveys (1983-2005) conducted by the Peruvian Marine Research Institute (IMARPE) and landing statistics for anchoveta ( Engraulis ringens) and sardine ( Sardinops sagax) along the Peruvian coast from 1961 to 2005. The multi-year trend of anchoveta population abundance varied consistently with zooplankton biovolume trend, suggesting bottom-up control on anchovy at the population scale (since oceanographic conditions and phytoplankton production support the changes in zooplankton abundance). For a finer-scale analysis (km) we statistically modelled zooplankton biovolume as a function of geographical (latitude and distance from the 200-m isobath), environmental (sea surface temperature), temporal (year, month and time-of-day) and biological (acoustic anchovy and sardine biomass within 5 km of each zooplankton sample) covariates over all survey using both classification and regression trees (CART) and generalized additive models (GAM). CART showed local anchoveta density to have the strongest effect on zooplankton biovolume, with significantly reduced levels of biovolume for higher neighbourhood anchoveta biomass. Additionally, zooplankton biovolume was higher offshore than on the shelf. GAM results corroborated the CART findings, also showing a clear diel effect on zooplankton biovolume, probably due to diel migration or daytime net avoidance. Apparently, the observed multi-year population scale bottom-up control is not inconsistent with local depletion of zooplankton when anchoveta are locally abundant, since the

  19. Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

    Science.gov (United States)

    Wagner, James M; Alper, Hal S

    2016-04-01

    Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. PMID:26701310

  20. DNA Nanostructures on Membranes as Tools for Synthetic Biology.

    Science.gov (United States)

    Czogalla, Aleksander; Franquelim, Henri G; Schwille, Petra

    2016-04-26

    Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompatible building material on the nanoscale. The possibility to chemically integrate functional groups into oligonucleotides, most notably with lipophilic anchors, enabled a widespread usage of DNA as a viable alternative to proteins with respect to functional activity on membranes. As described throughout this review, hybrid DNA-lipid nanostructures can mediate events such as vesicle docking and fusion, or selective partitioning of molecules into phase-separated membranes. Moreover, the major benefit of DNA structural constructs, such as DNA tiles and DNA origami, is the reproducibility and simplicity of their design. DNA nanotechnology can produce functional structures with subnanometer precision and allow for a tight control over their biochemical functionality, e.g., interaction partners. DNA-based membrane nanopores and origami structures able to assemble into two-dimensional networks on top of lipid bilayers are recent examples of the manifold of complex devices that can be achieved. In this review, we will shortly present some of the potentially most relevant avenues and accomplishments of membrane-anchored DNA nanostructures for investigating, engineering, and mimicking lipid membrane-related biophysical processes. PMID:27119630

  1. Improving microalgae for biotechnology--From genetics to synthetic biology.

    Science.gov (United States)

    Hlavova, Monika; Turoczy, Zoltan; Bisova, Katerina

    2015-11-01

    Microalgae have traditionally been used in many biotechnological applications, where each new application required a different species or strain expressing the required properties; the challenge therefore is to isolate or develop, characterize and optimize species or strains that can express more than one specific property. In agriculture, breeding of natural variants has been successfully used for centuries to improve production traits in many existing plant and animal species. With the discovery of the concepts of classical genetics, these new ideas have been extensively used in selective breeding. However, many biotechnologically relevant algae do not possess the sexual characteristics required for traditional breeding/crossing, although they can be modified by chemical and physical mutagens. The resulting mutants are not considered as genetically modified organisms (GMOs) and their cultivation is therefore not limited by legislation. On the other hand, mutants prepared by random or specific insertion of foreign DNA are considered to be GMOs. This review will compare the effects of two genetic approaches on model algal species and will summarize their advantages in basic research. Furthermore, we will discuss the potential of mutagenesis to improve microalgae as a biotechnological resource, to accelerate the process from specific strain isolation to growth optimization, and discuss the production of new products. Finally, we will explore the potential of algae in synthetic biology. PMID:25656099

  2. Visual anticipation biases conscious perception but not bottom-up visual processing

    Directory of Open Access Journals (Sweden)

    Paul F.M.J. Verschure

    2015-01-01

    Full Text Available Theories of consciousness can be grouped with respect to their stance on embodiment, sensori-motor contingencies, prediction and integration. In this list prediction plays a key role and it is not clear which aspects of prediction are most prominent in the conscious scene. An evolving view on the brain is that it can be seen as a prediction machine that optimizes its ability to predict states of the world and the self through the top-down propagation of predictions and the bottom-up presentation of prediction errors. There are competing views though on whether prediction or prediction errors dominate the conscious scene. Yet, due to the lack of efficient indirect measures, the dynamic effects of prediction on perception, decision making and consciousness have been difficult to assess and to model. We propose a novel mathematical framework and psychophysical paradigm that allows us to assess both the hierarchical structuring of perceptual consciousness, its content and the impact of predictions and / or errors on the conscious scene. Using a displacement detection task combined with reverse correlation we reveal signatures of the usage of prediction at three different levels of perception: bottom-up early saccades, top-down driven late saccades and conscious decisions. Our results suggest that the brain employs multiple parallel mechanisms at different levels of information processing to restrict the sensory field using predictions. We observe that cognitive load has a quantifiable effect on this dissociation of the bottom-up sensory and top-down predictive processes. We propose a probabilistic data association model from dynamical systems theory to model this predictive bias in different information processing levels.

  3. Neural activities in V1 create the bottom-up saliency map of natural scenes.

    Science.gov (United States)

    Chen, Cheng; Zhang, Xilin; Wang, Yizhou; Zhou, Tiangang; Fang, Fang

    2016-06-01

    A saliency map is the bottom-up contribution to the deployment of exogenous attention. It, as well as its underlying neural mechanism, is hard to identify because of the influence of top-down signals. A recent study showed that neural activities in V1 could create a bottom-up saliency map (Zhang et al. in Neuron 73(1):183-192, 2012). In this paper, we tested whether their conclusion can generalize to complex natural scenes. In order to avoid top-down influences, each image was presented with a low contrast for only 50 ms and was followed by a high contrast mask, which rendered the whole image invisible to participants (confirmed by a forced-choice test). The Posner cueing paradigm was adopted to measure the spatial cueing effect (i.e., saliency) by an orientation discrimination task. A positive cueing effect was found, and the magnitude of the cueing effect was consistent with the saliency prediction of a computational saliency model. In a following fMRI experiment, we used the same masked natural scenes as stimuli and measured BOLD signals responding to the predicted salient region (relative to the background). We found that the BOLD signal in V1, but not in other cortical areas, could well predict the cueing effect. These results suggest that the bottom-up saliency map of natural scenes could be created in V1, providing further evidence for the V1 saliency theory (Li in Trends Cogn Sci 6(1):9-16, 2002). PMID:26879771

  4. Coupled multi-physics simulation frameworks for reactor simulation: A bottom-up approach

    International Nuclear Information System (INIS)

    A 'bottom-up' approach to multi-physics frameworks is described, where first common interfaces to simulation data are developed, then existing physics modules are adapted to communicate through those interfaces. Physics modules read and write data through those common interfaces, which also provide access to common simulation services like parallel IO, mesh partitioning, etc.. Multi-physics codes are assembled as a combination of physics modules, services, interface implementations, and driver code which coordinates calling these various pieces. Examples of various physics modules and services connected to this framework are given. (author)

  5. Unsupervised tattoo segmentation combining bottom-up and top-down cues

    Science.gov (United States)

    Allen, Josef D.; Zhao, Nan; Yuan, Jiangbo; Liu, Xiuwen

    2011-06-01

    Tattoo segmentation is challenging due to the complexity and large variance in tattoo structures. We have developed a segmentation algorithm for finding tattoos in an image. Our basic idea is split-merge: split each tattoo image into clusters through a bottom-up process, learn to merge the clusters containing skin and then distinguish tattoo from the other skin via top-down prior in the image itself. Tattoo segmentation with unknown number of clusters is transferred to a figureground segmentation. We have applied our segmentation algorithm on a tattoo dataset and the results have shown that our tattoo segmentation system is efficient and suitable for further tattoo classification and retrieval purpose.

  6. Public engagement as a field of tension between bottom-up and top-down strategies

    DEFF Research Database (Denmark)

    Horsbøl, Anders; Lassen, Inger

    2012-01-01

    In the ongoing debate about climate change, public engagement is given increasing prominence as a possible solution to a general lack of citizen participation in climate change mitigation efforts. Recent years have seen a surge in public engagement initiatives in many countries in the Western world....... These initiatives often have to deal with dilemmas between participatory aspects and other considerations such as planning efficiency, dilemmas that potentially bring about tension between bottom-up and top-down strategies. Literature on climate change issues has addressed the failure of public response...... more knowledge and information about climate change has not significantly changed people’s behaviour towards higher involvement....

  7. Supporting Frequent Updates in R-Trees: A Bottom-Up Approach

    DEFF Research Database (Denmark)

    Lee, Mong Li; Hsu, Wynne; Jensen, Christian Søndergaard;

    2003-01-01

    locality. While the R-tree is the index of choice for multi-dimensional data with low dimensionality, and is thus relevant to these applications, R-tree updates are also relatively inefficient. We present a generalized bottom-up update strategy for R-trees that generalizes existing update techniques and......Advances in hardware-related technologies promise to enable new data management applications that monitor continuous processes. In these applications, enormous amounts of state samples are obtained via sensors and are streamed to a database. Further, updates are very frequent and may exhibit...

  8. NEMO. Netherlands Energy demand MOdel. A top-down model based on bottom-up information

    International Nuclear Information System (INIS)

    The title model links energy use to other production factors, (physical) production, energy prices, technological trends and government policies. It uses a 'putty-semiputty' vintage production structure, in which new investments, adaptations to existing capital goods (retrofit) and 'good-housekeeping' are discerned. Price elasticities are relatively large in the long term and small in the short term. Most predictions of energy use are based on either econometric models or on 'bottom-up information', i.e. disaggregated lists of technical possibilities for and costs of saving energy. Typically, one predicts more energy-efficiency improvements using bottom-up information than using econometric ('top-down') models. We bridged this so-called 'energy-efficiency gap' by designing our macro/meso model NEMO in such a way that we can use bottom-up (micro) information to estimate most model parameters. In our view, reflected in NEMO, the energy-efficiency gap arises for two reasons. The first is that firms and households use a fairly high discount rate of 15% when evaluating the profitability of energy-efficiency improvements. The second is that our bottom-up information ('ICARUS') for most economic sectors does not (as NEMO does) take account of the fact that implementation of new, energy-efficient technology in capital stock takes place only gradually. Parameter estimates for 19 sectors point at a long-term technological energy efficiency improvement trend in Netherlands final energy use of 0.8% per year. The long-term price elasticity is estimated to be 0.29. These values are comparable to other studies based on time series data. Simulations of the effects of the oil price shocks in the seventies and the subsequent fall of oil prices show that the NEMO's price elasticities are consistent with historical data. However, the present pace at which new technologies become available (reflected in NEMO) appears to be lower than in the seventies and eighties. This suggests that it

  9. Bottom-up approach for the fabrication of spin torque nano-oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Darques, M; De la Torre Medina, J; Abreu Araujo, F; Piraux, L [Institute of Condensed Matter and Nanosciences, Universite catholique de Louvain, Croix du Sud 1, Louvain-la-Neuve (Belgium); Dussaux, A; Khvalkovskiy, A V; Guillemet, R; Bouzehouane, K; Fusil, S; Grollier, J; Cros, V [Unite Mixte de Physique CNRS/Thales and Universite Paris Sud 11, Palaiseau (France); Avanesyan, G G; Zvezdin, K A, E-mail: michael.darques@uclouvain.be [A.M. Prokhorov General Physics Institute of RAS, Vavilova str. 38, Moscow (Russian Federation)

    2011-03-16

    We report on a bottom-up approach for the fabrication of spin-transfer nano-oscillators (STNOs). Porous alumina is used as a template for the growth by electrodeposition of metallic spin valves in series. Under specific magnetic field and injected current conditions, emission of microwave current is detected with frequency in the 1.5 GHz range and linewidth as low as 8 MHz. We find strong indications that the microwave emission is due to spin-transfer-driven vortex oscillations. This technique is promising for the fabrication of dense arrays of STNOs in view of device synchronization.

  10. Bottom-up assembly of hydrophobic nanocrystals and graphene nanosheets into mesoporous nanocomposites.

    Science.gov (United States)

    Huang, Jijiang; Liu, Wenxian; Wang, Li; Sun, Xiaoming; Huo, Fengwei; Liu, Junfeng

    2014-04-22

    A general strategy for constructing graphene-based nanocomposites is achieved by emulsion-based bottom-up self-assembly of hydrophobic nanocrystals (NCs) to positively charged colloidal spheres, followed by the electrostatic assembly of NC colloidal spheres with negatively charged graphene oxide in an acidulous aqueous solution. With a simple heat treatment, 3D mesoporous NC spheres/graphene composites are obtained. TiO2/graphene composites typically exhibit a better rate capability and cycle performance than do the corresponding isolated TiO2 spheres. PMID:24684553

  11. Assessment of the Bottom-up Budgeting Process for FY 2015

    OpenAIRE

    Manasan, Rosario G.

    2015-01-01

    The bottom-up budgeting (BUB) process is one of the major reform initiatives of the Aquino administration and has been tagged as such from several perspectives. First, it is seen as a component of its budget reform thrusts that are aimed at making the national government budgeting process more responsive to local needs. Second, the BUB is viewed as part of the democracy/empowerment reform as it opens another avenue for people`s participation in local planning and budgeting and for generating ...

  12. Representing energy technologies in top-down economic models using bottom-up information

    International Nuclear Information System (INIS)

    The rate and magnitude of technological change is a critical component in estimating future anthropogenic carbon emissions. We present a methodology for modeling low-carbon emitting technologies within the MIT Emissions Prediction and Policy Analysis (EPPA) model, a computable general equilibrium (CGE) model of the world economy. The methodology translates bottom-up engineering information for two carbon capture and sequestration (CCS) technologies in the electric power sector into the EPPA model and discusses issues that arise in assuring an accurate representation and realistic market penetration. We find that coal-based technologies with sequestration penetrate, despite their higher cost today, because of projected rising natural gas prices. (author)

  13. WORD-OF-MOUTH MARKETING AND ENTERPRISE STRATEGIES: A BOTTOM-UP DIFFUSION MODEL

    OpenAIRE

    Remondino, Marco

    2011-01-01

    A comprehensive simulation model is presented, aimed to show the dynamics of social diffusion based on the word of mouth (e.g.: viral marketing) over a social network of interconnected individuals. The model is build following a bottom-up approach and the agent based paradigm; this means that the dynamics of the diffusion is simulated in real time and generated at the micro level, not calculated by using mathematical formulas. This allows both to follow – step by step – the emergent process a...

  14. Supporting Frequent Updates in R-Trees: A Bottom-Up Approach

    DEFF Research Database (Denmark)

    Lee, Mong Li; Hsu, Wynne; Jensen, Christian Søndergaard; Cui, Bin; Teo, Keng Lik

    2004-01-01

    Advances in hardware-related technologies promise to enable new data management applications that monitor continuous processes. In these applications, enormous amounts of state samples are obtained via sensors and are streamed to a database. Further, updates are very frequent and may exhibit...... improve update performance. It has different levels of reorganization - ranging from global to local - during updates, avoiding expensive top-down updates. A compact main-memory summary structure that allows direct access to the R-tree index nodes is used together with efficient bottom-up algorithms...

  15. Life by design: Philosophical perspectives on synthetic biology

    Directory of Open Access Journals (Sweden)

    Bensaude Vincent Bernadette

    2015-01-01

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

  16. The Transnational Governance of Synthetic Biology: Scientific uncertainty, cross-borderness and the 'art' of governance

    OpenAIRE

    Zhang, Joy Y.; Marris, Claire; Rose, Nikolas

    2011-01-01

    Synthetic biology is a new field of research that aims to 'make biology easier to engineer'. Some claim that it could revolutionise biotechnology to deliver applications for the energy, medical and agricultural sectors. However there are concerns about potential environmental and health risks, the creation of monopolies dominated by large multinational corporations, and the ethics of creating artificial life. How should synthetic biology be best governed to maximise benefits and minimise risk...

  17. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    OpenAIRE

    Lewis, Daniel D.; Villarreal, Fernando D.; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the...

  18. Challenges for the European governance of synthetic biology for human health

    OpenAIRE

    Stemerding, D.; Douglas, C.

    2014-01-01

    Synthetic biology is a series of scientific and technological practices involved in the application of engineering principles to the design and production of predictable and robust biological systems. While policy discussions abound in this area, emerging technologies like synthetic biology present considerable challenges in the articulation of concrete policy options given that their introduction into society may still be in the distant future. This paper reports on a series of governance wo...

  19. Bottom-up reconstruction scenarios for (un)constrained MSSM parameters at the CERN LHC

    International Nuclear Information System (INIS)

    We consider some specific inverse problem or 'bottom-up' reconstruction strategies at the CERN LHC for both general and constrained minimal supersymmetric standard model (MSSM) parameters, starting from a plausibly limited set of sparticle identification and mass measurements, using mainly gluino/squark cascade decays, plus eventually the lightest Higgs boson mass. For the three naturally separated sectors of gaugino/Higgsino, squark/slepton, and Higgs parameters, we examine different step-by-step algorithms based on rather simple, entirely analytical, inverted relations between masses and basic MSSM parameters. This includes also reasonably good approximations of some of the relevant radiative correction calculations. We distinguish the constraints obtained for a general MSSM from those obtained with universality assumptions in the three different sectors. Our results are compared at different stages with the determination from more standard 'top-down' fit of models to data, and finally combined into a global determination of all the relevant parameters. Our approach gives complementary information to more conventional analysis, and is not restricted to the specific LHC measurement specificities. In addition, the bottom-up renormalization group evolution of general MSSM parameters, being an important ingredient in this framework, is illustrated as a new publicly available option of the MSSM spectrum calculation code SuSpect.

  20. Bottom-up approach for decentralised energy planning: Case study of Tumkur district in India

    International Nuclear Information System (INIS)

    Decentralized Energy Planning (DEP) is one of the options to meet the rural and small-scale energy needs in a reliable, affordable and environmentally sustainable way. The main aspect of the energy planning at decentralized level would be to prepare an area-based DEP to meet energy needs and development of alternate energy sources at least-cost to the economy and environment. Present work uses goal-programming method in order to analyze the DEP through bottom-up approach. This approach includes planning from the lowest scale of Tumkur district in India. The scale of analysis included village level-Ungra, panchayat level (local council)-Yedavani, block level-Kunigal and district level-Tumkur. The approach adopted was bottom-up (village to district) to allow a detailed description of energy services and the resulting demand for energy forms and supply technologies. Different scenarios are considered at four decentralized scales for the year 2005 and are developed and analyzed for the year 2020. Decentralized bioenergy system for producing biogas and electricity, using local biomass resources, are shown to promote development compared to other renewables. This is because, apart from meeting energy needs, multiple goals could be achieved such as self-reliance, local employment, and land reclamation apart from CO2 emissions reduction.

  1. Dynamic formulation of a top-down and bottom-up merging energy policy model

    International Nuclear Information System (INIS)

    The impact of energy policy measures is not restricted to the energy system and should therefore be analysed within an economy-wide framework, while keeping the essential details of the energy sector. The aim of this paper is to present new developments in the field of the consistent evaluation of indicators for the sustainability assessment of energy policy measures. Starting from the static concept of Boehringer (Energy Econ. 20 (1998) 233), this paper shows how the complementarity format can be used in computable general equilibrium (CGE) modelling for a dynamic formulation of bottom-up and top-down approach merging models. While a hybrid approach increases the credibility of CGE models in energy policy analysis by replacing the energy sector generic functional forms with a bottom-up activity analysis based on specific technologies, the endogenous formulation of investment decisions makes an explicit description of evolving specific capital stocks and technology mixes possible. Both features are essential when assessing effects of policy measures that may be affected by structural change--which is typically the case in the long-term assessment of energy policy measures

  2. Dynamic formulation of a top-down and bottom-up merging energy policy model

    Energy Technology Data Exchange (ETDEWEB)

    Frei, C.W. [Swiss Federal Inst. of Technology, Lausanne (Switzerland). Centre for Energy Policy and Economics; Haldi, P.A.; Sarlos, G. [Swiss Federal Inst. of Technology, Lausanne (Switzerland). Lab. of Energy Systems

    2003-08-01

    The impact of energy policy measures is not restricted to the energy system and should therefore be analysed within an economy-wide framework, while keeping the essential details of the energy sector. The aim of this paper is to present new developments in the field of the consistent evaluation of indicators for the sustainability assessment of energy policy measures. Starting from the static concept of Boehringer (Energy Econ. 20 (1998) 233), this paper shows how the complementarity format can be used in computable general equilibrium (CGE) modelling for a dynamic formulation of bottom-up and top-down approach merging models. While a hybrid approach increases the credibility of CGE models in energy policy analysis by replacing the energy sector generic functional forms with a bottom-up activity analysis based on specific technologies, the endogenous formulation of investment decisions makes an explicit description of evolving specific capital stocks and technology mixes possible. Both features are essential when assessing effects of policy measures that may be affected by structural change - which is typically the case in the long-term assessment of energy policy measures.(author)

  3. A bottom-up institutional approach to cooperative governance of risky commons

    Science.gov (United States)

    Vasconcelos, Vítor V.; Santos, Francisco C.; Pacheco, Jorge M.

    2013-09-01

    Avoiding the effects of climate change may be framed as a public goods dilemma, in which the risk of future losses is non-negligible, while realizing that the public good may be far in the future. The limited success of existing attempts to reach global cooperation has been also associated with a lack of sanctioning institutions and mechanisms to deal with those who do not contribute to the welfare of the planet or fail to abide by agreements. Here we investigate the emergence and impact of different types of sanctioning to deter non-cooperative behaviour in climate agreements. We show that a bottom-up approach, in which parties create local institutions that punish free-riders, promotes the emergence of widespread cooperation, mostly when risk perception is low, as it is at present. On the contrary, global institutions provide, at best, marginal improvements regarding overall cooperation. Our results clearly suggest that a polycentric approach involving multiple institutions is more effective than that associated with a single, global one, indicating that such a bottom-up, self-organization approach, set up at a local scale, provides a better ground on which to attempt a solution for such a complex and global dilemma.

  4. Top-down and bottom-up definitions of human failure events in human reliability analysis

    Energy Technology Data Exchange (ETDEWEB)

    Boring, Ronald Laurids [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2014-10-01

    In the probabilistic risk assessments (PRAs) used in the nuclear industry, human failure events (HFEs) are determined as a subset of hardware failures, namely those hardware failures that could be triggered by human action or inaction. This approach is top-down, starting with hardware faults and deducing human contributions to those faults. Elsewhere, more traditionally human factors driven approaches would tend to look at opportunities for human errors first in a task analysis and then identify which of those errors is risk significant. The intersection of top-down and bottom-up approaches to defining HFEs has not been carefully studied. Ideally, both approaches should arrive at the same set of HFEs. This question is crucial, however, as human reliability analysis (HRA) methods are generalized to new domains like oil and gas. The HFEs used in nuclear PRAs tend to be top-down—defined as a subset of the PRA—whereas the HFEs used in petroleum quantitative risk assessments (QRAs) often tend to be bottom-up—derived from a task analysis conducted by human factors experts. The marriage of these approaches is necessary in order to ensure that HRA methods developed for top-down HFEs are also sufficient for bottom-up applications.

  5. Formation of three-dimensional hepatic tissue by the bottom-up method using spheroids.

    Science.gov (United States)

    Okudaira, Tatsuya; Amimoto, Naoki; Mizumoto, Hiroshi; Kajiwara, Toshihisa

    2016-08-01

    Liver regenerative medicine has attracted attention as a possible alternative to organ transplantation. To address the challenge of liver regenerative medicine, the development of a construction method has been proposed for liver tissue in vitro with a high cell density and high functionality for transplantation into patients with severe liver failure. In this study, we fabricated highly functional three-dimensional hepatic tissue by a bottom-up method using spheroids. The hepatic tissue was formed by stacking hepatocyte spheroids covered with human umbilical vein endothelial cells (HUVECs). Hepatic tissue constructs were evaluated for cell survival, liver-specific functions, and histologically. As a result, we identified improvements in liver-specific functions (ammonia removal and albumin secretion) and cell survival. In addition, HUVECs were regularly distributed at every 100 μm within the tissue, and live cells were present within the whole tissue construct throughout the culture period. In summary, we successfully fabricated highly functional hepatic tissue by the bottom-up method using HUVEC-covered hepatocyte spheroids. PMID:26803704

  6. A bottom-up approach for the synthesis of highly ordered fullerene-intercalated graphene hybrids

    Directory of Open Access Journals (Sweden)

    Dimitrios eGournis

    2015-02-01

    Full Text Available Much of the research effort on graphene focuses on its use as a building block for the development of new hybrid nanostructures with well-defined dimensions and properties suitable for applications such as gas storage, heterogeneous catalysis, gas/liquid separations, nanosensing and biomedicine. Towards this aim, here we describe a new bottom-up approach, which combines self-assembly with the Langmuir Schaefer deposition technique to synthesize graphene-based layered hybrid materials hosting fullerene molecules within the interlayer space. Our film preparation consists in a bottom-up layer-by-layer process that proceeds via the formation of a hybrid organo-graphene oxide Langmuir film. The structure and composition of these hybrid fullerene-containing thin multilayers deposited on hydrophobic substrates were characterized by a combination of X-ray diffraction, Raman and X-ray photoelectron spectroscopies, atomic force microscopy and conductivity measurements. The latter revealed that the presence of C60 within the interlayer spacing leads to an increase in electrical conductivity of the hybrid material as compared to the organo-graphene matrix alone.

  7. Top-down (Prior Knowledge) and Bottom-up (Perceptual Modality) Influences on Spontaneous Interpersonal Synchronization.

    Science.gov (United States)

    Gipson, Christina L; Gorman, Jamie C; Hessler, Eric E

    2016-04-01

    Coordination with others is such a fundamental part of human activity that it can happen unintentionally. This unintentional coordination can manifest as synchronization and is observed in physical and human systems alike. We investigated the role of top-down influences (prior knowledge of the perceptual modality their partner is using) and bottom-up factors (perceptual modality combination) on spontaneous interpersonal synchronization. We examine this phenomena with respect to two different theoretical perspectives that differently emphasize top-down and bottom-up factors in interpersonal synchronization: joint-action/shared cognition theories and ecological-interactive theories. In an empirical study twelve dyads performed a finger oscillation task while attending to each other's movements through either visual, auditory, or visual and auditory perceptual modalities. Half of the participants were given prior knowledge of their partner's perceptual capabilities for coordinating across these different perceptual modality combinations. We found that the effect of top-down influence depends on the perceptual modality combination between two individuals. When people used the same perceptual modalities, top-down influence resulted in less synchronization and when people used different perceptual modalities, top-down influence resulted in more synchronization. Furthermore, persistence in the change in behavior as a result of having perceptual information about each other ('social memory') was stronger when this top-down influence was present. PMID:27033133

  8. The Challenge of Bottom-Up Paradigm and Popular Participation in Sustainable Rural Development of Nigeria: The Way Forward

    OpenAIRE

    J. O. Adefila

    2012-01-01

    The paper is entitled ‘The challenge of bottom-up paradigm and popular participation in rural economic development of Nigeria’. There is the clamour for a shift from centre-down to bottom-up paradigm particularly among the rural developers considering the back-wash effects of the latter which tends to undermine the economic growth and development of the rural areas. The paper aims at reinforcing the adoption of bottom-up and popular participation approaches to rural socio-economic transformat...

  9. Integrating the bottom-up and top-down approach to energy economy modelling. The case of Denmark

    DEFF Research Database (Denmark)

    Klinge Jacobsen, Henrik

    1998-01-01

    This paper presents results from an integration project covering Danish models based on bottom-up and top-down approaches to energy]economy modelling. The purpose of the project was to identify theoretical and methodological problems for integrating existing models for Denmark and to implement an...... integration of the models. The integration was established through a number of links between energy bottom-up modules and a macroeconomic model. In this integrated model it is possible to analyse both top-down instruments, such as taxes along with bottom-up instruments, such as regulation of technology...

  10. Comparison of Synthetic and Biologic Mesh in Ventral Hernia Repair Using Components Separation Technique.

    Science.gov (United States)

    Sandvall, Brinkley K; Suver, Daniel W; Said, Hakim K; Mathes, David W; Neligan, Peter C; Dellinger, E Patchen; Louie, Otway

    2016-06-01

    Ventral hernia repair (VHR) for large abdominal wall defects is challenging. Prior research established that the use of mesh is superior to suture closure alone and that component separation is an effective technique to combat loss of abdominal domain. Studies comparing component separation technique (CST) outcomes utilizing synthetic versus biologic mesh are limited. A retrospective review was conducted of 72 consecutive patients who underwent VHR with CST between 2006 and 2010 at our institution. Surgeon preference and the presence of contamination guided whether synthetic mesh (27 patients) or biologic mesh (45 patients) was used. Mean follow-up interval for all comers was 13.9 months and similar in both groups (P > 0.05). Degree of contamination and severity of premorbid medical conditions were significantly higher in the biologic mesh group, as reflected in the higher Ventral Hernia Working Group (VHWG) score (2.04 versus 2.86). Clinical outcomes, as measured by both minor and major complication rates and recurrence rates, were not significantly different. Minor complication rates were 26% in the synthetic group and 37% in the biologic group and major complication rates 15% in the synthetic group and 22% in the biologic group. There was 1 recurrence (4%) in the synthetic mesh group versus 5 (11%) in the biologic mesh group. Multivariable analysis for major complications revealed no significant difference for either synthetic or biologic mesh while controlling for other variables. Subset analysis of uncontaminated cases revealed recurrence rates of 4% in the synthetic mesh group and 6% in the biologic mesh group. VHR using CST and either synthetic mesh or biologic mesh resulted in low recurrence rates with similar overall complication profiles, despite the higher average VHWG grading score in the biologic mesh group. Our results support the VHWG recommendation for biologic mesh utilization in higher VHWG grade patients. In VHWG grade 2 patients, our clinical

  11. A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

    Science.gov (United States)

    Rothschild, Lynn J.

    2010-01-01

    The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

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

    Science.gov (United States)

    Rothschild, Lynn J.

    2016-01-01

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

  13. Landauer in the Age of Synthetic Biology: Energy Consumption and Information Processing in Biochemical Networks

    Science.gov (United States)

    Mehta, Pankaj; Lang, Alex H.; Schwab, David J.

    2016-03-01

    A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to understand and manipulate cellular information processing networks raises several fundamental physics questions: How do the molecular components of cellular circuits exploit energy consumption to improve information processing? Can one utilize ideas from thermodynamics to improve the design of synthetic cellular circuits and modules? Here, we summarize recent theoretical work addressing these questions. Energy consumption in cellular circuits serves five basic purposes: (1) increasing specificity, (2) manipulating dynamics, (3) reducing variability, (4) amplifying signal, and (5) erasing memory. We demonstrate these ideas using several simple examples and discuss the implications of these theoretical ideas for the emerging field of synthetic biology. We conclude by discussing how it may be possible to overcome these limitations using "post-translational" synthetic biology that exploits reversible protein modification.

  14. Bottom-up communication. Identifying opportunities and limitations through an exploratory field-based evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C.; Irvine, K.N. [Institute of Energy and Sustainable Development, De Montfort University, Leicester, LE1 9BH (United Kingdom)

    2013-02-15

    Communication to promote behaviours like energy saving can use significant resources. What is less clear is the comparative value of different approaches available to communicators. While it is generally agreed that 'bottom-up' approaches, where individuals are actively involved rather than passive, are preferable to 'top-down' authority-led projects, there is a dearth of evidence that verifies why this should be. Additionally, while the literature has examined the mechanics of the different approaches, there has been less attention paid to the associated psychological implications. This paper reports on an exploratory comparative study that examined the effects of six distinct communication activities. The activities used different communication approaches, some participative and others more top-down informational. Two theories, from behavioural studies and communication, were used to identify key variables for consideration in this field-based evaluation. The evaluation aimed to assess not just which activity might be most successful, as this has limited generalisability, but to also gain insight into what psychological impacts might contribute to success. Analysis found support for the general hypothesis that bottom-up approaches have more impact on behaviour change than top-down. The study also identified that, in this instance, the difference in reported behaviour across the activities related partly to the extent to which intentions to change behaviour were implemented. One possible explanation for the difference in reported behaviour change across the activities is that a bottom-up approach may offer a supportive environment where participants can discuss progress with like-minded individuals. A further possible explanation is that despite controlling for intention at an individual level, the pre-existence of strong intentions may have an effect on group success. These suggestive findings point toward the critical need for additional and larger-scale studies

  15. A bottom up approach for engineering catchments through sustainable runoff management

    Science.gov (United States)

    Wilkinson, M.; Quinn, P. F.; Jonczyk, J.; Burke, S.

    2010-12-01

    There is no doubt that our catchments are under great stress. There have been many accounts around the world of severe flood events and water quality issues within channels. As a result of these, ecological habitats in rivers are also under pressure. Within the United Kingdom, all these issues have been identified as key target areas for policy. Traditionally this has been managed by a policy driven top down approach which is usually ineffective. A one ‘size fits all’ attitude often does not work. This paper presents a case study in northern England whereby a bottom up approach is applied to multipurpose managing of catchments at the source (in the order of 1-10km2). This includes simultaneous tackling of water quality, flooding and ecological issues by creating sustainable runoff management solutions such as storage ponds, wetlands, beaver dams and willow riparian features. In order to identify the prevailing issues in a specific catchment, full and transparent stakeholder engagement is essential, with everybody who has a vested interest in the catchment being involved from the beginning. These problems can then be dealt with through the use of a novel catchment management toolkit, which is transferable to similar scale catchments. However, evidence collected on the ground also allows for upscaling of the toolkit. The process gathers the scientific evidence about the effectiveness of existing or new measures, which can really change the catchment functions. Still, we need to get better at communicating the science to policy makers and policy therefore must facilitate a bottom up approach to land and water management. We show a test site for this approach in the Belford burn catchment (6km2), northern England. This catchment has problems with flooding and water quality. Increased sediment loads are affecting the nearby estuary which is an important ecological zone and numerous floods have affected the local village. A catchment engineering toolkit has been

  16. Succumbing to Bottom-Up Biases on Task Choice Predicts Increased Switch Costs in the Voluntary Task Switching Paradigm

    OpenAIRE

    JosephMichaelOrr

    2011-01-01

    Bottom-up biases are widely thought to influence task choice in the voluntary task switching paradigm. Definitive support for this hypothesis is lacking, however, because task choice and task performance are usually confounded. We therefore revisited this hypothesis using a paradigm in which task choice and task performance are temporally separated. As predicted, participants tended to choose the task that was primed by bottom-up biases. Moreover, such choices were linked to increased swit...

  17. New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris

    OpenAIRE

    Vogl, Thomas; Franz S. Hartner; Glieder, Anton

    2013-01-01

    Biopharmaceuticals are an integral part of modern medicine and pharmacy. Both, the development and the biotechnological production of biopharmaceuticals are highly cost-intensive and require suitable expression systems. In this review we discuss established and emerging tools for reengineering the methylotrophic yeast Pichia pastoris for biopharmaceutical production. Recent advancements of this industrial expression system through synthetic biology include synthetic promoters to avoid methano...

  18. Unsupervised Tattoo Segmentation Combining Bottom-Up and Top-Down Cues

    Energy Technology Data Exchange (ETDEWEB)

    Allen, Josef D [ORNL

    2011-01-01

    Tattoo segmentation is challenging due to the complexity and large variance in tattoo structures. We have developed a segmentation algorithm for nding tattoos in an image. Our basic idea is split-merge: split each tattoo image into clusters through a bottom-up process, learn to merge the clusters containing skin and then distinguish tattoo from the other skin via top-down prior in the image itself. Tattoo segmentation with unknown number of clusters is transferred to a gure-ground segmentation. We have applied our segmentation algorithm on a tattoo dataset and the results have shown that our tattoo segmentation system is e cient and suitable for further tattoo classi cation and retrieval purpose.

  19. Bottom-up and top-down controls on picoplankton in the East China Sea

    Directory of Open Access Journals (Sweden)

    C. Guo

    2013-05-01

    Full Text Available Dynamics of picoplankton population distribution in the East China Sea (ECS, a marginal sea in the western North Pacific Ocean, were studied during two "CHOICE-C" cruises in August 2009 (summer and January 2010 (winter. Dilution experiments were conducted during the two cruises to investigate the growth and grazing among picophytoplantkon populations. Picoplankton accounted for an average of ~29% (2% to 88% of community carbon biomass in the ECS on average, with lower percentages in plume region than in shelf and kuroshio regions. Averaged growth rates (μ for Prochlorococcus (Pro, Synechococcus (Syn and picoeukaryotes (peuk were 0.36, 0.89, 0.90 d−1, respectively, in summer, and 0.46, 0.58, 0.56 d−1, respectively, in winter. Seawater salinity and nutrient availability exerted significant controls on picoplankton growth rate. Averaged grazing mortality (m were 0.46, 0.63, 0.68 d−1 in summer, and 0.22, 0.32, 0.22 d−1 in winter for Pro, Syn and peuk respectively. The three populations demonstrated very different distribution patterns regionally and seasonally affected by both bottom-up and top-down controls. In summer, Pro, Syn and peuk were dominant in Kuroshio, transitional and plume regions respectively. Protist grazing consumed 84%, 78%, 73% and 45%, 47%, 57% of production for Pro, Syn and peuk in summer and winter respectively, suggesting more significant top-down controls in summer. In winter, all three populations tended to distribute in offshore regions, although the area of coverage was different (peuk > Syn > Pro. Bottom-up factors can explain as much as 91.5%, 82% and 81.2% of Pro, Syn and peuk abundance variance in winter, while only 59.1% and 43.7% for Pro and peuk in summer. Regionally, Yangtze River discharge plays a significant role in affecting the intensity of top-down control, indicated by significant and negative association between salinity and grazing mortality of all three populations and higher grazing mortality to

  20. Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Erin Shammel [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Burnum-Johnson, Kristin E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Ibrahim, Yehia M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Orton, Daniel J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Monroe, Matthew E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kelly, Ryan T. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Moore, Ronald J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zhang, Xing [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Theberge, Roger [Boston Univ. of Medicine, MA (United States); Costello, Catherine E. [Boston Univ. of Medicine, MA (United States); Smith, Richard D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-07-03

    Proteomic measurements with greater throughput, sensitivity and additional structural information enhance the in-depth characterization of complex mixtures and targeted studies with additional information and higher confidence. While liquid chromatography separation coupled with mass spectrometry (LC-MS) measurements have provided information on thousands of proteins in different sample types, the additional of another rapid separation stage providing structural information has many benefits for analyses. Technical advances in ion funnels and multiplexing have enabled ion mobility separations to be easily and effectively coupled with LC-MS proteomics to enhance the information content of measurements. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.

  1. A bottom-up perspective on leadership of collaborative innovation in the public sector

    DEFF Research Database (Denmark)

    Hansen, Jesper Rohr

    organizations. A crucial condition for success is iterative leadership adaptation. In conclusion, the thesis finds that specialized professionals are indeed able to develop politically viable, innovative and collaborative solutions to wicked problems; and that such professionals are able to transform themselves......The thesis investigates how new forms of public leadership can contribute to solving complex problems in today’s welfare societies through innovation. A bottom-up type of leadership for collaborative innovation addressing wicked problems is theorised, displaying a social constructive process...... approach to leadership; a theoretical model emphasises that leadership emerges through social processes of recognition. Leadership is recognised by utilising the uncertainty of a wicked problem and innovation to influence collaborators’ sensemaking processes. The empirical setting is the City of Copenhagen...

  2. Bottom-up design of 2D organic photocatalysts for visible-light driven hydrogen evolution

    Science.gov (United States)

    Wang, Peng; Jiang, Xue; Zhao, Jijun

    2016-01-01

    To design two-dimensional (2D) organocatalysts, three series of covalent organic frameworks (COFs) are constructed using bottom-up strategies, i.e. molecular selection, tunable linkage, and functionalization. First-principles calculations are performed to confirm their photocatalytic activity under visible light. Two of our constructed 2D COF models (B1 and C3) are identified as a sufficiently efficient organocatalyst for visible light water splitting. The controllable construction of such COFs from suitable organic subunit, linkage, and functional groups paves the way for correlating band edge alignments and geometry parameters of 2D organic materials. Our theoretical prediction not only provides essential insights into designing 2D-COF photocatalysts for water splitting, but also sparks other technological applications for 2D organic materials.

  3. Bottom-Up Cost Analysis of a High Concentration PV Module; NREL (National Renewable Energy Laboratory)

    Energy Technology Data Exchange (ETDEWEB)

    Horowitz, K.; Woodhouse, M.; Lee, H.; Smestad, G.

    2015-04-13

    We present a bottom-up model of III-V multi-junction cells, as well as a high concentration PV (HCPV) module. We calculate $0.65/Wp(DC) manufacturing costs for our model HCPV module design with today’s capabilities, and find that reducing cell costs and increasing module efficiency offer the promising pathways for future cost reductions. Cell costs could be significantly reduced via an increase in manufacturing scale, substrate reuse, and improved manufacturing yields. We also identify several other significant drivers of HCPV module costs, including the Fresnel lens primary optic, module housing, thermal management, and the receiver board. These costs could potentially be lowered by employing innovative module designs.

  4. Coupled multi-physics simulation frameworks for reactor simulation: A bottom-up approach

    International Nuclear Information System (INIS)

    In this paper, we present a 'bottom-up' approach to multi-physics frameworks, where we first develop common interfaces to simulation data, then adapt existing physics modules to communicate through those interfaces. Interfaces are provided for geometry, mesh, and field data, and are independent of one another; a fourth interface is available for relating data between these interfaces. Physics modules read and write data through those common interfaces, which also provide access to common simulation services like parallel IO, mesh partitioning, etc. Multi-physics codes are assembled as a combination of physics modules, services, interface implementations, and driver code which coordinates calling these various pieces. The framework being constructed as part of this effort, referred to as SHARP, is shown

  5. Strain Response of Hot-Mix Asphalt Overlays for Bottom-Up Reflective Cracking

    CERN Document Server

    Ghauch, Ziad G

    2011-01-01

    This paper examines the strain response of typical HMA overlays above jointed PCC slabs prone to bottom-up reflective cracking. The occurrence of reflective cracking under the combined effect of traffic and environmental loading significantly reduces the design life of the HMA overlays and can lead to its premature failure. In this context, viscoelastic material properties combined with cyclic vehicle loadings and pavement temperature distribution were implemented in a series of FE models in order to study the evolution of horizontal tensile and shear strains at the bottom of the HMA overlay. The effect of several design parameters, such as subbase and subgrade moduli, vehicle speed, overlay thickness, and temperature condition, on the horizontal and shear strain response was investigated. Results obtained show that the rate of horizontal and shear strain increase at the bottom of the HMA overlay drop with higher vehicle speed, higher subgrade modulus, and higher subbase modulus. Moreover, the rate of horizon...

  6. Bottom-up design of 2D organic photocatalysts for visible-light driven hydrogen evolution

    International Nuclear Information System (INIS)

    To design two-dimensional (2D) organocatalysts, three series of covalent organic frameworks (COFs) are constructed using bottom-up strategies, i.e. molecular selection, tunable linkage, and functionalization. First-principles calculations are performed to confirm their photocatalytic activity under visible light. Two of our constructed 2D COF models (B1 and C3) are identified as a sufficiently efficient organocatalyst for visible light water splitting. The controllable construction of such COFs from suitable organic subunit, linkage, and functional groups paves the way for correlating band edge alignments and geometry parameters of 2D organic materials. Our theoretical prediction not only provides essential insights into designing 2D-COF photocatalysts for water splitting, but also sparks other technological applications for 2D organic materials. (paper)

  7. Collective Inclusioning: A Grounded Theory of a Bottom-Up Approach to Innovation and Leading

    Directory of Open Access Journals (Sweden)

    Michal Lysek

    2016-06-01

    Full Text Available This paper is a grounded theory study of how leaders (e.g., entrepreneurs, managers, etc. engage people in challenging undertakings (e.g., innovation that require everyone’s commitment to such a degree that they would have to go beyond what could be reasonably expected in order to succeed. Company leaders sometimes wonder why their employees no longer show the same responsibility towards their work, and why they are more concerned with internal politics than solving customer problems. It is because company leaders no longer apply collective inclusioning to the same extent as they did in the past. Collective inclusioning can be applied in four ways by convincing, afinitizing, goal congruencing, and engaging. It can lead to fostering strong units of people for taking on challenging undertakings. Collective inclusioning is a complementing theory to other strategic management and leading theories. It offers a new perspective on how to implement a bottom-up approach to innovation.

  8. Bottom-Up Nanofabrication of Supported Noble Metal Alloy Nanoparticle Arrays for Plasmonics

    DEFF Research Database (Denmark)

    Nugroho, Ferry A. A.; Iandolo, Beniamino; Wagner, Jakob Birkedal; Langhammer, Christoph

    2016-01-01

    concept, we focus on Au-based binary and ternary alloy systems with Ag, Cu, and Pd, due to their high relevance for nanoplasmonics and complete miscibility, and characterize their optical properties. Moreover, as an example for the relevance of the obtained materials for integration in devices, we......Mixing different elements at the nanoscale to obtain alloy nanostructures with fine-tuned physical and chemical properties offers appealing opportunities for nanotechnology and nanoscience. However, despite widespread successful application of alloy nanoparticles made by colloidal synthesis in...... optimization of the surface density. These cannot be fulfilled even using state-of-the-art self -assembly strategies of colloids. As a solution, we present here a generic bottom-up nanolithography-compatible fabrication approach for large-area arrays of alloy nanoparticles on surfaces. To illustrate the...

  9. Manufacturing at Nanoscale: Top-Down, Bottom-up and System Engineering

    International Nuclear Information System (INIS)

    The current nano-technology revolution is facing several major challenges: to manufacture nanodevices below 20 nm, to fabricate three-dimensional complex nano-structures, and to heterogeneously integrate multiple functionalities. To tackle these grand challenges, the Center for Scalable and Integrated NAno-Manufacturing (SINAM), a NSF Nanoscale Science and Engineering Center, set its goal to establish a new manufacturing paradigm that integrates an array of new nano-manufacturing technologies, including the plasmonic imaging lithography and ultramolding imprint lithography aiming toward critical resolution of 1-10 nm and the hybrid top-down and bottom-up technologies to achieve massively parallel integration of heterogeneous nanoscale components into higher-order structures and devices. Furthermore, SINAM will develop system engineering strategies to scale-up the nano-manufacturing technologies. SINAMs integrated research and education platform will shed light to a broad range of potential applications in computing, telecommunication, photonics, biotechnology, health care, and national security

  10. Blueprints for green biotech: development and application of standards for plant synthetic biology.

    Science.gov (United States)

    Patron, Nicola J

    2016-06-15

    Synthetic biology aims to apply engineering principles to the design and modification of biological systems and to the construction of biological parts and devices. The ability to programme cells by providing new instructions written in DNA is a foundational technology of the field. Large-scale de novo DNA synthesis has accelerated synthetic biology by offering custom-made molecules at ever decreasing costs. However, for large fragments and for experiments in which libraries of DNA sequences are assembled in different combinations, assembly in the laboratory is still desirable. Biological assembly standards allow DNA parts, even those from multiple laboratories and experiments, to be assembled together using the same reagents and protocols. The adoption of such standards for plant synthetic biology has been cohesive for the plant science community, facilitating the application of genome editing technologies to plant systems and streamlining progress in large-scale, multi-laboratory bioengineering projects. PMID:27284031

  11. Organism, machine, artifact: The conceptual and normative challenges of synthetic biology.

    Science.gov (United States)

    Holm, Sune; Powell, Russell

    2013-12-01

    Synthetic biology is an emerging discipline that aims to apply rational engineering principles in the design and creation of organisms that are exquisitely tailored to human ends. The creation of artificial life raises conceptual, methodological and normative challenges that are ripe for philosophical investigation. This special issue examines the defining concepts and methods of synthetic biology, details the contours of the organism-artifact distinction, situates the products of synthetic biology vis-à-vis this conceptual typology and against historical human manipulation of the living world, and explores the normative implications of these conclusions. In addressing the challenges posed by emerging biotechnologies, new light can be thrown on old problems in the philosophy of biology, such as the nature of the organism, the structure of biological teleology, the utility of engineering metaphors and methods in biological science, and humankind's relationship to nature. PMID:23810468

  12. Web-based software tool for constraint-based design specification of synthetic biological systems.

    Science.gov (United States)

    Oberortner, Ernst; Densmore, Douglas

    2015-06-19

    miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ). PMID:25426642

  13. Using dichotic listening to study bottom-up and top-down processing in children and adults.

    Science.gov (United States)

    Andersson, Martin; Llera, John Eric; Rimol, Lars M; Hugdahl, Kenneth

    2008-09-01

    The study examined top-down attention modulation of bottom-up processing in children and adults under conditions of varying bottom-up stimulus demands. Voiced and unvoiced consonant-vowel syllables were used in a dichotic-listening situation to manipulate the strength of the bottom-up stimulus-driven right ear advantage when subjects were instructed to focus attention on, and report, either the left or right ear stimulus. We predicted that children would differ from adults in their ability to use attention to modulate a lateralized ear advantage, and particularly when there was a conflict between the direction of the bottom-up ear advantage and the direction of the top-down attention instruction. Thirty children and 30 adults were presented with dichotic presentations of consonant-vowel syllables. The results showed that the voicing manipulation affected the strength of the ear advantage, and that the children performed significantly below the adults when the voicing parameter caused a strong conflict between bottom-up and top down processing. Thus, children seem to lack the cognitive flexibility necessary to modulate a stimulus-driven bottom-up ear advantage, particularly in situations where right ear advantage (REA) is enhanced by the acoustic properties of the stimuli and attentional demands require a left ear shift. It is suggested that varying the stimulus demands in a dichotic-listening situation may be a novel way to study cognitive development. PMID:18608228

  14. Synthetic Biology and Conservation of Nature: Wicked Problems and Wicked Solutions

    OpenAIRE

    Redford, K. H.; Adams, W; Mace, G. M.

    2013-01-01

    So far, conservation scientists have paid little attention to synthetic biology; this is unfortunate as the technology is likely to transform the operating space within which conservation functions, and therefore the prospects for maintaining biodiversity into the future.

  15. Gamification in citizen science: Projects in particle physics and synthetic biology

    OpenAIRE

    Jennett, C.; Iacovides, I.; Skands, P.; Shomar, H.; Cox, A. L.

    2013-01-01

    We present two new citizen cyberscience projects that are being developed in the research fields of Particle Physics and Synthetic Biology, and discuss several issues to be considered in relation to the gamification of these projects.

  16. Achieving social-ecological fit through bottom-up collaborative governance: an empirical investigation

    Directory of Open Access Journals (Sweden)

    Angela M. Guerrero

    2015-12-01

    Full Text Available Significant benefits can arise from collaborative forms of governance that foster self-organization and flexibility. Likewise, governance systems that fit with the extent and complexity of the system under management are considered essential to our ability to solve environmental problems. However, from an empirical perspective the fundamental question of whether self-organized (bottom-up collaborative forms of governance are able to accomplish adequate fit is unresolved. We used new theory and methodological approaches underpinned by interdisciplinary network analysis to address this gap by investigating three governance challenges that relate to the problem of fit: shared management of ecological resources, management of interconnected ecological resources, and cross-scale management. We first identified a set of social-ecological network configurations that represent the hypothesized ways in which collaborative arrangements can contribute to addressing these challenges. Using social and ecological data from a large-scale biodiversity conservation initiative in Australia, we empirically determined how well the observed patterns of stakeholder interactions reflect these network configurations. We found that stakeholders collaborate to manage individual parcels of native vegetation, but not for the management of interconnected parcels. In addition, our data show that the collaborative arrangements enable management across different scales (local, regional, supraregional. Our study provides empirical support for the ability of collaborative forms of governance to address the problem of fit, but also suggests that in some cases the establishment of bottom-up collaborative arrangements would likely benefit from specific guidance to facilitate the establishment of collaborations that better align with the ways ecological resources are interconnected across the landscape. In our case study region, this would improve the capacity of stakeholders to

  17. A bottom-up approach of stochastic demand allocation in water quality modelling

    Directory of Open Access Journals (Sweden)

    E. J. M. Blokker

    2010-04-01

    Full Text Available An "all pipes" hydraulic model of a drinking water distribution system was constructed with two types of demand allocations. One is constructed with the conventional top-down approach, i.e. a demand multiplier pattern from the booster station is allocated to all demand nodes with a correction factor to account for the average water demand on that node. The other is constructed with a bottom-up approach of demand allocation, i.e., each individual home is represented by one demand node with its own stochastic water demand pattern. This was done for a drinking water distribution system of approximately 10 km of mains and serving ca. 1000 homes. The system was tested in a real life situation.

    The stochastic water demand patterns were constructed with the end-use model SIMDEUM on a per second basis and per individual home. Before applying the demand patterns in a network model, some temporal aggregation was done. The flow entering the test area was measured and a tracer test with sodium chloride was performed to determine travel times. The two models were validated on the total sum of demands and on travel times.

    The study showed that the bottom-up approach leads to realistic water demand patterns and travel times, without the need for any flow measurements or calibration. In the periphery of the drinking water distribution system it is not possible to calibrate models on pressure, because head losses are too low. The study shows that in the periphery it is also difficult to calibrate on water quality (e.g. with tracer measurements, as a consequence of the high variability between days. The stochastic approach of hydraulic modelling gives insight into the variability of travel times as an added feature beyond the conventional way of modelling.

  18. Top-down and bottom-up approaches for cost estimating new reactor designs

    International Nuclear Information System (INIS)

    For several years, Generation-4 designs will be 'pre-conceptual' for the less mature concepts and 'preliminary' for the more mature concepts. In this situation, appropriate data for some of the plant systems may be lacking to develop a bottom-up cost estimate. Therefore, a more global approach, the Top-Down Approach (TDA), is needed to help the designers and decision makers in comparing design options. It utilizes more or less simple models for cost estimating the different parts of a design. TDA cost estimating effort applies to a whole functional element whose cost is approached by similar estimations coming from existing data, ratios and models, for a given range of variation of parameters. Modeling is used when direct analogy is not possible. There are two types of models, global and specific ones. Global models are applied to cost modules related to Code Of Account. Exponential formulae such as Ci = Ai + (Bi x Pin) are used when there are cost data for comparable modules in nuclear or other industries. Specific cost models are developed for major specific components of the plant: - process equipment such as reactor vessel, steam generators or large heat exchangers. - buildings, with formulae estimating the construction cost from base cost of m3 of building volume. - systems, when unit costs, cost ratios and models are used, depending on the level of detail of the design. Bottom Up Approach (BUA), which is based on unit prices coming from similar equipment or from manufacturer consulting, is very valuable and gives better cost estimations than TDA when it can be applied, that is at a rather late stage of the design. Both approaches are complementary when some parts of the design are detailed enough to be estimated by BUA, and when BUA results are used to check TDA results and to improve TDA models. This methodology is applied to the HTR (High Temperature Reactor) concept and to an advanced PWR design

  19. Top-down instead of bottom-up estimates of uncertainty in INAA results?

    International Nuclear Information System (INIS)

    The initial publication of the ISO Guide to the Expression of Uncertainty in Measurement (GUM) and many related documents has resulted in a worldwide awareness of the importance of a realistic estimate of the value reported after the +/- sign. The evaluation of uncertainty in measurement, as introduced by the GUM, is derived from the principles applied in physical measurements. Many testing laboratories have already experienced large problems in applying these principles in e.g. (bio)chemical measurements, resulting in time-consuming evaluations and costly additional experiments. Other, more pragmatic and less costly approaches have been proposed to obtain a realistic estimate of the range in which the true value of the measurement may be found with a certain degree of probability. One of these approaches, the 'top-down method', is based on the standard deviation in the results of intercomparison data. This approach is much easier for tests for which it is either difficult to establish a full measurement equation, or if e.g. matrix-matching reference materials are absent. It has been demonstrated that the GUM 'bottom-up' approach of evaluating uncertainty in measurement can easily be applied in instrumental neutron activation analysis (INAA) as all significant sources of uncertainty can be evaluated. INAA is therefore a valuable technique to test the validity of the top-down approach. In this contribution, examples of the top-down evaluation of uncertainty in INAA derived from participation in intercomparison rounds and proficiency testing schemes will be presented. The results will be compared with the bottom-up evaluation of uncertainty, and ease of applicability, validity and usefullness of both approaches will be discussed.

  20. Using synthetic biology to make cells tomorrow's test tubes

    OpenAIRE

    Garcia, HG; Brewster, RC; Phillips, R.

    2016-01-01

    The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In t...

  1. The path to next generation biofuels: successes and challenges in the era of synthetic biology

    OpenAIRE

    Gonzalez Ramon; Fava Fabio; Dellomonaco Clementina

    2010-01-01

    Abstract Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo path...

  2. A systematic design method for robust synthetic biology to satisfy design specifications

    OpenAIRE

    Wu Chih-Hung; Chen Bor-Sen

    2009-01-01

    Abstract Background Synthetic biology is foreseen to have important applications in biotechnology and medicine, and is expected to contribute significantly to a better understanding of the functioning of complex biological systems. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to intrinsic parameter uncertainties, external disturbances and functional variations of intra- and extra-cellular environments. The ...

  3. Promoting microbiology education through the iGEM synthetic biology competition.

    Science.gov (United States)

    Kelwick, Richard; Bowater, Laura; Yeoman, Kay H; Bowater, Richard P

    2015-08-01

    Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research. Synthetic biology projects have developed into wide-ranging training and educational experiences through iGEM, the International Genetically Engineered Machines competition. Elements of the competition are judged against specific criteria and teams can win medals and prizes across several categories. Collaboration is an important element of iGEM, and all DNA constructs synthesized by iGEM teams are made available to all researchers through the Registry for Standard Biological Parts. An overview of microbiological developments in the iGEM competition is provided. This review is targeted at educators that focus on microbiology and synthetic biology, but will also be of value to undergraduate and postgraduate students with an interest in this exciting subject area. PMID:26260156

  4. (Re-)Construction, characterization and modeling of genomes for synthetic biology

    OpenAIRE

    Suarez Diez, Maria; Lam, Carolyn; Leprince, Audrey; Martins Dos Santos, Vitor

    2009-01-01

    Abstract Synthetic biology is the rational (re-)design of biological systems with useful properties. In its engineering perspective, it aims at transforming biotechnology into a true engineering discipline with the corresponding reliabilities and accuracies in design. Under this view, the building blocks of complex systems are well-characterized biological modules, designed and optimized for specific functions that can be assembled into circuits to perform complex biological funct...

  5. Building momentum for systems and synthetic biology in India

    OpenAIRE

    Krishnan, Remya; Manjaly-Antony, Lijo Anto; Dhar, Pawan K.

    2010-01-01

    Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out) and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computat...

  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 throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental efforts. Clearly, what counts is the resultin 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. PMID:27075000

  7. Biochemistry-directed hollow porous microspheres: bottom-up self-assembled polyanion-based cathodes for sodium ion batteries

    Science.gov (United States)

    Lin, Bo; Li, Qiufeng; Liu, Baodong; Zhang, Sen; Deng, Chao

    2016-04-01

    Biochemistry-directed synthesis of functional nanomaterials has attracted great interest in energy storage, catalysis and other applications. The unique ability of biological systems to guide molecule self-assembling facilitates the construction of distinctive architectures with desirable physicochemical characteristics. Herein, we report a biochemistry-directed ``bottom-up'' approach to construct hollow porous microspheres of polyanion materials for sodium ion batteries. Two kinds of polyanions, i.e. Na3V2(PO4)3 and Na3.12Fe2.44(P2O7)2, are employed as cases in this study. The microalgae cell realizes the formation of a spherical ``bottom'' bio-precursor. Its tiny core is subjected to destruction and its tough shell tends to carbonize upon calcination, resulting in the hollow porous microspheres for the ``top'' product. The nanoscale crystals of the polyanion materials are tightly enwrapped by the highly-conductive framework in the hollow microsphere, resulting in the hierarchical nano-microstructure. The whole formation process is disclosed as a ``bottom-up'' mechanism. Moreover, the biochemistry-directed self-assembly process is confirmed to play a crucial role in the construction of the final architecture. Taking advantage of the well-defined hollow-microsphere architecture, the abundant interior voids and the highly-conductive framework, polyanion materials show favourable sodium-intercalation kinetics. Both materials are capable of high-rate long-term cycling. After five hundred cycles at 20 C and 10 C, Na3V2(PO4)3 and Na3.12Fe2.44(P2O7)2 retain 96.2% and 93.1% of the initial capacity, respectively. Therefore, the biochemistry-directed technique provides a low-cost, highly-efficient and widely applicable strategy to produce high-performance polyanion-based cathodes for sodium ion batteries.Biochemistry-directed synthesis of functional nanomaterials has attracted great interest in energy storage, catalysis and other applications. The unique ability of

  8. Synthetic biology devices for in vitro and in vivo diagnostics

    OpenAIRE

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

    2015-01-01

    There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging...

  9. Sucralose, A Synthetic Organochlorine Sweetener: Overview of Biological Issues

    OpenAIRE

    Schiffman, Susan S.; Rother, Kristina I.

    2013-01-01

    Sucralose is a synthetic organochlorine sweetener (OC) that is a common ingredient in the world's food supply. Sucralose interacts with chemosensors in the alimentary tract that play a role in sweet taste sensation and hormone secretion. In rats, sucralose ingestion was shown to increase the expression of the efflux transporter P-glycoprotein (P-gp) and two cytochrome P-450 (CYP) isozymes in the intestine. P-gp and CYP are key components of the presystemic detoxification system involved in fi...

  10. Metabolomics methods for the synthetic biology of secondary metabolism

    OpenAIRE

    Nguyen, Quoc-Thai; Merlo, Maria E.; Medema, Marnix H.; Jankevics, Andris; Breitling, Rainer; Takano, Eriko

    2012-01-01

    Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or “awakening” of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent...

  11. Deciphering the language between biological and synthetic materials

    Directory of Open Access Journals (Sweden)

    Paolo Antonio Netti

    2014-06-01

    Full Text Available Chemical signals propagating through aqueous environment are at the basis of the language utilized by living systems to exchange information. In the last years, molecular biology has partly disclosed the grammar and the syntax of this complex language revealing the fascinating world of molecular communication that is the foundation of biological development.

  12. Design, Mathematical Modelling, Construction and Testing of Synthetic Gene Network Oscillators to Establish Roseobacter Clade Bacteria and the Protozoan Trypanosoma brucei as Synthetic Biology Chassis.

    OpenAIRE

    Borg, Y.

    2015-01-01

    The aim of this project is to establish Roseobacter marine bacteria and Trypanosoma brucei (T. brucei) protozoa as synthetic biology chassis. This work addresses the gap within synthetic biology resulting from the limited choice of host cells available for use in practice. This was done by developing synthetic bacterial and trypanosomal genetic regulatory networks (GRNs) which function as an oscillator as well as by developing the necessary protocols and set-ups to allow for the analysis of G...

  13. Regime shift from phytoplankton to macrophyte dominance in a large river: Top-down versus bottom-up effects

    Energy Technology Data Exchange (ETDEWEB)

    Ibanez, Carles, E-mail: carles.ibanez@irta.cat [IRTA Aquatic Ecosystems, Carretera Poble Nou, Km 5.5, 43540 St. Carles de la Rapita, Catalonia (Spain); Alcaraz, Carles; Caiola, Nuno; Rovira, Albert; Trobajo, Rosa [IRTA Aquatic Ecosystems, Carretera Poble Nou, Km 5.5, 43540 St. Carles de la Rapita, Catalonia (Spain); Alonso, Miguel [United Research Services S.L., Urgell 143, 08036 Barcelona, Catalonia (Spain); Duran, Concha [Confederacion Hidrografica del Ebro, Sagasta 24-26, 50071 Zaragoza, Aragon (Spain); Jimenez, Pere J. [Grup Natura Freixe, Major 56, 43750 Flix, Catalonia (Spain); Munne, Antoni [Agencia Catalana de l' Aigua, Provenca 204-208, 08036 Barcelona, Catalonia (Spain); Prat, Narcis [Departament d' Ecologia, Universitat de Barcelona, Diagonal 645, 08028 Barcelona Catalonia (Spain)

    2012-02-01

    The lower Ebro River (Catalonia, Spain) has recently undergone a regime shift from a phytoplankton-dominated to a macrophyte-dominated system. This shift is well known in shallow lakes but apparently it has never been documented in rivers. Two initial hypotheses to explain the collapse of the phytoplankton were considered: a) the diminution of nutrients (bottom-up); b) the filtering effect due to the colonization of the zebra mussel (top-down). Data on water quality, hydrology and biological communities (phytoplankton, macrophytes and zebra mussel) was obtained both from existing data sets and new surveys. Results clearly indicate that the decrease in phosphorus is the main cause of a dramatic decrease in chlorophyll and large increase in water transparency, triggering the subsequent colonization of macrophytes in the river bed. A Generalized Linear Model analysis showed that the decrease in dissolved phosphorus had a relative importance 14 times higher than the increase in zebra mussel density to explain the variation of total chlorophyll. We suggest that the described changes in the lower Ebro River can be considered a novel ecosystem shift. This shift is triggering remarkable changes in the biological communities beyond the decrease of phytoplankton and the proliferation of macrophytes, such as massive colonization of Simulidae (black fly) and other changes in the benthic invertebrate communities that are currently investigated. - Highlights: Black-Right-Pointing-Pointer We show a regime shift in a large river from phytoplankton to macrophyte dominance. Black-Right-Pointing-Pointer Two main hypotheses are considered: nutrient decrease and zebra mussel grazing. Black-Right-Pointing-Pointer Phosphorus depletion is found to be the main cause of the phytoplankton decline. Black-Right-Pointing-Pointer We conclude that oligotrophication triggered the colonization of macrophytes. Black-Right-Pointing-Pointer This new regime shift in a river is similar to that described

  14. A bottom-up approach to estimating cost elements of REDD+ pilot projects in Tanzania

    Directory of Open Access Journals (Sweden)

    Merger Eduard

    2012-08-01

    Full Text Available Abstract Background Several previous global REDD+ cost studies have been conducted, demonstrating that payments for maintaining forest carbon stocks have significant potential to be a cost-effective mechanism for climate change mitigation. These studies have mostly followed highly aggregated top-down approaches without estimating the full range of REDD+ costs elements, thus underestimating the actual costs of REDD+. Based on three REDD+ pilot projects in Tanzania, representing an area of 327,825 ha, this study explicitly adopts a bottom-up approach to data assessment. By estimating opportunity, implementation, transaction and institutional costs of REDD+ we develop a practical and replicable methodological framework to consistently assess REDD+ cost elements. Results Based on historical land use change patterns, current region-specific economic conditions and carbon stocks, project-specific opportunity costs ranged between US$ -7.8 and 28.8 tCOxxxx for deforestation and forest degradation drivers such as agriculture, fuel wood production, unsustainable timber extraction and pasture expansion. The mean opportunity costs for the three projects ranged between US$ 10.1 – 12.5 tCO2. Implementation costs comprised between 89% and 95% of total project costs (excluding opportunity costs ranging between US$ 4.5 - 12.2 tCO2 for a period of 30 years. Transaction costs for measurement, reporting, verification (MRV, and other carbon market related compliance costs comprised a minor share, between US$ 0.21 - 1.46 tCO2. Similarly, the institutional costs comprised around 1% of total REDD+ costs in a range of US$ 0.06 – 0.11 tCO2. Conclusions The use of bottom-up approaches to estimate REDD+ economics by considering regional variations in economic conditions and carbon stocks has been shown to be an appropriate approach to provide policy and decision-makers robust economic information on REDD+. The assessment of opportunity costs is a crucial first step to

  15. Synthetic biology pioneer John Glass to kick off GenBioOrg seminar series

    OpenAIRE

    Bland, Susan

    2010-01-01

    GenBioOrg, an organization for students in Virginia Tech's Genetics, Bioinformatics, and Computational Biology Ph.D. program, is hosting an invited speaker series for the spring 2010 semester that will feature an opening talk by John Glass, professor in the J. Craig Venter Institute's (JCVI) Synthetic Biology Group.

  16. 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,…

  17. Bottom-up and top-down influences at untrained conditions determine perceptual learning specificity and transfer

    Science.gov (United States)

    Xiong, Ying-Zi; Zhang, Jun-Yun; Yu, Cong

    2016-01-01

    Perceptual learning is often orientation and location specific, which may indicate neuronal plasticity in early visual areas. However, learning specificity diminishes with additional exposure of the transfer orientation or location via irrelevant tasks, suggesting that the specificity is related to untrained conditions, likely because neurons representing untrained conditions are neither bottom-up stimulated nor top-down attended during training. To demonstrate these top-down and bottom-up contributions, we applied a “continuous flash suppression” technique to suppress the exposure stimulus into sub-consciousness, and with additional manipulations to achieve pure bottom-up stimulation or top-down attention with the transfer condition. We found that either bottom-up or top-down influences enabled significant transfer of orientation and Vernier discrimination learning. These results suggest that learning specificity may result from under-activations of untrained visual neurons due to insufficient bottom-up stimulation and/or top-down attention during training. High-level perceptual learning thus may not functionally connect to these neurons for learning transfer. DOI: http://dx.doi.org/10.7554/eLife.14614.001 PMID:27377357

  18. Synthetic Approaches and Biological Activities of 4-Hydroxycoumarin Derivatives

    OpenAIRE

    Oee-Sook Park; Jae-Chul Jung

    2009-01-01

    The main purpose of this review is to summarize recent chemical syntheses and structural modifications of 4-hydroxycoumarin and its derivatives, of interest due to their characteristic conjugated molecular architecture and biological activities.

  19. Synthetic Approaches and Biological Activities of 4-Hydroxycoumarin Derivatives

    Directory of Open Access Journals (Sweden)

    Oee-Sook Park

    2009-11-01

    Full Text Available The main purpose of this review is to summarize recent chemical syntheses and structural modifications of 4-hydroxycoumarin and its derivatives, of interest due to their characteristic conjugated molecular architecture and biological activities.

  20. Thiosemicarbazones: preparation methods, synthetic applications and biological importance

    International Nuclear Information System (INIS)

    Thiosemicarbazones are a class of compounds known by their chemical and biological properties, such as antitumor, antibacterial, antiviral and antiprotozoal activity. Their ability to form chelates with metals has great importance in their biological activities. Their synthesis is very simple, versatile and clean, usually giving high yields. They are largely employed as intermediates, in the synthesis of others compounds. This article is a survey of some of these characteristics showing their great importance to organic and medicinal chemistry. (author)

  1. Ambivalences of creating life societal and philosophical dimensions of synthetic biology

    CERN Document Server

    Engelhard, Margret; Toepfer, Georg

    2016-01-01

    "Synthetic biology" is the label of a new technoscientific field with many different facets and agendas. One common aim is to "create life", primarily by using engineering principles to design and modify biological systems for human use. In a wider context, the topic has become one of the big cases in the legitimization processes associated with the political agenda to solve global problems with the aid of (bio-)technological innovation. Conceptual-level and meta-level analyses are needed: we should sort out conceptual ambiguities to agree on what we talk about, and we need to spell out agendas to see the disagreements clearly. The book is based on the interdisciplinary summer school "Analyzing the societal dimensions of synthetic biology", which took place in Berlin in September 2014. The contributions address controversial discussions around the philosophical examination, public perception, moral evaluation and governance of synthetic biology.

  2. The Early Anthropogenic Hypothesis: Top-Down and Bottom-up Evidence

    Science.gov (United States)

    Ruddiman, W. F.

    2014-12-01

    Two complementary lines of evidence support the early anthropogenic hypothesis. Top-down evidence comes from comparing Holocene greenhouse-gas trends with those during equivalent intervals of previous interglaciations. The increases in CO2 and CH4 during the late Holocene are anomalous compared to the decreasing trends in a stacked average of previous interglaciations, thereby supporting an anthropogenic origin. During interglacial stage 19, the closest Holocene insolation analog, CO2 fell to 245 ppm by the time equivalent to the present, in contrast to the observed pre-industrial rise to 280-285 ppm. The 245-ppm level measured in stage 19 falls at the top of the natural range predicted by the original anthropogenic hypothesis of Ruddiman (2003). Bottom-up evidence comes from a growing list of archeological and other compilations showing major early anthropogenic transformations of Earth's surface. Key examples include: efforts by Dorian Fuller and colleagues mapping the spread of irrigated rice agriculture across southern Asia and its effects on CH4 emissions prior to the industrial era; an additional effort by Fuller showing the spread of methane-emitting domesticated livestock across Asia and Africa (coincident with the spread of fertile crescent livestock across Europe); historical compilations by Jed Kaplan and colleagues documenting very high early per-capita forest clearance in Europe, thus underpinning simulations of extensive pre-industrial clearance and large CO2 emissions; and wide-ranging studies by Erle Ellis and colleagues of early anthropogenic land transformations in China and elsewhere.

  3. Top-down silicon microcantilever with coupled bottom-up silicon nanowire for enhanced mass resolution

    International Nuclear Information System (INIS)

    A stepped cantilever composed of a bottom-up silicon nanowire coupled to a top-down silicon microcantilever electrostatically actuated and with capacitive or optical readout is fabricated and analyzed, both theoretically and experimentally, for mass sensing applications. The mass sensitivity at the nanowire free end and the frequency resolution considering thermomechanical noise are computed for different nanowire dimensions. The results obtained show that the coupled structure presents a very good mass sensitivity thanks to the nanowire, where the mass depositions take place, while also presenting a very good frequency resolution due to the microcantilever, where the transduction is carried out. A two-fold improvement in mass sensitivity with respect to that of the microcantilever standalone is experimentally demonstrated, and at least an order-of-magnitude improvement is theoretically predicted, only changing the nanowire length. Very close frequency resolutions are experimentally measured and theoretically predicted for a standalone microcantilever and for a microcantilever-nanowire coupled system. Thus, an improvement in mass sensing resolution of the microcantilever-nanowire stepped cantilever is demonstrated with respect to that of the microcantilever standalone. (paper)

  4. Optical and electronic properties study of bottom-up graphene nanoribbons for photovoltaic applications

    Science.gov (United States)

    Villegas, Cesar E. P.; Rocha, Alexandre

    2015-03-01

    Graphene nanoribbons (GNRs), turn out to be serious contender for several optolectronic applications due to their physical properties. Recently, bottom-up methods, using the assembly of appropriate precursor molecules were shown to be an exciting pathway towards making precise nanoribbons. In particular, it has been demonstrated that so-called cove-shaped GNRs absorb light in the visible part of the spectrum, suggesting they could be used for photovoltaic applications. In solar cells, the key ingredient is the presence excitons and their subsequent diffusion along a donor material. This is influenced by the character of the different excitations taking place, as well as, the exciton binding energy. Thus, In this work we use many-body corrected density functional theory to simulate the optical properties of these nanoribbons. We elucidate the most important transitions occurring in these systems, and identify types of excitatiions that have not been previously observed in conventional nanoribbons. We also find that the exciton binding energies for all the structures we considered are in the eV range, which enhances the diffusion lengths for the particle-hole pairs. Finally, we estimate the potencial of these systems as solar cells by calculating the short-circuit current. The Authors thank FAPESP for financial support.

  5. Bottom-Up, Wet Chemical Technique for the Continuous Synthesis of Inorganic Nanoparticles

    Directory of Open Access Journals (Sweden)

    Annika Betke

    2014-01-01

    Full Text Available Continuous wet chemical approaches for the production of inorganic nanoparticles are important for large scale production of nanoparticles. Here we describe a bottom-up, wet chemical method applying a microjet reactor. This technique allows the separation between nucleation and growth in a continuous reactor environment. Zinc oxide (ZnO, magnetite (Fe3O4, as well as brushite (CaHPO4·2H2O, particles with a small particle size distribution can be obtained continuously by using the rapid mixing of two precursor solutions and the fast removal of the nuclei from the reaction environment. The final particles were characterized by FT-IR, TGA, DLS, XRD and SEM techniques. Systematic studies on the influence of the different process parameters, such as flow rate and process temperature, show that the particle size can be influenced. Zinc oxide was obtained with particle sizes between 44 nm and 102 nm. The obtained magnetite particles have particle sizes in the range of 46 nm to 132 nm. Brushite behaves differently; the obtained particles were shaped like small plates with edge lengths between 100 nm and 500 nm.

  6. Achieving integrated urban water management: planning top-down or bottom-up?

    Science.gov (United States)

    Gabe, J; Trowsdale, S; Vale, R

    2009-01-01

    Integrated Urban Water Management (IUWM) acknowledges a broad range of environmental and socio-economic outcomes but the link between design intentions and operational performance is not always clear. This may be due in part to a lack of shared principles that remove bias and inconsistency in assessing the operational performance of IUWM. This paper investigates the possibility of developing shared principles through examination of shared objectives and shared indicators within two logical and integrated frameworks for urban residential developments that aspire for IUWM and sustainable development. The framework method was applied using very different approaches-one a top-down urban planning process, the other a bottom-up community consultation process. Both frameworks highlight the extent to which IUWM is part of a broad social and environmental system. Core environmental performance objectives and indicators were very similar, highlighting the potential to develop shared principles in reporting and benchmarking the environmental performance of neighbourhood developments. Socio-economic indicators were highly variable due to process and likely contextual differences, thus it is unclear if the influence of IUWM on these variables can transcend the social context unless the practice of urban water management can expand its core responsibility beyond "hard" physical infrastructure. PMID:19474495

  7. Evidence for differential top-down and bottom-up suppression in posterior parietal cortex.

    Science.gov (United States)

    Mirpour, Koorosh; Bisley, James W

    2013-10-19

    When searching for an object, we usually avoid items that are visually different from the target and objects or places that have been searched already. Previous studies have shown that neural activity in the lateral intraparietal area (LIP) can be used to guide this behaviour; responses to task irrelevant stimuli or to stimuli that have been fixated previously in the trial are reduced compared with responses to potential targets. Here, we test the hypothesis that these reduced responses have a different genesis. Two animals were trained on a visual foraging task, in which they had to find a target among a number of physically identical potential targets (T) and task irrelevant distractors. We recorded neural activity and local field potentials (LFPs) in LIP while the animals performed the task. We found that LFP power was similar for potential targets and distractors but was greater in the alpha and low beta bands when a previously fixated T was in the response field. We interpret these data to suggest that the reduced single-unit response to distractors is a bottom-up feed-forward result of processing in earlier areas and the reduced response to previously fixated Ts is a result of active top-down suppression. PMID:24018730

  8. Top-down and bottom-up regulation of macroalgal community structure on a Kenyan reef

    Science.gov (United States)

    Mörk, Erik; Sjöö, Gustaf Lilliesköld; Kautsky, Nils; McClanahan, Tim R.

    2009-09-01

    Top-down and bottom-up regulation in the form of grazing by herbivores and nutrient availability are important factors governing macroalgal communities in the coral reef ecosystem. Today, anthropogenic activities, such as over-harvesting of herbivorous fish and sea urchins and increased nutrient loading, are altering the interaction of these two structuring forces. The present study was conducted in Kenya and investigates the relative importance of herbivory and nutrient loading on macroalgal community dynamics, by looking at alterations in macroalgal functional groups, species diversity ( H') and biomass within experimental quadrats. The experiment was conducted in situ for 42 days during the dry season. Cages excluding large herbivorous fish and sea urchins were used in the study and nutrient addition was conducted using coated, slow-release fertilizer (nitrogen and phosphorous) at a site where herbivory is generally low and nutrient levels are relatively high for the region. Nutrient addition increased tissue nutrient content in the algae, and fertilized quadrats had 24% higher species diversity. Herbivore exclusion resulted in a 77% increase in algal biomass, mainly attributable to a >1000% increase in corticated forms. These results are in accordance with similar studies in other regions, but are unique in that they indicate that, even when prevailing nutrient levels are relatively high and herbivore pressure is relatively low, continued anthropogenic disturbance results in further ecological responses and increased reef degradation.

  9. Bottom-up and top-down mechanisms indirectly mediate interactions between benthic biotic ecosystem components

    Science.gov (United States)

    Van Colen, Carl; Thrush, Simon F.; Parkes, Samantha; Harris, Rachel; Woodin, Sally A.; Wethey, David S.; Pilditch, Conrad A.; Hewitt, Judi E.; Lohrer, Andrew M.; Vincx, Magda

    2015-04-01

    The loss or decline in population size of key species can instigate a cascade of effects that have implications for interacting species, therewith impacting biodiversity and ecosystem functioning. We examined how top-down and bottom-up interactions may mediate knock-on effects of a coastal deposit-feeding clam, Macomona liliana (hereafter Macomona), on sandflat meiobenthos densities. Therefore we manipulated densities of Macomona in combination with predator exclusion and experimental shading that was expected to alter microphytobenthos biomass. We show that Macomona regulated densities of meiobenthic (38-500 μm) nematodes, copepods, polychaetes, turbellarians, and ostracodes during the three months of incubation via indirect mechanisms. Predator pressure on Macomona by eagle rays (Myliobatis tenuicaudatus) was found to have a negative effect on densities of some meiobenthic taxa. Furthermore, experimental shading resulted in the loss of a positive relation between Macomona and microphytobenthos biomass, while concurrently increasing the density of some meiobenthic taxa. We suggest that this observation can be explained by the release from bioturbation interference effects of the cockle Austrovenus stutchburyi that was found to thrive in the presence of Macomona under non-shaded conditions. Our results highlight the importance of interactions between macrofaunal bioturbation, microphyte biomass, sediment stability, and predation pressure for the structuring of benthic communities. This experiment illustrates that manipulative field experiments may be particularly suitable to study such multiple indirect mechanisms that regulate ecosystem diversity and related functioning because such approaches may best capture the complex feedbacks and processes that determine ecosystem dynamics.

  10. Template-Free Bottom-Up Method for Fabricating Diblock Copolymer Patchy Particles.

    Science.gov (United States)

    Ye, Xianggui; Li, Zhan-Wei; Sun, Zhao-Yan; Khomami, Bamin

    2016-05-24

    Patchy particles are one of most important building blocks for hierarchical structures because of the discrete patches on their surface. We have demonstrated a convenient, simple, and scalable bottom-up method for fabricating diblock copolymer patchy particles through both experiments and dissipative particle dynamics (DPD) simulations. The experimental method simply involves reducing the solvent quality of the diblock copolymer solution by the slow addition of a nonsolvent. Specifically, the fabrication of diblock copolymer patchy particles begins with a crew-cut soft-core micelle, where the micelle core is significantly swelled by the solvent. With water addition at an extremely slow rate, the crew-cut soft-core micelles first form a larger crew-cut micelle. With further water addition, the corona-forming blocks of the crew-cut micelles begin to aggregate and eventually form well-defined patches. Both experiments and DPD simulations indicate that the number of patches has a very strong dependence on the diblock copolymer composition-the particle has more patches on the surface with a lower volume fraction of patch-forming blocks. Furthermore, particles with more patches have a greater ability to assemble, and particles with fewer patches have a greater ability to merge once assembled. PMID:27109249

  11. Bottom-up study of flaw tolerance properties of protein networks

    Science.gov (United States)

    Qin, Zhao; Buehler, Markus

    2012-02-01

    We study the material properties of an intermediate filament proten network by computational modeling using a bottom-up approach. We start with an atomic model of each filament's and obtain the mechanical behavior of them. We then use these parameters in setting up a mesoscale model of the network material at scales of micrometers. Using this multi-scale method, we report a detailed analysis of the associated deformation and failure mechanisms of this hierarchical material. Our modeling reveals that a structure transition that occurs at the proteins' secondary structure level is crucial for the networks' flaw tolerance property, which implies that the material retains its mechanical function despite the existence of large defects. We also examine the effect of crosslink strength on the failure properties. We discover that relatively weaker crosslinks lead to a more flaw tolerant network that is 23% stronger. This unexpected behavior is caused by that the crosslink strength functions as a switch to alter the failure mechanism. Weak crosslinks are able to efficiently diffuse the stress around the crack tip, making the crack more difficult to propagate. We compare our results to that of elastic and softening materials and find that the effect of crosslink strength is much smaller in those systems. These findings imply that the mechanical properties of both the filaments and interfaces among filaments are critical for bioinspired material designs, challenging the conventional paradigm in engineering design.

  12. A Bottom-Up Engineered Broadband Optical Nanoabsorber for Radiometry and Energy Harnessing Applications

    Science.gov (United States)

    Kaul, Anupama B.; Coles, James B.; Megerian, Krikor G.; Eastwood, Michael; Green, Robert O.; Bandaru, Prabhakar R.

    2013-01-01

    Optical absorbers based on vertically aligned multi-walled carbon nanotubes (MWCNTs), synthesized using electric-field assisted growth, are described here that show an ultra-low reflectance, 100X lower compared to Au-black from wavelength lamba approximately 350 nm - 2.5 micron. A bi-metallic Co/Ti layer was shown to catalyze a high site density of MWCNTs on metallic substrates and the optical properties of the absorbers were engineered by controlling the bottom-up synthesis conditions using dc plasma-enhanced chemical vapor deposition (PECVD). Reflectance measurements on the MWCNT absorbers after heating them in air to 400deg showed negligible changes in reflectance which was still low, approximately 0.022 % at lamba approximately 2 micron. In contrast, the percolated structure of the reference Au-black samples collapsed completely after heating, causing the optical response to degrade at temperatures as low as 200deg. The high optical absorption efficiency of the MWCNT absorbers, synthesized on metallic substrates, over a broad spectral range, coupled with their thermal ruggedness, suggests they have promise in solar energy harnessing applications, as well as thermal detectors for radiometry.

  13. Bottom-Up Abstract Modelling of Optical Networks-on-Chip: From Physical to Architectural Layer

    Directory of Open Access Journals (Sweden)

    Alberto Parini

    2012-01-01

    Full Text Available This work presents a bottom-up abstraction procedure based on the design-flow FDTD + SystemC suitable for the modelling of optical Networks-on-Chip. In this procedure, a complex network is decomposed into elementary switching elements whose input-output behavior is described by means of scattering parameters models. The parameters of each elementary block are then determined through 2D-FDTD simulation, and the resulting analytical models are exported within functional blocks in SystemC environment. The inherent modularity and scalability of the S-matrix formalism are preserved inside SystemC, thus allowing the incremental composition and successive characterization of complex topologies typically out of reach for full-vectorial electromagnetic simulators. The consistency of the outlined approach is verified, in the first instance, by performing a SystemC analysis of a four-input, four-output ports switch and making a comparison with the results of 2D-FDTD simulations of the same device. Finally, a further complex network encompassing 160 microrings is investigated, the losses over each routing path are calculated, and the minimum amount of power needed to guarantee an assigned BER is determined. This work is a basic step in the direction of an automatic technology-aware network-level simulation framework capable of assembling complex optical switching fabrics, while at the same time assessing the practical feasibility and effectiveness at the physical/technological level.

  14. Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis.

    Science.gov (United States)

    Kremer, Lukas P M; Leufken, Johannes; Oyunchimeg, Purevdulam; Schulze, Stefan; Fufezan, Christian

    2016-03-01

    Proteomics data integration has become a broad field with a variety of programs offering innovative algorithms to analyze increasing amounts of data. Unfortunately, this software diversity leads to many problems as soon as the data is analyzed using more than one algorithm for the same task. Although it was shown that the combination of multiple peptide identification algorithms yields more robust results, it is only recently that unified approaches are emerging; however, workflows that, for example, aim to optimize search parameters or that employ cascaded style searches can only be made accessible if data analysis becomes not only unified but also and most importantly scriptable. Here we introduce Ursgal, a Python interface to many commonly used bottom-up proteomics tools and to additional auxiliary programs. Complex workflows can thus be composed using the Python scripting language using a few lines of code. Ursgal is easily extensible, and we have made several database search engines (X!Tandem, OMSSA, MS-GF+, Myrimatch, MS Amanda), statistical postprocessing algorithms (qvality, Percolator), and one algorithm that combines statistically postprocessed outputs from multiple search engines ("combined FDR") accessible as an interface in Python. Furthermore, we have implemented a new algorithm ("combined PEP") that combines multiple search engines employing elements of "combined FDR", PeptideShaker, and Bayes' theorem. PMID:26709623

  15. Bottom-Up Visual Saliency Estimation With Deep Autoencoder-Based Sparse Reconstruction.

    Science.gov (United States)

    Xia, Chen; Qi, Fei; Shi, Guangming

    2016-06-01

    Research on visual perception indicates that the human visual system is sensitive to center-surround (C-S) contrast in the bottom-up saliency-driven attention process. Different from the traditional contrast computation of feature difference, models based on reconstruction have emerged to estimate saliency by starting from original images themselves instead of seeking for certain ad hoc features. However, in the existing reconstruction-based methods, the reconstruction parameters of each area are calculated independently without taking their global correlation into account. In this paper, inspired by the powerful feature learning and data reconstruction ability of deep autoencoders, we construct a deep C-S inference network and train it with the data sampled randomly from the entire image to obtain a unified reconstruction pattern for the current image. In this way, global competition in sampling and learning processes can be integrated into the nonlocal reconstruction and saliency estimation of each pixel, which can achieve better detection results than the models with separate consideration on local and global rarity. Moreover, by learning from the current scene, the proposed model can achieve the feature extraction and interaction simultaneously in an adaptive way, which can form a better generalization ability to handle more types of stimuli. Experimental results show that in accordance with different inputs, the network can learn distinct basic features for saliency modeling in its code layer. Furthermore, in a comprehensive evaluation on several benchmark data sets, the proposed method can outperform the existing state-of-the-art algorithms. PMID:26800552

  16. Visionmaker NYC: A bottom-up approach to finding shared socioeconomic pathways in New York City

    Science.gov (United States)

    Sanderson, E. W.; Fisher, K.; Giampieri, M.; Barr, J.; Meixler, M.; Allred, S. B.; Bunting-Howarth, K. E.; DuBois, B.; Parris, A. S.

    2015-12-01

    Visionmaker NYC is a free, public participatory, bottom-up web application to develop and share climate mitigation and adaptation strategies for New York City neighborhoods. The goal is to develop shared socioeconomic pathways by allowing a broad swath of community members - from schoolchildren to architects and developers to the general public - to input their concepts for a desired future. Visions are comprised of climate scenarios, lifestyle choices, and ecosystem arrangements, where ecosystems are broadly defined to include built ecosystems (e.g. apartment buildings, single family homes, etc.), transportation infrastructure (e.g. highways, connector roads, sidewalks), and natural land cover types (e.g. wetlands, forests, estuary.) Metrics of water flows, carbon cycling, biodiversity patterns, and population are estimated for the user's vision, for the same neighborhood today, and for that neighborhood as it existed in the pre-development state, based on the Welikia Project (welikia.org.) Users can keep visions private, share them with self-defined groups of other users, or distribute them publicly. Users can also propose "challenges" - specific desired states of metrics for specific parts of the city - and others can post visions in response. Visionmaker contributes by combining scenario planning, scientific modelling, and social media to create new, wide-open possibilities for discussion, collaboration, and imagination regarding future, shared socioeconomic pathways.

  17. Fabricating ordered functional nanostructures onto polycrystalline substrates from the bottom-up

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Maria, E-mail: mtorres@drexel.edu; Pardo, Lorena; Ricote, Jesus [Instituto de Ciencia de Materiales de Madrid (Spain); Fuentes-Cobas, Luis E. [Centro de Investigacion en Materiales Avanzados (Mexico); Rodriguez, Brian J. [University College Dublin, Belfield, School of Physics (Ireland); Calzada, M. Lourdes, E-mail: lcalzada@icmm.csic.es [Instituto de Ciencia de Materiales de Madrid (Spain)

    2012-10-15

    Microemulsion-mediated synthesis has emerged as a powerful bottom-up procedure for the preparation of ferroelectric nanostructures onto substrates. However, periodical order has yet to be achieved onto polycrystalline Pt-coated Si substrates. Here, we report a new methodology that involves microemulsion-mediated synthesis and the controlled modification of the surface of the substrate by coating it with a template-layer of water-micelles. This layer modifies the surface tension of the substrate and yields a periodic arrangement of ferroelectric crystalline nanostructures. The size of the nanostructures is decreased to the sub-50 nm range and they show a hexagonal order up to the third neighbors, which corresponds to a density of 275 Gb in{sup -2}. The structural analysis of the nanostructures by synchrotron X-ray diffraction confirms that the nanostructures have a PbTiO{sub 3} perovskite structure, with lattice parameters of a = b = 3.890(0) A and c = 4.056(7) A. Piezoresponse force microscopy confirmed the ferro-piezoelectric character of the nanostructures. This simple methodology is valid for the self-assembly of other functional oxides onto polycrystalline substrates, enabling their reliable integration into micro/nano devices.

  18. Bottom-up synthesis of ordered metal/oxide/metal nanodots on substrates for nanoscale resistive switching memory

    Science.gov (United States)

    Han, Un-Bin; Lee, Jang-Sik

    2016-05-01

    The bottom-up approach using self-assembled materials/processes is thought to be a promising solution for next-generation device fabrication, but it is often found to be not feasible for use in real device fabrication. Here, we report a feasible and versatile way to fabricate high-density, nanoscale memory devices by direct bottom-up filling of memory elements. An ordered array of metal/oxide/metal (copper/copper oxide/copper) nanodots was synthesized with a uniform size and thickness defined by self-organized nanotemplate mask by sequential electrochemical deposition (ECD) of each layer. The fabricated memory devices showed bipolar resistive switching behaviors confirmed by conductive atomic force microscopy. This study demonstrates that ECD with bottom-up growth has great potential to fabricate high-density nanoelectronic devices beyond the scaling limit of top-down device fabrication processes.

  19. Bottom-up synthesis of ordered metal/oxide/metal nanodots on substrates for nanoscale resistive switching memory

    Science.gov (United States)

    Han, Un-Bin; Lee, Jang-Sik

    2016-01-01

    The bottom-up approach using self-assembled materials/processes is thought to be a promising solution for next-generation device fabrication, but it is often found to be not feasible for use in real device fabrication. Here, we report a feasible and versatile way to fabricate high-density, nanoscale memory devices by direct bottom-up filling of memory elements. An ordered array of metal/oxide/metal (copper/copper oxide/copper) nanodots was synthesized with a uniform size and thickness defined by self-organized nanotemplate mask by sequential electrochemical deposition (ECD) of each layer. The fabricated memory devices showed bipolar resistive switching behaviors confirmed by conductive atomic force microscopy. This study demonstrates that ECD with bottom-up growth has great potential to fabricate high-density nanoelectronic devices beyond the scaling limit of top-down device fabrication processes. PMID:27157385

  20. Cosmo Cassette: A Microfluidic Microgravity Microbial System For Synthetic Biology Unit Tests and Satellite Missions

    Science.gov (United States)

    Berliner, Aaron J.

    2013-01-01

    Although methods in the design-build-test life cycle of the synthetic biology field have grown rapidly, the expansion has been non-uniform. The design and build stages in development have seen innovations in the form of biological CAD and more efficient means for building DNA, RNA, and other biological constructs. The testing phase of the cycle remains in need of innovation. Presented will be both a theoretical abstraction of biological measurement and a practical demonstration of a microfluidics-based platform for characterizing synthetic biological phenomena. Such a platform demonstrates a design of additive manufacturing (3D printing) for construction of a microbial fuel cell (MFC) to be used in experiments carried out in space. First, the biocompatibility of the polypropylene chassis will be demonstrated. The novel MFCs will be cheaper, and faster to make and iterate through designs. The novel design will contain a manifold switchingdistribution system and an integrated in-chip set of reagent reservoirs fabricated via 3D printing. The automated nature of the 3D printing yields itself to higher resolution switching valves and leads to smaller sized payloads, lower cost, reduced power and a standardized platform for synthetic biology unit tests on Earth and in space. It will be demonstrated that the application of unit testing in synthetic biology will lead to the automatic construction and validation of desired constructs. Unit testing methodologies offer benefits of preemptive problem identification, change of facility, simplicity of integration, ease of documentation, and separation of interface from implementation, and automated design.

  1. Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course

    OpenAIRE

    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, ...

  2. The Comparative Effect of Top-down Processing and Bottom-up Processing through TBLT on Extrovert and Introvert EFL

    Directory of Open Access Journals (Sweden)

    Pezhman Nourzad Haradasht

    2013-09-01

    Full Text Available This research seeks to examine the effect of two models of reading comprehension, namely top-down and bottom-up processing, on the reading comprehension of extrovert and introvert EFL learners’ reading comprehension. To do this, 120 learners out of a total number of 170 intermediate learners being educated at Iran Mehr English Language School were selected all taking a PET (Preliminary English Test first for homogenization prior to the study. They also answered the Eysenck Personality Inventory (EPI which in turn categorized them into two subgroups within each reading models consisting of introverts and extroverts. All in all, there were four subgroups: 30 introverts and 30 extroverts undergoing the top-down processing treatment, and 30 introverts and 30 extroverts experiencing the bottom-up processing treatment. The aforementioned PET was administered as the post test of the study after each group was exposed to the treatment for 18 sessions in six weeks. After the instructions finished, the mean scores of all four groups on this post test were computed and a two-way ANOVA was run to test all the four hypotheses raise in this study. the results showed that while learners generally benefitted more from the bottom-up processing setting compared  to the top-down processing one, the extrovert group was better off receiving top-down instruction. Furthermore, introverts outperformed extroverts in bottom-up group; yet between the two personalities subgroups in the top-down setting no difference was seen. A predictable pattern of benefitting from teaching procedures could not be drawn for introverts as in both top-down and bottom-up settings, they benefitted more than extroverts.Keywords: Reading comprehension, top-down processing, bottom-up processing, extrovert, introvert

  3. Advanced Drug Delivery Systems - a Synthetic and Biological Applied Evaluation

    DEFF Research Database (Denmark)

    Bjerg, Lise Nørkjær

    Specific delivery of drugs to diseased sites in the body is a major topic in the development of drug delivery system today. Especially, the field of cancer treatment needs improved drug delivery systems as the strong dose-limiting side effects of chemotherapy today often present a barrier for an...... unloading of the encapsulated drug have been tried optimized in a variety of ways. Many propose the use of small molecules, such as vitamins and peptides, for active targeting of the liposomes to overexpressed receptors on the cancerous tissue. Once located close to the diseased site a trigger mechanism for...... function as the targeting moiety on the surface of the liposomes. Several examples of synthetic procedures known from the literature are presented. The chapter is completed with a study covering the conjugation efficiencies of a variety of chemical functionalities. Large differences are revealed between...

  4. Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells.

    Science.gov (United States)

    Angelici, Bartolomeo; Mailand, Erik; Haefliger, Benjamin; Benenson, Yaakov

    2016-08-30

    One of the goals of synthetic biology is to develop programmable artificial gene networks that can transduce multiple endogenous molecular cues to precisely control cell behavior. Realizing this vision requires interfacing natural molecular inputs with synthetic components that generate functional molecular outputs. Interfacing synthetic circuits with endogenous mammalian transcription factors has been particularly difficult. Here, we describe a systematic approach that enables integration and transduction of multiple mammalian transcription factor inputs by a synthetic network. The approach is facilitated by a proportional amplifier sensor based on synergistic positive autoregulation. The circuits efficiently transduce endogenous transcription factor levels into RNAi, transcriptional transactivation, and site-specific recombination. They also enable AND logic between pairs of arbitrary transcription factors. The results establish a framework for developing synthetic gene networks that interface with cellular processes through transcriptional regulators. PMID:27545896

  5. Biomimetic Chemistry and Synthetic Biology: A Two-way Traffic Across the Borders

    OpenAIRE

    Bernadette Bensaude-Vincent

    2009-01-01

    Crossing the boundaries - between nature and artifact and between inanimate and living matter - is a major feature of the convergence between nanotechnology and biotechnology. This paper points to two symmetric ways of crossing the boundaries: chemists mimicking nature's structures and processes, and synthetic biologists mimicking synthetic chemists with biological materials. However to what extent are they symmetrical and do they converge toward a common view of life and machines? The questi...

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

    OpenAIRE

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

    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...

  7. Quantifying the uncertainties of a bottom-up emission inventory of anthropogenic atmospheric pollutants in China

    Directory of Open Access Journals (Sweden)

    Y. Zhao

    2010-11-01

    Full Text Available The uncertainties of a national, bottom-up inventory of Chinese emissions of anthropogenic SO2, NOx, and particulate matter (PM of different size classes and carbonaceous species are comprehensively quantified, for the first time, using Monte Carlo simulation. The inventory is structured by seven dominant sectors: coal-fired electric power, cement, iron and steel, other industry (boiler combustion, other industry (non-combustion processes, transportation, and residential. For each parameter related to emission factors or activity-level calculations, the uncertainties, represented as probability distributions, are either statistically fitted using results of domestic field tests or, when these are lacking, estimated based on foreign or other domestic data. The uncertainties (i.e., 95% confidence intervals around the central estimates of Chinese emissions of SO2, NOx, total PM, PM10, PM2.5, black carbon (BC, and organic carbon (OC in 2005 are estimated to be −14%~12%, −10%~36%, −10%~36%, −12%~42% −16%~52%, −23%~130%, and −37%~117%, respectively. Variations at activity levels (e.g., energy consumption or industrial production are not the main source of emission uncertainties. Due to narrow classification of source types, large sample sizes, and relatively high data quality, the coal-fired power sector is estimated to have the smallest emission uncertainties for all species except BC and OC. Due to poorer source classifications and a wider range of estimated emission factors, considerable uncertainties of NOx and PM emissions from cement production and boiler combustion in other industries are found. The probability distributions of emission factors for biomass burning, the largest source of BC and OC, are fitted based on very limited domestic field measurements, and special caution should thus be taken interpreting these emission uncertainties. Although Monte

  8. Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem.

    Science.gov (United States)

    Rudman, Seth M; Rodriguez-Cabal, Mariano A; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W; Crutsinger, Gregory M

    2015-08-01

    Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. PMID:26203004

  9. High thermoelectric figure of merit nanostructured pnictogen chalcogenides by bottom-up synthesis and assembly

    Science.gov (United States)

    Mehta, Rutvik J.

    Thermoelectric materials offer promise for realizing transformative environmentallyfriendly solid-state refrigeration technologies that could replace current technologies based on ozone-depleting liquid coolants. The fruition of this vision requires factorial enhancements in the figure of merit (ZT) of thermoelectric materials, necessitating high Seebeck coefficient (alpha), high electrical conductivity (sigma) and low thermal conductivity (kappa). This thesis reports a novel bottom-up approach to scalably sculpt large quantities (>10g/minute) of V 2VI3 nanocrystals with controllable shapes and sizes, and assemble them into bulk samples to obtain both high power factors alpha 2sigma as well as unprecedentedly low kappa through tunable doping and nanostructuring. The thesis demonstrates a surfactant-mediated microwave-solvothermal synthesis technique that selectively yields both n- and p-typed pnictogen chalcogenide (Bi2Te3, Sb2Te3, Bi2Se3) nanoplates and, nanowires and nanotubes (Sb 2Se3) that can be sintered to obtain 25-250 % increases in ZT>1 compared to their non-nanostructured and un-doped counterparts. A key result is that nanostructuring diminishes the lattice thermal conductivity kappa L to ultra-low values of 0.2-0.5 Wm-1K-1. Sub-atomic-percent sulfur doping and sulfurization of the pnictogen chalcogenides induced through mercaptan-terminated organic surfactants used in the synthesis result in large Seebeck coefficients between -240 nanocomposites by mixing nanoplates of different materials (e.g., S-doped Sb2Te3 and S-doped Bi2Te3) and forming heterostructures of metals and chalcogenides. The thesis finally demonstrates the extendibility of the novel synthesis and assembly approach to tailor the thermoelectric properties of other non-traditional thermoelectric materials systems.

  10. OBJCUT: efficient segmentation using top-down and bottom-up cues.

    Science.gov (United States)

    Kumar, M Pawan; Torr, P H S; Zisserman, A

    2010-03-01

    We present a probabilistic method for segmenting instances of a particular object category within an image. Our approach overcomes the deficiencies of previous segmentation techniques based on traditional grid conditional random fields (CRF), namely that 1) they require the user to provide seed pixels for the foreground and the background and 2) they provide a poor prior for specific shapes due to the small neighborhood size of grid CRF. Specifically, we automatically obtain the pose of the object in a given image instead of relying on manual interaction. Furthermore, we employ a probabilistic model which includes shape potentials for the object to incorporate top-down information that is global across the image, in addition to the grid clique potentials which provide the bottom-up information used in previous approaches. The shape potentials are provided by the pose of the object obtained using an object category model. We represent articulated object categories using a novel layered pictorial structures model. Nonarticulated object categories are modeled using a set of exemplars. These object category models have the advantage that they can handle large intraclass shape, appearance, and spatial variation. We develop an efficient method, OBJCUT, to obtain segmentations using our probabilistic framework. Novel aspects of this method include: 1) efficient algorithms for sampling the object category models of our choice and 2) the observation that a sampling-based approximation of the expected log-likelihood of the model can be increased by a single graph cut. Results are presented on several articulated (e.g., animals) and nonarticulated (e.g., fruits) object categories. We provide a favorable comparison of our method with the state of the art in object category specific image segmentation, specifically the methods of Leibe and Schiele and Schoenemann and Cremers. PMID:20075476

  11. Bottom-up model of self-organized criticality on networks.

    Science.gov (United States)

    Noël, Pierre-André; Brummitt, Charles D; D'Souza, Raissa M

    2014-01-01

    The Bak-Tang-Wiesenfeld (BTW) sandpile process is an archetypal, stylized model of complex systems with a critical point as an attractor of their dynamics. This phenomenon, called self-organized criticality, appears to occur ubiquitously in both nature and technology. Initially introduced on the two-dimensional lattice, the BTW process has been studied on network structures with great analytical successes in the estimation of macroscopic quantities, such as the exponents of asymptotically power-law distributions. In this article, we take a microscopic perspective and study the inner workings of the process through both numerical and rigorous analysis. Our simulations reveal fundamental flaws in the assumptions of past phenomenological models, the same models that allowed accurate macroscopic predictions; we mathematically justify why universality may explain these past successes. Next, starting from scratch, we obtain microscopic understanding that enables mechanistic models; such models can, for example, distinguish a cascade's area from its size. In the special case of a 3-regular network, we use self-consistency arguments to obtain a zero-parameter mechanistic (bottom-up) approximation that reproduces nontrivial correlations observed in simulations and that allows the study of the BTW process on networks in regimes otherwise prohibitively costly to investigate. We then generalize some of these results to configuration model networks and explain how one could continue the generalization. The numerous tools and methods presented herein are known to enable studying the effects of controlling the BTW process and other self-organizing systems. More broadly, our use of multitype branching processes to capture information bouncing back and forth in a network could inspire analogous models of systems in which consequences spread in a bidirectional fashion. PMID:24580281

  12. Bottom-up impact on the cecidomyiid leaf galler and its parasitism in a tropical rainforest.

    Science.gov (United States)

    Malinga, Geoffrey M; Valtonen, Anu; Nyeko, Philip; Vesterinen, Eero J; Roininen, Heikki

    2014-10-01

    The relative importance of host-plant resources, natural enemies or their interactions in controlling the population of galling insects and their parasitism is poorly known for tropical gallers. In this study, we assessed the impacts of plant quality and density of host trees in regulating the densities of a galler species, the cecidomyiid leaf galler (Cecidomyiini sp. 1EJV) and its parasitoids and inquilines on Neoboutonia macrocalyx trees in Uganda. We manipulated the nutritional quality (or vigour) and the resource concentration with four levels each of fertilization and the group size of host tree. We then recorded the effects of these treatments on the growth rate and total leaf area of host plants, the density of gallers and their mortality by parasitoids and inquilines. Higher levels of fertilization and host density resulted in significantly higher total leaf area than did ambient nutrient levels, and lowest tree densities, respectively. Fertilization also caused significant change in the growth rate of leaf area. Both higher fertilization and host density caused higher density of gallers. Total leaf area was positively associated with galler density, but within galled replicates, the galled leaves were larger than the ungalled leaves. Although highest levels of fertilization and density of host trees caused significant change in the densities of parasitoids, the rate of parasitism did not change. However, tree-density manipulations increased the rate of inquilinism, but on a very low level. Our results demonstrate a trophic cascade in the tropical galler and its parasitoids as a response to bottom-up effects. PMID:25124946

  13. Top-down and bottom-up processes in grassland and forested streams.

    Science.gov (United States)

    Nyström, Per; McIntosh, Angus R; Winterbourn, Michael J

    2003-08-01

    The influence of predatory fish on the structure of stream food webs may be altered by the presence of forest canopy cover, and consequent differences in allochthonous inputs and primary production. Eight sites containing introduced brown trout ( Salmo trutta) and eight sites that did not were sampled in the Cass region, South Island, New Zealand. For each predator category, half the sites were located in southern beech (Nothofagus) forest patches (range of canopy cover, 65-90%) and the other half were in tussock grassland. Food resources used by two dominant herbivores-detritivores were assessed using stable isotopes. (13)C/(12)C ratios were obtained for coarse particulate organic matter (CPOM), fine particulate organic matter (FPOM), algal dominated biofilm from rocks, and larvae of Deleatidium (Ephemeroptera) and Olinga (Trichoptera). Total abundance and biomass of macroinvertebrates did not differ between streams with and without trout, but were significantly higher at grassland sites than forested sites. However, taxon richness and species composition differed substantially between trout and no-trout sites, irrespective of whether streams were located in forest or not. Trout streams typically contained more taxa, had low biomass of predatory invertebrates and large shredders, but a high proportion of consumers with cases or shells. The standing stock of CPOM was higher at forested sites, but there was less FPOM and more algae at sites with trout, regardless of the presence or absence of forest cover. The stable carbon isotope range for biofilm on rocks was broad and encompassed the narrow CPOM and FPOM ranges. At trout sites, carbon isotope ratios of Deleatidium, the most abundant invertebrate primary consumer, were closely related to biofilm values, but no relationship was found at no-trout sites where algal biomass was much lower. These results support a role for both bottom-up and top-down processes in controlling the structure of the stream communities

  14. Top-down or bottom-up: Contrasting perspectives on psychiatric diagnoses

    Directory of Open Access Journals (Sweden)

    Willem MA Verhoeven

    2008-09-01

    Full Text Available Willem MA Verhoeven1,2, Siegfried Tuinier1, Ineke van der Burgt31Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands; 2Department of Psychiatry, Erasmus University Medical Centre, Rotterdam, The Netherlands; 3Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The NetherlandsAbstract: Clinical psychiatry is confronted with the expanding knowledge of medical genetics. Most of the research into the genetic underpinnings of major mental disorders as described in the categorical taxonomies, however, did reveal linkage with a variety of chromosomes. This heterogeneity of results is most probably due to the assumption that the nosological categories as used in these studies are disease entities with clear boundaries. If the reverse way of looking, the so-called bottom-up approach, is applied, it becomes clear that genetic abnormalities are in most cases not associated with a single psychiatric disorder but with a certain probability to develop a variety of aspecific psychiatric symptoms. The adequacy of the categorical taxonomy, the so-called top-down approach, seems to be inversely related to the amount of empirical etiological data. This is illustrated by four rather prevalent genetic syndromes, fragile X syndrome, Prader-Willi syndrome, 22q11 deletion syndrome, and Noonan syndrome, as well as by some cases with rare chromosomal abnormalities. From these examples, it becomes clear that psychotic symptoms as well as mood, anxiety, and autistic features can be found in a great variety of different genetic syndromes. A psychiatric phenotype exists, but comprises, apart from the chance to present several psychiatric symptoms, all elements from developmental, neurocognitive, and physical characteristics.Keywords: genetic disorders, psychiatric symptoms, phenotype, mental disorders

  15. Synthetic biology outside the cell: linking computational tools to cell-free systems.

    Science.gov (United States)

    Lewis, Daniel D; Villarreal, Fernando D; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems. PMID:25538941

  16. Synthetic Biology and the Moral Significance of Artificial Life: A Reply to Douglas, Powell and Savulescu.

    Science.gov (United States)

    Christiansen, Andreas

    2016-06-01

    I discuss the moral significance of artificial life within synthetic biology via a discussion of Douglas, Powell and Savulescu's paper 'Is the creation of artificial life morally significant'. I argue that the definitions of 'artificial life' and of 'moral significance' are too narrow. Douglas, Powell and Savulescu's definition of artificial life does not capture all core projects of synthetic biology or the ethical concerns that have been voiced, and their definition of moral significance fails to take into account the possibility that creating artificial life is conditionally acceptable. Finally, I show how several important objections to synthetic biology are plausibly understood as arguing that creating artificial life in a wide sense is only conditionally acceptable. PMID:26833578

  17. Recent progress in synthetic biology for microbial production of C3-C10 alcohols

    Directory of Open Access Journals (Sweden)

    Edna N. Lamsen

    2012-06-01

    Full Text Available The growing need to address current energy and environmental problems has sparked an interest in developing improved biological methods to produce liquid fuels from renewable sources. While microbial ethanol production is well established, higher chain alcohols possess chemical properties that are more similar to gasoline. Unfortunately, these alcohols (except 1-butanol are not produced efficiently in natural microorganisms, and thus economical production in industrial volumes remains a challenge. Synthetic biology, however, offers additional tools to engineer synthetic pathways in user-friendly hosts to help increase titers and productivity of these advanced biofuels. This review concentrates on recent developments in synthetic biology to produce higher-chain alcohols as viable renewable replacements for traditional fuel.

  18. Applications of membrane computing in systems and synthetic biology

    CERN Document Server

    Gheorghe, Marian; Pérez-Jiménez, Mario

    2014-01-01

    Membrane Computing was introduced as a computational paradigm in Natural Computing. The models introduced, called Membrane (or P) Systems, provide a coherent platform to describe and study living cells as computational systems. Membrane Systems have been investigated for their computational aspects and employed to model problems in other fields, like: Computer Science, Linguistics, Biology, Economy, Computer Graphics, Robotics, etc. Their inherent parallelism, heterogeneity and intrinsic versatility allow them to model a broad range of processes and phenomena, being also an efficient means to solve and analyze problems in a novel way. Membrane Computing has been used to model biological systems, becoming with time a thorough modeling paradigm comparable, in its modeling and predicting capabilities, to more established models in this area. This book is the result of the need to collect, in an organic way, different facets of this paradigm. The chapters of this book, together with the web pages accompanying th...

  19. Sender-receiver systems and applying information theory for quantitative synthetic biology.

    Science.gov (United States)

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-02-01

    Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. PMID:25282688

  20. Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Borodina, Irina; Li, Mingji

    2015-01-01

    biology has the potential to bring down this cost by improving our ability to predictably engineer biological systems. This review highlights synthetic biology applications for design, assembly, and optimization of non-native biochemical pathways in baker's yeast Saccharomyces cerevisiae. We describe...... computational tools for the prediction of biochemical pathways, molecular biology methods for assembly of DNA parts into pathways, and for introducing the pathways into the host, and finally approaches for optimizing performance of the introduced pathways.......Synthetic biology and metabolic engineering enable generation of novel cell factories that efficiently convert renewable feedstocks into biofuels, bulk, and fine chemicals, thus creating the basis for biosustainable economy independent on fossil resources. While over a hundred proof...

  1. Standardization, IPRs and open innovation in synthetic biology

    DEFF Research Database (Denmark)

    Minssen, Timo; Wested, Jakob

    2015-01-01

    (ICT) to biological standards? These and further legal issues related to IP, regulation, standardization, competition law & open innovation require a careful consideration of new user-generated models and solutions. Before this background this paper seeks to describe IP and standardization aspects of......, in which we will address standard setting efforts in SB and the relevance of various IPRs for specific SB standards. This provides the basis for section 3, in which we debate problematic issues and summarize our conclusions....

  2. C-Nucleosides: Synthetic Strategies and Biological Applications

    Czech Academy of Sciences Publication Activity Database

    Štambaský, J.; Hocek, Michal; Kočovský, P.

    2009-01-01

    Roč. 109, č. 12 (2009), s. 6729-6764. ISSN 0009-2665 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550902 Grant ostatní: NIH(US) 1R03TW007372-01 Institutional research plan: CEZ:AV0Z40550506 Keywords : nucleosides * nucleobases * biological activity * extension of genetic alphabet Subject RIV: CC - Organic Chemistry Impact factor: 35.957, year: 2009

  3. GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Adrien Basso-Blandin

    2012-11-01

    Full Text Available In this article, we propose a domain specific language, GUBS (Genomic Unified Behavior Specification, dedicated to the behavioral specification of synthetic biological devices, viewed as discrete open dynamical systems. GUBS is a rule-based declarative language. By contrast to a closed system, a program is always a partial description of the behavior of the system. The semantics of the language accounts the existence of some hidden non-specified actions possibly altering the behavior of the programmed device. The compilation framework follows a scheme similar to automatic theorem proving, aiming at improving synthetic biological design safety.

  4. Grain size engineering of bcc refractory metals: Top-down and bottom-up-Application to tungsten

    International Nuclear Information System (INIS)

    We have used two general methodologies for the production of ultrafine grained (UFG) and nanocrystalline (NC) tungsten (W) metal samples: top-down and bottom-up. In the first, Equal channel angular extrusion (ECAE), coupled with warm rolling has been used to fabricate UFG W, and high pressure torsion (HPT) was used to fabricate NC W. We demonstrate an abrupt shift in the deformation mechanism, particularly under dynamic compressive loading, in UFG and NC W. This novel deformation mechanism, a dramatic transition from a uniform deformation mode to that of localized shearing, is shared by other UFG and NC body-centerd cubic (BCC) metals. We have also conducted a series of bottom-up experiments to consolidate powdered UFG W precursors into solid bodies. The bottom-up approach relies on rapid, high-temperature consolidation, specifically designed for UFG and NC W powders. The mechanical property results from the top-down UFG and NC W were used as minimum property benchmarks to guide and design the experimental protocols and parameters for use in the bottom-up procedures. Preliminary results, showing rapid grain growth during the consolidation cycle, did not achieve full density in the W samples. Further development of high-purity W nanopowders and appropriate grain-growth inhibitors (e.g., Zener pinning) will be required to successfully produce bulk-sized UFG and NC W samples

  5. Leadership for Quality University Teaching: How Bottom-Up Academic Insights Can Inform Top-Down Leadership

    Science.gov (United States)

    Scott, Donald E.; Scott, Shelleyann

    2016-01-01

    This paper presents the leadership implications from a study that explored how to increase the quality of teaching in a university thereby presenting data from the bottom up--the academic perspective--to inform leadership, policies, and academic development which generally flows from the top down. We report academics' perceptions of and…

  6. On the Temporal Relation of Top-Down and Bottom-Up Mechanisms during Guidance of Attention

    Science.gov (United States)

    Wykowska, Agnieszka; Schubo, Anna

    2010-01-01

    Two mechanisms are said to be responsible for guiding focal attention in visual selection: bottom-up, saliency-driven capture and top-down control. These mechanisms were examined with a paradigm that combined a visual search task with postdisplay probe detection. Two SOAs between the search display and probe onsets were introduced to investigate…

  7. Addressing a "Black Box" of Bottom-Up Synthesis: Revealing the Structures of Growing Colloidal-Nanocrystal Nuclei.

    Science.gov (United States)

    Sobol, Oded; Gadot, Eyal; Wang, Yifeng; Weinstock, Ira A; Meshi, Louisa

    2015-11-16

    In bottom-up synthesis, products from reactions of structural building units rapidly pass from soluble molecular complexes to nanoscale intermediates, whose solution-state structures defy elucidation by any routine method. To address this, electron diffraction is used to reveal the structures of cryogenically "trapped" colloidal nanocrystals. PMID:26536393

  8. The Roles of Feature-Specific Task Set and Bottom-Up Salience in Attentional Capture: An ERP Study

    Science.gov (United States)

    Eimer, Martin; Kiss, Monika; Press, Clare; Sauter, Disa

    2009-01-01

    We investigated the roles of top-down task set and bottom-up stimulus salience for feature-specific attentional capture. Spatially nonpredictive cues preceded search arrays that included a color-defined target. For target-color singleton cues, behavioral spatial cueing effects were accompanied by cue-induced N2pc components, indicative of…

  9. Assessing the Gap Between Top-down and Bottom-up Measured Methane Emissions in Indianapolis, IN.

    Science.gov (United States)

    Prasad, K.; Lamb, B. K.; Cambaliza, M. O. L.; Shepson, P. B.; Stirm, B. H.; Salmon, O. E.; Lavoie, T. N.; Lauvaux, T.; Ferrara, T.; Howard, T.; Edburg, S. L.; Whetstone, J. R.

    2014-12-01

    Releases of methane (CH4) from the natural gas supply chain in the United States account for approximately 30% of the total US CH4 emissions. However, there continues to be large questions regarding the accuracy of current emission inventories for methane emissions from natural gas usage. In this paper, we describe results from top-down and bottom-up measurements of methane emissions from the large isolated city of Indianapolis. The top-down results are based on aircraft mass balance and tower based inverse modeling methods, while the bottom-up results are based on direct component sampling at metering and regulating stations, surface enclosure measurements of surveyed pipeline leaks, and tracer/modeling methods for other urban sources. Mobile mapping of methane urban concentrations was also used to identify significant sources and to show an urban-wide low level enhancement of methane levels. The residual difference between top-down and bottom-up measured emissions is large and cannot be fully explained in terms of the uncertainties in top-down and bottom-up emission measurements and estimates. Thus, the residual appears to be, at least partly, attributed to a significant wide-spread diffusive source. Analyses are included to estimate the size and nature of this diffusive source.

  10. Glutarimides: Biological activity, general synthetic methods and physicochemical properties

    Directory of Open Access Journals (Sweden)

    Popović-Đorđević Jelena B.

    2015-01-01

    Full Text Available Glutarimides, 2,6-dioxopiperidines are compounds that rarely occur in natural sources, but so far isolated ones exert widespread pharmacological activities, which makes them valuable as potential pharmacotherapeutics. Glutarimides act as androgen receptor antagonists, anti-inflammatory, anxiolytics, antibacterials, and tumor suppressing agents. Some synthetic glutarimide derivatives are already in use as immunosuppressive and sedative (e.g., thalidomide or anxiolytics (buspirone drugs. The wide applicability of this class of compounds, justify the interest of scientists to explore new pathways for its syntheses. General methods for synthesis of six-membered imide ring, are presented in this paper. These methods include: a reaction of dicarboxylic acids with ammonia or primary amine, b reactions of cyclization: amido-acids, diamides, dinitriles, nitrilo-acids, amido-nitriles, amido-esters, amidoacyl-chlorides or diacyl-chlorides, c adition of carbon-monoxide on a,b-unsaturated amides, d oxidation reactions, e Michael adition of active methylen compounds on methacrylamide or conjugated amides. Some of the described methods are used for closing glutarimide ring in syntheses of farmacological active compounds sesbanimide and aldose reductase inhibitors (ARI. Analyses of the geometry, as well as, the spectroscopic analyses (NMR and FT-IR of some glutarimides are presented because of their broad spectrum of pharmacological activity. To elucidate structures of glutarimides, geometrical parameters of newly synthesized tert-pentyl-1-benzyl-4-methyl-glutarimide-3-carboxylate (PBMG are analyzed and compared with the experimental data from X-ray analysis for glutarimide. Moreover, molecular electrostatic potential (MEP surface which is plotted over the optimized geometry to elucidate the reactivity of PBMG molecule is analyzed. The electronic properties of glutarimide derivatives are explained on the example of thalidomide. The Frontier Molecular Orbital

  11. [Impact of synthetic biology on patent law in view of of European jurisprudence].

    Science.gov (United States)

    Bernardo Alvarez, María Angela

    2014-01-01

    The roots of synthetic biology--the redesign of biological molecules, structures and organisms--can be traced to the research developed by Jacques L. Monod and François Jacob in 1961. This field has undergone significant growth in the past ten years and its emergence has raised the question of whether the patent system is suitable to protect inventions in emergent areas as synthetic biology. The article will analyze the numerous scientific, socio-economic, ethical and legal challenges faced by synthetic biology, introducing the European Patent Law related to biotechnology as the minimum common framework and considering if more changes are needed to adequately protect the inventor rights, while taking into account the arrival of a new research culture, characterized by embracing open-innovation and open-source initiatives. The discussion will review some biotechnological patent law cases and summarize questions as whether isolated molecules of DNA are eligible for patent or the patentability of living matter, under the terms of Directive 98/44/EC. The article will finally consider the impact of synthetic biology on the European patent system. PMID:25845209

  12. Can life be engineered? Epistemological roots and blind spots of Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Heams Thomas

    2015-01-01

    Full Text Available Synthetic Biology is the latest attempt in experimental biology to reach the long lasting goal of mastering processes of life by engineering them. This emergent discipline results from the novel convergence of biology and concept and tools from other fields such as computing and engineering sciences. It relies on rational design of bioparts, modules, or organisms, as opposed to the tinkering methods provided so far by the even most sophisticated biotechnologies. Such an approach could have major consequences, for both applied and fundamental research. But this appealing narrative may obscure important epistemological issues, some of them being rooted in old misconceptions or shortcomings in biology. By focusing mainly on the mechanistic dimension of living beings, Synthetic Biology partially recycle ancient debates and could miss the opportunity to provide an integrative account of what makes life actually specific in the natural world. A first insight into a critical reassessment of some of the goals, the lexicon, and the theoretical foundations of Synthetic Biology is proposed, as other natural dimensions of the biological world are highlighted. Taken as a whole, these considerations challenge several core concepts of the discipline, but may help to redefine some of its strategies and overcome some major hurdles.

  13. Reconciling Top-Down and Bottom-Up Estimates of Oil and Gas Methane Emissions in the Barnett Shale

    Science.gov (United States)

    Hamburg, S.

    2015-12-01

    Top-down approaches that use aircraft, tower, or satellite-based measurements of well-mixed air to quantify regional methane emissions have typically estimated higher emissions from the natural gas supply chain when compared to bottom-up inventories. A coordinated research campaign in October 2013 used simultaneous top-down and bottom-up approaches to quantify total and fossil methane emissions in the Barnett Shale region of Texas. Research teams have published individual results including aircraft mass-balance estimates of regional emissions and a bottom-up, 25-county region spatially-resolved inventory. This work synthesizes data from the campaign to directly compare top-down and bottom-up estimates. A new analytical approach uses statistical estimators to integrate facility emission rate distributions from unbiased and targeted high emission site datasets, which more rigorously incorporates the fat-tail of skewed distributions to estimate regional emissions of well pads, compressor stations, and processing plants. The updated spatially-resolved inventory was used to estimate total and fossil methane emissions from spatial domains that match seven individual aircraft mass balance flights. Source apportionment of top-down emissions between fossil and biogenic methane was corroborated with two independent analyses of methane and ethane ratios. Reconciling top-down and bottom-up estimates of fossil methane emissions leads to more accurate assessment of natural gas supply chain emission rates and the relative contribution of high emission sites. These results increase our confidence in our understanding of the climate impacts of natural gas relative to more carbon-intensive fossil fuels and the potential effectiveness of mitigation strategies.

  14. Selecting category specific visual information: Top-down and bottom-up control of object based attention.

    Science.gov (United States)

    Corradi-Dell'Acqua, Corrado; Fink, Gereon R; Weidner, Ralph

    2015-09-01

    The ability to select, within the complexity of sensory input, the information most relevant for our purposes is influenced by both internal settings (i.e., top-down control) and salient features of external stimuli (i.e., bottom-up control). We here investigated using fMRI the neural underpinning of the interaction of top-down and bottom-up processes, as well as their effects on extrastriate areas processing visual stimuli in a category-selective fashion. We presented photos of bodies or buildings embedded into frequency-matched visual noise to the subjects. Stimulus saliency changed gradually due to an altered degree to which photos stood-out in relation to the surrounding noise (hence generating stronger bottom-up control signals). Top-down settings were manipulated via instruction: participants were asked to attend one stimulus category (i.e., "is there a body?" or "is there a building?"). Highly salient stimuli that were inconsistent with participants' attentional top-down template activated the inferior frontal junction and dorsal parietal regions bilaterally. Stimuli consistent with participants' current attentional set additionally activated insular cortex and the parietal operculum. Furthermore, the extrastriate body area (EBA) exhibited increased neural activity when attention was directed to bodies. However, the latter effect was found only when stimuli were presented at intermediate saliency levels, thus suggesting a top-down modulation of this region only in the presence of weak bottom-up signals. Taken together, our results highlight the role of the inferior frontal junction and posterior parietal regions in integrating bottom-up and top-down attentional control signals. PMID:25735196

  15. A bottom-up approach to urban metabolism: the perspective of BRIDGE

    Science.gov (United States)

    Chrysoulakis, N.; Borrego, C.; San Josè, R.; Grimmond, S. B.; Jones, M. B.; Magliulo, V.; Klostermann, J.; Santamouris, M.

    2011-12-01

    Urban metabolism considers a city as a system and usually distinguishes between energy and material flows as its components. "Metabolic" studies are usually top-down approaches that assess the inputs and outputs of food, water, energy, and pollutants from a city, or that compare the changing metabolic process of several cities. In contrast, bottom-up approaches are based on quantitative estimates of urban metabolism components at local to regional scales. Such approaches consider the urban metabolism as the 3D exchange and transformation of energy and matter between a city and its environment. The city is considered as a system and the physical flows between this system and its environment are quantitatively estimated. The transformation of landscapes from primarily agricultural and forest uses to urbanized landscapes can greatly modify energy and material exchanges and it is, therefore, an important aspect of an urban area. Here we focus on the exchanges and transformation of energy, water, carbon and pollutants. Recent advances in bio-physical sciences have led to new methods and models to estimate local scale energy, water, carbon and pollutant fluxes. However, there is often poor communication of new knowledge and its implications to end-users, such as planners, architects and engineers. The FP7 Project BRIDGE (SustainaBle uRban plannIng Decision support accountinG for urban mEtabolism) aims at bridging this gap and at illustrating the advantages of considering environmental issues in urban planning. BRIDGE does not perform a complete life cycle analysis or calculate whole system urban metabolism, but rather focuses on specific metabolism components (energy, water, carbon and pollutants). Its main goal is the development of a Decision Suport System (DSS) with the potential to select planning actions which better fit the goal of changing the metabolism of urban systems towards sustainability. BRIDGE evaluates how planning alternatives can modify the physical

  16. 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.

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

    OpenAIRE

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

    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 ...

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

    OpenAIRE

    Toni, Tina; Tidor, Bruce

    2013-01-01

    Biological systems are inherently variable, with their dynamics influenced by intrinsic and extrinsic sources. These systems are often only partially characterized, with large uncertainties about specific sources of extrinsic variability and biochemical properties. Moreover, it is not yet well understood how different sources of variability combine and affect biological systems in concert. To successfully design biomedical therapies or synthetic circuits with robust performance, it is crucial...

  19. Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

    NARCIS (Netherlands)

    Medema, Marnix H.; Breitling, Rainer; Bovenberg, Roel; Takano, Eriko

    2011-01-01

    One of the most promising applications of synthetic biology is the biosynthesis of new drugs from secondary metabolites. Here, we survey a wide range of strategies that control the activity of biosynthetic modules in the cell in space and time, and illustrate how these strategies can be used to desi

  20. Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs.

    Science.gov (United States)

    Hillson, Nathan J; Plahar, Hector A; Beal, Jacob; Prithviraj, Ranjini

    2016-06-17

    Research is communicated more effectively and reproducibly when articles depict genetic designs consistently and fully disclose the complete sequences of all reported constructs. ACS Synthetic Biology is now providing authors with updated guidance and piloting a new tool and publication workflow that facilitate compliance with these recommended practices and standards for visual representation and data exchange. PMID:27267452

  1. Playing God in Frankenstein's Footsteps: Synthetic Biology and the Meaning of Life

    NARCIS (Netherlands)

    Belt, van den H.

    2009-01-01

    The emergent new science of synthetic biology is challenging entrenched distinctions between, amongst others, life and non-life, the natural and the artificial, the evolved and the designed, and even the material and the informational. Whenever such culturally sanctioned boundaries are breached, res

  2. Synthetic Biology R&D Risks: Social-Institutional Contexts Matter!

    Science.gov (United States)

    Wolfe, Amy K; Campa, Maria Fernanda; Bergmann, Rachael A; Stelling, Savannah C; Bjornstad, David J; Shumpert, Barry L

    2016-05-01

    Factors that shape actual research practices - 'social and institutional context' - typically are missing from considerations of synthetic biology R&D-related risk and containment. We argue that analyzing context is essential in identifying circumstances that create, amplify, or diminish risk, and in revealing new opportunities for avoiding or managing those risks. PMID:26900006

  3. Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism

    OpenAIRE

    Shahzad, Khuram; Juan J. Loor

    2012-01-01

    Systems biology is a computational field that has been used for several years across different scientific areas of biological research to uncover the complex interactions occurring in living organisms. Applications of systems concepts at the mammalian genome level are quite challenging, and new complimentary computational/experimental techniques are being introduced. Most recent work applying modern systems biology techniques has been conducted on bacteria, yeast, mouse, and human genomes. Ho...

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

    Science.gov (United States)

    Brown, Adam J; James, David C

    2016-01-01

    The next generation of mammalian cell factories for biopharmaceutical production will be genetically engineered to possess both generic and product-specific manufacturing capabilities that may not exist naturally. Introduction of entirely new combinations of synthetic functions (e.g. novel metabolic or stress-response pathways), and retro-engineering of existing functional cell modules will drive disruptive change in cellular manufacturing performance. However, before we can apply the core concepts underpinning synthetic biology (design, build, test) to CHO cell engineering we must first develop practical and robust enabling technologies. Fundamentally, we will require the ability to precisely control the relative stoichiometry of numerous functional components we simultaneously introduce into the host cell factory. In this review we discuss how this can be achieved by design of engineered promoters that enable concerted control of recombinant gene transcription. We describe the specific mechanisms of transcriptional regulation that affect promoter function during bioproduction processes, and detail the highly-specific promoter design criteria that are required in the context of CHO cell engineering. The relative applicability of diverse promoter development strategies are discussed, including re-engineering of natural sequences, design of synthetic transcription factor-based systems, and construction of synthetic promoters. This review highlights the potential of promoter engineering to achieve precision transcriptional control for CHO cell synthetic biology. PMID:26721629

  5. Top-down and bottom-up control of large herbivore populations: a review of natural and human-induced influences

    OpenAIRE

    Gandiwa, E.

    2013-01-01

    The question whether animal populations are top-down and/or bottom-up controlled has motivated a thriving body of research over the past five decades. In this review I address two questions: 1) how do top-down and bottom-up controls influence large herbivore populations? 2) How do human activities and control systems influence the top-down and bottom-up processes that affect large herbivore population dynamics? Previous studies suggest that the relative influence of top-down vs. bottom-up con...

  6. Immobilized Biofilm in Thermophilic Biohydrogen Production using Synthetic versus Biological Materials

    Directory of Open Access Journals (Sweden)

    Jaruwan Wongthanate

    2015-02-01

    Full Text Available Biohydrogen production was studied from the vermicelli processing wastewater using synthetic and biological materials as immobilizing substrate employing a mixed culture in a batch reactor operated at the initial pH 6.0 and thermophilic condition (55 ± 1ºC. Maximum cumulative hydrogen production (1,210 mL H2/L wastewater was observed at 5% (v/v addition of ring-shaped synthetic material, which was the ring-shaped hydrophobic acrylic. Regarding 5% (v/v addition of synthetic and biological materials, the maximum cumulative hydrogen production using immobilizing synthetic material of ball-shaped hydrophobic polyethylene (HBPE (1,256.5 mL H2/L wastewater was a two-fold increase of cumulative hydrogen production when compared to its production using immobilizing biological material of rope-shaped hydrophilic ramie (609.8 mL H2/L wastewater. SEM observation of immobilized biofilm on a ball-shaped HBPE or a rope-shaped hydrophilic ramie was the rod shape and gathered into group.

  7. Price elasticities, policy measures and actual developments in household energy consumption - A bottom up analysis for the Netherlands

    International Nuclear Information System (INIS)

    In the Netherlands it seems likely that the large number of new policy measures in the past decade has influenced the response of households to changing prices. To investigate this issue the energy trends in the period 1990-2000 have been simulated with a bottom-up model, applied earlier for scenario studies, and extensive data from surveys. For a number of alternative price cases the elasticity values found are explained using the bottom-up changes in energy trends. One finding is that the specific set of saving options defines for a great part the price response. The price effect has been analysed too in combination with the policy measures standards, subsidies and energy taxes. The simulation results indicate that the elasticity value could be 30-40% higher without these measures. (author)

  8. Robust aircraft segmentation from very high-resolution images based on bottom-up and top-down cue integration

    Science.gov (United States)

    Gao, Feng; Xu, Qizhi; Li, Bo

    2016-01-01

    Existing segmentation methods require manual interventions to optimally extract objects from cluttered background, so that they can hardly work well in automated surveillance systems. In order to automatically extract aircrafts from very high-resolution images, we proposed a segmentation method that combines bottom-up and top-down cues. Three essential principles from local contrast, global contrast, and center bias are involved to compute bottom-up cue. In addition, top-down cue is computed by incorporating aircraft shape priors, and it is achieved by training a classifier from a rich set of visual features. Iterative operations and adaptive fitting are designed to get refined results. Experimental results demonstrated that the proposed method can provide significant improvements on the segmentation accuracy.

  9. Laser-assisted production of tricalcium phosphate nanoparticles from biological and synthetic hydroxyapatite in aqueous medium

    Science.gov (United States)

    Boutinguiza, M.; Pou, J.; Lusquiños, F.; Comesaña, R.; Riveiro, A.

    2011-04-01

    Pulsed laser ablation technique has attracted great attention as a method for preparing nanoparticles. In this work, calcined fish bones and synthetic hydroxyapatite, have been used as target to be ablated in de-ionized water with a pulsed CO 2 laser to produce calcium phosphate nanoparticles. The obtained nanoparticles were amorphous and spherical in shape with a mean diameter of about 25 nm. The microanalyses revealed that nanoparticles obtained from the synthetic HA undergo transformation to tricalcium phosphate. While nanoparticles obtained from the biological hydroxyapatite mostly preserve the composition of precursor material.

  10. Tisza, Transmission and Innovation: An Innovative Bottom-up Model for Transmission and Promotion of Tisza Cultural Heritage

    OpenAIRE

    Barberis Rami, Matías Ezequiel; Berić, Dejan; Mátai, Anikó; Opriş, Lavinia-Ioana; Ricci, Giulia; Rustja, Dritan

    2015-01-01

    The project aims to promote and preserve both tangible and intangible cultural heritage in a particular region of the Danube river basin, Tisza Region (TR). The TR cultural heritage is less-well-known in the rest of Europe and is at risk of being lost or forgotten if not preserved and supported. In this project is presented an innovative and strategic bottom-up model which allows local people to manage how their heritage is disseminated through transmission and promotion of their ...

  11. Top-down but not bottom-up visual scanning is affected in hereditary pure cerebellar ataxia.

    Directory of Open Access Journals (Sweden)

    Shunichi Matsuda

    Full Text Available The aim of this study was to clarify the nature of visual processing deficits caused by cerebellar disorders. We studied the performance of two types of visual search (top-down visual scanning and bottom-up visual scanning in 18 patients with pure cerebellar types of spinocerebellar degeneration (SCA6: 11; SCA31: 7. The gaze fixation position was recorded with an eye-tracking device while the subjects performed two visual search tasks in which they looked for a target Landolt figure among distractors. In the serial search task, the target was similar to the distractors and the subject had to search for the target by processing each item with top-down visual scanning. In the pop-out search task, the target and distractor were clearly discernible and the visual salience of the target allowed the subjects to detect it by bottom-up visual scanning. The saliency maps clearly showed that the serial search task required top-down visual attention and the pop-out search task required bottom-up visual attention. In the serial search task, the search time to detect the target was significantly longer in SCA patients than in normal subjects, whereas the search time in the pop-out search task was comparable between the two groups. These findings suggested that SCA patients cannot efficiently scan a target using a top-down attentional process, whereas scanning with a bottom-up attentional process is not affected. In the serial search task, the amplitude of saccades was significantly smaller in SCA patients than in normal subjects. The variability of saccade amplitude (saccadic dysmetria, number of re-fixations, and unstable fixation (nystagmus were larger in SCA patients than in normal subjects, accounting for a substantial proportion of scattered fixations around the items. Saccadic dysmetria, re-fixation, and nystagmus may play important roles in the impaired top-down visual scanning in SCA, hampering precise visual processing of individual items.

  12. The Comparative Effect of Top-down Processing and Bottom-up Processing through TBLT on Extrovert and Introvert EFL

    OpenAIRE

    Pezhman Nourzad Haradasht; Abdollah Baradaran

    2013-01-01

    This research seeks to examine the effect of two models of reading comprehension, namely top-down and bottom-up processing, on the reading comprehension of extrovert and introvert EFL learners’ reading comprehension. To do this, 120 learners out of a total number of 170 intermediate learners being educated at Iran Mehr English Language School were selected all taking a PET (Preliminary English Test) first for homogenization prior to the study. They also answered the Eysenck Personality Invent...

  13. Community context mediates the top-down vs. bottom-up effects of grazers on rocky shores

    OpenAIRE

    Bracken, MES; Dolecal, RE; Long, JD

    2014-01-01

    Interactions between grazers and autotrophs are complex, including both topdown consumptive and bottom-up facilitative effects of grazers. Thus, in addition to consuming autotrophs, herbivores can also enhance autotroph biomass by recycling limiting nutrients, thereby increasing nutrient availability. Here, we evaluated these consumptive and facilitative interactions between snails (Littorina littorea) and seaweeds (Fucus vesiculosus and Ulva lactuca) on a rocky shore. We partitioned herbivor...

  14. Radiographic Evaluation of Children with Febrile Urinary Tract Infection: Bottom-Up, Top-Down, or None of the Above?

    OpenAIRE

    Prasad, Michaella M.; Cheng, Earl Y.

    2011-01-01

    The proper algorithm for the radiographic evaluation of children with febrile urinary tract infection (FUTI) is hotly debated. Three studies are commonly administered: renal-bladder ultrasound (RUS), voiding cystourethrogram (VCUG), and dimercapto-succinic acid (DMSA) scan. However, the order in which these tests are obtained depends on the methodology followed: bottom-up or top-down. Each strategy carries advantages and disadvantages, and some groups now advocate even less of a workup (no...

  15. Effects of pollutants on bottom-up and top-down processes in insect-plant interactions

    International Nuclear Information System (INIS)

    Bottom-up (host plant quality) and top-down (natural enemies) forces both influence the fitness and population dynamics of herbivores. However, the impact of pollutants acting on these forces has not been examined, which prompted us to review the literature to test hypotheses regarding this area of research. A comprehensive literature search found 126 references which examined fitness components and population dynamics of 203 insect herbivores. One hundred and fifty-three of the 203 herbivores (75.4%) had fitness impacted due to bottom-up factors in polluted environments. In contrast, only 20 of the 203 (9.9%) had fitness significantly impacted due to top-down factors in polluted environments. The paucity of results for top-down factors impacting fitness does not necessarily mean that top-down factors are less important, but rather that fewer studies include natural enemies. We provide a synthesis of available data by pollution type and herbivore guild, and suggest future research to address this issue. - Pollutants can affect insect herbivores through bottom-up and, possibly, top-down processes

  16. An integrated top-down and bottom-up proteomic approach to characterize the antigen binding fragment of antibodies

    Energy Technology Data Exchange (ETDEWEB)

    Dekker, Leendert J.; Wu, Si; vanDuijn, Martijn M.; Tolic, Nikola; Stingl, Christoph; Zhao, Rui; Luider, Theo N.; Pasa-Tolic, Ljiljana

    2014-05-31

    We have previously shown that different individuals exposed to the same antigen produce antibodies with identical mutations in their complementarity determining regions (CDR), suggesting that CDR tryptic peptides can serve as biomarkers for disease diagnosis and prognosis. Complete Fabs derived from disease specific antibodies have even higher potential; they could potentially be used for disease treatment and are required to identify the antigens towards which the antibodies are directed. However, complete Fab sequence characterization via LC-MS analysis of tryptic peptides (i.e. bottom-up) has proven to be impractical for mixtures of antibodies. To tackle this challenge, we have developed an integrated bottom-up and top-down MS approach, employing 2D chromatography coupled with Fourier transform mass spectrometry (FTMS), and applied this approach for full characterization of the variable parts of two pharmaceutical monoclonal antibodies with sensitivity comparable to the bottom-up standard. These efforts represent an essential step towards the identification of disease specific antibodies in patient samples with potentially significant clinical impact.

  17. A comprehensive estimate of recent carbon sinks in China using both top-down and bottom-up approaches

    Science.gov (United States)

    Jiang, Fei; Chen, Jing; Zhou, Linxi; Ju, Weimin; Zhang, Huifang; Machida, Toshinobu; Ciais, Philippe; Peters, Wouter; Wang, Hengmao; Chen, Baozhang; Liu, Linxin; Zhang, Chunhua; Matsueda, Hidekazu; Sawa, Yousuke

    2016-04-01

    Atmospheric inversions use measurements of atmospheric CO2 gradients to constrain regional surface fluxes. Current inversions indicate a net terrestrial CO2 sink in China between 0.16 and 0.35 PgC/yr. The uncertainty of these estimates is as large as the mean because the atmospheric network historically contained only one high altitude station in China. Here, we revisit the calculation of the terrestrial CO2 flux in China, excluding emissions from fossil fuel burning and cement production, by using two inversions with three new CO2 monitoring stations in China as well as aircraft observations over Asia. We estimate a net terrestrial CO2 uptake of 0.39-0.51 PgC/yr with a mean of 0.45 PgC/yr in 2006-2009. After considering the lateral transport of carbon in air and water and international trade, the annual mean carbon sink is adjusted to 0.35 PgC/yr. To evaluate this top-down estimate, we constructed an independent bottom-up estimate based on ecosystem data, and giving a net land sink of 0.33 PgC/yr. This demonstrates closure between the top-down and bottom-up estimates. Both top-down and bottom-up estimates give a higher carbon sink than previous estimates made for the 1980s and 1990s, suggesting a trend towards increased uptake by land ecosystems in China.

  18. A comprehensive estimate of recent carbon sinks in China using both top-down and bottom-up approaches

    Science.gov (United States)

    Jiang, Fei; Chen, Jing M.; Zhou, Lingxi; Ju, Weimin; Zhang, Huifang; Machida, Toshinobu; Ciais, Philippe; Peters, Wouter; Wang, Hengmao; Chen, Baozhang; Liu, Lixin; Zhang, Chunhua; Matsueda, Hidekazu; Sawa, Yousuke

    2016-02-01

    Atmospheric inversions use measurements of atmospheric CO2 gradients to constrain regional surface fluxes. Current inversions indicate a net terrestrial CO2 sink in China between 0.16 and 0.35 PgC/yr. The uncertainty of these estimates is as large as the mean because the atmospheric network historically contained only one high altitude station in China. Here, we revisit the calculation of the terrestrial CO2 flux in China, excluding emissions from fossil fuel burning and cement production, by using two inversions with three new CO2 monitoring stations in China as well as aircraft observations over Asia. We estimate a net terrestrial CO2 uptake of 0.39-0.51 PgC/yr with a mean of 0.45 PgC/yr in 2006-2009. After considering the lateral transport of carbon in air and water and international trade, the annual mean carbon sink is adjusted to 0.35 PgC/yr. To evaluate this top-down estimate, we constructed an independent bottom-up estimate based on ecosystem data, and giving a net land sink of 0.33 PgC/yr. This demonstrates closure between the top-down and bottom-up estimates. Both top-down and bottom-up estimates give a higher carbon sink than previous estimates made for the 1980s and 1990s, suggesting a trend towards increased uptake by land ecosystems in China.

  19. Sponge communities on Caribbean coral reefs are structured by factors that are top-down, not bottom-up.

    Directory of Open Access Journals (Sweden)

    Joseph R Pawlik

    Full Text Available Caribbean coral reefs have been transformed in the past few decades with the demise of reef-building corals, and sponges are now the dominant habitat-forming organisms on most reefs. Competing hypotheses propose that sponge communities are controlled primarily by predatory fishes (top-down or by the availability of picoplankton to suspension-feeding sponges (bottom-up. We tested these hypotheses on Conch Reef, off Key Largo, Florida, by placing sponges inside and outside predator-excluding cages at sites with less and more planktonic food availability (15 m vs. 30 m depth. There was no evidence of a bottom-up effect on the growth of any of 5 sponge species, and 2 of 5 species grew more when caged at the shallow site with lower food abundance. There was, however, a strong effect of predation by fishes on sponge species that lacked chemical defenses. Sponges with chemical defenses grew slower than undefended species, demonstrating a resource trade-off between growth and the production of secondary metabolites. Surveys of the benthic community on Conch Reef similarly did not support a bottom-up effect, with higher sponge cover at the shallower depth. We conclude that the structure of sponge communities on Caribbean coral reefs is primarily top-down, and predict that removal of sponge predators by overfishing will shift communities toward faster-growing, undefended species that better compete for space with threatened reef-building corals.

  20. Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.

    Directory of Open Access Journals (Sweden)

    Lesia Bilitchenko

    Full Text Available BACKGROUND: Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices from a collection of individual Parts. RESULTS: We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. CONCLUSIONS: Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly.

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

    Science.gov (United States)

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

    2016-06-17

    Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users. PMID:27268205

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

    Science.gov (United States)

    Beach, Dale L; Alvarez, Consuelo J

    2015-12-01

    Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic "parts," students construct a "reporter plasmid" expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a "sensor plasmid," the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses. PMID:26753032

  3. Synthetic

    Directory of Open Access Journals (Sweden)

    Anna Maria Manferdini

    2010-06-01

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

  4. BioModel Engineering: Its role in Systems Biology and Synthetic Biology

    OpenAIRE

    Gilbert, David Roger; Breitling, Rainer; Heiner, Monika

    2009-01-01

    BioModel Engineering takes place at the interface of computing science, mathematics, engineering and biology, and provides a systematic approach for designing, constructing and analyzing computational models of biological systems. Some of its central concepts are inspired by efficient software engineering strategies. BioModel Engineering does not aim at engineering biological systems per se, but rather aims at describing their structure and behavior, in particular at the le...

  5. Identifying the computational requirements of an integrated top-down-bottom-up model for overt visual attention within an active vision system.

    Directory of Open Access Journals (Sweden)

    Sebastian McBride

    Full Text Available Computational visual attention systems have been constructed in order for robots and other devices to detect and locate regions of interest in their visual world. Such systems often attempt to take account of what is known of the human visual system and employ concepts, such as 'active vision', to gain various perceived advantages. However, despite the potential for gaining insights from such experiments, the computational requirements for visual attention processing are often not clearly presented from a biological perspective. This was the primary objective of this study, attained through two specific phases of investigation: 1 conceptual modeling of a top-down-bottom-up framework through critical analysis of the psychophysical and neurophysiological literature, 2 implementation and validation of the model into robotic hardware (as a representative of an active vision system. Seven computational requirements were identified: 1 transformation of retinotopic to egocentric mappings, 2 spatial memory for the purposes of medium-term inhibition of return, 3 synchronization of 'where' and 'what' information from the two visual streams, 4 convergence of top-down and bottom-up information to a centralized point of information processing, 5 a threshold function to elicit saccade action, 6 a function to represent task relevance as a ratio of excitation and inhibition, and 7 derivation of excitation and inhibition values from object-associated feature classes. The model provides further insight into the nature of data representation and transfer between brain regions associated with the vertebrate 'active' visual attention system. In particular, the model lends strong support to the functional role of the lateral intraparietal region of the brain as a primary area of information consolidation that directs putative action through the use of a 'priority map'.

  6. 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 imp...... 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.......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...

  7. The prospects of synthetic biology for the production of fuel from biomass

    International Nuclear Information System (INIS)

    When applied to engineering the metabolism of microorganisms, synthetic biology produces a broad spectrum of biomolecules from carbohydrates and, in the near future, from the biomass in general. The markets for biofuels and for chemicals are thus hooked up through a common technological core. Synthetic biology also opens new possibilities for switching from different types of biomass to different products, thus allowing for more flexibility in development strategies and eventually in industrial operations. This opening is welcomed even though the economic and societal environments hardly favors biofuels. A few more years of research and development are needed to bring these new possibilities to industrial maturity. Advanced biofuels will pass the threshold at which they become profitable and will no longer need subsidies. (author)

  8. 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.

  9. 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. PMID:27030440

  10. Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology.

    Science.gov (United States)

    Kanigowska, Paulina; Shen, Yue; Zheng, Yijing; Rosser, Susan; Cai, Yizhi

    2016-02-01

    Acoustic droplet ejection (ADE) technology uses focused acoustic energy to transfer nanoliter-scale liquid droplets with high precision and accuracy. This noncontact, tipless, low-volume dispensing technology minimizes the possibility of cross-contamination and potentially reduces the costs of reagents and consumables. To date, acoustic dispensers have mainly been used in screening libraries of compounds. In this paper, we describe the first application of this powerful technology to the rapidly developing field of synthetic biology, for DNA synthesis and assembly at the nanoliter scale using a Labcyte Echo 550 acoustic dispenser. We were able to successfully downscale PCRs and the popular one-pot DNA assembly methods, Golden Gate and Gibson assemblies, from the microliter to the nanoliter scale with high assembly efficiency, which effectively cut the reagent cost by 20- to 100-fold. We envision that acoustic dispensing will become an instrumental technology in synthetic biology, in particular in the era of DNA foundries. PMID:26163567

  11. Integrated experimental platforms to study blast injuries: a bottom-up approach

    Science.gov (United States)

    Bo, C.; Williams, A.; Rankin, S.; Proud, W. G.; Brown, K. A.

    2014-05-01

    We are developing experimental models of blast injury using data from live biological samples. An integrated research strategy is followed to study material and biological properties of cells, tissues and organs, that are subjected to dynamic and static pressures, relevant to those of battlefield blast. We have developed a confined Split Hopkinson Pressure Bar (SHPB) system, which allows cells, either in suspension or as a monolayer, to be subjected to compression waves with pressures on the order of a few MPa and durations of hundreds of microseconds. The chamber design enables recovery of biological samples for cellular and molecular analysis. The SHPB platform, coupled with Quasi-Static experiments, is used to determine stress-strain curves of soft biological tissues under compression at low, medium and high strain rates. Tissue samples are examined, using histological techniques, to study macro- and microscopic changes induced by compression waves. In addition, a shock tube enables application of single or multiple air blasts with pressures on the order of kPa and a few milliseconds duration; this platform was used for initial studies on mesenchymal stem cells responses to blast pressures.

  12. Biological Removal of Phosphate Using Phosphate Solubilizing Bacterial Consortium from Synthetic Wastewater: A Laboratory Scale

    OpenAIRE

    Dipak Paul; Sankar Narayan Sinha

    2015-01-01

    Biological phosphate removal is an important process having gained worldwide attention and widely used for removing phosphorus from wastewater. The present investigation was aimed to screen the efficient phosphate solubilizing bacterial isolates and used to remove phosphate from synthetic wastewater under shaking flasks conditions. Pseudomonas sp. JPSB12, Enterobacter sp. TPSB20, Flavobacterium sp. TPSB23 and mixed bacterial consortium (Pseudomonas sp. JPSB12+Enterobacter sp. TPSB20+Flavobact...

  13. Playing God in Frankenstein’s Footsteps: Synthetic Biology and the Meaning of Life

    OpenAIRE

    van den Belt, Henk

    2009-01-01

    The emergent new science of synthetic biology is challenging entrenched distinctions between, amongst others, life and non-life, the natural and the artificial, the evolved and the designed, and even the material and the informational. Whenever such culturally sanctioned boundaries are breached, researchers are inevitably accused of playing God or treading in Frankenstein’s footsteps. Bioethicists, theologians and editors of scientific journals feel obliged to provide an authoritative answer ...

  14. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

    OpenAIRE

    Currin, Andrew; Swainston, Neil; Philip J. Day; Kell, Douglas B.

    2014-01-01

    The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions....

  15. Biological Treatment of a Synthetic Dye Water and an Industrial Textile Wastewater Containing Azo Dye Compounds

    OpenAIRE

    Wallace, Trevor Haig

    2001-01-01

    In this research, the ability of anaerobic and aerobic biological sludges to reduce and stabilize azo dye compounds was studied. Synthetic dye solutions and an industrial textile wastewater were both treated using anaerobic and aerobic biomass, separately and in sequential step-treatment processes. The primary objective was to reduce the wastewater color to an intensity that complies with the Virginia Pollutant Discharge Elimination System (VPDES) permit level. This level is set at 300 Ame...

  16. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle.

    Science.gov (United States)

    Carbonell, Pablo; Currin, Andrew; Jervis, Adrian J; Rattray, Nicholas J W; Swainston, Neil; Yan, Cunyu; Takano, Eriko; Breitling, Rainer

    2016-08-27

    Covering: 2000 to 2016Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted. PMID:27185383

  17. Synthetic Biology and Microbial Fuel Cells: Towards Self-Sustaining Life Support Systems

    Science.gov (United States)

    Hogan, John Andrew

    2014-01-01

    NASA ARC and the J. Craig Venter Institute (JCVI) collaborated to investigate the development of advanced microbial fuels cells (MFCs) for biological wastewater treatment and electricity production (electrogenesis). Synthetic biology techniques and integrated hardware advances were investigated to increase system efficiency and robustness, with the intent of increasing power self-sufficiency and potential product formation from carbon dioxide. MFCs possess numerous advantages for space missions, including rapid processing, reduced biomass and effective removal of organics, nitrogen and phosphorus. Project efforts include developing space-based MFC concepts, integration analyses, increasing energy efficiency, and investigating novel bioelectrochemical system applications

  18. Biological armors under impact—effect of keratin coating, and synthetic bio-inspired analogues

    International Nuclear Information System (INIS)

    A number of biological armors, such as turtle shells, consist of a strong exoskeleton covered with a thin keratin coating. The mechanical role upon impact of this keratin coating has surprisingly not been investigated thus far. Low-velocity impact tests on the turtle shell reveal a unique toughening phenomenon attributed to the thin covering keratin layer, the presence of which noticeably improves the fracture energy and shell integrity. Synthetic substrate/coating analogues were subsequently prepared and exhibit an impact behavior similar to the biological ones. The results of the present study may improve our understanding, and even future designs, of impact-tolerant structures. (paper)

  19. Mapping the patent landscape of synthetic biology for fine chemical production pathways.

    Science.gov (United States)

    Carbonell, Pablo; Gök, Abdullah; Shapira, Philip; Faulon, Jean-Loup

    2016-09-01

    A goal of synthetic biology bio-foundries is to innovate through an iterative design/build/test/learn pipeline. In assessing the value of new chemical production routes, the intellectual property (IP) novelty of the pathway is important. Exploratory studies can be carried using knowledge of the patent/IP landscape for synthetic biology and metabolic engineering. In this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable chemicals in the extended metabolic space of chassis organisms, as computed by the retrosynthesis-based algorithm RetroPath. Our database for reactions processed by sequences in heterologous pathways was screened against the PatSeq database, a comprehensive collection of more than 150M sequences present in patent grants and applications. We also examine related patent families using Derwent Innovations. This large-scale computational study provides useful insights into the IP landscape of synthetic biology for fine and specialty chemicals production. PMID:27489206

  20. Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition

    OpenAIRE

    Karpievitch, Yuliya V.; Taverner, Thomas; Adkins, Joshua N.; Stephen J Callister; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2009-01-01

    Motivation: LC-MS allows for the identification and quantification of proteins from biological samples. As with any high-throughput technology, systematic biases are often observed in LC-MS data, making normalization an important preprocessing step. Normalization models need to be flexible enough to capture biases of arbitrary complexity, while avoiding overfitting that would invalidate downstream statistical inference. Careful normalization of MS peak intensities would enable greater accurac...

  1. A comparison of top-down and bottom-up approaches to benthic habitat mapping to inform offshore wind energy development

    Science.gov (United States)

    LaFrance, Monique; King, John W.; Oakley, Bryan A.; Pratt, Sheldon

    2014-07-01

    Recent interest in offshore renewable energy within the United States has amplified the need for marine spatial planning to direct management strategies and address competing user demands. To assist this effort in Rhode Island, benthic habitat classification maps were developed for two sites in offshore waters being considered for wind turbine installation. Maps characterizing and representing the distribution and extent of benthic habitats are valuable tools for improving understanding of ecosystem patterns and processes, and promoting scientifically-sound management decisions. This project presented the opportunity to conduct a comparison of the methodologies and resulting map outputs of two classification approaches, “top-down” and “bottom-up” in the two study areas. This comparison was undertaken to improve understanding of mapping methodologies and their applicability, including the bottom-up approach in offshore environments where data density tends to be lower, as well as to provide case studies for scientists and managers to consider for their own areas of interest. Such case studies can offer guidance for future work for assessing methodologies and translating them to other areas. The traditional top-down mapping approach identifies biological community patterns based on communities occurring within geologically defined habitat map units, under the concept that geologic environments contain distinct biological assemblages. Alternatively, the bottom-up approach aims to establish habitat map units centered on biological similarity and then uses statistics to identify relationships with associated environmental parameters and determine habitat boundaries. When applied to the two study areas, both mapping approaches produced habitat classes with distinct macrofaunal assemblages and each established statistically strong and significant biotic-abiotic relationships with geologic features, sediment characteristics, water depth, and/or habitat

  2. Synthetic biology and microbioreactor platforms for programmable production of biologics at the point-of-care

    Science.gov (United States)

    Perez-Pinera, Pablo; Han, Ningren; Cleto, Sara; Cao, Jicong; Purcell, Oliver; Shah, Kartik A.; Lee, Kevin; Ram, Rajeev; Lu, Timothy K.

    2016-01-01

    Current biopharmaceutical manufacturing systems are not compatible with portable or distributed production of biologics, as they typically require the development of single biologic-producing cell lines followed by their cultivation at very large scales. Therefore, it remains challenging to treat patients in short time frames, especially in remote locations with limited infrastructure. To overcome these barriers, we developed a platform using genetically engineered Pichia pastoris strains designed to secrete multiple proteins on programmable cues in an integrated, benchtop, millilitre-scale microfluidic device. We use this platform for rapid and switchable production of two biologics from a single yeast strain as specified by the operator. Our results demonstrate selectable and near-single-dose production of these biologics in system with analytical, purification and polishing technologies could lead to a small-scale, portable and fully integrated personal biomanufacturing platform that could advance disease treatment at point-of-care. PMID:27470089

  3. Governing synthetic biology in the light of the Access and Benefit Sharing regulation (ABS).

    Science.gov (United States)

    Augusto, Carlos; Gutiérrez, Conde

    2014-01-01

    Synthetic biology is a change of paradigm, i.e. from the exploitation of natural and genetic resources to lab production of biological entities. This transitional shift represents a great challenge for developing countries, particularly those which host biodiversity, and users of genetic resources, since the latter might not be longer required to access to actual genetic resources (tangible genetic resources) but rather genetic resources' information (intangible genetic resources) in order to replicate those resources in labs. This could mean that users of genetic resource would not have to comply with the Convention on Biological Diversity (CBD) and its complementary treaty, the Nagoya Protocol, known also as the Access and Benefit Sharing regime (ABS). Both international instrument demands that States create legal mechanisms to secure access and benefit sharing, i.e., users of genetic resources are required to obtain prior informed consent (PIC) from host countries of biodiversity and reach mutual agreed terms (MATs), in which users and countries agree how to share the benefits arise from the utilization of genetic resources. The ABS regime is particularly relevant since its implementation at national and regional level has created tensions between users of genetic resources and developing countries. This situation could lead to users removing interest in the exploitation of genetic resources, subsequently, meaning that their focus would move towards technologies that rely less on tangible genetic resources, including synthetic biology. This papers aim to discuss the scope of the CBD and the Nagoya Protocol in the light of synthetic biology and the implications for developing countries. PMID:25845206

  4. Bottom-up effects of climate on fish populations: data from the Continuous Plankton Recorder

    DEFF Research Database (Denmark)

    Pitois, S.G.; Lynam, C.P.; Jansen, Teunis;

    2012-01-01

    unique opportunity to investigate long-term changes over decadal scales in the abundance and distribution of fish larvae in relation to physical and biological factors. A principal component analysis (PCA) using 7 biotic and abiotic parameters is applied to investigate the impact of environmental changes......) impacting on the hydro dynamic features of the North Sea, in turn impacting on the plankton available as prey for fish larvae. The responses and adaptability of fish larvae to changing environmental conditions, parti cularly to changes in prey availability, are complex and species-specific. This complexity...

  5. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    International Nuclear Information System (INIS)

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model

  6. Benchmarking energy scenarios for China: perspectives from top-down, economic and bottom-up, technical modelling

    DEFF Research Database (Denmark)

    This study uses a soft-linking methodology to harmonise two complex global top-down and bottom-up models with a regional China focus. The baseline follows the GDP and demographic trends of the Shared Socio-economic Pathways (SSP2) scenario, down-scaled for China, while the carbon tax scenario fol......-specific modelling results further. These new sub-regional China features can now be used for a more detailed analysis of China's regional developments in a global context....

  7. Top-down and Bottom-up. Testing a mixed approach to the generation of priorities for sustainable urban mobility

    OpenAIRE

    E. Pieralice; F. Mameli; G. Marletto

    2015-01-01

    This paper contributes to the debate on how to make operational the concept of sustainable urban mobility and advocates the use of a mixed – top-down and bottom-up – approach to the generation of priorities for sustainable urban mobility. In particular, we tested whether a common list of priorities remain valid after a participated scrutiny performed in seven urban areas of southern Italy. The test was based on a 3-steps procedure. In step 1, we used a common conceptual framework (based on Ma...

  8. Bottom-up modelling of continuous renovation and energy balance of existing building stock: case study Kočevje

    OpenAIRE

    Šijanec Zavrl, Marjana; Stegnar, Gašper; Rakušček, Andraž; Gjerkeš, Henrik

    2016-01-01

    A dynamic bottom-up model of the building stock is developed and implemented in a case study of Kočevje urban region. In the model, national register of real estate is cross-linked to data from other registers, e.g. the energy performance certificates (EPC) and the subsidized energy renovation measures. Regular updates of the data in registers enable continual improvement of the model. Therenovation potential is determined with respect to the age of building components after the last renovati...

  9. Bottom-Up Nano-heteroepitaxy of Wafer-Scale Semipolar GaN on (001) Si

    KAUST Repository

    Hus, Jui Wei

    2015-07-15

    Semipolar {101¯1} InGaN quantum wells are grown on (001) Si substrates with an Al-free buffer and wafer-scale uniformity. The novel structure is achieved by a bottom-up nano-heteroepitaxy employing self-organized ZnO nanorods as the strain-relieving layer. This ZnO nanostructure unlocks the problems encountered by the conventional AlN-based buffer, which grows slowly and contaminates the growth chamber. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Land claim settlements and their impacts : regional dynamics and bottom-up economic development in Nunavik and Nunatsiavut (Canada)

    OpenAIRE

    Fugmann, Gerlis

    2011-01-01

    Since the 1970s, land claim and self-government agreements have provided the Inuit in the Arctic with a variety of tools, granting them considerable rights and benefits within their traditional settlement areas. One of the central purposes of these regional agreements was to create an economic base in order to enhance development from within the various regions and thus promote economic self-reliance for the Inuit beneficiaries. This bottom-up approach is a clear shift from the top-down devel...

  11. A statistical mixture method to reveal bottom-up and top-down factors guiding the eye-movements

    OpenAIRE

    Couronné, Thomas; Guérin-Dugué, Anne; Michel DUBOIS; Faye, Pauline; MARENDAZ, Christian

    2010-01-01

    When people gaze at real scenes, their visual attention is driven both by a set of bottom-up processes coming from the signal properties of the scene and also from top-down effects such as the task, the affective state, prior knowledge, or the semantic context. The context of this study is an assessment of manufactured objects (here car cab interior). From this dedicated context, this work describes a set of methods to analyze the eye-movements during the visual scene evaluation. But these me...

  12. A bottom-up approach for optimization of friction stir processing parameters; a study on aluminium 2024-T3 alloy

    International Nuclear Information System (INIS)

    Highlights: • An experimental bottom-up approach has been developed for optimizing the process parameters for friction stir processing. • Optimum parameter processed samples were tested and characterized in detail. • Ultimate tensile strength of 1.3 times the base metal strength was obtained. • Residual stresses on the processed surface were only 10% of the yield strength of base metal. • Microstructure observations revealed fine equi-axed grains with precipitate particles at the grain boundaries. - Abstract: Friction stir processing (FSP) is emerging as one of the most competent severe plastic deformation (SPD) method for producing bulk ultra-fine grained materials with improved properties. Optimizing the process parameters for a defect free process is one of the challenging aspects of FSP to mark its commercial use. For the commercial aluminium alloy 2024-T3 plate of 6 mm thickness, a bottom-up approach has been attempted to optimize major independent parameters of the process such as plunge depth, tool rotation speed and traverse speed. Tensile properties of the optimum friction stir processed sample were correlated with the microstructural characterization done using Scanning Electron Microscope (SEM) and Electron Back-Scattered Diffraction (EBSD). Optimum parameters from the bottom-up approach have led to a defect free FSP having a maximum strength of 93% the base material strength. Micro tensile testing of the samples taken from the center of processed zone has shown an increased strength of 1.3 times the base material. Measured maximum longitudinal residual stress on the processed surface was only 30 MPa which was attributed to the solid state nature of FSP. Microstructural observation reveals significant grain refinement with less variation in the grain size across the thickness and a large amount of grain boundary precipitation compared to the base metal. The proposed experimental bottom-up approach can be applied as an effective method for

  13. Benchmarking energy scenarios for China: perspectives from top-down, economic and bottom-up, technical modelling

    OpenAIRE

    Mischke, Peggy

    2014-01-01

    This study uses a soft-linking methodology to harmonise two complex global top-down and bottom-up models with a regional China focus. The baseline follows the GDP and demographic trends of the Shared Socio-economic Pathways (SSP2) scenario, down-scaled for China, while the carbon tax scenario follows the pathway of the Asia Modelling Exercise.We find that soft-linking allows "bridging the gap" and reducing uncertainty between these models. Without soft-linking, baseline result ranges for Chin...

  14. The drastic outcomes from voting alliances in three-party bottom-up democratic voting (1990 $\\rightarrow$ 2013)

    OpenAIRE

    Galam, Serge

    2013-01-01

    The drastic effect of local alliances in three-party competition is investigated in democratic hierarchical bottom-up voting. The results are obtained analytically using a model which extends a sociophysics frame introduced in 1986 \\cite{psy} and 1990 \\cite{lebo} to study two-party systems and the spontaneous formation of democratic dictatorship. It is worth stressing that the 1990 paper was published in the Journal of Statistical Physics, the first paper of its kind in the journal. It was sh...

  15. Una implementación computacional de un modelo de atención visual Bottom-up aplicado a escenas naturales/A Computational Implementation of a Bottom-up Visual Attention Model Applied to Natural Scenes

    Directory of Open Access Journals (Sweden)

    Juan F. Ramírez Villegas

    2011-12-01

    Full Text Available El modelo de atención visual bottom-up propuesto por Itti et al., 2000 [1], ha sido un modelo popular en tanto exhibe cierta evidencia neurobiológica de la visión en primates. Este trabajo complementa el modelo computacional de este fenómeno desde la dinámica realista de una red neuronal. Asimismo, esta aproximación se basa en la existencia de mapas topográficos que representan la prominencia de los objetos del campo visual para la formación de una representación general (mapa de prominencia, esta representación es la entrada de una red neuronal dinámica con interacciones locales y globales de colaboración y competencia que convergen sobre las principales particularidades (objetos de la escena.The bottom-up visual attention model proposed by Itti et al. 2000 [1], has been a popular model since it exhibits certain neurobiological evidence of primates’ vision. This work complements the computational model of this phenomenon using a neural network with realistic dynamics. This approximation is based on several topographical maps representing the objects saliency that construct a general representation (saliency map, which is the input for a dynamic neural network, whose local and global collaborative and competitive interactions converge to the main particularities (objects presented by the visual scene as well.

  16. Protein-polymer nano-machines. Towards synthetic control of biological processes

    Directory of Open Access Journals (Sweden)

    Alexander Cameron

    2004-09-01

    Full Text Available Abstract The exploitation of nature's machinery at length scales below the dimensions of a cell is an exciting challenge for biologists, chemists and physicists, while advances in our understanding of these biological motifs are now providing an opportunity to develop real single molecule devices for technological applications. Single molecule studies are already well advanced and biological molecular motors are being used to guide the design of nano-scale machines. However, controlling the specific functions of these devices in biological systems under changing conditions is difficult. In this review we describe the principles underlying the development of a molecular motor with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for control of the motor function. The molecular motor is a derivative of a TypeI Restriction-Modification (R-M enzyme and the synthetic polymer is drawn from the class of materials that exhibit a temperature-dependent phase transition. The potential exploitation of single molecules as functional devices has been heralded as the dawn of new era in biotechnology and medicine. It is not surprising, therefore, that the efforts of numerous multidisciplinary teams 12. have been focused in attempts to develop these systems. as machines capable of functioning at the low sub-micron and nanometre length-scales 3. However, one of the obstacles for the practical application of single molecule devices is the lack of functional control methods in biological media, under changing conditions. In this review we describe the conceptual basis for a molecular motor (a derivative of a TypeI Restriction-Modification enzyme with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for controlling the motor function 4.

  17. Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

    Directory of Open Access Journals (Sweden)

    E.V.Krishnamurthy

    2012-03-01

    Full Text Available We describe a multiset of agents based modeling and simulation paradigm for synthetic biology. The multiset of agents –based programming paradigm, can be interpreted as the outcome arising out of deterministic, nondeterministic or stochastic interaction among elements in a multiset object space, that includes the environment. These interactions are like chemical reactions and the evolution of the multiset can emulate the system biological functions. Since the reaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward equilibrium or emergent state. Practical realization of this paradigm for system biological simulation is achieved through the concept of transactional style programming with agents, as well as soft computing (neural- network principles. Also we briefly describe currently available tools for agent-based-modeling, simulation and animation.

  18. Linking top-down and bottom-up approaches for assessing the vulnerability of a 100 % renewable energy system in Northern-Italy

    Science.gov (United States)

    Borga, Marco; Francois, Baptiste; Hingray, Benoit; Zoccatelli, Davide; Creutin, Jean-Dominique; brown, Casey

    2016-04-01

    Due to their variable and un-controllable features, integration of Variable Renewable Energies (e.g. solar-power, wind-power and hydropower, denoted as VRE) into the electricity network implies higher production variability and increased risk of not meeting demand. Two approaches are commonly used for assessing this risk and especially its evolution in a global change context (i.e. climate and societal changes); top-down and bottom-up approaches. The general idea of a top-down approach is to drive analysis of global change or of some key aspects of global change on their systems (e.g., the effects of the COP 21, of the deployment of Smart Grids, or of climate change) with chains of loosely linked simulation models within a predictive framework. The bottom-up approach aims to improve understanding of the dependencies between the vulnerability of regional systems and large-scale phenomenon from knowledge gained through detailed exploration of the response to change of the system of interest, which may reveal vulnerability thresholds, tipping points as well as potential opportunities. Brown et al. (2012) defined an analytical framework to merge these two approaches. The objective is to build, a set of Climate Response Functions (CRFs) putting in perspective i) indicators of desired states ("success") and undesired states ("failure") of a system as defined in collaboration with stakeholders 2) exhaustive exploration of the effects of uncertain forcings and imperfect system understanding on the response of the system itself to a plausible set of possible changes, implemented a with multi-dimensionally consistent "stress test" algorithm, and 3) a set "ex post" hydroclimatic and socioeconomic scenarios that provide insight into the differential effectiveness of alternative policies and serve as entry points for the provision of climate information to inform policy evaluation and choice. We adapted this approach for analyzing a 100 % renewable energy system within a region

  19. Source attribution of methane emissions from global oil and gas production: results of bottom-up simulations over three decades

    Science.gov (United States)

    Höglund-Isaksson, Lena

    2016-04-01

    Existing bottom-up emission inventories of historical methane and ethane emissions from global oil and gas systems do not well explain year-on-year variations estimated by top-down models from atmospheric measurements. This paper develops a bottom-up methodology which allows for country- and year specific source attribution of methane and ethane emissions from global oil and natural gas production for the period 1980 to 2012. The analysis rests on country-specific simulations of associated gas flows which are converted into methane and ethane emissions. The associated gas flows are constructed from country-specific information on oil and gas production and associated gas generation and recovery, and coupled with generic assumptions to bridge regional information gaps on the fractions of unrecovered associated gas that is vented instead of flared. Summing up emissions from associated gas flows with global estimates of emissions from unintended leakage and natural gas transmission and distribution, the resulting global emissions of methane and ethane from oil and gas systems are reasonably consistent with corresponding estimates from top-down models. Also revealed is that the fall of the Soviet Union in 1990 had a significant impact on methane and ethane emissions from global oil and gas systems.

  20. Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics.

    Science.gov (United States)

    Blein-Nicolas, Mélisande; Zivy, Michel

    2016-08-01

    How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. peptide counting, spectral counting), while the second makes use of extracted ion currents to quantify chromatographic peaks and infer protein abundances based on peptide quantification. These two approaches actually refer to multiple methods which have been developed during the last decade, but were submitted to deep evaluations only recently. In this paper, we compiled these different methods as exhaustively as possible. We also summarized the way they address the different problems raised by bottom-up protein quantification such as normalization, the presence of shared peptides, unequal peptide measurability and missing data. This article is part of a Special Issue entitled: Plant Proteomics- a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26947242

  1. Bottom-up versus top-down effects on ciliate community composition in four eutrophic lakes (China).

    Science.gov (United States)

    Li, Jing; Chen, Feizhou; Liu, Zhengwen; Zhao, Xiuxia; Yang, Kun; Lu, Wenxuan; Cui, Kai

    2016-04-01

    Previous studies have shown that ciliate plankton is generally controlled by food resources (e.g., algae) and predators (e.g., metazooplankton). Among lakes with similar trophic levels but different distributions of phyto- and metazooplankton, the main forces acting on ciliate assemblages may be different. We investigated the relationship between ciliate communities and bottom-up versus top-down variables based on a survey of four subtropical eutrophic lakes (China). Two of the lakes (Chaohu, Taihu) are located on the Mid-lower Yangtze Plain near sea level, and the other two (Dianchi, Xingyunhu) on the Yunnan-Kweichow Plateau at 1700m above sea level. Blooms of cyanobacteria developed during summer in Lakes Chaohu and Taihu and throughout the year in Lakes Dianchi and Xingyunhu. Ciliate functional feeding groups differed significantly between lakes. The results of canonical correspondence analysis (CCA) and variation partitioning showed that cyanobacteria significantly influence ciliate species, whereas 'edible' algae (cryptophytes, diatoms) and cladocerans were the important variables in explaining the ciliate community structure of Lakes Dianchi and Xingyunhu compared with Lakes Taihu and Chaohu. Our results highlight the importance of consistent cyanobacterial blooms in shaping the ciliate community in subtropical eutrophic shallow lakes by interacting with top-down and bottom-up factors. PMID:26773905

  2. Galvanostatic bottom-up filling of TSV-like trenches: Choline-based leveler containing two quaternary ammoniums

    International Nuclear Information System (INIS)

    Highlights: • The choline-based leveler having two quaternary ammoniums was synthesized. • The adsorption of this leveler with suppressor and accelerator was examined. • Galvanostatic Cu bottom-up filling was achieved with three-additive system. • The mechanism of gap-filling was elucidated based on the additive adsorption. - Abstract: Through Silicon Via (TSV) technology is essential to accomplish 3-dimensional packaging of electronics. Hence, more reliable and faster TSV filling by Cu electrodeposition is required. Our approach to improve Cu gap-filling in TSV is based on the development of new organic additives for feature filling. Here, we introduce our achievements from the synthesis of choline-based leveler to the feature filling using a synthesized leveler. The choline-based leveler, which includes two quaternary ammoniums at both ends of the molecule, is synthesized from glutaric acid. The characteristics of the choline-based additive are examined by the electrochemical analyses, and it is confirmed that the choline-based leveler shows a convection dependent adsorption behavior, which is essential for leveling. The interactions between the polymeric suppressor, accelerator, and the choline-based leveler are also investigated by changing the convection condition. Using the combination of suppressor, accelerator, and the choline-based leveler, the extreme bottom-up filling of Cu at trenches with dimensions similar to TSV are fulfilled. The mechanism of Cu gap-filling is demonstrated based on the results of electrochemical analyses and feature filling

  3. Orchestrated structure evolution: accelerating direct-write nanomanufacturing by combining top-down patterning with bottom-up growth

    International Nuclear Information System (INIS)

    Direct-write nanomanufacturing with scanning beams and probes is flexible and can produce high quality products, but it is normally slow and expensive to raster point-by-point over a pattern. We demonstrate the use of an accelerated direct-write nanomanufacturing method called 'orchestrated structure evolution' (OSE), where a direct-write tool patterns a small number of growth 'seeds' that subsequently grow into the final thin film pattern. Through control of seed size and spacing, it is possible to vary the ratio of 'top-down' to 'bottom-up' character of the patterning processes, ranging from conventional top-down raster patterning to nearly pure bottom-up space-filling via seed growth. Electron beam lithography (EBL) and copper electrodeposition were used to demonstrate trade-offs between process time and product quality over nano- to microlength scales. OSE can reduce process times for high-cost EBL patterning by orders of magnitude, at the expense of longer (but inexpensive) copper electrodeposition processing times. We quantify the degradation of pattern quality that accompanies fast OSE patterning by measuring deviations from the desired patterned area and perimeter. We also show that the density of OSE-induced grain boundaries depends upon the seed separation and size. As the seed size is reduced, the uniformity of an OSE film becomes more dependent on details of seed nucleation processes than normally seen for conventionally patterned films.

  4. The drastic outcomes from voting alliances in three-party bottom-up democratic voting (1990 $\\rightarrow$ 2013)

    CERN Document Server

    Galam, Serge

    2013-01-01

    The drastic effect of local alliances in three-party competition is investigated in democratic hierarchical bottom-up voting. The results are obtained analytically using a model which extends a sociophysics frame introduced in 1986 \\cite{psy} and 1990 \\cite{lebo} to study two-party systems and the spontaneous formation of democratic dictatorship. It is worth stressing that the 1990 paper was published in the Journal of Statistical Physics, the first paper of its kind in the journal. It was shown how a minority in power can preserve its leadership using bottom-up democratic elections. However such a bias holds only down to some critical value of minimum support. The results were used latter to explain the sudden collapse of European communist parties in the nineties. The extension to three-party competition reveals the mechanisms by which a very small minority party can get a substantial representation at higher levels of the hierarchy when the other two competing parties are big. Additional surprising results...

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

    OpenAIRE

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

  6. Drought-Stressed Tomato Plants Trigger Bottom-Up Effects on the Invasive Tetranychus evansi.

    Directory of Open Access Journals (Sweden)

    Miguel G Ximénez-Embún

    Full Text Available Climate change will bring more drought periods that will have an impact on the irrigation practices of some crops like tomato, from standard water regime to deficit irrigation. This will promote changes in plant metabolism and alter their interactions with biotic stressors. We have tested if mild or moderate drought-stressed tomato plants (simulating deficit irrigation have an effect on the biological traits of the invasive tomato red spider mite, Tetranychus evansi. Our data reveal that T evansi caused more leaf damage to drought-stressed tomato plants (≥1.5 fold for both drought scenarios. Mite performance was also enhanced, as revealed by significant increases of eggs laid (≥2 fold at 4 days post infestation (dpi, and of mobile forms (≥2 fold and 1.5 fold for moderate and mild drought, respectively at 10 dpi. The levels of several essential amino acids (histidine, isoleucine, leucine, tyrosine, valine and free sugars in tomato leaves were significantly induced by drought in combination with mites. The non-essential amino acid proline was also strongly induced, stimulating mite feeding and egg laying when added to tomato leaf disks at levels equivalent to that estimated on drought-infested tomato plants at 10 dpi. Tomato plant defense proteins were also affected by drought and/or mite infestation, but T. evansi was capable of circumventing their potential adverse effects. Altogether, our data indicate that significant increases of available free sugars and essential amino acids, jointly with their phagostimulant effect, created a favorable environment for a better T. evansi performance on drought-stressed tomato leaves. Thus, drought-stressed tomato plants, even at mild levels, may be more prone to T evansi outbreaks in a climate change scenario, which might negatively affect tomato production on area-wide scales.

  7. Drought-Stressed Tomato Plants Trigger Bottom-Up Effects on the Invasive Tetranychus evansi.

    Science.gov (United States)

    Ximénez-Embún, Miguel G; Ortego, Félix; Castañera, Pedro

    2016-01-01

    Climate change will bring more drought periods that will have an impact on the irrigation practices of some crops like tomato, from standard water regime to deficit irrigation. This will promote changes in plant metabolism and alter their interactions with biotic stressors. We have tested if mild or moderate drought-stressed tomato plants (simulating deficit irrigation) have an effect on the biological traits of the invasive tomato red spider mite, Tetranychus evansi. Our data reveal that T evansi caused more leaf damage to drought-stressed tomato plants (≥1.5 fold for both drought scenarios). Mite performance was also enhanced, as revealed by significant increases of eggs laid (≥2 fold) at 4 days post infestation (dpi), and of mobile forms (≥2 fold and 1.5 fold for moderate and mild drought, respectively) at 10 dpi. The levels of several essential amino acids (histidine, isoleucine, leucine, tyrosine, valine) and free sugars in tomato leaves were significantly induced by drought in combination with mites. The non-essential amino acid proline was also strongly induced, stimulating mite feeding and egg laying when added to tomato leaf disks at levels equivalent to that estimated on drought-infested tomato plants at 10 dpi. Tomato plant defense proteins were also affected by drought and/or mite infestation, but T. evansi was capable of circumventing their potential adverse effects. Altogether, our data indicate that significant increases of available free sugars and essential amino acids, jointly with their phagostimulant effect, created a favorable environment for a better T. evansi performance on drought-stressed tomato leaves. Thus, drought-stressed tomato plants, even at mild levels, may be more prone to T evansi outbreaks in a climate change scenario, which might negatively affect tomato production on area-wide scales. PMID:26735490

  8. Bioassessment of a combined chemical-biological treatment for synthetic acid mine drainage.

    Science.gov (United States)

    Pagnanelli, F; De Michelis, I; Di Muzio, S; Ferella, F; Vegliò, F

    2008-11-30

    In this work, ecotoxicological characteristics of synthetic samples of acid mine drainage (AMD) before and after a combined chemical-biological treatment were investigated by using Lepidium sativum and Daphnia magna. AMD treatment was performed in a two-column apparatus consisting of chemical precipitation by limestone and biological refinement by sulphate reducing bacteria. Synthetic samples of AMD before treatment were toxic for both L. sativum (germination index, G, lower than 10%) and D. magna (100% immobility) due to acid pH and presence of copper and zinc. Chemical treatment (raising pH to 5-6 and eliminating copper) generated effluents with reduced toxicity for L. sativum (G=33%), while 100% immobility was still observed for D. magna. Dynamic trends of toxicity for the first and fifth outputs of the biological column denoted a gradual improvement leading to hormesis for Lepidium (after the initial release of organic excess), while a constant residual toxicity remained for Daphnia (probably due to H(2)S produced by sulphate reducing bacteria). PMID:18394799

  9. Diversity-Oriented Synthetic Strategies Applied to Cancer Chemical Biology and Drug Discovery

    Directory of Open Access Journals (Sweden)

    Ian Collins

    2014-10-01

    Full Text Available How can diversity-oriented strategies for chemical synthesis provide chemical tools to help shape our understanding of complex cancer pathways and progress anti-cancer drug discovery efforts? This review (surveying the literature from 2003 to the present considers the applications of diversity-oriented synthesis (DOS, biology-oriented synthesis (BIOS and associated strategies to cancer biology and drug discovery, summarising the syntheses of novel and often highly complex scaffolds from pluripotent or synthetically versatile building blocks. We highlight the role of diversity-oriented synthetic strategies in producing new chemical tools to interrogate cancer biology pathways through the assembly of relevant libraries and their application to phenotypic and biochemical screens. The use of diversity-oriented strategies to explore structure-activity relationships in more advanced drug discovery projects is discussed. We show how considering appropriate and variable focus in library design has provided a spectrum of DOS approaches relevant at all stages in anti-cancer drug discovery.

  10. Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options

    Energy Technology Data Exchange (ETDEWEB)

    Carter, Sarah R. [J. Craig Venter Institute; Rodemeyer, Michael [University of Virginia; Garfinkel, Michele S. [EMBO; Friedman, Robert M [J. Craig Venter Institute

    2014-05-01

    Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options Sarah R. Carter, Ph.D., J. Craig Venter Institute; Michael Rodemeyer, J.D., University of Virginia; Michele S. Garfinkel, Ph.D., EMBO; Robert M. Friedman, Ph.D., J. Craig Venter Institute In recent years, a range of genetic engineering techniques referred to as “synthetic biology” has significantly expanded the tool kit available to scientists and engineers, providing them with far greater capabilities to engineer organisms than previous techniques allowed. The field of synthetic biology includes the relatively new ability to synthesize long pieces of DNA from chemicals, as well as improved methods for genetic manipulation and design of genetic pathways to achieve more precise control of biological systems. These advances will help usher in a new generation of genetically engineered microbes, plants, and animals. The JCVI Policy Center team, along with researchers at the University of Virginia and EMBO, examined how well the current U.S. regulatory system for genetically engineered products will handle the near-term introduction of organisms engineered using synthetic biology. In particular, the focus was on those organisms intended to be used or grown directly in the environment, outside of a contained facility. The study concludes that the U.S. regulatory agencies have adequate legal authority to address most, but not all, potential environmental, health and safety concerns posed by these organisms. Such near-term products are likely to represent incremental changes rather than a marked departure from previous genetically engineered organisms. However, the study also identified two key challenges for the regulatory system, which are detailed in the report. First, USDA’s authority over genetically engineered plants depends on the use of an older engineering technique that is no longer necessary for many applications. The shift to synthetic biology and other newer genetic

  11. New Synthetic Biology Tools to Track Microbial Dynamics in the Earth System

    Science.gov (United States)

    Silberg, J. J.; Masiello, C. A.; Cheng, H. Y.

    2015-12-01

    Microbes drive processes in the Earth system far exceeding their physical scale, mediating significant fluxes in the global C and N cycles. The tools of synthetic biology have the potential to significantly improve our understanding of microbes' role in the Earth system; however, these tools have not yet seen wide laboratory use because synthetically "programmed" microbes typically report by fluorescing (expressing green fluorescent protein), making them challenging to deploy into many Earth materials, the majority of which are not transparent and are heterogeneous (soils, sediments, and biomass). We are developing a new suite of biosensors that report instead by releasing gases. We will provide an overview of the use of gas-reporting biosensors in biogeochemistry and will report the development of the systematics of these sensors. These sensors will make tractable the testing of gene expression hypotheses derived from metagenomics data. Examples of processes that could be tracked non-invasively with gas sensors include coordination of biofilm formation, nitrification, rhizobial infection of plant roots, and at least some forms of methanogenesis, all of which are managed by an easily-engineered cell-cell communication system. Another relatively simple process to track with gas sensors is horizontal gene transfer. Successful development of gas biosensors for Earth science applications will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise using the tools of synthetic biology; normalizing the gas reporter signal to cell population size, since the number of cells and gene expression both contribute to gas production; managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel to report on multiple biological processes in parallel. We will report on progress addressing each of these issues.

  12. Carbon balance: the top-down and bottom-up emissions accounting methodologies; Balanco de carbono: a contabilidade das emissoes nas metodologias 'Top-Down' estendida ('Top-Bottom') e 'Bottom-Up'

    Energy Technology Data Exchange (ETDEWEB)

    Alvim, Carlos Feu; Eidelman, Frida; Ferreira, Omar Campos

    2005-08-15

    The Economy and Energy Organization has carried out together with the Ministry of Science and Technology a study on the carbon balance of energy use and transformation. The publication of its results has been made through the e and e periodical in its 48 and 50 issues. In the present issue we are publishing the results corresponding to the extended Top-Down accounting process and those corresponding to the use of the coefficients calculated for the Brazilian inventory from 1990 to 1994, using the Bottom-Up process, to estimate the emissions from 1970 to 2002. By comparing the two results it is possible to evaluate their deficiencies and the possible incoherence in the use of the two methodologies. (author)

  13. Comparison of Single Channel Potassium Current in Biological and Synthetic Systems - Dependence on Voltage

    International Nuclear Information System (INIS)

    The influence of an external field on an ion current pattern in biological and synthetic systems was investigated. The patch clamp recordings of potassium current through a big conductance locust potassium channel (BK-channel) and a track-etched polyethylene terephthalate membrane were examined by the power spectrum, fractal analysis and relative dispersion analysis. A similar dependence of potassium current behaviour on the external voltage in both systems was found. The generalized dimension formalism is redefined to make it applicable to the analysis of time series. (author)

  14. Frankenstein 2.0.: Identifying and characterising synthetic biology engineers in science fiction films

    OpenAIRE

    Meyer, Angela; Cserer, Amelie; Schmidt, Markus

    2013-01-01

    Synthetic biology (SB) has emerged as one of the newest and promising areas of bio-technology. Issues typically associated to SB, notably in the media, like the idea of artificial life creation and “real” engineering of life also appear in many popular films. Drawing upon the analysis of 48 films, the article discusses how scientists applying technologies that can be related to SB are represented in these movies. It hereby discusses that traditional clichés of scientists in general tend to be...

  15. Methanol regulated yeast promoters: production vehicles and toolbox for synthetic biology.

    Science.gov (United States)

    Gasser, Brigitte; Steiger, Matthias G; Mattanovich, Diethard

    2015-01-01

    Promoters are indispensable elements of a standardized parts collection for synthetic biology. Regulated promoters of a wide variety of well-defined induction ratios and expression strengths are highly interesting for many applications. Exemplarily, we discuss the application of published genome scale transcriptomics data for the primary selection of methanol inducible promoters of the yeast Pichia pastoris (Komagataella sp.). Such a promoter collection can serve as an excellent toolbox for cell and metabolic engineering, and for gene expression to produce heterologous proteins. PMID:26627685

  16. Atomic layer deposition-Sequential self-limiting surface reactions for advanced catalyst "bottom-up" synthesis

    Science.gov (United States)

    Lu, Junling; Elam, Jeffrey W.; Stair, Peter C.

    2016-06-01

    Catalyst synthesis with precise control over the structure of catalytic active sites at the atomic level is of essential importance for the scientific understanding of reaction mechanisms and for rational design of advanced catalysts with high performance. Such precise control is achievable using atomic layer deposition (ALD). ALD is similar to chemical vapor deposition (CVD), except that the deposition is split into a sequence of two self-limiting surface reactions between gaseous precursor molecules and a substrate. The unique self-limiting feature of ALD allows conformal deposition of catalytic materials on a high surface area catalyst support at the atomic level. The deposited catalytic materials can be precisely constructed on the support by varying the number and type of ALD cycles. As an alternative to the wet-chemistry based conventional methods, ALD provides a cycle-by-cycle "bottom-up" approach for nanostructuring supported catalysts with near atomic precision. In this review, we summarize recent attempts to synthesize supported catalysts with ALD. Nucleation and growth of metals by ALD on oxides and carbon materials for precise synthesis of supported monometallic catalyst are reviewed. The capability of achieving precise control over the particle size of monometallic nanoparticles by ALD is emphasized. The resulting metal catalysts with high dispersions and uniformity often show comparable or remarkably higher activity than those prepared by conventional methods. For supported bimetallic catalyst synthesis, we summarize the strategies for controlling the deposition of the secondary metal selectively on the primary metal nanoparticle but not on the support to exclude monometallic formation. As a review of the surface chemistry and growth behavior of metal ALD on metal surfaces, we demonstrate the ways to precisely tune size, composition and structure of bimetallic metal nanoparticles. The cycle-by-cycle "bottom up" construction of bimetallic (or multiple

  17. Biological Removal of Phosphate Using Phosphate Solubilizing Bacterial Consortium from Synthetic Wastewater: A Laboratory Scale

    Directory of Open Access Journals (Sweden)

    Dipak Paul

    2015-01-01

    Full Text Available Biological phosphate removal is an important process having gained worldwide attention and widely used for removing phosphorus from wastewater. The present investigation was aimed to screen the efficient phosphate solubilizing bacterial isolates and used to remove phosphate from synthetic wastewater under shaking flasks conditions. Pseudomonas sp. JPSB12, Enterobacter sp. TPSB20, Flavobacterium sp. TPSB23 and mixed bacterial consortium (Pseudomonas sp. JPSB12+Enterobacter sp. TPSB20+Flavobacterium sp. TPSB23 were used for the removal of phosphate. Among the individual strains, Enterobacter sp. TPSB20 was removed maximum phosphate (61.75% from synthetic wastewater in presence of glucose as a carbon source. The consortium was effectively removed phosphate (74.15-82.50% in the synthetic wastewater when compared to individual strains. The pH changes in culture medium with time and extracellular phosphatase activity (acid and alkaline were also investigated. The efficient removal of phosphate by the consortium may be due to the synergistic activity among the individual strains and phosphatase enzyme activity. The use of bacterial consortium in the remediation of phosphate contaminated aquatic environments has been discussed.

  18. Building Better Scientists through Cross-Disciplinary Collaboration in Synthetic Biology: A Report from the Genome Consortium for Active Teaching Workshop 2010

    Science.gov (United States)

    Wolyniak, Michael J.; Alvarez, Consuelo J.; Chandrasekaran, Vidya; Grana, Theresa M.; Holgado, Andrea; Jones, Christopher J.; Morris, Robert W.; Pereira, Anil L.; Stamm, Joyce; Washington, Talitha M.; Yang, Yixin

    2010-01-01

    Synthetic biology is the application of engineering and mathematical principles to develop novel biological devices and circuits. What separates synthetic biology from traditional molecular biology is the development of standardized interchangeable DNA "parts," just as advances in engineering in the nineteenth century brought about standardized…

  19. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    Directory of Open Access Journals (Sweden)

    Daniel eLewis

    2014-12-01

    Full Text Available As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo systems, with only a few examples of prominent work done on predicting the dynamics of cell-free systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  20. Direct and indirect bottom-up and top-down forces shape the abundance of the orb-web spider Argiope bruennichi

    OpenAIRE

    Bruggisser, Odile T; Sandau, Nadine; Blandenier, Gilles; Fabian, Yvonne; Kehrli, Patrik; Aebi, Alex; Russell E Naisbit; Bersier, Louis-Félix

    2014-01-01

    Species abundance in local communities is determined by bottom-up and top-down processes, which can act directly and indirectly on the focal species. Studies examining these effects simultaneously are rare. Here we explore the direct top-down and direct and indirect bottom-up forces regulating the abundance and predation success of an intermediate predator, the web-building spider Argiope bruennichi (Araneae: Araneidae). We manipulated plant diversity (2, 6, 12 or 20 sown species) in 9 wildfl...

  1. The influence of top-down, bottom-up and abiotic factors on the moose (Alces alces) population of Isle Royale.

    OpenAIRE

    Vucetich, John A.; Rolf O Peterson

    2004-01-01

    Long-term, concurrent measurement of population dynamics and associated top-down and bottom-up processes are rare for unmanipulated, terrestrial systems. Here, we analyse populations of moose, their predators (wolves, Canis lupus), their primary winter forage (balsam fir, Abies balsamea) and several climatic variables that were monitored for 40 consecutive years in Isle Royale National Park (544 km2), Lake Superior, USA. We judged the relative importance of top-down, bottom-up and abiotic fac...

  2. Balancing Top-Down, Bottom-Up, and Peer-to-Peer Approaches to Sustaining Distance Training

    Directory of Open Access Journals (Sweden)

    Zane BERGE

    2006-07-01

    Full Text Available Many distance training case studies identify distance training leadership as bottom-up, whereas much of the literature suggests a need for strategic, top-down approaches. With change management as an overarching framework, approaches to sustaining distance training that originate at different levels of the organization are explored. Special attention is paid to the content of the change messages involved, guided by Rogers’ five attributes of innovations. Research of change management and distance training literature suggests a combination of approaches that should fit the organizational culture as well as correctly address genuine concerns at the various organizational levels. A properly balanced approach could lead to new levels of communication and understanding in a learning organization and to distance training being sustained as a business process

  3. Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing

    Science.gov (United States)

    Gillet, Ludovic C.; Leitner, Alexander; Aebersold, Ruedi

    2016-06-01

    Proteins constitute a key class of molecular components that perform essential biochemical reactions in living cells. Whether the aim is to extensively characterize a given protein or to perform high-throughput qualitative and quantitative analysis of the proteome content of a sample, liquid chromatography coupled to tandem mass spectrometry has become the technology of choice. In this review, we summarize the current state of mass spectrometry applied to bottom-up proteomics, the approach that focuses on analyzing peptides obtained from proteolytic digestion of proteins. With the recent advances in instrumentation and methodology, we show that the field is moving away from providing qualitative identification of long lists of proteins to delivering highly consistent and accurate quantification values for large numbers of proteins across large numbers of samples. We believe that this shift will have a profound impact for the field of proteomics and life science research in general.

  4. The faith of a physicist reflections of a bottom-up thinker : the Gifford lectures for 1993-4

    CERN Document Server

    Polkinghorne, John C

    1994-01-01

    Is it possible to think like a scientist and yet have the faith of a Christian? Although many Westerners might say no, there are also many critically minded individuals who entertain what John Polkinghorne calls a "wistful wariness" toward religion--they feel unable to accept religion on rational grounds yet cannot dismiss it completely. Polkinghorne, both a particle physicist and Anglican priest, here explores just what rational grounds there could be for Christian beliefs, maintaining that the quest for motivated understanding is a concern shared by scientists and religious thinkers alike. Anyone who assumes that religion is based on unquestioning certainties, or that it need not take into account empirical knowledge, will be challenged by Polkinghorne's bottom-up examination of Christian beliefs about events ranging from creation to the resurrection. The author organizes his inquiry around the Nicene Creed, an early statement that continues to summarize Christian beliefs. He applies to each of its tenets ...

  5. Aid effectiveness from Rome to Busan: some progress but lacking bottom-up approaches or behaviour changes.

    Science.gov (United States)

    Martini, Jessica; Mongo, Roch; Kalambay, Hyppolite; Fromont, Anne; Ribesse, Nathalie; Dujardin, Bruno

    2012-07-01

    The Busan partnership adopted at the 4th High Level Forum on Aid Effectiveness at the end of last year is a significant step forward towards the improvement of aid quality and the promotion of development. In particular, the inclusiveness achieved in Busan and the shift in discourse from 'aid effectiveness' to 'development effectiveness' are emblematic. However, key challenges still remain. Firstly, decision-making should be more bottom-up, finding ways to take into account the populations' needs and experiences and to enhance self-learning dynamics during the policy process. Today, it is particularly necessary to define what 'development' means at country level, according to the aspirations of particular categories of people and meeting operational and local expectations. Secondly, changes in language should be followed by a real change in mindset. Development stakeholders should further adapt their procedures to the reality of complex systems in which development interventions are being dealt with. PMID:22583911

  6. Radiographic Evaluation of Children with Febrile Urinary Tract Infection: Bottom-Up, Top-Down, or None of the Above?

    Directory of Open Access Journals (Sweden)

    Michaella M. Prasad

    2012-01-01

    Full Text Available The proper algorithm for the radiographic evaluation of children with febrile urinary tract infection (FUTI is hotly debated. Three studies are commonly administered: renal-bladder ultrasound (RUS, voiding cystourethrogram (VCUG, and dimercapto-succinic acid (DMSA scan. However, the order in which these tests are obtained depends on the methodology followed: bottom-up or top-down. Each strategy carries advantages and disadvantages, and some groups now advocate even less of a workup (none of the above due to the current controversies about treatment when abnormalities are diagnosed. New technology is available and still under investigation, but it may help to clarify the interplay between vesicoureteral reflux, renal scarring, and dysfunctional elimination in the future.

  7. Bottom-Up Fabrication of Nanopatterned Polymers on DNA Origami by In Situ Atom-Transfer Radical Polymerization.

    Science.gov (United States)

    Tokura, Yu; Jiang, Yanyan; Welle, Alexander; Stenzel, Martina H; Krzemien, Katarzyna M; Michaelis, Jens; Berger, Rüdiger; Barner-Kowollik, Christopher; Wu, Yuzhou; Weil, Tanja

    2016-05-01

    Bottom-up strategies to fabricate patterned polymers at the nanoscale represent an emerging field in the development of advanced nanodevices, such as biosensors, nanofluidics, and nanophotonics. DNA origami techniques provide access to distinct architectures of various sizes and shapes and present manifold opportunities for functionalization at the nanoscale with the highest precision. Herein, we conduct in situ atom-transfer radical polymerization (ATRP) on DNA origami, yielding differently nanopatterned polymers of various heights. After cross-linking, the grafted polymeric nanostructures can even stably exist in solution without the DNA origami template. This straightforward approach allows for the fabrication of patterned polymers with low nanometer resolution, which provides access to unique DNA-based functional hybrid materials. PMID:27058968

  8. Applications of microbial cytochrome P450 enzymes in biotechnology and synthetic biology.

    Science.gov (United States)

    Girvan, Hazel M; Munro, Andrew W

    2016-04-01

    Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenase enzymes with enormous potential for synthetic biology applications. Across Nature, their substrate range is vast and exceeds that of other enzymes. The range of different chemical transformations performed by P450s is also substantial, and continues to expand through interrogation of the properties of novel P450s and by protein engineering studies. The ability of P450s to introduce oxygen atoms at specific positions on complex molecules makes these enzymes particularly valuable for applications in synthetic biology. This review focuses on the enzymatic properties and reaction mechanisms of P450 enzymes, and on recent studies that highlight their broad applications in the production of oxychemicals. For selected soluble bacterial P450s (notably the high-activity P450-cytochrome P450 reductase enzyme P450 BM3), variants with a multitude of diverse substrate selectivities have been generated both rationally and by random mutagenesis/directed evolution approaches. This highlights the robustness and malleability of the P450 fold, and the capacity of these biocatalysts to oxidise a wide range of chemical scaffolds. This article reviews recent research on the application of wild-type and engineered P450s in the production of important chemicals, including pharmaceuticals and drug metabolites, steroids and antibiotics. In addition, the properties of unusual members of the P450 superfamily that do not follow the canonical P450 catalytic pathway are described. PMID:27015292

  9. Easing the global burden of diarrhoeal disease: can synthetic biology help?

    Science.gov (United States)

    Vohra, Prerna; Blakely, Garry W

    2013-09-01

    The Millennium Declaration committed the 193 member states of the United Nations to end poverty by 2015. Despite the efforts of the UN and World Health Organisation, and the G8 commitment to spend a fixed proportion of gross national income on overseas aid, more than 2.6 billion people still lack access to proper sanitation. The absence of effective public health strategies in developing countries results in significant health burdens following gastrointestinal infections. Diarrhoea associated with infections resulting from oral-faecal contamination is the second leading cause of death in children under 5 years of age, primarily in Africa and South Asia. Currently there are no appropriate vaccines that could be easily administered on a global scale to prevent these infections. Synthetic biology has the potential to contribute to development of such vaccines. Our work is directed at developing a range of multivalent oral vaccines against the most common diarrhoea-causing bacteria, e.g., Escherichia coli, Shigella and Salmonella. If synthetic biology is to avoid the suspicion and possible revulsion of the public, scientists need to demonstrate that this new field has something real to offer. PMID:24432144

  10. Reconciling Long-Term Trends in Air Quality with Bottom-up Emission Inventories for Los Angeles

    Science.gov (United States)

    Mcdonald, B. C.; Kim, S. W.; Frost, G. J.; Harley, R.; Trainer, M.

    2014-12-01

    Significant long-term changes in air quality have been observed in the United States over several decades. However, reconciling ambient observations with bottom-up emission inventories has proved challenging. In this study, we perform WRF-Chem modeling in the Los Angeles basin for carbon monoxide (CO), nitrogen oxides (NOx), volatile organic compounds (VOCs), and ozone (O3) over a long time period (1987-2010). To improve reconciliation of emission inventories with atmospheric observations, we incorporate new high-resolution emissions maps of a major to dominant source of urban air pollution, motor vehicles. A fuel-based approach is used to estimate motor vehicle emissions utilizing annual fuel sales reports, traffic count data that capture spatial and temporal patterns of vehicle activity, and pollutant emission factors measured from roadway studies performed over the last twenty years. We also update emissions from stationary sources using Continuous Emissions Monitoring Systems (CEMS) data when available, and use emission inventories developed by the South Coast Air Quality Management District (SCAQMD) and California Air Resources Board (ARB) for other important emission source categories. WRF-Chem modeling is performed in three years where field-intensive measurements were made: 1987 (SCAQS: Southern California Air Quality Study), 2002 (ITCT: Intercontinental Transport and Chemical Transformation Study), and 2010 (CALNEX). We assess the ability of the improved bottom-up emissions inventory to predict long-term changes in ambient levels of CO, NOx, and O3, which are known to have occurred over this time period. We also assess changing spatial and temporal patterns of primary (CO and NOx) and secondary (O3) pollutant concentrations across the Los Angeles basin, which has important implications on human health.

  11. China's energy and emissions outlook to 2050: Perspectives from bottom-up energy end-use model

    International Nuclear Information System (INIS)

    Although China became the world's largest CO2 emitter in 2007, the country has also taken serious actions to reduce its energy and carbon intensity. This study uses the bottom-up LBNL China End-Use Energy Model to assess the role of energy efficiency policies in transitioning China to a lower emission trajectory and meeting its 2020 intensity reduction goals. Two scenarios – Continued Improvement and Accelerated Improvement – were developed to assess the impact of actions already taken by the Chinese government as well as planned and potential actions, and to evaluate the potential for China to reduce energy demand and emissions. This scenario analysis presents an important modeling approach based in the diffusion of end-use technologies and physical drivers of energy demand and thereby help illuminate China's complex and dynamic drivers of energy consumption and implications of energy efficiency policies. The findings suggest that China's CO2 emissions will not likely continue growing throughout this century because of saturation effects in appliances, residential and commercial floor area, roadways, fertilizer use; and population peak around 2030 with slowing urban population growth. The scenarios also underscore the significant role that policy-driven efficiency improvements will play in meeting 2020 carbon mitigation goals along with a decarbonized power supply. - Highlights: ► Bottom-up model of China's energy and CO2 reductions through sectoral policies. ► 2 scenarios evaluate impact of actions already taken/planned and future potential. ► China's CO2 will not likely continue growing through 2050 due to saturation effects. ► Results emphasize both policy-driven efficiency and decarbonized power supply.

  12. A bottom-up analysis of China’s iron and steel industrial energy consumption and CO2 emissions

    International Nuclear Information System (INIS)

    Highlights: • This paper analyses future steel demand and steel scrap consumption through bottom-up analysis. • Steel scrap consumption is analyzed individually by different sources. • Steel consumption and energy consumption will peak at around 2020 and 2015 respectively. • Energy intensity and CO2 intensity of steel production will decrease obviously in the future. • Energy efficiency improvement and structural change will play different roles in near- and long-term CO2 mitigations. - Abstract: China’s steel industry has grown significantly since the mid-1990s, and has been the backbone of Chinese heavy industry. It is also the most energy intensive industrial sector in China, accounting for 16.1% of total energy consumption in 2010. To assess energy consumption and CO2 emissions from China’s steel industry, a system dynamics model and a bottom-up energy system model-TIMES (The Integrated MARKAL-EFOM System) were used to analyze steel demand, energy consumption and CO2 emissions from China’s iron and steel industry from 2010 to 2050. The model results suggest that steel production in China will rise from 627 Mt in 2010, to a peak of 772 Mt in 2020, and then gradually decrease to 527 Mt in 2050. The share of Electric Arc Furnace (EAF) steel production will also increase significantly from 9.8% in 2010, to 45.6% in 2050. With the deployment of energy conservation technologies, such as Coke Dry Quenching, exhaust gas and heat recovery equipment, energy intensity and CO2 intensity of steel production will keep decreasing during the modeling period. In the near future, reductions in energy intensity and CO2 intensity will rely more on energy efficiency improvements; however, from a long-term perspective, structural change-the increasing share of EAF steel production, will be of great significance

  13. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

    DEFF Research Database (Denmark)

    Aziz, Ramy K.; Monk, Jonathan M.; Lewis, R. M.;

    2015-01-01

    % and 43%. The most common failure modes were incorrect computation of single gene essentiality and biological information that was missing from the model. Moreover, we performed virtual and biological screening against several synthetic lethal pairs to explore whether two-compound formulations could be...

  14. The Biological Property of Synthetic Evolved Digital Circuits with ESD Immunity-Redundancy or Degeneracy?

    Institute of Scientific and Technical Information of China (English)

    Menghua Man; Shanghe Liu; Xiaolong Chang; Mai Lu

    2013-01-01

    In the ongoing evolutionary process,biological systems have displayed a fundamental and remarkable property of robustness,i.e.,the property allows the system to maintain its functions despite external and internal perturbations.Redundancy and degeneracy are thought to be the underlying structural mechanisms of biological robustness.Inspired by this,we explored the proximate cause of the immunity of the synthetic evolved digital circuits to ESD interference and discussed the biological characteristics behind the evolutionary circuits.First,we proposed an evolutionary method for intrinsic immune circuit design.The circuits' immunity was evaluated using the functional fault models based on probability distributions.Then,several benchmark circuits,including ADDER,MAJORITY,and C17,were evolved for high intrinsic immunity.Finally,using the quantitative definitions based on information theory,we measured the topological characteristics of redundancy and degeneracy in the evolved circuits and compared their contributions to the immunity.The results show that redundant elements are necessary for the ESD immune circuit design,whereas degeneracy is the key to making use of the redundancy robustly and efficiently.

  15. Terminator Operon Reporter: combining a transcription termination switch with reporter technology for improved gene synthesis and synthetic biology applications.

    Science.gov (United States)

    Zampini, Massimiliano; Mur, Luis A J; Rees Stevens, Pauline; Pachebat, Justin A; Newbold, C James; Hayes, Finbarr; Kingston-Smith, Alison

    2016-01-01

    Synthetic biology is characterized by the development of novel and powerful DNA fabrication methods and by the application of engineering principles to biology. The current study describes Terminator Operon Reporter (TOR), a new gene assembly technology based on the conditional activation of a reporter gene in response to sequence errors occurring at the assembly stage of the synthetic element. These errors are monitored by a transcription terminator that is placed between the synthetic gene and reporter gene. Switching of this terminator between active and inactive states dictates the transcription status of the downstream reporter gene to provide a rapid and facile readout of the accuracy of synthetic assembly. Designed specifically and uniquely for the synthesis of protein coding genes in bacteria, TOR allows the rapid and cost-effective fabrication of synthetic constructs by employing oligonucleotides at the most basic purification level (desalted) and without the need for costly and time-consuming post-synthesis correction methods. Thus, TOR streamlines gene assembly approaches, which are central to the future development of synthetic biology. PMID:27220405

  16. Metabolism and toxicological analysis of synthetic cannabinoids in biological fluids and tissues.

    Science.gov (United States)

    Presley, B C; Gurney, S M R; Scott, K S; Kacinko, S L; Logan, B K

    2016-07-01

    Synthetic cannabinoids, which began proliferating in the United States in 2009, have gone through numerous iterations of modification to their chemical structures. More recent generations of compounds have been associated with significant adverse outcomes following use, including cognitive and psychomotor impairment, seizures, psychosis, tissue injury and death. These effects increase the urgency for forensic and public health laboratories to develop methods for the detection and identification of novel substances, and apply these to the determination of their metabolism and disposition in biological samples. This comprehensive review describes the history of the appearance of the drugs in the United States, discusses the naming conventions emerging to designate new structures, and describes the most prominent new compounds linked to the adverse effects now associated with their use. We review in depth the metabolic pathways that have been elucidated for the major members of each of the prevalent synthetic cannabinoid drug subclasses, the enzyme systems responsible for their metabolism, and the use of in silico approaches to assist in predicting and identifying the metabolites of novel compounds and drug subclasses that will continue to appear. Finally, we review and critique analytical methods applied to the detection of the drugs and their metabolites, including immunoassay screening, and liquid chromatography mass spectrometry confirmatory techniques applied to urine, serum, whole blood, oral fluid, hair, and tissues. PMID:27257717

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

    Science.gov (United States)

    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. PMID:27096615

  18. 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. PMID:27226765

  19. Hybrid bottom-up/top-down energy and economy outlooks: a survey of the IMACLIM-S experiments

    Directory of Open Access Journals (Sweden)

    Frédéric eGhersi

    2015-11-01

    Full Text Available In this paper we survey the research undertaken at the Centre International de Recherche sur l’Environnement et le Développement (CIRED on the combination of the IMACLIM-S macroeconomic model with ‘bottom-up’ energy modeling, with a view to associate the strengths and circumvent the limitations of both approaches to energy-economy-environment (E3 prospective modeling. We start by presenting the two methodological avenues of coupling IMACLIM-S with detailed energy systems models pursued at CIRED since the late 1990s’: (1 the calibration of the behavioral functions of IMACLIM-S that represent the producers’ and consumers’ trade-offs between inputs or consumptions, on a large set of bottom-up modeling results; (2 the coupling of IMACLIM-S to some bottom-up model through the iterative exchange of some of each model’s outputs as the other model’s inputs until convergence of the exchanged data, comprising the main macroeconomic drivers and energy systems variables. In the following section, we turn to numerical application and address the prerequisite of harmonizing national accounts, energy balance and energy price data to produce consistent hybrid input-output matrices as a basis of scenario exploration. We highlight how this data treatment step reveals the discrepancies and biases induced by sticking to the conventional modeling usage of uniform pricing of homogeneous goods. IMACLIM-S rather calibrates agent-specific margins, which we introduce and comment upon. In a further section we sum up the results of 4 IMACLIM-S experiments, insisting upon the value-added of hybrid modeling. These varied experiments regard international climate policy burden sharing; the more general numerical consequences of shifting from a biased standard CGE model perspective to the hybrid IMACLIM approach; the macroeconomic consequences of a strong development of electric mobility in the European Union; and the resilience of public debts to energy shocks

  20. 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. PMID:25796071