WorldWideScience

Sample records for biological part assembly

  1. Asmparts: assembly of biological model parts.

    Science.gov (United States)

    Rodrigo, Guillermo; Carrera, Javier; Jaramillo, Alfonso

    2007-12-01

    We propose a new computational tool to produce models of biological systems by assembling models from biological parts. Our software not only takes advantage of modularity, but it also enforces standardisation in part characterisation by considering a model of each part. We have used model parts in SBML to design transcriptional networks. Our software is open source, it works in linux and windows platforms, and it could be used to automatically produce models in a server. Our tool not only facilitates model design, but it will also help to promote the establishment of a registry of model parts.

  2. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

    Energy Technology Data Exchange (ETDEWEB)

    Torella, JP; Lienert, F; Boehm, CR; Chen, JH; Way, JC; Silver, PA

    2014-08-07

    Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.

  3. Standard biological parts knowledgebase.

    Science.gov (United States)

    Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

    2011-02-24

    We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  4. Standard biological parts knowledgebase.

    Directory of Open Access Journals (Sweden)

    Michal Galdzicki

    Full Text Available We have created the Knowledgebase of Standard Biological Parts (SBPkb as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org. The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org. SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL, a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  5. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  6. Ultrasonic Assembly of Thermoplastic Parts

    Energy Technology Data Exchange (ETDEWEB)

    Schurman, W. R.

    1970-03-31

    Four ultrasonic methods were evaluated for assembly of experimental plastic parts for detonators: (1) welding, (2) crimping and staking, (3) insertion, and (4) reactivation of adhesives. For welding, staking and insertion, plastics with low elastic moduli, such as acrylics and polycarbonate, produced the best results. Thermosetting, hot-melt, and solution adhesives could all be activated ultrasonically to form good bonds on plastics and other materials. This evaluation indicated that thermoplastic detonator parts could be assembled ultrasonically in shorter times than by present production techniques with high bond strengths and high product acceptance rates.

  7. DNA assembly for plant biology: techniques and tools.

    Science.gov (United States)

    Patron, Nicola J

    2014-06-01

    As the speed and accuracy of genome sequencing improves, there are ever-increasing resources available for the design and construction of synthetic DNA parts. These can be used to engineer plant genomes to produce new functions or to elucidate the function of endogenous sequences. Until recently the assembly of amplified or cloned sequences into large and complex designs was a limiting step in plant synthetic biology and biotechnology. A number of new methods for assembling DNA molecules have been developed in the last few years, several of which have been applied to the production of molecules used to modify plant genomes.

  8. Chapter 8: Biological knowledge assembly and interpretation.

    Directory of Open Access Journals (Sweden)

    Ju Han Kim

    Full Text Available Most methods for large-scale gene expression microarray and RNA-Seq data analysis are designed to determine the lists of genes or gene products that show distinct patterns and/or significant differences. The most challenging and rate-liming step, however, is to determine what the resulting lists of genes and/or transcripts biologically mean. Biomedical ontology and pathway-based functional enrichment analysis is widely used to interpret the functional role of tightly correlated or differentially expressed genes. The groups of genes are assigned to the associated biological annotations using Gene Ontology terms or biological pathways and then tested if they are significantly enriched with the corresponding annotations. Unlike previous approaches, Gene Set Enrichment Analysis takes quite the reverse approach by using pre-defined gene sets. Differential co-expression analysis determines the degree of co-expression difference of paired gene sets across different conditions. Outcomes in DNA microarray and RNA-Seq data can be transformed into the graphical structure that represents biological semantics. A number of biomedical annotation and external repositories including clinical resources can be systematically integrated by biological semantics within the framework of concept lattice analysis. This array of methods for biological knowledge assembly and interpretation has been developed during the past decade and clearly improved our biological understanding of large-scale genomic data from the high-throughput technologies.

  9. Supramolecular Assemblies Responsive to Biomolecules toward Biological Applications.

    Science.gov (United States)

    Shigemitsu, Hajime; Hamachi, Itaru

    2015-10-01

    Stimuli-responsive supramolecular assemblies consisting of small molecules are attractive functional materials for biological applications such as drug delivery, medical diagnosis, enzyme immobilization, and tissue engineering. By use of their dynamic and reversible properties, many supramolecular assemblies responsive to a variety of biomolecules have been designed and synthesized. This review focuses on promising strategies for the construction of such dynamic supramolecular assemblies and their functions. While studies of biomolecule-responsive supramolecular assemblies have mainly been performed in vitro, it has recently been demonstrated that some of them can work in live cells. Supramolecular assemblies now open up new avenues in chemical biology and biofunctional materials.

  10. CAD Parts-Based Assembly Modeling by Probabilistic Reasoning

    KAUST Repository

    Zhang, Kai-Ke

    2016-04-11

    Nowadays, increasing amount of parts and sub-assemblies are publicly available, which can be used directly for product development instead of creating from scratch. In this paper, we propose an interactive design framework for efficient and smart assembly modeling, in order to improve the design efficiency. Our approach is based on a probabilistic reasoning. Given a collection of industrial assemblies, we learn a probabilistic graphical model from the relationships between the parts of assemblies. Then in the modeling stage, this probabilistic model is used to suggest the most likely used parts compatible with the current assembly. Finally, the parts are assembled under certain geometric constraints. We demonstrate the effectiveness of our framework through a variety of assembly models produced by our prototype system. © 2015 IEEE.

  11. Self-assembling hybrid diamond-biological quantum devices

    Science.gov (United States)

    Albrecht, A.; Koplovitz, G.; Retzker, A.; Jelezko, F.; Yochelis, S.; Porath, D.; Nevo, Y.; Shoseyov, O.; Paltiel, Y.; Plenio, M. B.

    2014-09-01

    The realization of scalable arrangements of nitrogen vacancy (NV) centers in diamond remains a key challenge on the way towards efficient quantum information processing, quantum simulation and quantum sensing applications. Although technologies based on implanting NV-centers in bulk diamond crystals or hybrid device approaches have been developed, they are limited by the achievable spatial resolution and by the intricate technological complexities involved in achieving scalability. We propose and demonstrate a novel approach for creating an arrangement of NV-centers, based on the self-assembling capabilities of biological systems and their beneficial nanometer spatial resolution. Here, a self-assembled protein structure serves as a structural scaffold for surface functionalized nanodiamonds, in this way allowing for the controlled creation of NV-structures on the nanoscale and providing a new avenue towards bridging the bio-nano interface. One-, two- as well as three-dimensional structures are within the scope of biological structural assembling techniques. We realized experimentally the formation of regular structures by interconnecting nanodiamonds using biological protein scaffolds. Based on the achievable NV-center distances of 11 nm, we evaluate the expected dipolar coupling interaction with neighboring NV-centers as well as the expected decoherence time. Moreover, by exploiting these couplings, we provide a detailed theoretical analysis on the viability of multiqubit quantum operations, suggest the possibility of individual addressing based on the random distribution of the NV intrinsic symmetry axes and address the challenges posed by decoherence and imperfect couplings. We then demonstrate in the last part that our scheme allows for the high-fidelity creation of entanglement, cluster states and quantum simulation applications.

  12. Physical mechanisms and biological significance of supramolecular protein self-assembly.

    Science.gov (United States)

    Kentsis, Alex; Borden, Katherine L B

    2004-04-01

    In living cells, chemical reactions of metabolism, information processing, growth and development are organized in a complex network of interactions. At least in part, the organization of this network is accomplished as a result of physical assembly by supramolecular scaffolds. Indeed, most proteins function in cells within the context of multimeric or supramolecular assemblies. With the increasing availability of atomic structures and molecular thermodynamics, it is possible to recast the problem of non-covalent molecular self-assembly from a unified perspective of structural thermodynamics and kinetics. Here, we present a generalized theory of self-assembly based on Wegner's kinetic model and use it to delineate three physical mechanisms of self-assembly: as limited by association of assembly units (nucleation), by association of monomers (isodesmic), and by conformational reorganization of monomers that is coupled to assembly (conformational). Thus, we discuss actin, tubulin, clathrin, and the capsid of icosahedral cowpea chlorotic mottle virus with respect to assembly of architectural scaffolds that perform largely mechanical functions, and pyruvate dehydrogenase, and RING domain proteins PML, arenaviral Z, and BRCA1:BARD1 with regard to assembly of supramolecular enzymes with metabolic and chemically directive functions. In addition to the biological functions made possible by supramolecular self-assembly, such as mesoscale mechanics of architectural scaffolds and metabolic coupling of supramolecular enzymes, we show that the physical mechanisms of self-assembly and their structural bases are biologically significant as well, having regulatory roles in both formation and function of the assembled structures in health and disease.

  13. PaperClip: rapid multi-part DNA assembly from existing libraries.

    Science.gov (United States)

    Trubitsyna, Maryia; Michlewski, Gracjan; Cai, Yizhi; Elfick, Alistair; French, Christopher E

    2014-11-10

    Assembly of DNA 'parts' to create larger constructs is an essential enabling technique for bioengineering and synthetic biology. Here we describe a simple method, PaperClip, which allows flexible assembly of multiple DNA parts from currently existing libraries cloned in any vector. No restriction enzymes, mutagenesis of internal restriction sites, or reamplification to add end homology are required. Order of assembly is directed by double stranded oligonucleotides-'Clips'. Clips are formed by ligation of pairs of oligonucleotides corresponding to the ends of each part. PaperClip assembly can be performed by polymerase chain reaction or by cell extract-mediated recombination. Once multi-use Clips have been prepared, assembly of at least six DNA parts in any order can be accomplished with high efficiency within several hours.

  14. Automated assembly of micro mechanical parts in a Microfactory setup

    DEFF Research Database (Denmark)

    Eriksson, Torbjörn Gerhard; Hansen, Hans Nørgaard; Gegeckaite, Asta

    2006-01-01

    Many micro products in use today are manufactured using semi-automatic assembly. Handling, assembly and transport of the parts are especially labour intense processes. Automation of these processes holds a large potential, especially if flexible, modular microfactories can be developed. This pape...

  15. Precise Truss Assembly Using Commodity Parts and Low Precision Welding

    Science.gov (United States)

    Komendera, Erik; Reishus, Dustin; Dorsey, John T.; Doggett, W. R.; Correll, Nikolaus

    2014-01-01

    Hardware and software design and system integration for an intelligent precision jigging robot (IPJR), which allows high precision assembly using commodity parts and low-precision bonding, is described. Preliminary 2D experiments that are motivated by the problem of assembling space telescope optical benches and very large manipulators on orbit using inexpensive, stock hardware and low-precision welding are also described. An IPJR is a robot that acts as the precise "jigging", holding parts of a local structure assembly site in place, while an external low precision assembly agent cuts and welds members. The prototype presented in this paper allows an assembly agent (for this prototype, a human using only low precision tools), to assemble a 2D truss made of wooden dowels to a precision on the order of millimeters over a span on the order of meters. The analysis of the assembly error and the results of building a square structure and a ring structure are discussed. Options for future work, to extend the IPJR paradigm to building in 3D structures at micron precision are also summarized.

  16. One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy.

    Science.gov (United States)

    Casini, Arturo; MacDonald, James T; De Jonghe, Joachim; Christodoulou, Georgia; Freemont, Paul S; Baldwin, Geoff S; Ellis, Tom

    2014-01-01

    Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications.

  17. Targeted development of registries of biological parts.

    Directory of Open Access Journals (Sweden)

    Jean Peccoud

    Full Text Available BACKGROUND: The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry is the most advanced implementation of this idea. METHODS/PRINCIPAL FINDINGS: By analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified. CONCLUSIONS/SIGNIFICANCE: Organizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users.

  18. An Easy-to-Assemble Three-Part Galvanic Cell

    Science.gov (United States)

    Eggen, Per-Odd; Skaugrud, Brit

    2015-01-01

    The galvanic cell presented in this article is made of only three parts, is easy to assemble, and can light a red light emitting diode (LED). The three cell components consist of a piece of paper with copper sulfate, a piece of paper with sodium sulfate, and a piece of magnesium ribbon. Within less than 1 h, students have time to discuss the…

  19. Biology and Mechanics of Blood Flows Part I: Biology

    CERN Document Server

    Thiriet, Marc

    2008-01-01

    Biology and Mechanics of Blood Flows presents the basic knowledge and state-of-the-art techniques necessary to carry out investigations of the cardiovascular system using modeling and simulation. Part I of this two-volume sequence, Biology, addresses the nanoscopic and microscopic scales. The nanoscale corresponds to the scale of biochemical reaction cascades involved in cell adaptation to mechanical stresses among other stimuli. The microscale is the scale of stress-induced tissue remodeling associated with acute or chronic loadings. The cardiovascular system, like any physiological system, has a complicated three-dimensional structure and composition. Its time dependent behavior is regulated, and this complex system has many components. In this authoritative work, the author provides a survey of relevant cell components and processes, with detailed coverage of the electrical and mechanical behaviors of vascular cells, tissues, and organs. Because the behaviors of vascular cells and tissues are tightly coupl...

  20. Research on Micromanipulating Robot Based on Micro Parts Assembly

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    At present, micro parts assembly is one of the key problems in the fields of micromachine and microelectro mechanical system (MEMS). Performing microassembly by micromanipulating robots is put forward in this paper. Thus based, the general structure of a micromanipulating robot is analyzed briefly. A micro telemanipulating robot developed by the authors with visual monitoring and bilateral force feedback is introduced. The peg in hole task of 0.2mm has been finished successfully by telemanipulation. The operator has gained durative and stable contacting force perceiving.

  1. Part identification in robotic assembly using vision system

    Science.gov (United States)

    Balabantaray, Bunil Kumar; Biswal, Bibhuti Bhusan

    2013-12-01

    Machine vision system acts an important role in making robotic assembly system autonomous. Identification of the correct part is an important task which needs to be carefully done by a vision system to feed the robot with correct information for further processing. This process consists of many sub-processes wherein, the image capturing, digitizing and enhancing, etc. do account for reconstructive the part for subsequent operations. Interest point detection of the grabbed image, therefore, plays an important role in the entire image processing activity. Thus it needs to choose the correct tool for the process with respect to the given environment. In this paper analysis of three major corner detection algorithms is performed on the basis of their accuracy, speed and robustness to noise. The work is performed on the Matlab R2012a. An attempt has been made to find the best algorithm for the problem.

  2. Prions and Protein Assemblies that Convey Biological Information in Health and Disease.

    Science.gov (United States)

    Sanders, David W; Kaufman, Sarah K; Holmes, Brandon B; Diamond, Marc I

    2016-02-03

    Prions derived from the prion protein (PrP) were first characterized as infectious agents that transmit pathology between individuals. However, the majority of cases of neurodegeneration caused by PrP prions occur sporadically. Proteins that self-assemble as cross-beta sheet amyloids are a defining pathological feature of infectious prion disorders and all major age-associated neurodegenerative diseases. In fact, multiple non-infectious proteins exhibit properties of template-driven self-assembly that are strikingly similar to PrP. Evidence suggests that like PrP, many proteins form aggregates that propagate between cells and convert cognate monomer into ordered assemblies. We now recognize that numerous proteins assemble into macromolecular complexes as part of normal physiology, some of which are self-amplifying. This review highlights similarities among infectious and non-infectious neurodegenerative diseases associated with prions, emphasizing the normal and pathogenic roles of higher-order protein assemblies. We propose that studies of the structural and cellular biology of pathological versus physiological aggregates will be mutually informative.

  3. Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

    Science.gov (United States)

    Patron, Nicola J; Orzaez, Diego; Marillonnet, Sylvestre; Warzecha, Heribert; Matthewman, Colette; Youles, Mark; Raitskin, Oleg; Leveau, Aymeric; Farré, Gemma; Rogers, Christian; Smith, Alison; Hibberd, Julian; Webb, Alex A R; Locke, James; Schornack, Sebastian; Ajioka, Jim; Baulcombe, David C; Zipfel, Cyril; Kamoun, Sophien; Jones, Jonathan D G; Kuhn, Hannah; Robatzek, Silke; Van Esse, H Peter; Sanders, Dale; Oldroyd, Giles; Martin, Cathie; Field, Rob; O'Connor, Sarah; Fox, Samantha; Wulff, Brande; Miller, Ben; Breakspear, Andy; Radhakrishnan, Guru; Delaux, Pierre-Marc; Loqué, Dominique; Granell, Antonio; Tissier, Alain; Shih, Patrick; Brutnell, Thomas P; Quick, W Paul; Rischer, Heiko; Fraser, Paul D; Aharoni, Asaph; Raines, Christine; South, Paul F; Ané, Jean-Michel; Hamberger, Björn R; Langdale, Jane; Stougaard, Jens; Bouwmeester, Harro; Udvardi, Michael; Murray, James A H; Ntoukakis, Vardis; Schäfer, Patrick; Denby, Katherine; Edwards, Keith J; Osbourn, Anne; Haseloff, Jim

    2015-10-01

    Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.

  4. Molecular self-assembly for biological investigations and nanoscale lithography

    Science.gov (United States)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  5. Substrate chemistry influences the morphology and biological function of adsorbed extracellular matrix assemblies.

    Science.gov (United States)

    Sherratt, Michael J; Bax, Daniel V; Chaudhry, Shazia S; Hodson, Nigel; Lu, Jian R; Saravanapavan, Priya; Kielty, Cay M

    2005-12-01

    In addition to mediating cell signalling events, native extracellular matrix (ECM) assemblies interact with other ECM components, act as reservoirs for soluble signalling molecules and perform structural roles. The potential of native ECM assemblies in the manufacture of biomimetic materials has not been fully exploited due, in part, to the effects of substrate interactions on their morphology. We have previously demonstrated that the ECM components, fibrillin and type VI collagen microfibrils, exhibit substrate dependent morphologies on chemically and topographically variable heterogeneous surfaces. Using both cleaning and coating approaches on silicon wafers and glass coverslips we have produced chemically homogeneous, topographically similar substrates which cover a large amphiphilic range. Extremes of substrate amphiphilicity induced morphological changes in periodicity, curvature and lateral spreading which may mask binding sites or disrupt domain structure. Biological functionality, as assayed by the ability to support cell spreading, was significantly reduced for fibrillin microfibrils adsorbed on highly hydrophilic substrates (contact angle 20.7 degrees) compared with less hydrophilic (contact angle 38.3 degrees) and hydrophobic (contact angle 92.8 degrees) substrates. With an appropriate choice of surface chemistry, multifunctional ECM assemblies retain their native morphology and biological functionality.

  6. Critical appraisal: dental amalgam update--part II: biological effects.

    Science.gov (United States)

    Wahl, Michael J; Swift, Edward J

    2013-12-01

    Dental amalgam restorations have been controversial for over 150 years. In Part I of this Critical Appraisal, the clinical efficacy of dental amalgam was updated. Here in Part II, the biological effects of dental amalgam are addressed.

  7. Analysis and optimization of assembly variations for non-rigid parts

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Traditional variation analysis methods are not applicable to non-rigid assemblies due to possible part deformation during the assembly process. This paper presents the use of finite element methods to simulate assembly deformation. The relationship between the parts' variation and the variation of the key points in final assembly for quality control is set up by calculating the spring back deformation after assembly. Moreover, the optimization method for non-rigid assembly variations based on finite element analysis is presented. The optimal objective is to reduce the manufacturing cost. The approach is implemented by using ANSYS and MATLAB. The test example shows that the proposed method is effective and applicable.

  8. Method of Measuring Fixture Automatic Design and Assembly for Auto-Body Part

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A method of 3-D measuring fixture automatic assembly for auto-body part is presented. Locating constraint mapping technique and assembly rule-based reasoning are applied. Calculating algorithm of the position and pose for the part model, fixture configuration and fixture elements in virtual auto-body assembly space are given. Transforming fixture element from itself coordinate system space to assembly space with homogeneous transformation matrix is realized. Based on the second development technique of unigraphics(UG), the automated assembly is implemented with application program interface (API) function. Lastly the automated assembly of measuring fixture for rear longeron as a case is implemented.

  9. High molecular weight DNA assembly in vivo for synthetic biology applications.

    Science.gov (United States)

    Juhas, Mario; Ajioka, James W

    2017-05-01

    DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

  10. Programming biological operating systems: genome design, assembly and activation.

    Science.gov (United States)

    Gibson, Daniel G

    2014-05-01

    The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.

  11. Scar-less multi-part DNA assembly design automation

    Science.gov (United States)

    Hillson, Nathan J.

    2016-06-07

    The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

  12. Interfacial interactions involved in the biological assembly of Chandipura virus nucleocapsid protein.

    Science.gov (United States)

    Sreejith, R; Gulati, Sahil; Gupta, Sanjay

    2013-06-01

    The biological assembly of Chandipura virus nucleocapsid (N) protein has been modeled and the amino acid residues involved in specific intermolecular interactions among N monomers during oligomerisation have been predicted.

  13. Direct Electron Transfer of Enzymes in a Biologically Assembled Conductive Nanomesh Enzyme Platform.

    Science.gov (United States)

    Lee, Seung-Woo; Lee, Ki-Young; Song, Yong-Won; Choi, Won Kook; Chang, Joonyeon; Yi, Hyunjung

    2016-02-24

    Nondestructive assembly of a nanostructured enzyme platform is developed in combination of the specific biomolecular attraction and electrostatic coupling for highly efficient direct electron transfer (DET) of enzymes with unprecedented applicability and versatility. The biologically assembled conductive nanomesh enzyme platform enables DET-based flexible integrated biosensors and DET of eight different enzyme with various catalytic activities.

  14. Simulations of curved assemblies in soft matter and biological systems

    Science.gov (United States)

    Qiao, Cong

    Viruses are small infectious agents that replicate only inside living cells of other organisms. In the viral life cycle, the self-assembly of the outer protein shell (capsid) is an essential step. We study this process in the hope of shedding light on development of antiviral drugs, gene therapy and other virus-related technologies that can benefit the humankind. More fundamentally, learning about the process of viral capsid assembly can elucidate the assembly mechanisms of a wide range of complex structures. In this work, we use molecular dynamics simulations and coarse-grained computational models to study viral capsid assembly in several situations where geometric constraints play a role in dictating assembly outcomes. We first focus on icosahedral viruses with single-stranded RNA genomes, in which case the capsid usually assembles around the genomic RNA. It is consistently observed in experiments that such viral particles are ''overcharged'', meaning the net negative charge on the viral genome is greater than the net positive charge on the viral capsid. We computationally investigate the mechanisms that lead to ``overcharging'', and more broadly, how the encapsidated genome length is influenced by the capsid. We perform both dynamical simulations of the assembly process and equilibrium calculations to determine the optimal genome length (meaning that which maximizes the assembly yield and/or minimizes the free energy of the assembled virus). We find that the optimal genome length is determined by the interplay between capsid size, net capsid charge, distribution of capsid charge and nucleic acid structures. Our simulations demonstrate that overcharging results from a combination of electrostatic screening and the geometric constraints associated with encapsulating a nucleic acid inside of a spherical virus. We then study the assembly of the immature HIV. In contrast to icosahedral viruses, the immature HIV forms an asymmetric particle, consisting of continuous

  15. Interference between Parts of a Mechanical Assembly Contained in a STEP File

    Directory of Open Access Journals (Sweden)

    Edwin Estévez Parra

    2015-01-01

    Full Text Available Obtaining interferences among parts of a product contributes to determine the feasibility of the assembly sequences according to the geometry of the parts involved. However, in assembly may exist partswith freeform surfaces which make difficult to determine the interference relationship between themautomatically. The objective of this research is to present a method for obtaining interference among assembly parts with prismatic, cylindric and form free surfaces. The method is automated with a software developed on PythonOCC open source framework, which is based on OpenCascade. The techniques for extracting assembly geometric information which is contained in a 3D CAD file withSTEP standard format, the detection of collisions between the parts in disassembly directions, and the generation of interference matrices are described. Two examples of mechanical assemblies are analyzed to demonstrate the effectiveness of the method and the interferences matrices corresponding to the six principal axis disassembly directions are obtained as a result.

  16. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools

    OpenAIRE

    Ham, Timothy S.; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna (Kuei-Yen); Nathan J Hillson; Jay D Keasling

    2012-01-01

    The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE install...

  17. Biology coming full circle: joining the whole and the parts.

    Science.gov (United States)

    Wikswo, John P; Porter, Andrew P

    2015-01-01

    The new cover of Experimental Biology and Medicine features the hermeneutic circle of biology, a concept we have adapted from the hermeneutic principle that one understands the whole only in terms of each part and the parts only in terms of the whole. Our hermeneutic circle summarizes the course of experimental biology through 2500 years of the achievements of reductionist research (understanding the parts), which culminates in our ability to rapidly sequence the genome. Rather than returning along the same path in a constructionist approach that simply builds upon this knowledge, but in reverse, an alternative is to close the circle with synthetic constructions that seek to integrate the full complexity of biological and physiological systems (understanding the whole), of which organs-on-chips are one example. This closing of the circle cannot be a comprehensively accurate representation of biology, but it can be a synthetic one that effectively defines particular biological subsystems. The illustration of the hermeneutic circle of biology is also intended to suggest both the multiple cycles that may be required to reach such a synthesis and the expansion of the circle in an outward spiral as knowledge increases. Our commentary explains the symbolism of the new cover in a philosophical and scientific discussion.

  18. Conformational assembly and biological properties of collagen mimetic peptides and their thermally responsive polymer conjugates

    Science.gov (United States)

    Krishna, Ohm Divyam

    2011-12-01

    Collagens are one of the most abundant proteins found in body tissues and organs, endowing structural integrity, mechanical strength, and multiple biological functions. Destabilized collagen inside human body leads to various degenerative diseases (ex. osteoarthritis) and ageing. This has continued to motivate the design of synthetic peptides and bio-synthetic polypeptides to closely mimic the native collagens in terms of triple helix structure and stability, potential for higher order assembly, and biological properties. However, the widespread application of de novo collagens has been limited in part by the need for hydroxylated proline in the formation of stable triple helical structures. To address this continued need, a hydroxyproline-free, thermally stable collagen-mimetic peptide (CLP-Cys) was rationally designed via the incorporation of electrostatically stabilized amino acid triplets. CLP-Cys was synthesized via solid phase peptide synthesis. The formation and stability of the triple helical structure were indicated via circular dichroism (CD) experiments and confirmed via differential scanning calorimetry (DSC) results. CLP-Cys also self-assembled into nano-rods and micro-fibrils, as evidenced via a combination of dynamic light scattering and transmission electron microscopy. Given the high thermal stability and its propensity for higher-order assembly, CLP-Cys was further functionalized at both the ends with a thermally responsive polymer, poly(diethylene glycol methyl ether methacrylate), (PDEGMEMA) to synthesize a biohybrid triblock copolymer. The CD results indicated that the triple helical form is retained, the thermal unfolding is sustained and helix to coil transition is reversible in the triblock hybrid context. The LCST of PDEGMEMA homopolymer (26 °C) is increased (to 35 °C) upon conjugation to the hydrophilic collagen peptide domain. Further, a combination of static light scattering, Cryo-SEM, TEM and confocal microscopy elucidated that the

  19. Prediction of phenotypes of missense mutations in human proteins from biological assemblies.

    Science.gov (United States)

    Wei, Qiong; Xu, Qifang; Dunbrack, Roland L

    2013-02-01

    Single nucleotide polymorphisms (SNPs) are the most frequent variation in the human genome. Nonsynonymous SNPs that lead to missense mutations can be neutral or deleterious, and several computational methods have been presented that predict the phenotype of human missense mutations. These methods use sequence-based and structure-based features in various combinations, relying on different statistical distributions of these features for deleterious and neutral mutations. One structure-based feature that has not been studied significantly is the accessible surface area within biologically relevant oligomeric assemblies. These assemblies are different from the crystallographic asymmetric unit for more than half of X-ray crystal structures. We find that mutations in the core of proteins or in the interfaces in biological assemblies are significantly more likely to be disease-associated than those on the surface of the biological assemblies. For structures with more than one protein in the biological assembly (whether the same sequence or different), we find the accessible surface area from biological assemblies provides a statistically significant improvement in prediction over the accessible surface area of monomers from protein crystal structures (P = 6e-5). When adding this information to sequence-based features such as the difference between wildtype and mutant position-specific profile scores, the improvement from biological assemblies is statistically significant but much smaller (P = 0.018). Combining this information with sequence-based features in a support vector machine leads to 82% accuracy on a balanced dataset of 50% disease-associated mutations from SwissVar and 50% neutral mutations from human/primate sequence differences in orthologous proteins.

  20. Directed self-assembly defectivity assessment. Part II

    Science.gov (United States)

    Bencher, Chris; Yi, He; Zhou, Jessica; Cai, Manping; Smith, Jeffrey; Miao, Liyan; Montal, Ofir; Blitshtein, Shiran; Lavi, Alon; Dotan, Kfir; Dai, Huixiong; Cheng, Joy Y.; Sanders, Daniel P.; Tjio, Melia; Holmes, Steven

    2012-03-01

    The main concern for the commercialization of directed self-assembly (DSA) for semiconductor manufacturing continues to be the uncertainty in capability and control of defect density. Our research investigates the defect densities of various DSA process applications in the context of a 300mm wafer fab cleanroom environment; this paper expands substantially on the previously published DSA defectivity study by reporting a defect density process window relative to chemical epitaxial pre-pattern registration lines; as well as investigated DSA based contact hole shrinking and report critical dimension statistics for the phase separated polymers before and after etch, along with positional accuracy measurements and missing via defect density.

  1. Interest in biology. Part I: A multidimensional construct

    Science.gov (United States)

    Gardner, Paul L.; Tamir, Pinchas

    Interest in a school subject (e.g., biology) is conceptualized in terms of three components: topics, activities, and motives, each of which has several dimensions. In this study, seven instruments were developed and administered to grade-10 biology students in Israel. Factor analysis provided support for the conceptualization which underlies the development of the instruments. Topic dimensions included biochemical processes, nonhuman organisms, human biology, personal hygiene, and practical applications; the activity dimensions were experiential learning, reception learning, writing/summarizing and group discussion; motives included environmental issues, moral issues, examination success, personal independence, problem solving, and four career dimensions (research, high-status professions, lower-status careers, woodsy-birdsy careers). In an analysis described in Part II of this paper, the students were classified into four groups on the basis of their grade-11 subject enrollment intentions: H (high-level biology), L (low-level biology), P (physical science), and N (no science). Zero-order and multiple correlations were found between interest and other variables and membership/nonmembership of the four groups. Students in Group H were characterized by higher achievement in year-10 biology, higher levels of enjoyment of biology, career orientations towards research or high-status biology-based professions, greater interest in various biology topics, especially reproduction/cell division/genetics, and a greater tendency to regard the Bagrut (grade-12) examination as interesting. Students in Group N displayed lower levels of interest in various topics (especially the microscope, plants, and reproduction), were less motivated to solve problems, had poorer grades in biology (and chemistry), were less likely to perceive biology as useful, were less likely to regard the Bagrut examination as fair, and were less likely to be interested in social modes of learning. There

  2. The year's new drugs & biologics 2015: Part I.

    Science.gov (United States)

    Graul, A I; Cruces, E; Stringer, M

    2016-01-01

    Nearly 100 new drugs and biologics, including important new line extensions, were approved or launched for the first time globally in 2015. These products are covered in depth in part I of our annual review of the pharma and biotech industry.

  3. World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia, part 1

    DEFF Research Database (Denmark)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas;

    2012-01-01

    These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry Guidelines for Biological Treatment of Schizophrenia published in 2005. For this 2012 revision, all available publications pertaining to the biological treatment of schizophrenia were...... efficacy and then categorised into six levels of evidence (A-F; Bandelow et al. 2008b, World J Biol Psychiatry 9:242). This first part of the updated guidelines covers the general descriptions of antipsychotics and their side effects, the biological treatment of acute schizophrenia and the management...

  4. World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia, Part 2

    DEFF Research Database (Denmark)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas;

    2013-01-01

    These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in 2006. For this 2012 revision, all available publications pertaining to the biological treatment of schizoph......These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in 2006. For this 2012 revision, all available publications pertaining to the biological treatment...... efficacy and then categorised into six levels of evidence (A-F) and five levels of recommendation (1-5) ( Bandelow et al. 2008a ,b, World J Biol Psychiatry 9:242, see Table 1 ). This second part of the updated guidelines covers long-term treatment as well as the management of relevant side effects...

  5. Solid-phase cloning for high-throughput assembly of single and multiple DNA parts

    DEFF Research Database (Denmark)

    Lundqvist, Magnus; Edfors, Fredrik; Sivertsson, Åsa;

    2015-01-01

    We describe solid-phase cloning (SPC) for high-throughput assembly of expression plasmids. Our method allows PCR products to be put directly into a liquid handler for capture and purification using paramagnetic streptavidin beads and conversion into constructs by subsequent cloning reactions. We...... present a robust automated protocol for restriction enzyme based SPC and its performance for the cloning of >60 000 unique human gene fragments into expression vectors. In addition, we report on SPC-based single-strand assembly for applications where exact control of the sequence between fragments...... is needed or where multiple inserts are to be assembled. In this approach, the solid support allows for head-to-tail assembly of DNA fragments based on hybridization and polymerase fill-in. The usefulness of head-to-tail SPC was demonstrated by assembly of >150 constructs with up to four DNA parts...

  6. YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae.

    Science.gov (United States)

    Guo, Yakun; Dong, Junkai; Zhou, Tong; Auxillos, Jamie; Li, Tianyi; Zhang, Weimin; Wang, Lihui; Shen, Yue; Luo, Yisha; Zheng, Yijing; Lin, Jiwei; Chen, Guo-Qiang; Wu, Qingyu; Cai, Yizhi; Dai, Junbiao

    2015-07-27

    It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts.

  7. Lineage-specific biology revealed by a finished genome assembly of the mouse.

    Directory of Open Access Journals (Sweden)

    Deanna M Church

    2009-05-01

    Full Text Available The mouse (Mus musculus is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes. In addition, we identified 439 long, non-protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.

  8. The year's new drugs & biologics 2014 - Part II: trends & challenges.

    Science.gov (United States)

    Graul, A I; Serebrov, M; Cruces, E; Tracy, M; Dulsat, C

    2015-02-01

    2014 was a year of continued high activity in the pharma and biotech industry, as evidenced in part I of this annual two-part review article published last month in this journal (1). As of December 23, 2014, a total of 55 new chemical and biological entities had reached their first markets worldwide, together with another 29 important new line extensions. Another 19 products were approved for the first time during the year but not yet launched by December 23. Furthermore, during the now-traditional year-end sprint, several regulatory agencies issued last-minute approvals for other compounds that missed the deadline for inclusion in that article, bringing the total of new approvals for the year to a somewhat higher number. In addition to the successful development, registration and launch of new drugs and biologics, there are various other trends and tendencies that serve as indicators of the overall health and status of the industry. These include the pursuit of novel programs designed by regulators to stimulate the development of drugs for diseases that are currently under-treated; the regular and pragmatic culling by companies of their R&D pipelines; and the decision to unify pipelines, portfolios and sales forces through mergers and acquisitions.

  9. Self-Assembling Biological Springs Force Transducers on the Micron Nanoscale

    Energy Technology Data Exchange (ETDEWEB)

    Benedek, George [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Casparay, Alfred H. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2016-08-19

    In this project, we are developing a new system for measuring forces within and between nanoscale biological molecules based on mesoscopic springs made of cholesterol helical ribbons. These ribbons self-assemble in a wide variety of complex fluids containing sterol, a mixture of surfactants and water [1] and have spring constants in the range from 0.5 to 500 pN/nm [2-4]. By the end of this project, we have demonstrated that the cholesterol helical ribbons can be used for measuring forces between biological objects and for mapping the strain fields in hydrogels.

  10. Biologically templated assembly of hybrid semiconducting nanomesh for high performance field effect transistors and sensors

    Science.gov (United States)

    Byeon, Hye-Hyeon; Lee, Seung-Woo; Lee, Eun-Hee; Kim, Woong; Yi, Hyunjung

    2016-10-01

    Delicately assembled composites of semiconducting nanomaterials and biological materials provide an attractive interface for emerging applications, such as chemical/biological sensors, wearable health monitoring devices, and therapeutic agent releasing devices. The nanostructure of composites as a channel and a sensing material plays a critical role in the performance of field effect transistors (FETs). Therefore, it is highly desirable to prepare elaborate composite that can allow the fabrication of high performance FETs and also provide high sensitivity and selectivity in detecting specific chemical/biological targets. In this work, we demonstrate that high performance FETs can be fabricated with a hydrodynamically assembled composite, a semiconducting nanomesh, of semiconducting single-walled carbon nanotubes (S-SWNTs) and a genetically engineered M13 phage to show strong binding affinity toward SWNTs. The semiconducting nanomesh enables a high on/off ratio (~104) of FETs. We also show that the threshold voltage and the channel current of the nanomesh FETs are sensitive to the change of the M13 phage surface charge. This biological gate effect of the phage enables the detection of biologically important molecules such as dopamine and bisphenol A using nanomesh-based FETs. Our results provide a new insight for the preparation of composite material platform for highly controllable bio/electronics interfaces.

  11. Biologically templated assembly of hybrid semiconducting nanomesh for high performance field effect transistors and sensors

    Science.gov (United States)

    Byeon, Hye-Hyeon; Lee, Seung-Woo; Lee, Eun-Hee; Kim, Woong; Yi, Hyunjung

    2016-01-01

    Delicately assembled composites of semiconducting nanomaterials and biological materials provide an attractive interface for emerging applications, such as chemical/biological sensors, wearable health monitoring devices, and therapeutic agent releasing devices. The nanostructure of composites as a channel and a sensing material plays a critical role in the performance of field effect transistors (FETs). Therefore, it is highly desirable to prepare elaborate composite that can allow the fabrication of high performance FETs and also provide high sensitivity and selectivity in detecting specific chemical/biological targets. In this work, we demonstrate that high performance FETs can be fabricated with a hydrodynamically assembled composite, a semiconducting nanomesh, of semiconducting single-walled carbon nanotubes (S-SWNTs) and a genetically engineered M13 phage to show strong binding affinity toward SWNTs. The semiconducting nanomesh enables a high on/off ratio (~104) of FETs. We also show that the threshold voltage and the channel current of the nanomesh FETs are sensitive to the change of the M13 phage surface charge. This biological gate effect of the phage enables the detection of biologically important molecules such as dopamine and bisphenol A using nanomesh-based FETs. Our results provide a new insight for the preparation of composite material platform for highly controllable bio/electronics interfaces. PMID:27762315

  12. Understanding recognition and self-assembly in biology using the chemist's toolbox. Insight into medicinal chemistry.

    Science.gov (United States)

    Quirolo, Z B; Benedini, L A; Sequeira, M A; Herrera, M G; Veuthey, T V; Dodero, V I

    2014-01-01

    Medicinal chemistry is intimately connected with basic science such as organic synthesis, chemical biology and biophysical chemistry among other disciplines. The reason of such connections is due to the power of organic synthesis to provide designed molecules; chemical biology to give tools to discover biological and/or pathological pathways and biophysical chemistry which provides the techniques to characterize and the theoretical background to understand molecular behaviour. The present review provides some selective examples of these research areas. Initially, template dsDNA organic synthesis and the spatio-temporal control of transcription are presenting following by the supramolecular entities used in drug delivery, such as liposomes and liquid crystal among others. Finally, peptides and protein self-assembly is connected with biomaterials and as an important event in the balance between health and disease. The final aim of the present review is to show the power of chemical tools not only for the synthesis of new molecules but also to improve our understanding of recognition and self-assembly in the biological context.

  13. Self-Assembly of Microscale Parts through Magnetic and Capillary Interactions

    Directory of Open Access Journals (Sweden)

    Madan Dubey

    2011-03-01

    Full Text Available Self-assembly is a promising technique to overcome fundamental limitations with integrating, packaging, and general handling of individual electronic-related components with characteristic lengths significantly smaller than 1 mm. Here we describe the use of magnetic and capillary forces to self-assemble 280 µm sized silicon building blocks into interconnected structures which approach a three-dimensional crystalline configuration. Integrated permanent magnet microstructures provided magnetic forces, while a low-melting-point solder alloy provided capillary forces. A finite element model of forces between the magnetic features demonstrated the utility of magnetic forces at this size scale. Despite a slight departure from designed dimensions in the actual fabricated parts, the combination of magnetic and capillary forces improved the assembly yield to 8%, over approximately 0.1% achieved previously with capillary forces alone.

  14. Solid-phase cloning for high-throughput assembly of single and multiple DNA parts.

    Science.gov (United States)

    Lundqvist, Magnus; Edfors, Fredrik; Sivertsson, Åsa; Hallström, Björn M; Hudson, Elton P; Tegel, Hanna; Holmberg, Anders; Uhlén, Mathias; Rockberg, Johan

    2015-04-20

    We describe solid-phase cloning (SPC) for high-throughput assembly of expression plasmids. Our method allows PCR products to be put directly into a liquid handler for capture and purification using paramagnetic streptavidin beads and conversion into constructs by subsequent cloning reactions. We present a robust automated protocol for restriction enzyme based SPC and its performance for the cloning of >60 000 unique human gene fragments into expression vectors. In addition, we report on SPC-based single-strand assembly for applications where exact control of the sequence between fragments is needed or where multiple inserts are to be assembled. In this approach, the solid support allows for head-to-tail assembly of DNA fragments based on hybridization and polymerase fill-in. The usefulness of head-to-tail SPC was demonstrated by assembly of >150 constructs with up to four DNA parts at an average success rate above 80%. We report on several applications for SPC and we suggest it to be particularly suitable for high-throughput efforts using laboratory workstations.

  15. Frameworks for programming biological function through RNA parts and devices.

    Science.gov (United States)

    Win, Maung Nyan; Liang, Joe C; Smolke, Christina D

    2009-03-27

    One of the long-term goals of synthetic biology is to reliably engineer biological systems that perform human-defined functions. Currently, researchers face several scientific and technical challenges in designing and building biological systems, one of which is associated with our limited ability to access, transmit, and control molecular information through the design of functional biomolecules exhibiting novel properties. The fields of RNA biology and nucleic acid engineering, along with the tremendous interdisciplinary growth of synthetic biology, are fueling advances in the emerging field of RNA programming in living systems. Researchers are designing functional RNA molecules that exhibit increasingly complex functions and integrating these molecules into cellular circuits to program higher-level biological functions. The continued integration and growth of RNA design and synthetic biology presents exciting potential to transform how we interact with and program biology.

  16. Effects of demographic stochasticity on biological community assembly on evolutionary time scales

    KAUST Repository

    Murase, Yohsuke

    2010-04-13

    We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the noise consist of species strongly coupled with each other and have stronger linear stability around the fixed-point populations than the corresponding noiseless model. The dynamics on evolutionary time scales for the predator-prey model are also altered by the noise. Approximate 1/f fluctuations are observed with noise, while 1/ f2 fluctuations are found for the model without demographic noise. © 2010 The American Physical Society.

  17. DNA assembler: a synthetic biology tool for characterizing and engineering natural product gene clusters.

    Science.gov (United States)

    Shao, Zengyi; Zhao, Huimin

    2012-01-01

    The majority of existing antibacterial and anticancer drugs are natural products or their derivatives. However, the characterization and engineering of these compounds are often hampered by limited ability to manipulate the corresponding biosynthetic pathways. Recently, we developed a genomics-driven, synthetic biology-based method, DNA assembler, for discovery, characterization, and engineering of natural product biosynthetic pathways (Shao, Luo, & Zhao, 2011). By taking advantage of the highly efficient yeast in vivo homologous recombination mechanism, this method synthesizes the entire expression vector containing the target biosynthetic pathway and the genetic elements needed for DNA maintenance and replication in individual hosts in a single-step manner. In this chapter, we describe the general guidelines for construct design. By using two distinct biosynthetic pathways, we demonstrate that DNA assembler can perform multiple tasks, including heterologous expression, introduction of single or multiple point mutations, scar-less gene deletion, generation of product derivatives, and creation of artificial gene clusters. As such, this method offers unprecedented flexibility and versatility in pathway manipulations.

  18. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

    Science.gov (United States)

    Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

    2012-10-01

    The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

  19. 78 FR 23940 - Use of International Standard ISO-10993, “Biological Evaluation of Medical Devices Part 1...

    Science.gov (United States)

    2013-04-23

    ... HUMAN SERVICES Food and Drug Administration Use of International Standard ISO-10993, ``Biological... International Standard ISO-10993, `Biological Evaluation of Medical Devices Part 1: Evaluation and Testing... entitled ``Use of International Standard ISO-10993, `Biological Evaluation of Medical Devices Part...

  20. The year's new drugs & biologics, 2014: Part I.

    Science.gov (United States)

    Graul, A I; Cruces, E; Stringer, M

    2015-01-01

    A year-end wrap-up of new drug approvals and launches reveals that activity in the pharmaceutical industry continues at a high level, with 55 new drugs and biologics introduced on their first markets in 2014 (as of December 23, 2014). Additionally, 29 important new line extensions (new formulations, new combinations or new indications for previously marketed products) also reached their first markets during the year. The most active therapeutic group in terms of new launches was anti-infective therapies, with 11 new drugs and biologics launched, most for the treatment of multidrug-resistant bacterial infections or hepatitis C. The most active market for new launches was again the U.S., site of more than half of all new launches in 2014. However new launch activity increased considerably last year in Japan, which actually pulled ahead of the E.U. for the first time in many years. In another important new development, 15 of the new drugs and biologics launched last year had orphan drug status, 5 had breakthrough therapy designation and 3 had Qualified Infectious Disease Product (QIDP) status. Another 19 products were approved for the first time during the year but not yet launched by close of this article; most are slated for launch in the first months of the new year.

  1. Probing self assembly in biological mixed colloids by SANS, deuteration and molecular manipulation

    Energy Technology Data Exchange (ETDEWEB)

    Hjelm, R.P. [Los Alamos National Laboratory, NM (United States); Thiyagarajan, P. [Argonne National Laboratory, IL (United States); Hoffman, A. [Univ. of California, San Diego, CA (United States); Alkan-Onyuksel, H. [Univ. of Illinois, Chicago, IL (United States)

    1994-12-31

    Small-angle neutron scattering was used to obtain information on the form and molecular arrangement of particles in mixed colloids of bile salts with phosphatidylcholine, and bile salts with monoolein. Both types of systems showed the same general characteristics. The particle form was highly dependent on total lipid concentration. At the highest concentrations the particles were globular mixed micelles with an overall size of 50{Angstrom}. As the concentration was reduced the mixed micelles elongated, becoming rodlike with diameter about 50{Angstrom}. The rods had a radial core-shell structure in which the phosphatidylcholine or monoolein fatty tails were arranged radially to form the core with the headgroups pointing outward to form the shell. The bile salts were at the interface between the shell and core with the hydrophilic parts facing outward as part of the shell. The lengths of the rods increased and became more polydispersed with dilution. At sufficiently low concentrations the mixed micelles transformed into single bilayer vesicles. These results give insight on the physiological function of bile and on the rules governing the self assembly of bile particles in the hepatic duct and the small intestine.

  2. Characterization of Delayed-Particle Emission Signatures for Pyroprocessing. Part 1: ABTR Fuel Assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Durkee, Jr., Joe W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-06-19

    A three-part study is conducted using the MCNP6 Monte Carlo radiation-transport code to calculate delayed-neutron (DN) and delayed-gamma (DG) emission signatures for nondestructive assay (NDA) metal-fuel pyroprocessing. In Part 1, MCNP6 is used to produce irradiation-induced used nuclear fuel (UNF) isotopic inventories for an Argonne National Laboratory (ANL) Advanced Burner Test Reactor (ABTR) preconceptual design fuel assembly (FA) model. The initial fuel inventory consists of uranium mixed with light-water-reactor transuranic (TRU) waste and 10 wt% zirconium (U-LWR-SFTRU-10%Zr). To facilitate understanding, parametric evaluation is done using models for 3% and 5% initial 235U a% enrichments, burnups of 5, 10, 15, 20, 30, …, 120 GWd/MTIHM, and 3-, 5-, 10-, 20-, and 30- year cooling times. Detailed delayed-particle radioisotope source terms for the irradiate FA are created using BAMF-DRT and SOURCES3A. Using simulation tallies, DG activity ratios (DGARs) are developed for 134Cs/137Cs 134Cs/154Eu, and 154Eu/137Cs markers as a function of (1) burnup and (2) actinide mass, including elemental uranium, neptunium, plutonium, americium, and curium. Spectral-integrated DN emission is also tallied. The study reveals a rich assortment of DGAR behavior as a function of DGAR type, enrichment, burnup, and cooling time. Similarly, DN emission plots show variation as a function of burnup and of actinide mass. Sensitivity of DGAR and DN signatures to initial 235U enrichment, burnup, and cooling time is evident. Comparisons of the ABTR radiation signatures and radiation signatures previously reported for a generic Westinghouse oxide-fuel assembly indicate that there are pronounced differences in the ABTR and Westinghouse oxide-fuel DN and DG signatures. These differences are largely attributable to the initial TRU inventory in the ABTR fuel. The actinide and nonactinide inventories for the

  3. 1994 Baseline biological studies for the Device Assembly Facility at the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Townsend, Y.E. [ed.; Woodward, B.D.; Hunter, R.B.; Greger, P.D.; Saethre, M.B.

    1995-02-01

    This report describes environmental work performed at the Device Assembly Facility (DAF) in 1994 by the Basic Environmental Monitoring and Compliance Program (BECAMP). The DAF is located near the Mojave-Great Basin desert transition zone 27 km north of Mercury. The area immediately around the DAF building complex is a gentle slope cut by 1 to 3 m deep arroyos, and occupied by transitional vegetation. In 1994, construction activities were largely limited to work inside the perimeter fence. The DAF was still in a preoperational mode in 1994, and no nuclear materials were present. The DAF facilities were being occupied so there was water in the sewage settling pond, and the roads and lights were in use. Sampling activities in 1994 represent the first year in the proposed monitoring scheme. The proposed biological monitoring plan gives detailed experimental protocols. Plant, lizard, tortoise, small mammal, and bird surveys were performed in 1994. The authors briefly outline procedures employed in 1994. Studies performed on each taxon are reviewed separately then summarized in a concluding section.

  4. Exploring the elastic features of spherically shaped biological assemblies and soft matter systems

    Energy Technology Data Exchange (ETDEWEB)

    Asfaw, Mesfin, E-mail: mesfin.taye@csun.edu [Department of Physics and Astronomy, California State University, Northridge, CA (United States)

    2011-03-16

    Using a numerical simulation, we study the elastic features of biological assemblies (e.g. viruses and bacteria) and soft matter systems (e.g. colloidosomes and nanoparticle covered droplets) that possess a spherical shape in which the proteins (particles) on the colloidosomes or virus shells are mechanically linked to form a stress-bearing spherical structure that may dramatically enhance the surface rigidity. The dependence of the rigidity enhancement upon the density of the cross-linked proteins situated on the surface of the virus is explored. We determine the percolation threshold P{sub ce} by considering bond percolation on the spherical elastic networks involving nearest neighbor forces. The percolation threshold of such networks is very different from that of a two-dimensional triangular lattice due to the topological effect. We find that the threshold probability for the spherical elastic network is considerably smaller than for an unwrapped network, which reveals that the spherical topology induces more rigidity to the network.

  5. 15 CFR Supplement No. 1 to Part 742 - Nonproliferation of Chemical and Biological Weapons

    Science.gov (United States)

    2010-01-01

    ... Biological Weapons No. Supplement No. 1 to Part 742 Commerce and Foreign Trade Regulations Relating to...—Nonproliferation of Chemical and Biological Weapons Note: Exports and reexports of items in performance of...: (i) Equipment (for producing chemical weapon precursors and chemical warfare agents) described...

  6. MISSA 2.0: an updated synthetic biology toolbox for assembly of orthogonal CRISPR/Cas systems

    Science.gov (United States)

    Zhang, Hai-Yan; Wang, Xing-Hui; Dong, Li; Wang, Zhi-Ping; Liu, Bing; Lv, Jie; Xing, Hui-Li; Han, Chun-Yan; Wang, Xue-Chen; Chen, Qi-Jun

    2017-01-01

    Efficient generation of plants carrying mutations in multiple genes remains a challenge. Using two or more orthogonal CRISPR/Cas systems can generate plants with multi-gene mutations, but assembly of these systems requires a robust, high-capacity toolkit. Here, we describe MISSA 2.0 (multiple-round in vivo site-specific assembly 2.0), an extensively updated toolkit for assembly of two or more CRISPR/Cas systems. We developed a novel suicide donor vector system based on plasmid RK2, which has much higher cloning capacity than the original, plasmid R6K-based system. We validated the utility of MISSA 2.0 by assembling multiple DNA fragments into the E. coli chromosome, and by creating transgenic Arabidopsis thaliana that constitutively or inducibly overexpress multiple genes. We then demonstrated that the higher cloning capacity of the RK2-derived MISSA 2.0 donor vectors facilitated the assembly of two orthogonal CRISPR/Cas systems including SpCas9 and SaCas9, and thus facilitated the creation of transgenic lines harboring these systems. We anticipate that MISSA 2.0 will enable substantial advancements in multiplex genome editing based on two or more orthogonal CRISPR/Cas9 systems, as well as in plant synthetic biology. PMID:28155921

  7. Monte Carlo modeling and analyses of YALINA booster subcritical assembly, Part III : low enriched uranium conversion analyses.

    Energy Technology Data Exchange (ETDEWEB)

    Talamo, A.; Gohar, Y. (Nuclear Engineering Division)

    2011-05-12

    This study investigates the performance of the YALINA Booster subcritical assembly, located in Belarus, during operation with high (90%), medium (36%), and low (21%) enriched uranium fuels in the assembly's fast zone. The YALINA Booster is a zero-power, subcritical assembly driven by a conventional neutron generator. It was constructed for the purpose of investigating the static and dynamic neutronics properties of accelerator driven subcritical systems, and to serve as a fast neutron source for investigating the properties of nuclear reactions, in particular transmutation reactions involving minor-actinides. The first part of this study analyzes the assembly's performance with several fuel types. The MCNPX and MONK Monte Carlo codes were used to determine effective and source neutron multiplication factors, effective delayed neutron fraction, prompt neutron lifetime, neutron flux profiles and spectra, and neutron reaction rates produced from the use of three neutron sources: californium, deuterium-deuterium, and deuterium-tritium. In the latter two cases, the external neutron source operates in pulsed mode. The results discussed in the first part of this report show that the use of low enriched fuel in the fast zone of the assembly diminishes neutron multiplication. Therefore, the discussion in the second part of the report focuses on finding alternative fuel loading configurations that enhance neutron multiplication while using low enriched uranium fuel. It was found that arranging the interface absorber between the fast and the thermal zones in a circular rather than a square array is an effective method of operating the YALINA Booster subcritical assembly without downgrading neutron multiplication relative to the original value obtained with the use of the high enriched uranium fuels in the fast zone.

  8. CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Jakociunas, Tadas; Rajkumar, Arun Stephen; Zhang, Jie

    2015-01-01

    , we present a method for marker-free multiloci integration of in vivo assembled DNA parts. By the use of CRISPR/Cas9-mediated one-step double-strand breaks at single, double and triple integration sites we report the successful in vivo assembly and chromosomal integration of DNA parts. We call our...

  9. Biological designer self-assembling peptide nanofiber scaffolds significantly enhance osteoblast proliferation, differentiation and 3-D migration.

    Directory of Open Access Journals (Sweden)

    Akihiro Horii

    Full Text Available A class of self-assembling peptide nanofiber scaffolds has been shown to be an excellent biological material for 3-dimension cell culture and stimulating cell migration into the scaffold, as well as for repairing tissue defects in animals. We report here the development of several peptide nanofiber scaffolds designed specifically for osteoblasts. We designed one of the pure self-assembling peptide scaffolds RADA16-I through direct coupling to short biologically active motifs. The motifs included osteogenic growth peptide ALK (ALKRQGRTLYGF bone-cell secreted-signal peptide, osteopontin cell adhesion motif DGR (DGRGDSVAYG and 2-unit RGD binding sequence PGR (PRGDSGYRGDS. We made the new peptide scaffolds by mixing the pure RAD16 and designer-peptide solutions, and we examined the molecular integration of the mixed nanofiber scaffolds using AFM. Compared to pure RAD16 scaffold, we found that these designer peptide scaffolds significantly promoted mouse pre-osteoblast MC3T3-E1 cell proliferation. Moreover, alkaline phosphatase (ALP activity and osteocalcin secretion, which are early and late markers for osteoblastic differentiation, were also significantly increased. We demonstrated that the designer, self-assembling peptide scaffolds promoted the proliferation and osteogenic differentiation of MC3T3-E1. Under the identical culture medium condition, confocal images unequivocally demonstrated that the designer PRG peptide scaffold stimulated cell migration into the 3-D scaffold. Our results suggest that these designer peptide scaffolds may be very useful for promoting bone tissue regeneration.

  10. World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia. Part 3

    DEFF Research Database (Denmark)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas

    2015-01-01

    treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations which are clinically and scientifically relevant. They are intended to be used by all physicians diagnosing and treating patients with schizophrenia....... Based on the first version of these guidelines a systematic review, as well as a data extraction from national guidelines have been performed for this update. The identified literature was evaluated with respect to the strength of evidence for its efficacy and subsequently categorised into six levels...... of evidence (A-F) and five levels of recommendation (1-5). This third part of the updated guidelines covers the management of the following specific treatment circumstances: comorbid depression, suicidality, various comorbid substance use disorders (legal and illegal drugs), and pregnancy and lactation...

  11. Biological materials: (Part A): Temperature-responsive polymers and drug delivery, and, (Part B): Polymer modification of fish scale and their nano-mechanical properties

    Science.gov (United States)

    Xiang, Xu

    This research has three parts. Two parts deal with novel nanoparticle assemblies for drug delivery, and are described in Part A, while the third part looks at properties of fish scales, an abundant and little-used waste resource, that can be modified to have value in medical and other areas. Part A describes fundamental research into the affects of block sequence of amphiphilic block copolymers prepared from on a new and versatile class of monomers, oligo(ethylene glycol) methyl ether acrylate (OEGA) and the more hydrophobic di(ethylene glycol) methyl ether methacrylate (DEGMA). Polymers from these monomers are biologically safe and give polymers with thermoresponsive properties that can be manipulated over a broader temperature range than the more researched N-isopropylacrylamide polymers. Using RAFT polymerization and different Chain Transfer Agents (CTAs) amphiphilic block copolymers were prepared to study the effect of block sequence (hydrophilic OEGA and more hydrophobic DEGMA) on their thermo-responsive properties. Pairing hydrophilic chain ends to a hydrophobic DEGMA block and hydrophobic chain ends to hydrophilic blocks ("mis-matched polarity") significantly affected thermoresponsive properties for linear and star diblock copolymers, but little affected symmetric triblock copolymers. Specifically matching polarity in diblock copolymers yielded nanoparticles with higher cloud points (CP), narrow temperature ranges for coil collapse above CP, and smaller hydrodynamic diameter than mis-matched polarity. Using this knowledge two linear OEGA/DEGMA diblock copolymers were prepared with thiol end groups and assembled into hybrid nanoparticles with a gold nanoparticle core (GNP-polymer hybrids). This design was made using the hypothesis that a hybrid polymer drug carrier with a high CP (50-60 °C) and a diblock structure could be designed with low levels of drug release below 37 °C (body temperature) allowing the drug carrier to reach a target (tumor) site with

  12. A Digital Interface for the Part Designers and the Fixture Designers for a Reconfigurable Assembly System

    Directory of Open Access Journals (Sweden)

    Vishwa V. Kumar

    2013-01-01

    Full Text Available This paper presents a web-based framework for interfacing product designers and fixture designers to fetch the benefits of early supplier involvement (ESI to a reconfigurable assembly system (RAS. The interfacing of the two members requires four steps, namely, collaboration chain, fixture supplier selection, knowledge share, and accommodation of service facilities so as to produce multiple products on a single assembly line. The interfacing not only provokes concurrency in the activities of product and fixture designer but also enables the assembly systems to tackle the spatial and generational variety. Among the four stages of interfacing, two steps are characterized by optimization issues, one from the product customer side and the other from the fixture designer side. To impart promptness in the optimization and hence the interaction, computationally economic tools are also presented in the paper for both of the supplier selection and fixture design optimization.

  13. Molecular Self-Assembly of Short Aromatic Peptides: From Biology to Nanotechnology and Material Science

    Science.gov (United States)

    Gazit, Ehud

    2013-03-01

    The formation of ordered amyloid fibrils is the hallmark of several diseases of unrelated origin. In spite of grave clinical consequence, the mechanism of amyloid formation is not fully understood. We have suggested, based on experimental and bioinformatic analysis, that aromatic interactions may provide energetic contribution as well as order and directionality in the molecular-recognition and self-association processes that lead to the formation of these assemblies. This is in line with the well-known central role of aromatic-stacking interactions in self-assembly processes. Our works on the mechanism of aromatic peptide self-assembly, lead to the discovery that the diphenylalanine recognition motif self-assembles into peptide nanotubes with a remarkable persistence length. Other aromatic homodipeptides could self-assemble in nano-spheres, nano-plates, nano-fibrils and hydrogels with nano-scale order. We demonstrated that the peptide nanostructures have unique chemical, physical and mechanical properties including ultra-rigidity as aramides, semi-conductive, piezoelectric and non-linear optic properties. We also demonstrated the ability to use these peptide nanostructures as casting mold for the fabrication of metallic nano-wires and coaxial nano-cables. The application of the nanostructures was demonstrated in various fields including electrochemical biosensors, tissue engineering, and molecular imaging. Finally, we had developed ways for depositing of the peptide nanostructures and their organization. We had use inkjet technology as well as vapour deposition methods to coat surface and from the peptide ``nano-forests''. We recently demonstrated that even a single phenylalanine amino-acid can form well-ordered fibrilar assemblies.

  14. Assembly, start and operation of an activated sludge reactor for the industrial effluents treatment: physico chemical and biological parameters

    Directory of Open Access Journals (Sweden)

    Márcia Regina Assalin

    2008-05-01

    Full Text Available Although of the immense available bibliography regarding the activated sludge process, little it is found in relation to the basic procedure to be adopted to implant, to activate and to monitor a reactor of activated sludge in laboratory scales. This article describes the assembly, departure and operation of an activated sludge system, operating in continuous process, at a laboratory scale, to study effluents treatments, using as example, Kraft E1 pulp mill effluent. Factors as biodegradability of the effluent to be treated, stationary state of the reactor, conventional operation parameters as physical chemistry and biological parameters are presented.

  15. Using Synthetic Biological Parts and Microbioreactors to Explore the Protein Expression Characteristics of Escherichia coli

    NARCIS (Netherlands)

    Gorochowski, Thomas E.; van den Berg, Eric; Kerkman, Richard; Roubos, Johannes A.; Bovenberg, Roel A. L.

    2014-01-01

    Synthetic biology has developed numerous parts for the precise control of protein expression. However, relatively little is known about the burden these place on a host, or their reliability under varying environmental conditions. To address this, we made use of synthetic transcriptional and transla

  16. Physical Activity: A Tool for Improving Health (Part 1--Biological Health Benefits)

    Science.gov (United States)

    Gallaway, Patrick J.; Hongu, Nobuko

    2015-01-01

    Extension educators have been promoting and incorporating physical activities into their community-based programs and improving the health of individuals, particularly those with limited resources. This article is the first of a three-part series describing the benefits of physical activity for human health: 1) biological health benefits of…

  17. Information theory in systems biology. Part II: protein-protein interaction and signaling networks.

    Science.gov (United States)

    Mousavian, Zaynab; Díaz, José; Masoudi-Nejad, Ali

    2016-03-01

    By the development of information theory in 1948 by Claude Shannon to address the problems in the field of data storage and data communication over (noisy) communication channel, it has been successfully applied in many other research areas such as bioinformatics and systems biology. In this manuscript, we attempt to review some of the existing literatures in systems biology, which are using the information theory measures in their calculations. As we have reviewed most of the existing information-theoretic methods in gene regulatory and metabolic networks in the first part of the review, so in the second part of our study, the application of information theory in other types of biological networks including protein-protein interaction and signaling networks will be surveyed.

  18. Atomic structure and handedness of the building block of a biological assembly.

    Science.gov (United States)

    Loquet, Antoine; Habenstein, Birgit; Chevelkov, Veniamin; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Lange, Adam

    2013-12-26

    Noncovalent supramolecular assemblies possess in general several unique subunit-subunit interfaces.The basic building block of such an assembly consists of several subunits and contains all unique interfaces. Atomic-resolution structures of monomeric subunits are typically accessed by crystallography or solution NMR and fitted into electron microscopy density maps. However, the structure of the intact building block in the assembled state remains unknown with this hybrid approach. Here, we present the solid-state NMR atomic structure of the building block of the type III secretion system needle. The building block structure consists of a homotetrameric subunit complex with three unique supramolecular interfaces. Side-chain positions at the interfaces were solved at atomic detail. The high-resolution structure reveals unambiguously the helical handedness of the assembly, determined to be right-handed for the type III secretion system needle.Additionally, the axial rise per subunit could be extracted from the tetramer structure and independently validated by mass-per-length measurements.

  19. In vitro production and characterization of partly assembled human CD3 complexes

    DEFF Research Database (Denmark)

    Kastrup, J; Pedersen, L Ø; Dietrich, J

    2002-01-01

    in Golgi apparatus before the fully assembled T-cell receptor is transported to the cell surface. To study the structural properties of the human CD3 chains, we have developed new methods to produce and fold the extracellular domains of CD3 gamma, CD3 delta and CD3 epsilon. Proteins were expressed...

  20. Information theory in systems biology. Part I: Gene regulatory and metabolic networks.

    Science.gov (United States)

    Mousavian, Zaynab; Kavousi, Kaveh; Masoudi-Nejad, Ali

    2016-03-01

    "A Mathematical Theory of Communication", was published in 1948 by Claude Shannon to establish a framework that is now known as information theory. In recent decades, information theory has gained much attention in the area of systems biology. The aim of this paper is to provide a systematic review of those contributions that have applied information theory in inferring or understanding of biological systems. Based on the type of system components and the interactions between them, we classify the biological systems into 4 main classes: gene regulatory, metabolic, protein-protein interaction and signaling networks. In the first part of this review, we attempt to introduce most of the existing studies on two types of biological networks, including gene regulatory and metabolic networks, which are founded on the concepts of information theory.

  1. Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.

    Science.gov (United States)

    Levy, Roie; Borenstein, Elhanan

    2014-01-01

    The human microbiome is a key contributor to health and development. Yet little is known about the ecological forces that are at play in defining the composition of such host-associated communities. Metagenomics-based studies have uncovered clear patterns of community structure but are often incapable of distinguishing alternative structuring paradigms. In a recent study, we integrated metagenomic analysis with a systems biology approach, using a reverse ecology framework to model numerous human microbiota species and to infer metabolic interactions between species. Comparing predicted interactions with species composition data revealed that the assembly of the human microbiome is dominated at the community level by habitat filtering. Furthermore, we demonstrated that this habitat filtering cannot be accounted for by known host phenotypes or by the metabolic versatility of the various species. Here we provide a summary of our findings and offer a brief perspective on related studies and on future approaches utilizing this metagenomic systems biology framework.

  2. Biological Activation of Inert Ceramics: Recent Advances Using Tailored Self-Assembled Monolayers on Implant Ceramic Surfaces

    Directory of Open Access Journals (Sweden)

    Frederik Böke

    2014-06-01

    Full Text Available High-strength ceramics as materials for medical implants have a long, research-intensive history. Yet, especially on applications where the ceramic components are in direct contact with the surrounding tissue, an unresolved issue is its inherent property of biological inertness. To combat this, several strategies have been investigated over the last couple of years. One promising approach investigates the technique of Self-Assembled Monolayers (SAM and subsequent chemical functionalization to create a biologically active tissue-facing surface layer. Implementation of this would have a beneficial impact on several fields in modern implant medicine such as hip and knee arthroplasty, dental applications and related fields. This review aims to give a summarizing overview of the latest advances in this recently emerging field, along with thorough introductions of the underlying mechanism of SAMs and surface cell attachment mechanics on the cell side.

  3. Assembly of Designed Oligonucleotides: a useful tool in synthetic biology for creating high-quality combinatorial DNA libraries.

    Science.gov (United States)

    Acevedo-Rocha, Carlos G; Reetz, Manfred T

    2014-01-01

    The method dubbed Assembly of Designed Oligonucleotides (ADO) is a powerful tool in synthetic biology to create combinatorial DNA libraries for gene, protein, metabolic, and genome engineering. In directed evolution of proteins, ADO benefits from using reduced amino acid alphabets for saturation mutagenesis and/or DNA shuffling, but all 20 canonical amino acids can be also used as building blocks. ADO is performed in a two-step reaction. The first involves a primer-free, polymerase cycling assembly or overlap extension PCR step using carefully designed overlapping oligonucleotides. The second step is a PCR amplification using the outer primers, resulting in a high-quality and bias-free double-stranded DNA library that can be assembled with other gene fragments and/or cloned into a suitable plasmid subsequently. The protocol can be performed in a few hours. In theory, neither the length of the DNA library nor the number of DNA changes has any limits. Furthermore, with the costs of synthetic DNA dropping every year, after an initial investment is made in the oligonucleotides, these can be exchanged for alternative ones with different sequences at any point in the process, fully exploiting the potential of creating highly diverse combinatorial libraries. In the example chosen here, we show the construction of a high-quality combinatorial ADO library targeting sixteen different codons simultaneously with nonredundant degenerate codons encoding various reduced alphabets of four amino acids along the heme region of the monooxygenase P450-BM3.

  4. The 1993 baseline biological studies and proposed monitoring plan for the Device Assembly Facility at the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, B.D.; Hunter, R.B.; Greger, P.D.; Saethre, M.B.

    1995-02-01

    This report contains baseline data and recommendations for future monitoring of plants and animals near the new Device Assembly Facility (DAF) on the Nevada Test Site (NTS). The facility is a large structure designed for safely assembling nuclear weapons. Baseline data was collected in 1993, prior to the scheduled beginning of DAF operations in early 1995. Studies were not performed prior to construction and part of the task of monitoring operational effects will be to distinguish those effects from the extensive disturbance effects resulting from construction. Baseline information on species abundances and distributions was collected on ephemeral and perennial plants, mammals, reptiles, and birds in the desert ecosystems within three kilometers (km) of the DAF. Particular attention was paid to effects of selected disturbances, such as the paved road, sewage pond, and the flood-control dike, associated with the facility. Radiological monitoring of areas surrounding the DAF is not included in this report.

  5. Application of real-time holographic interferometry in the nondestructive inspection of electronic parts and assemblies

    Science.gov (United States)

    Wood, Craig P.; Trolinger, James D.

    1991-01-01

    Nondestructive inspection by holographic interferometry (HI) is quickly gaining acceptance in the electronics industry as a sensitive and accurate method of locating manufacturing and assembly flaws in a wide range of electronics, from individual components to assembled modules. This paper describes the specific application of real-time HI in the nondestructive analysis of circuit board heat exchangers and multiple-layer printed wiring boards to locate areas of debonding and delamination. In the application of HI, the choice of a stressing method is often as important as the choice of a specific HI technique. Methods for component stressing include thermal, vibrational, and pressure-induced stressing methods, and these are described in detail. In addition, two techniques for sensitivity enhancement, phase shift interferometry and beam tilt correction, are discussed in detail.

  6. Engineering BioBrick vectors from BioBrick parts

    OpenAIRE

    Knight Thomas F; Endy Drew; Shetty Reshma P

    2008-01-01

    Abstract Background The underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts. The technical standard that has gained the most traction in the synthetic biology community is the BioBrick standard for physical composition of genetic parts. Parts that conform to the BioBrick assembly standard are BioBrick standard biological parts. To date, over 2,000 BioBrick parts have ...

  7. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  8. Monte Carlo modeling and analyses of YALINA- booster subcritical assembly Part II : pulsed neutron source.

    Energy Technology Data Exchange (ETDEWEB)

    Talamo, A.; Gohar, M. Y. A.; Rabiti, C.; Nuclear Engineering Division

    2008-10-22

    One of the most reliable experimental methods for measuring the kinetic parameters of a subcritical assembly is the Sjoestrand method applied to the reaction rate generated from a pulsed neutron source. This study developed a new analytical methodology for characterizing the kinetic parameters of a subcritical assembly using the Sjoestrand method, which allows comparing the analytical and experimental time dependent reaction rates and the reactivity measurements. In this methodology, the reaction rate, detector response, is calculated due to a single neutron pulse using MCNP/MCNPX computer code or any other neutron transport code that explicitly simulates the fission delayed neutrons. The calculation simulates a single neutron pulse over a long time period until the delayed neutron contribution to the reaction is vanished. The obtained reaction rate is superimposed to itself, with respect to the time, to simulate the repeated pulse operation until the asymptotic level of the reaction rate, set by the delayed neutrons, is achieved. The superimposition of the pulse to itself was calculated by a simple C computer program. A parallel version of the C program is used due to the large amount of data being processed, e.g. by the Message Passing Interface (MPI). The new calculation methodology has shown an excellent agreement with the experimental results available from the YALINA-Booster facility of Belarus. The facility has been driven by a Deuterium-Deuterium or Deuterium-Tritium pulsed neutron source and the (n,p) reaction rate has been experimentally measured by a {sup 3}He detector. The MCNP calculation has utilized the weight window and delayed neutron biasing variance reduction techniques since the detector volume is small compared to the assembly volume. Finally, this methodology was used to calculate the IAEA benchmark of the YALINA-Booster experiment.

  9. Design of casting blanks in CAPP system for parts of piston-cylinder assembly of internal combustion engines

    Directory of Open Access Journals (Sweden)

    V. Todić

    2012-01-01

    Full Text Available Development of information technology industry provided great possibilities in the area of integration of diff erent CAx systems, such as CAD, CAM, CAE and others. In order to successfully link systems of automated-design (or Computer Aided Design - CAD with automated manufacturing systems (or Computer Aided Manufacturing – CAM, automation of manufacturing process planning is needed, i.e. CAPP (Computer-Aided Process Planning systems can bridge a gap between design and manufacturing. In this paper is shown design of casting blanks in CAPP system for parts of piston-cylinder assembly of internal combustion engines in a manufacturing system.

  10. Invasive Species Biology, Control, and Research. Part 2. Multiflora Rose (Rosa multiflora)

    Science.gov (United States)

    2008-11-01

    this agent should be considered in concert with other biological control methods. The dying canes are incapable of asexual reproduction via layering...two, Multiflora Rose seedlings grow inconspicuously, but quickly become well anchored. Multiflora Rose reproduces asexually by suckering and...mowing the remaining topgrowth eliminates any remaining live plant parts that could asexually reproduce. ERDC TR-08-11 8 Table 1. Herbicides that

  11. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Science.gov (United States)

    2010-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time of... to be not adulterated. (b) When a lot of poultry suspected of containing biological residues...

  12. Self Assembly of Biogenic Surfactants at Mineral Surfaces and Their Effect on Biological Iron Acquisition

    Science.gov (United States)

    Kraemer, S. M.

    2005-12-01

    Microorganisms exude biogenic surfactants to modify the physical and chemical properties of mineral-water interfaces. Surfactants with negatively charged hydrophilic head groups interact strongly with oppositely charged mineral surfaces such as iron or aluminum oxides. Surfactant self assembly at mineral surfaces can result in the formation of admicelles that have a significant effect on the surface charge and hydrophobicity. These effects are exploited by microorganisms to facilitate attachment to mineral surfaces. Similarly, plants exude surfactants into the rhizosphere and change the surface tension and flow of soil water. Other surface active compounds that are typically found in soils and surface waters are humic substances and fatty acids that are produced by degradation of biomass. In general, surface active compounds are ubiquitous in natural systems. In this study we investigated how surfactants influence bio-mineral interactions using the example of siderophore promoted iron acquisition. Siderophore promoted iron acquisition involves the adsorption of a biogenic iron specific ligand (i.e. the siderophore) to iron oxides and the subsequent siderophore promoted iron oxide dissolution. The hypothesis of this project is that the modification of the iron oxide surface charge and hydrophobicity by adsorbed surfactants will have an important effect on siderophore adsorption and dissolution kinetics. We approached this subject by investigating the adsorption of a natural surfactant (rhamnolipids: RhL) and the synthetic surfactant (sodium dodecyl sulfate: SDS) on goethite (α-FeOOH, a common pedogenic iron oxide) and observing the effect of surfactant self assembly on the properties of the mineral water interface. We observed fast adsorption kinetics at pH 3 and slow adsorption at pH 6. The adsorbed surfactants reversed the surface potential of goethite (as evidenced by electrophoretic mobility measurements) at soluble surfactant concentrations below 10 μM (SDS

  13. Binary self-assembled monolayers modified Au nanoparticles as carriers in biological applications.

    Science.gov (United States)

    Chang, Hsun-Yun; You, Yun-Wen; Liao, Hua-Yang; Shyue, Jing-Jong

    2014-12-01

    Gold nanoparticles (AuNPs) are good nonviral carriers because of their ease of synthesis and conjugation in biochemistry, and self-assembled monolayers (SAMs) provide a tunable system to change their interfacial properties. Using homogeneously mixed carboxylic acid and amine functional groups, a series of surface potentials and isoelectric points (IEPs) could be obtained and allow systematic study of the effect of surface potential. In this work, the result of the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay revealed that binary-SAM modified AuNPs have high biocompatibility with HEK293T cells. The amount of AuNPs ingested by the cells was found to increase with increasing surface potential and the difference was also confirmed with a scanning transmission electron microscope. The ability of binary-SAM modified AuNPs as carriers was examined, and the plasmid deoxyribose nucleic acid (DNA)-containing eGFP reporter gene was used as the model cargo. Fluorescence imaging revealed that the transfection efficiency generally increased with increasing surface potential. More importantly, when the IEP of the AuNPs was higher than that of the environment of the endosome but lower than that of the cytoplasm, the plasmid DNA can be protected better and released more easily during the endocytosis process hence higher efficiency is obtained with 60% NH2 and 40% COOH in the binary-SAM.

  14. Biological activities and phytochemical profiles of extracts from different parts of bamboo (Phyllostachys pubescens).

    Science.gov (United States)

    Tanaka, Akinobu; Zhu, Qinchang; Tan, Hui; Horiba, Hiroki; Ohnuki, Koichiro; Mori, Yasuhiro; Yamauchi, Ryoko; Ishikawa, Hiroya; Iwamoto, Akira; Kawahara, Hiroharu; Shimizu, Kuniyoshi

    2014-06-18

    Besides being a useful building material, bamboo also is a potential source of bioactive substances. Although some studies have been performed to examine its use in terms of the biological activity, only certain parts of bamboo, especially the leaves or shoots, have been studied. Comprehensive and comparative studies among different parts of bamboo would contribute to a better understanding and application of this knowledge. In this study, the biological activities of ethanol and water extracts from the leaves, branches, outer culm, inner culm, knots, rhizomes and roots of Phyllostachys pubescens, the major species of bamboo in Japan, were comparatively evaluated. The phytochemical profiles of these extracts were tentatively determined by liquid chromatography-mass spectrometry (LC-MS) analysis. The results showed that extracts from different parts of bamboo had different chemical compositions and different antioxidative, antibacterial and antiallergic activities, as well as on on melanin biosynthesis. Outer culm and inner culm were found to be the most important sources of active compounds. 8-C-Glucosylapigenin, luteolin derivatives and chlorogenic acid were the most probable compounds responsible for the anti-allergy activity of these bamboo extracts. Our study suggests the potential use of bamboo as a functional ingredient in cosmetics or other health-related products.

  15. Biological Activities and Phytochemical Profiles of Extracts from Different Parts of Bamboo (Phyllostachys pubescens

    Directory of Open Access Journals (Sweden)

    Akinobu Tanaka

    2014-06-01

    Full Text Available Besides being a useful building material, bamboo also is a potential source of bioactive substances. Although some studies have been performed to examine its use in terms of the biological activity, only certain parts of bamboo, especially the leaves or shoots, have been studied. Comprehensive and comparative studies among different parts of bamboo would contribute to a better understanding and application of this knowledge. In this study, the biological activities of ethanol and water extracts from the leaves, branches, outer culm, inner culm, knots, rhizomes and roots of Phyllostachys pubescens, the major species of bamboo in Japan, were comparatively evaluated. The phytochemical profiles of these extracts were tentatively determined by liquid chromatography-mass spectrometry (LC-MS analysis. The results showed that extracts from different parts of bamboo had different chemical compositions and different antioxidative, antibacterial and antiallergic activities, as well as on on melanin biosynthesis. Outer culm and inner culm were found to be the most important sources of active compounds. 8-C-Glucosylapigenin, luteolin derivatives and chlorogenic acid were the most probable compounds responsible for the anti-allergy activity of these bamboo extracts. Our study suggests the potential use of bamboo as a functional ingredient in cosmetics or other health-related products.

  16. Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios.

    Science.gov (United States)

    Núñez, Andrés; Amo de Paz, Guillermo; Rastrojo, Alberto; García, Ana M; Alcamí, Antonio; Gutiérrez-Bustillo, A Montserrat; Moreno, Diego A

    2016-03-01

    The first part of this review ("Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios") describes the current knowledge on the major biological particles present in the air regarding their global distribution, concentrations, ratios and influence of meteorological factors in an attempt to provide a framework for monitoring their biodiversity and variability in such a singular environment as the atmosphere. Viruses, bacteria, fungi, pollen and fragments thereof are the most abundant microscopic biological particles in the air outdoors. Some of them can cause allergy and severe diseases in humans, other animals and plants, with the subsequent economic impact. Despite the harsh conditions, they can be found from land and sea surfaces to beyond the troposphere and have been proposed to play a role also in weather conditions and climate change by acting as nucleation particles and inducing water vapour condensation. In regards to their global distribution, marine environments act mostly as a source for bacteria while continents additionally provide fungal and pollen elements. Within terrestrial environments, their abundances and diversity seem to be influenced by the land-use type (rural, urban, coastal) and their particularities. Temporal variability has been observed for all these organisms, mostly triggered by global changes in temperature, relative humidity, et cetera. Local fluctuations in meteorological factors may also result in pronounced changes in the airbiota. Although biological particles can be transported several hundreds of meters from the original source, and even intercontinentally, the time and final distance travelled are strongly influenced by factors such as wind speed and direction. [Int Microbiol 2016; 19(1):1-1 3].

  17. Cytosol-dependent membrane fusion in ER, nuclear envelope and nuclear pore assembly: biological implications.

    Science.gov (United States)

    Rafikova, Elvira R; Melikov, Kamran; Chernomordik, Leonid V

    2010-01-01

    Endoplasmic reticulum and nuclear envelope rearrangements after mitosis are often studied in the reconstitution system based on Xenopus egg extract. In our recent work we partially replaced the membrane vesicles in the reconstitution mix with protein-free liposomes to explore the relative contributions of cytosolic and transmembrane proteins. Here we discuss our finding that cytosolic proteins mediate fusion between membranes lacking functional transmembrane proteins and the role of membrane fusion in endoplasmic reticulum and nuclear envelope reorganization. Cytosol-dependent liposome fusion has allowed us to restore, without adding transmembrane nucleoporins, functionality of nuclear pores, their spatial distribution and chromatin decondensation in nuclei formed at insufficient amounts of membrane material and characterized by only partial decondensation of chromatin and lack of nuclear transport. Both the mechanisms and the biological implications of the discovered coupling between spatial distribution of nuclear pores, chromatin decondensation and nuclear transport are discussed.

  18. Biology and Mechanics of Blood Flows Part II: Mechanics and Medical Aspects

    CERN Document Server

    Thiriet, Marc

    2008-01-01

    Biology and Mechanics of Blood Flows presents the basic knowledge and state-of-the-art techniques necessary to carry out investigations of the cardiovascular system using modeling and simulation. Part II of this two-volume sequence, Mechanics and Medical Aspects, refers to the extraction of input data at the macroscopic scale for modeling the cardiovascular system, and complements Part I, which focuses on nanoscopic and microscopic components and processes. This volume contains chapters on anatomy, physiology, continuum mechanics, as well as pathological changes in the vasculature walls including the heart and their treatments. Methods of numerical simulations are given and illustrated in particular by application to wall diseases. This authoritative book will appeal to any biologist, chemist, physicist, or applied mathematician interested in the functioning of the cardiovascular system.

  19. Evolution of the cephalopod head complex by assembly of multiple molluscan body parts: Evidence from Nautilus embryonic development.

    Science.gov (United States)

    Shigeno, Shuichi; Sasaki, Takenori; Moritaki, Takeya; Kasugai, Takashi; Vecchione, Michael; Agata, Kiyokazu

    2008-01-01

    Cephalopod head parts are among the most complex occurring in all invertebrates. Hypotheses for the evolutionary process require a drastic body-plan transition in relation to the life-style changes from benthos to active nekton. Determining these transitions, however, has been elusive because of scarcity of fossil records of soft tissues and lack of some of the early developmental stages of the basal species. Here we report the first embryological evidence in the nautiloid cephalopod Nautilus pompilius for the morphological development of the head complex by a unique assembly of multiple archetypical molluscan body parts. Using a specialized aquarium system, we successfully obtained a series of developmental stages that enabled us to test previous controversial scenarios. Our results demonstrate that the embryonic organs exhibit body plans that are primarily bilateral and antero-posteriorly elongated at stereotyped positions. The distinct cephalic compartment, foot, brain cords, mantle, and shell resemble the body plans of monoplacophorans and basal gastropods. The numerous digital tentacles of Nautilus develop from simple serial and spatially-patterned bud-like anlagen along the anterior-posterior axis, indicating that origins of digital tentacles or arms of all other cephalopods develop not from the head but from the foot. In middle and late embryos, the primary body plans largely change to those of juveniles or adults, and finally form a "head" complex assembled by anlagen of the foot, cephalic hood, collar, hyponome (funnel), and the foot-derived epidermal covers. We suggest that extensions of the collar-funnel compartment and free epidermal folds derived from multiple topological foot regions may play an important role in forming the head complex, which is thought to be an important feature during the body plan transition.

  20. Monte Carlo modeling and analyses of YALINA-booster subcritical assembly part 1: analytical models and main neutronics parameters.

    Energy Technology Data Exchange (ETDEWEB)

    Talamo, A.; Gohar, M. Y. A.; Nuclear Engineering Division

    2008-09-11

    This study was carried out to model and analyze the YALINA-Booster facility, of the Joint Institute for Power and Nuclear Research of Belarus, with the long term objective of advancing the utilization of accelerator driven systems for the incineration of nuclear waste. The YALINA-Booster facility is a subcritical assembly, driven by an external neutron source, which has been constructed to study the neutron physics and to develop and refine methodologies to control the operation of accelerator driven systems. The external neutron source consists of Californium-252 spontaneous fission neutrons, 2.45 MeV neutrons from Deuterium-Deuterium reactions, or 14.1 MeV neutrons from Deuterium-Tritium reactions. In the latter two cases a deuteron beam is used to generate the neutrons. This study is a part of the collaborative activity between Argonne National Laboratory (ANL) of USA and the Joint Institute for Power and Nuclear Research of Belarus. In addition, the International Atomic Energy Agency (IAEA) has a coordinated research project benchmarking and comparing the results of different numerical codes with the experimental data available from the YALINA-Booster facility and ANL has a leading role coordinating the IAEA activity. The YALINA-Booster facility has been modeled according to the benchmark specifications defined for the IAEA activity without any geometrical homogenization using the Monte Carlo codes MONK and MCNP/MCNPX/MCB. The MONK model perfectly matches the MCNP one. The computational analyses have been extended through the MCB code, which is an extension of the MCNP code with burnup capability because of its additional feature for analyzing source driven multiplying assemblies. The main neutronics parameters of the YALINA-Booster facility were calculated using these computer codes with different nuclear data libraries based on ENDF/B-VI-0, -6, JEF-2.2, and JEF-3.1.

  1. 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

  2. A Class of Methods for the Analysis of Blade Tip Timing Data from Bladed Assemblies Undergoing Simultaneous Resonances—Part II: Experimental Validation

    Directory of Open Access Journals (Sweden)

    J. Gallego-Garrido

    2007-01-01

    Full Text Available Blade tip timing is a technique for the measurement of vibrations in rotating bladed assemblies. In Part I of this work a class of methods for the analysis of blade tip timing data from bladed assemblies undergoing two simultaneous synchronous resonances was developed. The approaches were demonstrated using data from a mathematical simulation of tip timing data. In Part II the methods are validated on an experimental test rig. First, the construction and characteristics of the rig will be discussed. Then, the performance of the analysis techniques when applied to data from the rig will be compared and analysed. It is shown that accurate frequency estimates are obtained by all the methods for both single and double resonances. Furthermore, the recovered frequencies are used to calculate the amplitudes of the blade tip responses. The presence of mistuning in the bladed assembly does not affect the performance of the new techniques.

  3. BioBrick assembly standards and techniques and associated software tools.

    Science.gov (United States)

    Røkke, Gunvor; Korvald, Eirin; Pahr, Jarle; Oyås, Ove; Lale, Rahmi

    2014-01-01

    The BioBrick idea was developed to introduce the engineering principles of abstraction and standardization into synthetic biology. BioBricks are DNA sequences that serve a defined biological function and can be readily assembled with any other BioBrick parts to create new BioBricks with novel properties. In order to achieve this, several assembly standards can be used. Which assembly standards a BioBrick is compatible with, depends on the prefix and suffix sequences surrounding the part. In this chapter, five of the most common assembly standards will be described, as well as some of the most used assembly techniques, cloning procedures, and a presentation of the available software tools that can be used for deciding on the best method for assembling of different BioBricks, and searching for BioBrick parts in the Registry of Standard Biological Parts database.

  4. Tratamento sistêmico da psoríase - Parte II: Imunomoduladores biológicos Systemic treatment of psoriasis - Part II: Biologic immunomodulator agents

    Directory of Open Access Journals (Sweden)

    Lúcia Arruda

    2004-08-01

    Full Text Available Em continuidade ao capítulo da edição anterior dos Anais Brasileiros de Dermatologia, nesta segunda parte da EMC-D serão discutidas as novas drogas, os imunomoduladores biológicos, que agem em determinadas fases da imunopatogênese da doença, modificando fenotipicamente sua evolução. Também serão discutidos alguns aspectos imunológicos que, atualmente, são responsáveis pelo desencadeamento da doençaAs part of its continued studies of psoriasis, this second part of the Continuing Medical Education in Dermatology segment of the Anais Brasileiros de Dermatologia introduces biological immunomodulators. Also known as "biologics", these drugs act on the immunopathogenetic steps of psoriasis by changing its features and progression. This paper also reviews some of the immunologic aspects of psoriasis.

  5. Elastic-Plastic Nonlinear Response of a Space Shuttle External Tank Stringer. Part 1; Stringer-Feet Imperfections and Assembly

    Science.gov (United States)

    Knight, Norman F., Jr.; Song, Kyongchan; Elliott, Kenny B.; Raju, Ivatury S.; Warren, Jerry E.

    2012-01-01

    Elastic-plastic, large-deflection nonlinear stress analyses are performed for the external hat-shaped stringers (or stiffeners) on the intertank portion of the Space Shuttle s external tank. These stringers are subjected to assembly strains when the stringers are initially installed on an intertank panel. Four different stringer-feet configurations including the baseline flat-feet, the heels-up, the diving-board, and the toes-up configurations are considered. The assembly procedure is analytically simulated for each of these stringer configurations. The location, size, and amplitude of the strain field associated with the stringer assembly are sensitive to the assumed geometry and assembly procedure. The von Mises stress distributions from these simulations indicate that localized plasticity will develop around the first eight fasteners for each stringer-feet configuration examined. However, only the toes-up configuration resulted in high assembly hoop strains.

  6. Independent in vitro assembly of all three major morphological parts of the 30S ribosomal subunit of Thermus thermophilus.

    Science.gov (United States)

    Agalarov, S C; Selivanova, O M; Zheleznyakova, E N; Zheleznaya, L A; Matvienko, N I; Spirin, A S

    1999-12-01

    Fragments of the 16S rRNA of Thermus thermophilus representing the 3' domain (nucleotides 890-1515) and the 5' domain (nucleotides 1-539) have been prepared by transcription in vitro. Incubation of these fragments with total 30S ribosomal proteins of T. thermophilus resulted in formation of specific RNPs. The particle assembled on the 3' RNA domain contained seven proteins corresponding to Escherichia coli ribosomal proteins S3, S7, S9, S10, S13, S14, and S19. All of them have previously been shown to interact with the 3' domain of the 16S RNA and to be localized in the head of the 30S ribosomal subunit. The particle formed on the 5' RNA domain contained five ribosomal proteins corresponding to E. coli proteins S4, S12, S17, S16, and S20. These proteins are known to be localized in the main part of the body of the 30S subunit. Both types of particle were compact and had sedimentation coefficients of 15.5 S and 13 S, respectively. Together with our recent demonstration of the reconstitution of the RNA particle representing the platform of the T. thermophilus 30S ribosomal subunit [Agalarov, S.C., Zheleznyakova, E.N., Selivanova, O.M., Zheleznaya, L.A., Matvienko, N.I., Vasiliev, V.D. & Spirin, A.S. (1998) Proc. Natl Acad. Sci. USA 95, 999-1003], these experiments establish that all three main structural lobes of the small ribosomal subunit can be reconstituted independently of each other and prepared in the individual state.

  7. CFD ANALYSIS OF THE SPACER GRIDS AND MIXING VANES EFFECT ON THE FLOW IN THE CHOSEN PART OF THE TVSA-T FUEL ASSEMBLY

    Directory of Open Access Journals (Sweden)

    Jakub Juklíček

    2015-10-01

    Full Text Available CFD is a promising and widely spread tool for a flow simulation in nuclear reactor fuel assemblies. One of the limiting factors is the complicated geometry of a spacer grid. It leads to the computational mesh with high number of cells and with possibility of decreasing quality. Therefore an approach to simulate the flow as precisely as possible and simultaneously in a reasonable computational expense has to be chosen. The goal of the following CFD analysis is to obtain the detailed velocity field in a precise geometry of a chosen part of the TVSA-T fuel assembly. This kind of simulation provides data for comparison that can be applied in many situations, for instance, for comparison with simulations when a porous media boundary condition is applied as a replacement of the spacer grid.TVSA-T fuel assembly is equipped with combined spacer grids. Combined spacer grid has two functions - support of the fuel pins as a part of assembly skeleton and mixing vanes which ensures coolant mixing. The support part is geometrically very complicated and it is impossible to prepare a good quality computational mesh there. It is also difficult to create a mesh in the support part and the mixing part joint area because of inaccurate connection between these two parts.A representative part of the TVSA-T fuel assembly with a combined spacer grid segment was chosen to perform the CFD simulation. Some inevitable geometry simplifications of the spacer grid geometry were performed. These simplifications were as insignificant as possible to preserve the flow character and to make it possible to prepare a quality mesh at the same time.Steady state CFD simulation was performed with k-ε realizable turbulence model. Heat transfer was not simulated and only velocity field was investigated. Detailed flow characterization which was obtained from this calculation shown, that mixing vanes already affect the flow in the support part of the grid thanks to suction effect. Vortex

  8. In vitro drug release and biological evaluation of biomimetic polymeric micelles self-assembled from amphiphilic deoxycholic acid–phosphorylcholine–chitosan conjugate

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Minming; Guo, Kai; Dong, Hongwei; Zeng, Rong, E-mail: tzengronga@jnu.edu.cn; Tu, Mei; Zhao, Jianhao

    2014-12-01

    Novel biomimetic amphiphilic chitosan derivative, deoxycholic acid–phosphorylcholine–chitosan conjugate (DCA–PCCs) was synthesized based on the combination of Atherton–Todd reaction for coupling phosphorylcholine (PC) and carbodiimide coupling reaction for linking deoxycholic acid (DCA) to chitosan. The chemical structure of DCA–PCCs was characterized by {sup 1}H and {sup 31}P nuclear magnetic resonance (NMR). The self-assembly of DCA–PCCs in water was analyzed by fluorescence measurements, dynamic laser light-scattering (DLS), zeta potential and transmission electron microscopy (TEM) technologies. The results confirmed that the amphiphilic DCA–PCCs can self-assemble to form nanosized spherical micelles with biomimetic PC shell. In vitro biological evaluation revealed that DCA–PCCs micelles had low toxicity against NIH/3T3 mouse embryonic fibroblasts as well as good hemocompatibility. Using quercetin as a hydrophobic model drug, drug loading and release study suggested that biomimetic DCA–PCCs micelles could be used as a promising nanocarrier avoiding unfavorable biological response for hydrophobic drug delivery applications. - Highlights: • DCA–PCCs with phosphorylcholine and deoxycholic acid was synthesized. • DCA–PCCs can self-assemble to form spherical micelles in aqueous system. • DCA–PCCs micelles had excellent cytocompatibility and hemocompatibility. • DCA–PCCs micelles loaded with quercetin exhibited a sustained drug release behavior.

  9. Design of Auto Generating Tool of Part Sub Assembly Drawing%零件小组立图自动生成程序设计

    Institute of Scientific and Technical Information of China (English)

    周玉飞

    2014-01-01

    The part sub assembly drawing is still in the stage of manual drawing mode in many shipyards for .By using the Python language of Tribon system for secondary development , the part sub assembly drawing can be automatically generated .This program is verified by a series of ship design , showing that it is feasible .%针对目前很多船厂对于零件小组立图的生成还处于手工出图模式的问题,通过利用Python语言对Tribon系统进行二次开发,实现零件小组立图的自动批量生成。一系列船型的实践证明该程序是可行的且实用性很强。

  10. Nanoscale device architectures derived from biological assemblies: The case of tobacco mosaic virus and (apo)ferritin

    Science.gov (United States)

    Calò, Annalisa; Eiben, Sabine; Okuda, Mitsuhiro; Bittner, Alexander M.

    2016-03-01

    Virus particles and proteins are excellent examples of naturally occurring structures with well-defined nanoscale architectures, for example, cages and tubes. These structures can be employed in a bottom-up assembly strategy to fabricate repetitive patterns of hybrid organic-inorganic materials. In this paper, we review methods of assembly that make use of protein and virus scaffolds to fabricate patterned nanostructures with very high spatial control. We chose (apo)ferritin and tobacco mosaic virus (TMV) as model examples that have already been applied successfully in nanobiotechnology. Their interior space and their exterior surfaces can be mineralized with inorganic layers or nanoparticles. Furthermore, their native assembly abilities can be exploited to generate periodic architectures for integration in electrical and magnetic devices. We introduce the state of the art and describe recent advances in biomineralization techniques, patterning and device production with (apo)ferritin and TMV.

  11. The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass; Heazlewood, Joshua; Millar, Harvey

    2009-12-01

    In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) established a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online

  12. A Multidisciplinary Workshop: Self-Assembling Peptide Systems in Biology, Medicine and Engineering, Crete, Greece, July 1-6, 1999

    Science.gov (United States)

    2013-01-31

    Lausanne, Switzerland Novel Functional Assays for Screening Ligand-Receptor Interactions Day 6, Tuesday July 6 Session 6. Morning: Thermodynamics... fungal amphipathic protein hydrophobin SELF-ASSEMBLING AMPHIPATHIC FUNGAL PROTEINS HYDROPHOBINS. Hydrophobins comprise a class of proteins with similar...Selective ablation of differentiated cells permits isolation of embryonic stem cell lines from murine embryos with a non-permissive genetic background

  13. Bioactivity of marine organisms. Part 3. Screening of marine algae of Indian coast for biological activity

    Digital Repository Service at National Institute of Oceanography (India)

    Kamat, S.Y.; Wahidullah, S.; Naik, C.G.; DeSouza, L.; Jayasree, V.; Ambiye, V.; Bhakuni, D.S.; Goel, A.K.; Garg, H.S.; Srimal, R.C.

    Ethanolic extracts from Indian marine algae have been tested for anti-viral, anti-bacterial, anti-fungal, anti-fertility, hypoglycaemic and a wide range of pharmacological activities. Of 34 species investigated 17 appeared biologically active. Six...

  14. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 2. Structures of DNA

    Energy Technology Data Exchange (ETDEWEB)

    1983-01-01

    This is Volume 2 of the proceedings of the 1982 Cold Springs Harbor Symposium on Quantitative Biology. The volume contains papers on DNA methylation, DNA replication, gene recombination, organization of genes along DNA, molecular structure and enzymology of DNA.

  15. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 2: Peptide Identification via Molecular Mass Determination

    Science.gov (United States)

    Arnquist, Isaac J.; Beussman, Douglas J.

    2009-01-01

    Mass spectrometry has become a routine analytical tool in the undergraduate curriculum in the form of GC-MS. While relatively few undergraduate programs have incorporated biological mass spectrometry into their programs, the importance of these techniques, as demonstrated by their recognition with the 2002 Nobel Prize, will hopefully lead to…

  16. From microbiology to cell biology: when an intracellular bacterium becomes part of its host cell.

    Science.gov (United States)

    McCutcheon, John P

    2016-08-01

    Mitochondria and chloroplasts are now called organelles, but they used to be bacteria. As they transitioned from endosymbionts to organelles, they became more and more integrated into the biochemistry and cell biology of their hosts. Work over the last 15 years has shown that other symbioses show striking similarities to mitochondria and chloroplasts. In particular, many sap-feeding insects house intracellular bacteria that have genomes that overlap mitochondria and chloroplasts in terms of size and coding capacity. The massive levels of gene loss in some of these bacteria suggest that they, too, are becoming highly integrated with their host cells. Understanding these bacteria will require inspiration from eukaryotic cell biology, because a traditional microbiological framework is insufficient for understanding how they work.

  17. The Sum of the Parts: Large-scale Modeling in Systems Biology

    DEFF Research Database (Denmark)

    Fridolin, Gross; Green, Sara

    2017-01-01

    these questions, we distinguish between two types of reductionism, namely 'modular reductionism' and 'bottom-up reductionism'. Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies of molecular processes. We ask whether systems...... biology provides novel ways to ​ ​recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium ​ ​M. genitalium. Secondly, we examine the attempt to recompose...... processes across different spatial scales via multi-scale cardiac models. Although these models also rely on a number of idealizations and simplifying assumptions, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising...

  18. Endobiogeny: A Global Approach to Systems Biology (Part 1 of 2)

    OpenAIRE

    Lapraz, Jean-Claude; Hedayat, Kamyar M.

    2013-01-01

    Endobiogeny is a global systems approach to human biology that may offer an advancement in clinical medicine based in scientific principles of rigor and experimentation and the humanistic principles of individualization of care and alleviation of suffering with minimization of harm. Endobiogeny is neither a movement away from modern science nor an uncritical embracing of pre-rational methods of inquiry but a synthesis of quantitative and qualitative relationships reflected in a systems-approa...

  19. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 1. Structures of DNA

    Energy Technology Data Exchange (ETDEWEB)

    1983-01-01

    The proceedings for the 47th Annual Cold Spring Harbor Symposia on Quantitative Biology are presented. This symposium focused on the Structure of DNA. Topics presented covered research in the handedness of DNA, conformational analysis, chemically modified DNA, chemical synthesis of DNA, DNA-protein interactions, DNA within nucleosomes, DNA methylation, DNA replication, gyrases and topoisomerases, recombining and mutating DNA, transcription of DNA and its regulation, the organization of genes along DNA, repetitive DNA and pseudogenes, and origins of replication, centromeres, and teleomeres.

  20. Somatostatin receptor biology in neuroendocrine and pituitary tumours: part 1--molecular pathways.

    Science.gov (United States)

    Cakir, Mehtap; Dworakowska, Dorota; Grossman, Ashley

    2010-11-01

    Neuroendocrine tumours (NETs) may occur at many sites in the body although the majority occur within the gastroenteropancreatic axis. Non-gastroenteropancreatic NETs encompass phaeochromocytomas and paragangliomas, medullary thyroid carcinoma, anterior pituitary tumour, broncho-pulmonary NETs and parathyroid tumours. Like most endocrine tumours, NETs also express somatostatin (SST) receptors (subtypes 1-5) whose ligand SST is known to inhibit endocrine and exocrine secretions and have anti-tumour effects. In the light of this knowledge, the idea of using SST analogues in the treatment of NETs has become increasingly popular and new studies have centred upon the development of new SST analogues. We attempt to review SST receptor (SSTR) biology primarily in neuroendocrine tissues, focusing on pituitary tumours. A full data search was performed through PubMed over the years 2000-2009 with keywords 'somatostatin, molecular biology, somatostatin receptors, somatostatin signalling, NET, pituitary' and all relevant publications have been included, together with selected publications prior to that date. SSTR signalling in non-neuroendocrine solid tumours is beyond the scope of this review. SST is a potent anti-proliferative and anti-secretory agent for some NETs. The successful therapeutic use of SST analogues in the treatment of these tumours depends on a thorough understanding of the diverse effects of SSTR subtypes in different tissues and cell types. Further studies will focus on critical points of SSTR biology such as homo- and heterodimerization of SSTRs and the differences between post-receptor signalling pathways of SSTR subtypes.

  1. Bibliographical database of radiation biological dosimetry and risk assessment: Part 1, through June 1988

    Energy Technology Data Exchange (ETDEWEB)

    Straume, T.; Ricker, Y.; Thut, M.

    1988-08-29

    This database was constructed to support research in radiation biological dosimetry and risk assessment. Relevant publications were identified through detailed searches of national and international electronic databases and through our personal knowledge of the subject. Publications were numbered and key worded, and referenced in an electronic data-retrieval system that permits quick access through computerized searches on publication number, authors, key words, title, year, and journal name. Photocopies of all publications contained in the database are maintained in a file that is numerically arranged by citation number. This report of the database is provided as a useful reference and overview. It should be emphasized that the database will grow as new citations are added to it. With that in mind, we arranged this report in order of ascending citation number so that follow-up reports will simply extend this document. The database cite 1212 publications. Publications are from 119 different scientific journals, 27 of these journals are cited at least 5 times. It also contains reference to 42 books and published symposia, and 129 reports. Information relevant to radiation biological dosimetry and risk assessment is widely distributed among the scientific literature, although a few journals clearly dominate. The four journals publishing the largest number of relevant papers are Health Physics, Mutation Research, Radiation Research, and International Journal of Radiation Biology. Publications in Health Physics make up almost 10% of the current database.

  2. Programmable Self-Assembly of DNA-Protein Hybrid Hydrogel for Enzyme Encapsulation with Enhanced Biological Stability.

    Science.gov (United States)

    Wan, Lan; Chen, Qiaoshu; Liu, Jianbo; Yang, Xiaohai; Huang, Jin; Li, Li; Guo, Xi; Zhang, Jue; Wang, Kemin

    2016-04-11

    A DNA-protein hybrid hydrogel was constructed based on a programmable assembly approach, which served as a biomimetic physiologic matrix for efficient enzyme encapsulation. A dsDNA building block tailored with precise biotin residues was fabricated based on supersandwich hybridization, and then the addition of streptavidin triggered the formation of the DNA-protein hybrid hydrogel. The biocompatible hydrogel, which formed a flower-like porous structure that was 6.7 ± 2.1 μm in size, served as a reservoir system for enzyme encapsulation. Alcohol oxidase (AOx), which served as a representative enzyme, was encapsulated in the hybrid hydrogel using a synchronous assembly approach. The enzyme-encapsulated hydrogel was utilized to extend the duration time for ethanol removal in serum plasma and the enzyme retained 78% activity after incubation with human serum for 24 h. The DNA-protein hybrid hydrogel can mediate the intact immobilization on a streptavidin-modified and positively charged substrate, which is very beneficial to solid-phase biosensing applications. The hydrogel-encapsulated enzyme exhibited improved stability in the presence of various denaturants. For example, the encapsulated enzyme retained 60% activity after incubation at 55 °C for 30 min. The encapsulated enzyme also retains its total activity after five freeze-thaw cycles and even suspended in solution containing organic solvents.

  3. Somatostatin receptor biology in neuroendocrine and pituitary tumours: part 1 – molecular pathways

    Science.gov (United States)

    Cakir, Mehtap; Dworakowska, Dorota; Grossman, Ashley

    2010-01-01

    Abstract Neuroendocrine tumours (NETs) may occur at many sites in the body although the majority occur within the gastroenteropancreatic axis. Non-gastroenteropancreatic NETs encompass phaeochromocytomas and paragangliomas, medullary thyroid carcinoma, anterior pituitary tumour, broncho-pulmonary NETs and parathyroid tumours. Like most endocrine tumours, NETs also express somatostatin (SST) receptors (subtypes 1–5) whose ligand SST is known to inhibit endocrine and exocrine secretions and have anti-tumour effects. In the light of this knowledge, the idea of using SST analogues in the treatment of NETs has become increasingly popular and new studies have centred upon the development of new SST analogues. We attempt to review SST receptor (SSTR) biology primarily in neuroendocrine tissues, focusing on pituitary tumours. A full data search was performed through PubMed over the years 2000–2009 with keywords ‘somatostatin, molecular biology, somatostatin receptors, somatostatin signalling, NET, pituitary’ and all relevant publications have been included, together with selected publications prior to that date. SSTR signalling in non-neuroendocrine solid tumours is beyond the scope of this review. SST is a potent anti-proliferative and anti-secretory agent for some NETs. The successful therapeutic use of SST analogues in the treatment of these tumours depends on a thorough understanding of the diverse effects of SSTR subtypes in different tissues and cell types. Further studies will focus on critical points of SSTR biology such as homo- and heterodimerization of SSTRs and the differences between post-receptor signalling pathways of SSTR subtypes. PMID:20629989

  4. Chemical variability and biological activities of Brassica rapa var. rapifera parts essential oils depending on geographic variation and extraction technique.

    Science.gov (United States)

    Saka, Boualem; Djouahri, Abderrahmane; Djerrad, Zineb; Souhila, Terfi; Aberrane, Sihem; Sabaou, Nasserdine; Baaliouamer, Aoumeur; Boudarene, Lynda

    2017-02-01

    In the present work, the Brassica rapa var. rapifera parts essential oils and their antioxidant and antimicrobial activities were investigated for the first time depending on geographic origin and extraction technique. GC and GC-MS analyses showed several constituents, including alcohols, aldehydes, esters, ketones, norisoprenoids, terpenic, nitrogen and sulphur compounds, totalizing 38 and 41 compounds in leaves and root essential oils, respectively. Nitrogen compounds were the main volatiles in leaves essential oils and sulphur compounds were the main volatiles in root essential oils. Qualitative and quantitative differences were found among B. rapa var. rapifera parts essential oils collected from different locations and extracted by hydrodistillation (HD) and microwave-assisted hydrodistillation (MAHD) techniques. Furthermore, our findings showed a high variability for both antioxidant and antimicrobial activities. The highlighted variability reflects the high impact of plant part, geographic variation and extraction technique on chemical composition and biological activities, which led to conclude that we should select essential oils to be investigated carefully depending on these factors, in order to isolate the bioactive components or to have the best quality of essential oil in terms of biological activities and preventive effects in food. This article is protected by copyright. All rights reserved.

  5. The Subcritical Assembly in Dubna (SAD)—Part II: Research program for ADS-demo experiment

    Science.gov (United States)

    Gudowski, Waclaw; Shvetsov, Valery; Polanski, Aleksander; Broeders, Cornelis

    2006-06-01

    Subcritical Assembly in Dubna (SAD), a project funded by the International Science and Technology Centre, driven in collaboration with many European partners, may become the first Accelerator Driven Subcritical experiment coupling an existing proton accelerator of 660 MeV with a compact MQX-fuelled subcritical core. The main objective of the SAD experiment is to study physics of Accelerator Driven System ranging from a very deep subcriticality up to keff of 0.98. All experiences with subcriticality monitoring from previous subcritical experiments like MUSE, Yalina and IBR-30 booster mode will be verified in order to select the most reliable subcriticality monitoring technique. Particular attention will be given to validation of the core power-beam current relation. Moreover, some studies have been done to assess possibility of power upgrade for SAD.

  6. Can virtual reality predict body part discomfort and performance of people in realistic world for assembling tasks?

    CERN Document Server

    Hu, Bo; Zhang, Wei; Salvendy, Gaverial; Chablat, Damien; Bennis, Fouad

    2011-01-01

    This paper presents our work on relationship of evaluation results between virtual environment (VE) and realistic environment (RE) for assembling tasks. Evaluation results consist of subjective results (BPD and RPE) and objective results (posture and physical performance). Same tasks were performed with same experimental configurations and evaluation results were measured in RE and VE respectively. Then these evaluation results were compared. Slight difference of posture between VE and RE was found but not great difference of effect on people according to conventional ergonomics posture assessment method. Correlation of BPD and performance results between VE and RE are found by linear regression method. Moreover, results of BPD, physical performance, and RPE in VE are higher than that in RE with significant difference. Furthermore, these results indicates that subjects feel more discomfort and fatigue in VE than RE because of additional effort required in VE.

  7. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.

    Science.gov (United States)

    Greenbury, S F; Ahnert, S E

    2015-12-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.

  8. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

    Science.gov (United States)

    Greenbury, S. F.; Ahnert, S. E.

    2015-01-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained' and ‘unconstrained' sequences, in the broadest possible sense. As ‘constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding' and ‘non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  9. Biologic indicators of exposure to cadmium and lead palmerton, Pennsylvania. Part 2. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Sarasua, S.M.; McGeehin, M.A.; Stallings, F.L.; Terracciano, G.L.; Amler, R.W.

    1995-05-01

    In Part 2 of this study, no difference was reported in the results of medical tests of the blood, liver, kidney, and immune systems of participants living in the two study areas. No relationships was found between exposure to cadmium and lead and the immune, liver, and blood system tests. No community wide medical action is needed in Palmerton based on the results of this study. No further site-specific health studies are recommended.

  10. Observations on the biology of Afrotropical Hesperiidae (Lepidoptera). Part 6. Hesperiinae incertae sedis: palm feeders.

    Science.gov (United States)

    Cock, Matthew J W; Congdon, T Colin E; Collins, Steve C

    2014-07-08

    Partial life histories for 12 Hesperiinae incertae sedis that feed on palms (Arecaceae) are described and illustrated. The genera dealt with are: Perrotia (part), Ploetzia, Zophopetes, Gretna (part), Pteroteinon, Leona, and Caenides (part) (all from Evans' Ploetzia genera group). Although Gamia spp. have been reported to feed on palms, these records are considered to be in error, as caterpillars of this genus feed on Dracaena spp. (Asparagaceae). The life histories of the species documented are fairly uniform, in that caterpillars of most species have rounded brown heads, wider basally, with or without limited black markings, smooth bodies and make simple shelters by rolling leaves. Variation in caterpillar markings and male genitalia of Zophopetes dysmephila (Trimen) and caterpillar and adult markings of Gretna carmen Evans merit further study. In G. carmen, G. waga (Plötz) and G. balenge (Holland), the caterpillars' head and body are covered with hair-like setae, and develop an extensive covering of white waxy powder, which in G. balenge also covers the long setae. Furthermore, the pupa of G. balenge is unusual in having a pair of large, elaborate processes frontally on the head; when disturbed, the pupa vibrates violently and rattles noisily against the sides of the shelter. Ploetzia amygdalis (Mabille) and Pteroteinon laufella (Hewitson) have gregarious caterpillars, whereas the remaining species are solitary. After eclosion, the first instar caterpillars of Gretna spp. moult to the second instar without feeding. The implications of a palm-feeding life-style are discussed, and economic damage and plant quarantine risks to coconut, oil palm and ornamental palms pointed out. The known life histories suggest that all Afrotropical palm-feeding Hesperiidae will belong in the same tribe when the incertae sedis section is further elucidated, although the affinities of Gretna deserve further consideration. 

  11. Fixed-wing MAV attitude stability in atmospheric turbulence-Part 2: Investigating biologically-inspired sensors

    Science.gov (United States)

    Mohamed, A.; Watkins, S.; Clothier, R.; Abdulrahim, M.; Massey, K.; Sabatini, R.

    2014-11-01

    Challenges associated with flight control of agile fixed-wing Micro Air Vehicles (MAVs) operating in complex environments is significantly different to any larger scale vehicle. The micro-scale of MAVs can make them particularly sensitive to atmospheric disturbances thus limiting their operation. As described in Part 1, current conventional reactive attitude sensing systems lack the necessary response times for attitude control in high turbulence environments. This paper reviews in greater detail novel and emerging biologically inspired sensors, which can sense the disturbances before a perturbation is induced. A number of biological mechanoreceptors used by flying animals are explored for their utility in MAVs. Man-made attempts of replicating mechanoreceptors have thus been reviewed. Bio-inspired flow and pressure-based sensors were found to be the most promising for complementing or replacing current inertial-based reactive attitude sensors. Achieving practical implementations that meet the size, weight and power constraints of MAVs remains a significant challenge. Biological systems were found to rely on multiple sensors, potentially implying a number of research opportunities in the exploration of heterogeneous bio-inspired sensing solutions.

  12. Water Complexes Take Part in Biological Effect Created by Weak Combined Magnetic Field

    Science.gov (United States)

    Sheykina, Nadiia

    2016-07-01

    It was revealed experimentally that at small level of magnetic field's noise (less than 4µT/Hz0.5) the dependence of gravitropc reaction of cress roots on frequency had a fine structure/ The peak that corresponded to the cyclotron frequency of Ca2+ ions for the static component of combined magnetic field that was equal to 40µT became split up into three peaks ( f1 = 31/3Hz, f2 = 32.5Hz i f3 = 34 Hz./ . The frequency f1 corresponded to the Ca2+ ion (theoretical value 31.6 Hz), the frequency f2 corresponded to the hydronium ion H3O+ (theoretical value 32.9 Hz), the frequency f3 corresponded to OH- ion (theoretical value 35 Hz). Taking into account the influence of combined magnetic field on hydronium ions and Del Giudice' hypothesis one may throw away doubts about the possibility of ion cyclotron resonance. The hydronium ions are unusual because they have a long free path length. It was revealed that pH of the distillated water changed under the treatment in combined magnetic field tuned to cyclotron frequency of hydronium ion. Such changes in pH had to lead to the biological effects on the molecular ,cell and organism levels.

  13. Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly.

    Science.gov (United States)

    Moore, Tyler G; Garzon, Max H; Deaton, Russell J

    2015-01-01

    Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are "strong" assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self-assembly systems

  14. Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly.

    Directory of Open Access Journals (Sweden)

    Tyler G Moore

    Full Text Available Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are "strong" assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic

  15. Y-12 development organization technical progress report. Part 4, Assembly technology/compatibility and surveillance period ending September 30, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Northcutt, W.G. Jr. [comp.

    1993-12-27

    The Super Collider is a high-energy scientific instrument composed of a 53-mile-long ring of proton accelerators designed to collide protons and evaluate the emanating particles. The Oak Ridge Y-12 Plant is under contract to perform work for the Superconducting Super Collider Laboratory (SSCL) and has been asked to develop manufacturing processes for components of the gammas, electrons, muons (GEM) detector. Three welded subassemblies are involved in the fabrication of these conductors. The superconducting cable is enclosed in a stainless steel conduit, which is then enclosed in an aluminum sheath. The ends of the conductor are terminated with a connector assembly joined to the superconductor, the conduit, and the sheath. Initially, the conduit weld was to be a single-pass, autogenous gas-tungsten arc weld. The authors made a great effort to get full penetration without root reinforcement on the inside of the tube. When the authors were unable to meet all of the weld requirements with an autogenous weld, they shifted development efforts to making the weld using an automatic gas-tungsten arc tube welding head with an integral wire feeder. Because reinforcement at the root continued to be a problem, the authors decided to make the weld in two passes. To achieve the desired weld reinforcement on the outside of the tube, the authors developed a welding procedure in which an autogenous pass is used to join the tube ends with the necessary minimum pushthrough on the inside of the tube and filler metal is supplied during the second pass. This two-pass weld required a weld joint with a flat butt for the root pass and a V-groove for the filler metal pass. A 272-ft conduit was made using this two-pass welding procedure for a test at the University of Wisconsin.

  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. QUICK ASSESSMENT METHODOLOGY FOR RELIABILITY OF SOLDER JOINTS IN BALL GRID ARRAY (BGA)ASSEMBLY--PART Ⅱ: RELIABILITY EXPERIMENT AND NUMERICAL SIMULATION

    Institute of Scientific and Technical Information of China (English)

    史训清; John HL Pang; 杨前进; 王志平; 聂景旭

    2002-01-01

    In the present study, a facility, i.e., a mechanical deflection system(MDS), was established and applied to assess the long-term reliability of the solder joints in plastic ball grid array (BGA) assembly. It was found that the MDS not only quickly assesses the long-term reliability of solder joints within days, but can also mimic similar failure mechanisms in accelerated thermal cycling (ATC) tests.Based on the MDS and ATC reliability experiments, the acceleration factors (AF)were obtained for different reliability testing conditions. Furthermore, by using the creep constitutive relation and fatigue life model developed in part I, a numerical approach was established for the purpose of virtual life prediction of solder joints.The simulation results were found to be in good agreement with the test results from the MDS. As a result, a new reliability assessment methodology was established as an alternative to ATC for the evaluation of long-term reliability of plastic BGA assembly.

  18. Chemical constituents and biological investigations of the aerial parts of Egyptian Clerodendrum inerme

    Directory of Open Access Journals (Sweden)

    Sabrin R.M. Ibrahim

    2014-12-01

    Full Text Available B-friedoolean-5-ene-3-β-ol (1, β-sitosterol (2, stigmasta-5,22,25-trien-3-β-ol (3, betulinic acid (4, and 5-hydroxy-6,7,4′-trimethoxyflavone (5 were isolated from the aerial parts of Clerodendrum inerme L. (Verbenaceae. Their structures were established based on analyses of physical and spectroscopic data. Compounds 1, 4, and 5 were isolated for the first time from the plant. C. inerme L. was known as a rich source of terpenes, sterols, and phenolic compounds, so the antioxidant and anti-inflammatory activities were evaluated. The total methanolic extract (TME and compound 5 showed scavenging activity with maximum inhibition of 61.84% for TME (100 μg/mL and 37.19% for 5 (20 μM, respectively, using DPPH assay. In addition, the TME exhibited anti-inflammatory activity more than indomethacin at dose 200 mg/kg using the formalin induced hind paw edema method.

  19. 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.

  20. Biologically Inspired Self-assembling Synthesis of Bone-like Nano-hydroxyapatite/PLGA- (PEG-ASP)n Composite: A New Biomimetic Bone Tissue Engineering Scaffold Material

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A new biomimetic bone tissue engineering scaffold material, nano-HA/ PLGA-( PEG- ASP )n composite, was synthesized by a biologically inspired self assembling approach. A novel biodegradable PLGA( PEG-ASP ) n copolymer with pendant amine functional groups and enhanced hydrophilicity was synthesized by bulk ring-opening copolymerization by DL-lactide( DLLA ) and glycolide( GA ) with Aspartic acid ( ASP )-Polyethylene glycol( PEG ) alt-prepolymer. A Three-dimensional, porous scaffold of the PLGA-( PEG-ASP )n copolymer was fabricated by a solvent casting, particulate leaching process. The scaffold was then incubated in modified simulated body fluid ( mSBF ) . Growth of HA nanocrystals on the inner pore surfaces of the porous scaffold is confirmed by calcium ion binding analyses, SEM, mass increase measurements and quantification of phosphate content within scaffolds . SEM analysis demonstrated the nucleation and growth of a continuous bonelike, low crystalline carbonated HA nanocrystals on the inner pore surfawes of the PLGA-( PEG-ASP)n scaffolds. The amount of calcium binding, total mass and the mass of pbosphate on experimental PLGA-( PEG- ASP )n scaffolds at different incubation times in mSBF was significantly greater than that of control PLGA scaffolds . This nano-HA/ PLGA- ( PEG-ASP )n composite shows some features of natural bone both in main composition and hierarchical microstructure. The ASPPEG alt-prepolymer modified PLGA copolymer provide a controllable high surface density and distribution of anionic functional groups which would enhauce nucleation and growth of bonelike mineral following exposure to mSBF. This biomimetic treatment provides a simple method for surface funetionalization and subsequent mineral nucleation and self-assembling on biodegradable polymer scaffolds for tissue engineering.

  1. Gaseous VOCs rapidly modify particulate matter and its biological effects - Part 1: Simple VOCs and model PM

    Science.gov (United States)

    Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y.-H.; Jaspers, I.; Jeffries, H. E.

    2012-12-01

    This is the first of a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOC), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of biological effects, using cultured human lung cells as model indicators. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. The exposure systems permit virtually gas-only- or PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure. Our simple experiments in this part of the study were designed to eliminate many competing atmospheric processes to reduce ambiguity in our results. Simple volatile and semi-volatile organic gases that have inherent cellular toxic properties were tested individually for biological effect in the dark (at constant humidity). Airborne mixtures were then created with each compound to which we added PM that has no inherent cellular toxic properties for another cellular exposure. Acrolein and p-tolualdehyde were used as model VOCs and mineral oil aerosol (MOA) was selected as a surrogate for organic-containing PM. MOA is appropriately complex in composition to represent ambient PM, and exhibits no inherent cellular toxic effects and thus did not contribute any biological detrimental effects on its own. Chemical measurements, combined with the responses of our biological exposures, clearly demonstrate that gas-phase pollutants can modify the composition of PM (and its resulting detrimental effects on lung cells). We observed that, even if the gas-phase pollutants are not

  2. Gaseous VOCs rapidly modify particulate matter and its biological effects – Part 1: Simple VOCs and model PM

    Directory of Open Access Journals (Sweden)

    H. E. Jeffries

    2012-02-01

    Full Text Available This is the first of a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOC, particulate matter (PM, and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model indicators. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects from cells exposed to chamber air relative to cells exposed to clean air. The exposure systems permit gas-only- or PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure. Our simple experiments in this part of the study were designed to eliminate many competing atmospheric processes to reduce ambiguity in our results. Simple volatile and semi-volatile organic gases that have inherent cellular toxic properties were tested individually for biological effect in the dark (at constant humidity. Airborne mixtures were then created with each compound and PM that has no inherent cellular toxic properties for another cellular exposure. Acrolein and p-tolualdehyde were used as model VOCs and mineral oil aerosol (MOA was selected as a surrogate for organic-containing PM. MOA is appropriately complex in composition to represent ambient PM, and it exhibits no inherent cellular toxic effects and thus did not contribute any biological detrimental effects on its own. Chemical measurements, combined with the responses of our biological exposures, clearly demonstrate that gas-phase pollutants can modify the composition of PM (and its resulting detrimental effects on lung cells – even if the gas-phase pollutants are not

  3. Gaseous VOCs rapidly modify particulate matter and its biological effects – Part 1: Simple VOCs and model PM

    Directory of Open Access Journals (Sweden)

    H. E. Jeffries

    2012-12-01

    Full Text Available This is the first of a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOC, particulate matter (PM, and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of biological effects, using cultured human lung cells as model indicators. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects from cells exposed to chamber air relative to cells exposed to clean air. The exposure systems permit virtually gas-only- or PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure. Our simple experiments in this part of the study were designed to eliminate many competing atmospheric processes to reduce ambiguity in our results. Simple volatile and semi-volatile organic gases that have inherent cellular toxic properties were tested individually for biological effect in the dark (at constant humidity. Airborne mixtures were then created with each compound to which we added PM that has no inherent cellular toxic properties for another cellular exposure. Acrolein and p-tolualdehyde were used as model VOCs and mineral oil aerosol (MOA was selected as a surrogate for organic-containing PM. MOA is appropriately complex in composition to represent ambient PM, and exhibits no inherent cellular toxic effects and thus did not contribute any biological detrimental effects on its own. Chemical measurements, combined with the responses of our biological exposures, clearly demonstrate that gas-phase pollutants can modify the composition of PM (and its resulting detrimental effects on lung cells. We observed that, even if the gas-phase pollutants

  4. Biologic Treatments for Sports Injuries II Think Tank-Current Concepts, Future Research, and Barriers to Advancement, Part 1: Biologics Overview, Ligament Injury, Tendinopathy.

    Science.gov (United States)

    LaPrade, Robert F; Geeslin, Andrew G; Murray, Iain R; Musahl, Volker; Zlotnicki, Jason P; Petrigliano, Frank; Mann, Barton J

    2016-12-01

    Biologic therapies, including stem cells, platelet-rich plasma, growth factors, and other biologically active adjuncts, have recently received increased attention in the basic science and clinical literature. At the 2015 AOSSM Biologics II Think Tank held in Colorado Springs, Colorado, a group of orthopaedic surgeons, basic scientists, veterinarians, and other investigators gathered to review the state of the science for biologics and barriers to implementation of biologics for the treatment of sports medicine injuries. This series of current concepts reviews reports the summary of the scientific presentations, roundtable discussions, and recommendations from this think tank.

  5. Implementation and evaluation of a training program as part of the Cooperative Biological Engagement Program in Azerbaijan

    Directory of Open Access Journals (Sweden)

    April eJohnson

    2015-10-01

    Full Text Available A training program for animal and human health professionals has been implemented in Azerbaijan through a joint agreement between the United States Defense Threat Reduction Agency and the Government of Azerbaijan. The training program is administered as part of the Cooperative Biological Engagement Program, and targets key employees in Azerbaijan’s disease surveillance system including physicians, veterinarians, epidemiologists, and laboratory personnel. Training is aimed at improving detection, diagnosis, and response to especially dangerous pathogens, although the techniques and methodologies can be applied to other pathogens and diseases of concern. Biosafety and biosecurity training is provided to all trainees within the program. Prior to 2014, a variety of international agencies and organizations provided training, which resulted in gaps related to lack of coordination of training materials and content. In 2014 a new training program was implemented in order to address those gaps. This paper provides an overview of the Cooperative Biological Engagement Program training program in Azerbaijan, a description of how the program fits into existing national training infrastructure, and an evaluation of the new program’s effectiveness to date. Long-term sustainability of the program is also discussed.

  6. Nitric oxide and redox regulation in the liver: Part I. General considerations and redox biology in hepatitis.

    Science.gov (United States)

    Diesen, Diana L; Kuo, Paul C

    2010-07-01

    Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are created in normal hepatocytes and are critical for normal physiologic processes, including oxidative respiration, growth, regeneration, apoptosis, and microsomal defense. When the levels of oxidation products exceed the capacity of normal antioxidant systems, oxidative stress occurs. This type of stress, in the form of ROS and RNS, can be damaging to all liver cells, including hepatocytes, Kupffer cells, stellate cells, and endothelial cells, through induction of inflammation, ischemia, fibrosis, necrosis, apoptosis, or through malignant transformation by damaging lipids, proteins, and/or DNA. In Part I of this review, we will discuss basic redox biology in the liver, including a review of ROS, RNS, and antioxidants, with a focus on nitric oxide as a common source of RNS. We will then review the evidence for oxidative stress as a mechanism of liver injury in hepatitis (alcoholic, viral, nonalcoholic). In Part II of this review, we will review oxidative stress in common pathophysiologic conditions, including ischemia/reperfusion injury, fibrosis, hepatocellular carcinoma, iron overload, Wilson's disease, sepsis, and acetaminophen overdose. Finally, biomarkers, proteomic, and antioxidant therapies will be discussed as areas for future therapeutic interventions.

  7. Nitric oxide and redox regulation in the liver: part II. Redox biology in pathologic hepatocytes and implications for intervention.

    Science.gov (United States)

    Diesen, Diana L; Kuo, Paul C

    2011-05-01

    Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are created in normal hepatocytes and are critical for normal physiologic processes, including oxidative respiration, growth, regeneration, apoptosis, and microsomal defense. When the levels of oxidation products exceed the capacity of normal antioxidant systems, oxidative stress occurs. This type of stress, in the form of ROS and RNS, can be damaging to all liver cells, including hepatocytes, Kupffer cells, stellate cells, and endothelial cells, through induction of inflammation, ischemia, fibrosis, necrosis, apoptosis, or through malignant transformation by damaging lipids, proteins, and/or DNA. In Part I of this review, we will discuss basic redox biology in the liver, including a review of ROS, RNS, and antioxidants, with a focus on nitric oxide as a common source of RNS. We will then review the evidence for oxidative stress as a mechanism of liver injury in hepatitis (alcoholic, viral, nonalcoholic). In Part II of this review, we will review oxidative stress in common pathophysiologic conditions, including ischemia/reperfusion injury, fibrosis, hepatocellular carcinoma, iron overload, Wilson's disease, sepsis, and acetaminophen overdose. Finally, biomarkers, proteomic, and antioxidant therapies will be discussed as areas for future therapeutic interventions.

  8. Gaseous VOCs rapidly modify particulate matter and its biological effects – Part 2: Complex urban VOCs and model PM

    Directory of Open Access Journals (Sweden)

    S. Ebersviller

    2012-03-01

    Full Text Available This is the second study in a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOCs, particulate matter (PM, and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber, both in the dark and in sunlight. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model living receptors. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects from cells exposed to chamber air relative to cells exposed to clean air. Our exposure systems permit side-by-side, gas-only- and PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure for either gases or PM.

    In Part 1 (Ebersviller et al., 2012a, we demonstrated the existence of PM "effect modification" (NAS, 2004 for the case of a single gas-phase toxicant and an inherently non-toxic PM (mineral oil aerosol, MOA. That is, in the presence of the single gas-phase toxicant in the dark, the initially non-toxic PM became toxic to lung cells in the PM-only-biological exposure system. In this Part 2 study, we used sunlit-reactive systems to create a large variety of gas-phase toxicants from a complex mixture of oxides of nitrogen and 54 VOCs representative of those measured in US city air. In these mostly day-long experiments, we have designated the period in the dark just after injection (but before sunrise as the "Fresh" condition and the period in the dark after sunset as the "Aged" condition. These two conditions were used to expose cells and to collect chemical characterization samples. We used the same inherently non-toxic PM from the Part 1 study as the

  9. Gaseous VOCs rapidly modify particulate matter and its biological effects – Part 2: Complex urban VOCs and model PM

    Directory of Open Access Journals (Sweden)

    H. E. Jeffries

    2012-12-01

    Full Text Available This is the second study in a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOCs, particulate matter (PM, and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber, both in the dark and in sunlight. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model living receptors. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects from cells exposed to chamber air relative to cells exposed to clean air. Our exposure systems permit side-by-side, gas-only- and PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure for either gases or PM. In Part 1 (Ebersviller et al., 2012a, we demonstrated the existence of PM "effect modification" (NAS, 2004 for the case of a single gas-phase toxicant and an inherently non-toxic PM (mineral oil aerosol, MOA. That is, in the presence of the single gas-phase toxicant in the dark, the initially non-toxic PM became toxic to lung cells in the PM-only-biological exposure system. In this Part 2 study, we used sunlit-reactive systems to create a large variety of gas-phase toxicants from a complex mixture of oxides of nitrogen and 54 VOCs representative of those measured in US city air. In these mostly day-long experiments, we have designated the period in the dark just after injection (but before sunrise as the "Fresh" condition and the period in the dark after sunset as the "Aged" condition. These two conditions were used to expose cells and to collect chemical characterization samples. We used the same inherently non-toxic PM from the Part 1 study as the target PM

  10. Gaseous VOCs rapidly modify particulate matter and its biological effects - Part 2: Complex urban VOCs and model PM

    Science.gov (United States)

    Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y.-H.; Jaspers, I.; Jeffries, H. E.

    2012-12-01

    This is the second study in a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOCs), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber, both in the dark and in sunlight. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model living receptors. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. Our exposure systems permit side-by-side, gas-only- and PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure for either gases or PM. In Part 1 (Ebersviller et al., 2012a), we demonstrated the existence of PM "effect modification" (NAS, 2004) for the case of a single gas-phase toxicant and an inherently non-toxic PM (mineral oil aerosol, MOA). That is, in the presence of the single gas-phase toxicant in the dark, the initially non-toxic PM became toxic to lung cells in the PM-only-biological exposure system. In this Part 2 study, we used sunlit-reactive systems to create a large variety of gas-phase toxicants from a complex mixture of oxides of nitrogen and 54 VOCs representative of those measured in US city air. In these mostly day-long experiments, we have designated the period in the dark just after injection (but before sunrise) as the "Fresh" condition and the period in the dark after sunset as the "Aged" condition. These two conditions were used to expose cells and to collect chemical characterization samples. We used the same inherently non-toxic PM from the Part 1 study as the target PM for "effect

  11. STAR: a simple TAL effector assembly reaction using isothermal assembly.

    Science.gov (United States)

    Gogolok, Sabine; Garcia-Diaz, Claudia; Pollard, Steven M

    2016-09-12

    Transcription activator-like effectors (TALEs) contain modular programmable DNA binding domains. Fusing TALEs with effector domains creates synthetic transcription factors (TALE-TFs) or nucleases (TALENs), enabling precise gene manipulations. The construction of TALEs remains challenging due to their repetitive sequences. Here we report a simple TALE assembly reaction (STAR) that enables individual laboratories to generate multiple TALEs in a facile manner. STAR uses an isothermal assembly ('Gibson assembly') that is labour- and cost-effective, accessible, rapid and scalable. A small 68-part fragment library is employed, and the specific TALE repeat sequence is generated within ~8 hours. Sequence-verified TALENs or TALE-TF plasmids targeting 17 bp target sequences can be produced within three days, without the need for stepwise intermediate plasmid production. We demonstrate the utility of STAR through production of functional TALE-TFs capable of activating human SOX2 expression. STAR addresses some of the shortcomings of existing Golden Gate or solid-phase assembly protocols and enables routine production of TALE-TFs that will complement emerging CRISPR/Cas9-based reagents across diverse applications in mammalian stem cell and synthetic biology.

  12. Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

    Science.gov (United States)

    Whitesides, George M.; Mathias, John P.; Seto, Christopher T.

    1991-12-01

    Molecular self assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by non-covalent bonds. Molecular self-assembly is ubiquitous in biological systems, and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated non-covalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating non-biological structures having dimensions of 1-10(exp 2) nanometers. Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

  13. General Assembly

    CERN Multimedia

    Staff Association

    2016-01-01

    5th April, 2016 – Ordinary General Assembly of the Staff Association! In the first semester of each year, the Staff Association (SA) invites its members to attend and participate in the Ordinary General Assembly (OGA). This year the OGA will be held on Tuesday, April 5th 2016 from 11:00 to 12:00 in BE Auditorium, Meyrin (6-2-024). During the Ordinary General Assembly, the activity and financial reports of the SA are presented and submitted for approval to the members. This is the occasion to get a global view on the activities of the SA, its financial management, and an opportunity to express one’s opinion, including taking part in the votes. Other points are listed on the agenda, as proposed by the Staff Council. Who can vote? Only “ordinary” members (MPE) of the SA can vote. Associated members (MPA) of the SA and/or affiliated pensioners have a right to vote on those topics that are of direct interest to them. Who can give his/her opinion? The Ordinary General Asse...

  14. STUDIES REGARDING THE DETERMINATION OF THE ADEQUATE ASSEMBLY TOLERANCES DEPENDING ON THE MANUFACTURING COSTS OF THE PARTS PROCESSED ON CLASSIC MACHINE TOOLS

    Directory of Open Access Journals (Sweden)

    Constanţa RĂDULESCU

    2010-06-01

    Full Text Available The paper deals with a study case regarding the determination of adequate assembly tolerances. The study concerned the assembly of two bearings on an axle. Determining the adequate tolerances of the sizes chains is based on Lagrange’s multipliers use. The optimization criterion for determining the assembly tolerances is the minimization of the product achievement cost. The relation between tolerances and cost will be revealed in a graphic component

  15. Biologically Assembled Quantum Electronic Arrays

    Science.gov (United States)

    2013-06-07

    effect mobility of carotenoid polyenes " Vol. 146, pp. 43-46, 2004. (b) He, ].; Chen, F.; Li, ].; Sankey, 0. F.; Terazono, Y.; Herrero, C.; Gust, D...Moore, T. A.; Moore, A. L.; Lindsay, S. M. "Electronic Decay Constant of Carotenoid Polyenes from Single-Molecule Measurements",]. Am. Chern. Soc...Krouse, K A.; Schrock, R. R. ]. Am. Chern. Soc., "Preparation and isolation of polyenes containing up to 15 double bonds", Vol. 110, pp. 4424-4425

  16. Biological Activities and Nutraceutical Potentials of Water Extracts from Different Parts of Cynomorium Coccineum L. (Maltese Mushroom

    Directory of Open Access Journals (Sweden)

    Zucca Paolo

    2016-07-01

    Full Text Available Maltese Mushroom (Cynomorium coccineum L. is a non-photosynthetic plant that has been used in traditional medicine for many centuries. In this paper, water extracts from the whole plant, external layer and peeled plant were studied to determine the main components responsible for its biological activities, i.e., its antimicrobial, antioxidant, and anti-tyrosinase activities; its cytotoxicity against mouse melanoma B16F10 cells; and its pro-erectile activity in adult male rats. The results of electron transfer and hydrogen transfer assays showed that the antioxidant activity was mainly due to anthocyanins in the external layer, whereas the external layer and peeled plant extracts both inhibited the microbial growth of several Gram-positive strains. In contrast, the whole plant extract had the highest anti-tyrosinase activity and exhibited pro-erectile activity when administered subcutaneously. Overall, this study elucidated which parts of Maltese Mushroom are responsible for its antimicrobial, antioxidant, and anti-tyrosinase activities and thus which extracts have potential for use in nutraceutical formulations.

  17. Engineering BioBrick vectors from BioBrick parts

    Directory of Open Access Journals (Sweden)

    Knight Thomas F

    2008-04-01

    Full Text Available Abstract Background The underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts. The technical standard that has gained the most traction in the synthetic biology community is the BioBrick standard for physical composition of genetic parts. Parts that conform to the BioBrick assembly standard are BioBrick standard biological parts. To date, over 2,000 BioBrick parts have been contributed to, and are available from, the Registry of Standard Biological Parts. Results Here we extended the same advantages of BioBrick standard biological parts to the plasmid-based vectors that are used to provide and propagate BioBrick parts. We developed a process for engineering BioBrick vectors from BioBrick parts. We designed a new set of BioBrick parts that encode many useful vector functions. We combined the new parts to make a BioBrick base vector that facilitates BioBrick vector construction. We demonstrated the utility of the process by constructing seven new BioBrick vectors. We also successfully used the resulting vectors to assemble and propagate other BioBrick standard biological parts. Conclusion We extended the principles of part reuse and standardization to BioBrick vectors. As a result, myriad new BioBrick vectors can be readily produced from all existing and newly designed BioBrick parts. We invite the synthetic biology community to (1 use the process to make and share new BioBrick vectors; (2 expand the current collection of BioBrick vector parts; and (3 characterize and improve the available collection of BioBrick vector parts.

  18. Molecular self-assembly advances and applications

    CERN Document Server

    Dequan, Alex Li

    2012-01-01

    In the past several decades, molecular self-assembly has emerged as one of the main themes in chemistry, biology, and materials science. This book compiles and details cutting-edge research in molecular assemblies ranging from self-organized peptide nanostructures and DNA-chromophore foldamers to supramolecular systems and metal-directed assemblies, even to nanocrystal superparticles and self-assembled microdevices

  19. Self-assembled nanostructures

    CERN Document Server

    Zhang, Jin Z; Liu, Jun; Chen, Shaowei; Liu, Gang-yu

    2003-01-01

    Nanostructures refer to materials that have relevant dimensions on the nanometer length scales and reside in the mesoscopic regime between isolated atoms and molecules in bulk matter. These materials have unique physical properties that are distinctly different from bulk materials. Self-Assembled Nanostructures provides systematic coverage of basic nanomaterials science including materials assembly and synthesis, characterization, and application. Suitable for both beginners and experts, it balances the chemistry aspects of nanomaterials with physical principles. It also highlights nanomaterial-based architectures including assembled or self-assembled systems. Filled with in-depth discussion of important applications of nano-architectures as well as potential applications ranging from physical to chemical and biological systems, Self-Assembled Nanostructures is the essential reference or text for scientists involved with nanostructures.

  20. STAR: a simple TAL effector assembly reaction using isothermal assembly

    Science.gov (United States)

    Gogolok, Sabine; Garcia-Diaz, Claudia; Pollard, Steven M.

    2016-01-01

    Transcription activator-like effectors (TALEs) contain modular programmable DNA binding domains. Fusing TALEs with effector domains creates synthetic transcription factors (TALE-TFs) or nucleases (TALENs), enabling precise gene manipulations. The construction of TALEs remains challenging due to their repetitive sequences. Here we report a simple TALE assembly reaction (STAR) that enables individual laboratories to generate multiple TALEs in a facile manner. STAR uses an isothermal assembly (‘Gibson assembly’) that is labour- and cost-effective, accessible, rapid and scalable. A small 68-part fragment library is employed, and the specific TALE repeat sequence is generated within ~8 hours. Sequence-verified TALENs or TALE-TF plasmids targeting 17 bp target sequences can be produced within three days, without the need for stepwise intermediate plasmid production. We demonstrate the utility of STAR through production of functional TALE-TFs capable of activating human SOX2 expression. STAR addresses some of the shortcomings of existing Golden Gate or solid-phase assembly protocols and enables routine production of TALE-TFs that will complement emerging CRISPR/Cas9-based reagents across diverse applications in mammalian stem cell and synthetic biology. PMID:27615025

  1. Acute and impaired wound healing: pathophysiology and current methods for drug delivery, part 1: normal and chronic wounds: biology, causes, and approaches to care.

    Science.gov (United States)

    Demidova-Rice, Tatiana N; Hamblin, Michael R; Herman, Ira M

    2012-07-01

    This is the first installment of 2 articles that discuss the biology and pathophysiology of wound healing, review the role that growth factors play in this process, and describe current ways of growth factor delivery into the wound bed. Part 1 discusses the latest advances in clinicians' understanding of the control points that regulate wound healing. Importantly, biological similarities and differences between acute and chronic wounds are considered, including the signaling pathways that initiate cellular and tissue responses after injury, which may be impeded during chronic wound healing.

  2. DeviceEditor visual biological CAD canvas

    Directory of Open Access Journals (Sweden)

    Chen Joanna

    2012-02-01

    Full Text Available Abstract Background Biological Computer Aided Design (bioCAD assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.

  3. The biological restoration of central nervous system architecture and function: part 1-foundations and historical landmarks in contemporary stem cell biology.

    Science.gov (United States)

    Farin, Azadeh; Liu, Charles Y; Elder, James B; Langmoen, Iver A; Apuzzo, Michael L J

    2009-01-01

    Since their discovery, stem cells have fascinated scientists with their ultimate potential: the ability to cure disease, repair altered physiology, and reverse neurological deficit. Stem cell science unquestionably promises to eliminate many of the tragic limitations contemporary medicine must acknowledge, and cloning may provide young cells for an aging population. Although it is widely believed that stem cells will transform the way medicine is practiced, therapeutic interventions using stem cell technology are still in their infancy. The 3 most common stem cell sources studied today are umbilical cord blood, bone marrow, and human embryos. Although cord blood is currently used to treat dozens of disorders and bone marrow stem cells have been used clinically since the 1960s, human embryonic stem cells have yet to be successfully applied to any disease. Undeniably, stem cell therapy has the potential to be one of the most powerful therapeutic options available. In this introductory article of a 5-part series on stem cells, we narrate the evolution of modern stem cell science, delineating major landmarks that will prove responsible for taking stem cell technology from the laboratory into revolutionary clinical applications: from the first milestone of identifying the mouse hematopoietic stem cell to the latest feats of producing pluripotent stem cells without embryos at all. In Part 2, we present the evidence demonstrating the certainty of adult mammalian neurogenesis; in Parts 3 and 4, we describe neurosurgical applications of stem cell technology; and in Part 5, we discuss the philosophical and ethical issues surrounding stem cell therapy, as well as future areas of exploration.

  4. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  5. From self-organization to self-assembly: a new materialism?

    Science.gov (United States)

    Vincent, Bernadette Bensaude

    2016-09-01

    While self-organization has been an integral part of academic discussions about the distinctive features of living organisms, at least since Immanuel Kant's Critique of Judgement, the term 'self-assembly' has only been used for a few decades as it became a hot research topic with the emergence of nanotechnology. Could it be considered as an attempt at reducing vital organization to a sort of assembly line of molecules? Considering the context of research on self-assembly I argue that the shift of attention from self-organization to self-assembly does not really challenge the boundary between chemistry and biology. Self-assembly was first and foremost investigated in an engineering context as a strategy for manufacturing without human intervention and did not raise new perspectives on the emergence of vital organization itself. However self-assembly implies metaphysical assumptions that this paper tries to disentangle. It first describes the emergence of self-assembly as a research field in the context of materials science and nanotechnology. The second section outlines the metaphysical implications and will emphasize a sharp contrast between the ontology underlying two practices of self-assembly developed under the umbrella of synthetic biology. And unexpectedly, we shall see that chemists are less on the reductionist side than most synthetic biologists. Finally, the third section ventures some reflections on the kind of design involved in self-assembly practices.

  6. Biochemical ripening of dredged sediments. Part 1. Kinetics of biological organic matter mineralization and chemical sulfur oxidation

    NARCIS (Netherlands)

    Vermeulen, J.; Gool, M.P.M. van; Dorleijn, A.S.; Joziasse, J.; Bruning, H.; Rulkens, W.H.; Grotenhuis, J.T.C.

    2007-01-01

    After dredged sediments have settled in a temporary upland disposal site, ripening starts, which turns waterlogged sediment into aerated soil. Aerobic biological mineralization of organic matter (OM) and chemical oxidation of reduced sulfur compounds are the major biochemical ripening processes. Qua

  7. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Science.gov (United States)

    2010-07-01

    ... constant, L/g mixed liquor volatile suspended solids (MLVSS)-hr KL=Liquid-phase mass transfer coefficient, m/s Ks=Monod biorate constant at half the maximum rate, g/m3 III. Test Procedure for Determination... of the open biological treatment unit. An appropriate value of the biorate constant, Ks,...

  8. Development of a coupled physical-biological ecosystem model ECOSMO - Part I: Model description and validation for the North Sea

    DEFF Research Database (Denmark)

    Schrum, Corinna; Alekseeva, I.; St. John, Michael

    2006-01-01

    A 3-D coupled biophysical model ECOSMO (ECOSystem MOdel) has been developed. The biological module of ECOSMO is based on lower trophic level interactions between two phyto- and two zooplankton components. The dynamics of the different phytoplankton components are governed by the availability of t...... trophic level. (c) 2006 Elsevier B.V All rights reserved....

  9. Design and development of pneumatic riveting pressure assembly machine for shell parts%壳体类零件气动铆压装配机床设计开发

    Institute of Scientific and Technical Information of China (English)

    杨孟涛; 金红伟; 王晓梅; 杨永刚

    2012-01-01

    为了实现壳体类零件需要从圆周或周边进行铆压装配的工艺要求,创新设计了新颖的机械执行结构,开发制造了一种新型的气动铆压装配机床.根据机床工艺流程,采用基于PLC和文本编辑器的控制方式,实现了机床的自动化.该机床为铆压装配机床的设计开发提供了新的思路和方法.%In order to achieve riveting assembly process requirements for the shell parts from the circumference or perimeter, a novel pneumatic riveting pressure assembly machine with innovative mechanical actuator was developed and fabricated. According to the assembly process, using the control method based on PLC and text editor to realize automatic machine. The machine provides new ideas and methods for the design and development of riveting assembly machine.

  10. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

    Energy Technology Data Exchange (ETDEWEB)

    Torella, JP; Boehm, CR; Lienert, F; Chen, JH; Way, JC; Silver, PA

    2013-12-28

    In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.

  11. On rapeseed meals. Part XXVI. Some remarks on the biological value of rapeseed meal proteins after silage.

    Science.gov (United States)

    Borowska, J; Cichon, R; Kozłowska, H; Rutkowski

    1978-01-01

    The influence of propionic bacteria on the biological value of potato-rapeseed meal protein ensilage was investigated. The inoculation of the ensilage with Propionibacterium Petersoni T 112 led to the reduction of the content of goitrogenous compounds (isothiocyanates and oxazolidinethiones) and to an increase of the nutritive value (NPU, PER) of the rapeseed protein. The increase of the protein value is greater by the application of propionic bacteria than by toasting of rapeseed meal.

  12. Systematic Review of Breast Cancer Biology in Developing Countries (Part 2): Asian Subcontinent and South East Asia

    Energy Technology Data Exchange (ETDEWEB)

    Bhikoo, Riyaz, E-mail: riyazbhikoo@gmail.com; Srinivasa, Sanket; Yu, Tzu-Chieh [Department of Surgery, South Auckland Clinical School, University of Auckland, Auckland 1640 (New Zealand); Moss, David [Department of Surgery, Middlemore Hospital, Auckland 1640 (New Zealand); Hill, Andrew G [Department of Surgery, South Auckland Clinical School, University of Auckland, Auckland 1640 (New Zealand)

    2011-05-13

    There has been no systematic appraisal of ethnicity-based variations in breast cancer (BC) biology amongst women from developing countries. A qualitative systematic review was conducted of breast cancer size, stage, grade, histological type, extra-mammary involvement, hormone receptor status as well as patient demographics. This review includes patients from Africa, the Middle East, Eastern Europe, Mexico, the Caribbean and South America. BC in these regions present at an earlier age with large aggressive tumours. Distant metastases are frequently present at the time of diagnosis. African women have a higher frequency of triple negative tumours. Over half of Middle Eastern women have lymph node involvement at the time of diagnosis. Despite experiencing a lower incidence compared to the Ashkenazi Jewish population, Palestinian women have poorer five-year survival outcomes. The majority of women from Mexico and South America have stage two or three disease whilst over sixty percent of women from Eastern Europe have either stage one or stage two disease. The biological characteristics of BC in the Caribbean cannot be fully assessed due to a paucity of data from the region. BC amongst the developing world is characterised by an early peak age of onset with aggressive biological characteristics. Strategies that improve breast cancer awareness, address amenable risk factors and improve early detection are essential.

  13. Systematic Review of Breast Cancer Biology in Developing Countries (Part 2: Asian Subcontinent and South East Asia

    Directory of Open Access Journals (Sweden)

    Andrew G Hill

    2011-05-01

    Full Text Available There has been no systematic appraisal of ethnicity-based variations in breast cancer (BC biology amongst women from developing countries. A qualitative systematic review was conducted of breast cancer size, stage, grade, histological type, extra-mammary involvement, hormone receptor status as well as patient demographics. This review includes patients from Africa, the Middle East, Eastern Europe, Mexico, the Caribbean and South America. BC in these regions present at an earlier age with large aggressive tumours. Distant metastases are frequently present at the time of diagnosis. African women have a higher frequency of triple negative tumours. Over half of Middle Eastern women have lymph node involvement at the time of diagnosis. Despite experiencing a lower incidence compared to the Ashkenazi Jewish population, Palestinian women have poorer five-year survival outcomes. The majority of women from Mexico and South America have stage two or three disease whilst over sixty percent of women from Eastern Europe have either stage one or stage two disease. The biological characteristics of BC in the Caribbean cannot be fully assessed due to a paucity of data from the region. BC amongst the developing world is characterised by an early peak age of onset with aggressive biological characteristics. Strategies that improve breast cancer awareness, address amenable risk factors and improve early detection are essential.

  14. World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia. Part 3: Update 2015 Management of special circumstances: Depression, Suicidality, substance use disorders and pregnancy and lactation.

    Science.gov (United States)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas; Lieberman, Jeffrey; Glenthøj, Birte; Gattaz, Wagner F; Thibaut, Florence; Möller, Hans-Jürgen

    2015-04-01

    These updated guidelines are based on the first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in the years 2005 and 2006. For this 2015 revision, all available publications pertaining to the biological treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations which are clinically and scientifically relevant. They are intended to be used by all physicians diagnosing and treating patients with schizophrenia. Based on the first version of these guidelines a systematic review, as well as a data extraction from national guidelines have been performed for this update. The identified literature was evaluated with respect to the strength of evidence for its efficacy and subsequently categorised into six levels of evidence (A-F) and five levels of recommendation (1-5). This third part of the updated guidelines covers the management of the following specific treatment circumstances: comorbid depression, suicidality, various comorbid substance use disorders (legal and illegal drugs), and pregnancy and lactation. These guidelines are primarily concerned with the biological treatment (including antipsychotic medication and other pharmacological treatment options) of patients with schizophrenia.

  15. World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia, part 2: update 2012 on the long-term treatment of schizophrenia and management of antipsychotic-induced side effects.

    Science.gov (United States)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas; Lieberman, Jeffrey; Glenthoj, Birte; Gattaz, Wagner F; Thibaut, Florence; Möller, Hans-Jürgen

    2013-02-01

    Abstract These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in 2006. For this 2012 revision, all available publications pertaining to the biological treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations that are clinically and scientifically meaningful. They are intended to be used by all physicians diagnosing and treating people suffering from schizophrenia. Based on the first version of these guidelines, a systematic review of the MEDLINE/PUBMED database and the Cochrane Library, in addition to data extraction from national treatment guidelines, has been performed for this update. The identified literature was evaluated with respect to the strength of evidence for its efficacy and then categorised into six levels of evidence (A-F) and five levels of recommendation (1-5) ( Bandelow et al. 2008a ,b, World J Biol Psychiatry 9:242, see Table 1 ). This second part of the updated guidelines covers long-term treatment as well as the management of relevant side effects. These guidelines are primarily concerned with the biological treatment (including antipsychotic medication and other pharmacological treatment options) of adults suffering from schizophrenia.

  16. DMSP and DMS dynamics during a mesoscale iron fertilization experiment in the Northeast Pacific Part II: Biological cycling

    Science.gov (United States)

    Merzouk, Anissa; Levasseur, Maurice; Scarratt, Michael G.; Michaud, Sonia; Rivkin, Richard B.; Hale, Michelle S.; Kiene, Ronald P.; Price, Neil M.; Li, William K. W.

    2006-10-01

    Dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) biological cycling rates were determined during SERIES, a mesoscale iron-fertilization experiment conducted in the high-nutrient low-chlorophyll (HNLC) waters of the northeast subarctic Pacific. The iron fertilization resulted in the rapid development of a nanoplankton assemblage that persisted for 11 days before abruptly crashing. The nanoplankton bloom was followed by a diatom bloom, accompanied by an important increase in bacterial abundance and production. These iron-induced alterations of the plankton assemblage coincided with changes in the size and biological cycling of the DMSP and DMS pools. The initial nanoplankton bloom resulted in increases in particulate DMSP (DMSPp; 77-180 nmol L -1), dissolved DMSP (DMSPd; 1-24 nmol L -1), and biological gross (0.11-0.78 nmol L -1 h -1) and net (0.04-0.74 nmol L -1 h -1) DMS production rates. During the nanoplankton bloom, DMSPd consumption by bacteria exceeded their sulfur demand and the excess sulfur was probably released as DMS, consistent with the high gross DMS production rates observed during that period. The crash of the nanoplankton bloom was marked by the rapid decline of DMSPp, DMSPd, and gross DMS production to their initial values. Following the crash of the nanoplankton bloom, bacterial production and estimated sulfur demand reached transient maxima of 9.3 μg C L -1 d -1 and 14.2 nmol S L -1 d -1, respectively. During this period of high bacterial production, bacterial DMSPd consumption was also very high (6 nmol L -1 h -1), but none of the consumed DMSPd was converted into DMS and a net biological DMS consumption was measured. This transient period initiated a rapid decrease in DMS concentrations inside the iron-enriched patch, which persisted during the following diatom bloom due to low biological gross and net DMS production that prevented the replenishment of DMS. Our results show that the impact of Fe fertilization on DMS production in

  17. Top-down assembly design using assembly features

    Institute of Scientific and Technical Information of China (English)

    石万凯; DENEUX; Dominique; 等

    2002-01-01

    The primary task of top-down assembly desig is to define a product's detailed physical description satisfying its functional requirements identified during the functional design phase.The implementation of this design process requires two things,that is ,product functional representation and a general assembly model.Product functions are not only the formulation of a customer's needs,but also the input data of assembly design.A general assembly model is to support the evolving process of the elaboration of a product structure.The assembly feature of extended concept is taken as a functional carrier,which is a generic relation among assembly-modeled entities.The model of assembly features describes the link between product functions and form features of parts.On the basis of this link,the propagation of design modifications is discussed so as to preserve the functionality and the coherence of the assembly model.The formal model of assembly design process describes the top-down process of creating an assembly model.This formal model is represented by the combination of assembly feature operations,the assembly model and the evaluation process.A design case study is conducted to verify the applicability of the presented approaches.

  18. Geometric reasoning about assembly tools

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, R.H.

    1997-01-01

    Planning for assembly requires reasoning about various tools used by humans, robots, or other automation to manipulate, attach, and test parts and subassemblies. This paper presents a general framework to represent and reason about geometric accessibility issues for a wide variety of such assembly tools. Central to the framework is a use volume encoding a minimum space that must be free in an assembly state to apply a given tool, and placement constraints on where that volume must be placed relative to the parts on which the tool acts. Determining whether a tool can be applied in a given assembly state is then reduced to an instance of the FINDPLACE problem. In addition, the author presents more efficient methods to integrate the framework into assembly planning. For tools that are applied either before or after their target parts are mated, one method pre-processes a single tool application for all possible states of assembly of a product in polynomial time, reducing all later state-tool queries to evaluations of a simple expression. For tools applied after their target parts are mated, a complementary method guarantees polynomial-time assembly planning. The author presents a wide variety of tools that can be described adequately using the approach, and surveys tool catalogs to determine coverage of standard tools. Finally, the author describes an implementation of the approach in an assembly planning system and experiments with a library of over one hundred manual and robotic tools and several complex assemblies.

  19. 40 CFR Appendix C to Part 63 - Determination of the Fraction Biodegraded (Fbio) in a Biological Treatment Unit

    Science.gov (United States)

    2010-07-01

    ... Units with Multiple Mixing Zones,” is a source for further information concerning how to determine the... AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED) Pt. 63, App. C Appendix C to Part 63—Determination of... covered and vented through a closed vent system to an air pollution control device. The determination...

  20. [Investigation of biologically active compounds at the Department of Organic Chemistry of University of Debrecen 1992-2009. Part III].

    Science.gov (United States)

    Antus, Sándor

    2010-01-01

    The author briefly reviews the beginning of the carbohydrate chemistry in Hungary with special regard to the results achieved at the Department of Organic Chemistry of University of Debrecen and summarizes the most important synthetic and pharmaceutical results obtained in this field between 1992-2009, part III.

  1. Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

    Science.gov (United States)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

  2. Surface functionalization of bioactive glasses with natural molecules of biological significance, part II: Grafting of polyphenols extracted from grape skin

    Science.gov (United States)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Polyphenols, as one of the most important family of phytochemicals protective substances from grape fruit, possess various biological activities and health-promoting benefits, for example: inhibition of some degenerative diseases, cardiovascular diseases and certain types of cancers, reduction of plasma oxidative stress and slowing aging. The combination of polyphenols and biomaterials may have good potential to reach good bioavailability and controlled release, as well as to give biological signaling properties to the biomaterial surfaces. In this research, conventional solvent extraction was developed for obtaining polyphenols from dry grape skins. The Folin&Ciocalteu method was used to determine the amount of total polyphenols in the extracts. Surface functionalization of two bioactive glasses (SCNA and CEL2) was performed by grafting the extracted polyphenols on their surfaces. The effectiveness of the functionalization was tested by UV spectroscopy, which analyzes the amount of polyphenols in the uptake solution (before and after functionalization) and on solid samples, and XPS, which analyzes the presence of phenols on the material surface.

  3. Observations on the biology of Afrotropical Hesperiidae (Lepidoptera) with particular reference to Kenya. Part 10. Pyrginae, Carcharodini.

    Science.gov (United States)

    Cock, Matthew J W

    2016-10-05

    Partial life histories are presented for Spialia kituina (Karsch), S. spio (Linnaeus), S. diomus (Hopffer), S. colotes transvaaliae (Trimen), S. dromus (Plötz), S. ploetzi (Aurivillius), S. zebra bifida Higgins and Gomalia elma elma (Trimen). All feed on species of Malvaceae. An earlier record from Kenya of Melhania velutina as the food plant of S. depauperata depauperata (Strand) was based on a misidentification and there are no known records of the food plant of this subspecies. Spialia ferax (Wallengren) stat. rev. is considered a valid species rather than a subspecies of S. diomus, based on significant differences in wing patterns, the shape of the valves, a zone where neither occurs, no signs that a cline is involved, and differences in the colouring and markings of the caterpillars. The convergence of the biology of the chequered skippers of the tribes Carcharodini, Pyrgini and Celaenorrhini is discussed.

  4. Illustrating how mechanical assemblies work

    KAUST Repository

    Mitra, Niloy J.

    2010-07-26

    How things work visualizations use a variety of visual techniques to depict the operation of complex mechanical assemblies. We present an automated approach for generating such visualizations. Starting with a 3D CAD model of an assembly, we first infer the motions of individual parts and the interactions between parts based on their geometry and a few user specified constraints. We then use this information to generate visualizations that incorporate motion arrows, frame sequences and animation to convey the causal chain of motions and mechanical interactions between parts. We present results for a wide variety of assemblies. © 2010 ACM.

  5. Illustrating how mechanical assemblies work

    KAUST Repository

    Mitra, Niloy J.

    2013-01-01

    How-things-work visualizations use a variety of visual techniques to depict the operation of complex mechanical assemblies. We present an automated approach for generating such visualizations. Starting with a 3D CAD model of an assembly, we first infer the motions of the individual parts and the interactions across the parts based on their geometry and a few user-specified constraints. We then use this information to generate visualizations that incorporate motion arrows, frame sequences, and animation to convey the causal chain of motions and mechanical interactions across parts. We demonstrate our system on a wide variety of assemblies. © 2013 ACM 0001-0782/13/01.

  6. Part project 1. Methods and concepts of biological waste composting. Comparison - evaluation - recommendations; Teilbericht 1. Verfahren und Konzepte der Bioabfallkompostierung. Vergleich - Bewertung - Empfehlungen

    Energy Technology Data Exchange (ETDEWEB)

    Gronauer, A.; Helm, M.; Schoen, H. [Bayerische Landesanstalt fuer Landtechnik der Technischen Univ. Muenchen-Weihenstephan (Germany)

    1997-12-31

    Topics of this article are: composting of biological wastes; techniques, operation modes, regional concepts, engineering, hygienical, ecological, economical aspects. (SR) gardening plots. The project comprised three parts: Composting techniques, applications of compost in agriculture and gardening, and applications in landscaping. This volume comprises the summaries of the three part-projects. (orig./SR) [Deutsch] Das uebergeordnete Ziel des Weihenstephaner Verbundvorhabens bestand darin, fachliche Grundlagen und Entscheidungshilfen fuer den Bereich der Kompostierung und der Verwertung von biogenen Reststoffen, insbesondere der getrennt erfassten organischen Abfaelle aus den Haushaltungen (Bioabfall), zu schaffen. In diesem Rahmen sollen sowohl verschiedene Verfahren und Techniken der Kompostierung als auch regionale Konzepte hinsichtlich verfahrenstechnischer, hygienischer, oekologischer, oekonomischer und die Entsorgungssicherheit betreffender Aspekte untersucht und bewertet werden. (orig./SR)

  7. New insights into the structure, assembly and biological roles of 10-12 nm connective tissue microfibrils from fibrillin-1 studies.

    Science.gov (United States)

    Jensen, Sacha A; Handford, Penny A

    2016-04-01

    The 10-12 nm diameter microfibrils of the extracellular matrix (ECM) impart both structural and regulatory properties to load-bearing connective tissues. The main protein component is the calcium-dependent glycoprotein fibrillin, which assembles into microfibrils at the cell surface in a highly regulated process involving specific proteolysis, multimerization and glycosaminoglycan interactions. In higher metazoans, microfibrils act as a framework for elastin deposition and modification, resulting in the formation of elastic fibres, but they can also occur in elastin-free tissues where they perform structural roles. Fibrillin microfibrils are further engaged in a number of cell matrix interactions such as with integrins, bone morphogenetic proteins (BMPs) and the large latent complex of transforming growth factor-β (TGFβ). Fibrillin-1 (FBN1) mutations are associated with a range of heritable connective disorders, including Marfan syndrome (MFS) and the acromelic dysplasias, suggesting that the roles of 10-12 nm diameter microfibrils are pleiotropic. In recent years the use of molecular, cellular and whole-organism studies has revealed that the microfibril is not just a structural component of the ECM, but through its network of cell and matrix interactions it can exert profound regulatory effects on cell function. In this review we assess what is known about the molecular properties of fibrillin that enable it to assemble into the 10-12 nm diameter microfibril and perform such diverse roles.

  8. A Self-Assembled Aggregate Composed of a Fatty Acid Membrane and the Building Blocks of Biological Polymers Provides a First Step in the Emergence of Protocells

    Science.gov (United States)

    Black, Roy A.; Blosser, Matthew C.

    2016-01-01

    We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then explain how the conformational constraints and altered chemical environment due to binding of the components to the membrane could facilitate the formation of nucleosides, oligonucleotides and peptides. We conclude by discussing how the resulting oligomers, even if short and random, could have increased vesicle stability and growth more than their building blocks did, and how competition among these vesicles could have led to longer polymers with complex functions. PMID:27529283

  9. Self-assembled drug delivery systems. Part 7: hepatocyte-targeted nanoassemblies of an adefovir lipid derivative with cytochrome P450-triggered drug release.

    Science.gov (United States)

    Du, Lina; Wu, Lailong; Jin, Yiguang; Jia, Junwei; Li, Miao; Wang, Yu

    2014-09-10

    A novel strategy was used in the design of self-assembled drug delivery systems (SADDSs) in this study. The nanoassemblies of an amphiphilic adefovir lipid derivative were prepared and demonstrated to have the functions of hepatocyte targeting, enzyme-triggered drug release and high anti-hepatitis effect. An amphiphilic adefovir lipid derivative, N-lauroyl-1-(3-chlorophenyl)-1,3-propanyl phosphonyl adefovir (LCPA) was prepared and formed the nanoassemblies by injecting the mixture of LCPA and another amphiphilic polymer, d-galactide polyoxyethylene (20) cetyl ether (GPCE) (ca. 20:1, mol/mol) into water. The nanoassemblies were very stable and showed negative charge. LCPA was sensitive to the cytochrome P450 isozymes that were expressed predominantly in the hepatocytes to produce adefovir. GPCE contained a long hydrophilic chain and a galactose ligand targeting the asialoglycoprotein receptors overexpressed on the surface of hepatocytes. The nanoassemblies showed the long-circulating and liver targeting effects according to the results of pharmacokinetics, tissue distribution and fluorescence imagination after bolus intravenous administration of the nanoassemblies to the mice. The highly efficient hepatitis B treatment was achieved by 10 day continuous administration of the nanoassemblies to the HBV-infected mice. Many functions were combined in the nanoassemblies, including prodrug, molecular self-assembly, nanotechnology, long-circulating, hepatocyte targeting and hepatocyte over expressing enzyme-triggered drug release.

  10. On Constraints in Assembly Planning

    Energy Technology Data Exchange (ETDEWEB)

    Calton, T.L.; Jones, R.E.; Wilson, R.H.

    1998-12-17

    Constraints on assembly plans vary depending on product, assembly facility, assembly volume, and many other factors. Assembly costs and other measures to optimize vary just as widely. To be effective, computer-aided assembly planning systems must allow users to express the plan selection criteria that appIy to their products and production environments. We begin this article by surveying the types of user criteria, both constraints and quality measures, that have been accepted by assembly planning systems to date. The survey is organized along several dimensions, including strategic vs. tactical criteria; manufacturing requirements VS. requirements of the automated planning process itself and the information needed to assess compliance with each criterion. The latter strongly influences the efficiency of planning. We then focus on constraints. We describe a framework to support a wide variety of user constraints for intuitive and efficient assembly planning. Our framework expresses all constraints on a sequencing level, specifying orders and conditions on part mating operations in a number of ways. Constraints are implemented as simple procedures that either accept or reject assembly operations proposed by the planner. For efficiency, some constraints are supplemented with special-purpose modifications to the planner's algorithms. Fast replanning enables an interactive plan-view-constrain-replan cycle that aids in constraint discovery and documentation. We describe an implementation of the framework in a computer-aided assembly planning system and experiments applying the system to a number of complex assemblies, including one with 472 parts.

  11. Diretrizes da World Federation of Societies of Biological Psychiatry (WFSBP para tratamento biológico de transtornos depressivos unipolares, 1ª parte: tratamento agudo e de continuação do transtorno depressivo maior World Federation of Societies of Biological Psychiatry (WFSBP Guidelines for biological treatment of unipolar depressive disorders, part 1: acute and continuation treatment of major depressive disorder

    Directory of Open Access Journals (Sweden)

    Michael Bauer

    2009-01-01

    Full Text Available Estas diretrizes práticas para o tratamento biológico de transtornos depressivos unipolares foram desenvolvidas por uma Força-Tarefa internacional da Federação Mundial de Sociedades de Psiquiatria Biológica (WFSBP. O objetivo ao desenvolver tais diretrizes foi rever sistematicamente todas as evidências existentes referentes ao tratamento de transtornos depressivos unipolares e produzir uma série de recomendações práticas com significado clínico e científico, baseadas nas evidências existentes. Têm como objetivo seu uso por todos os médicos que atendam e tratem pacientes com essas afecções. Os dados usados para o desenvolvimento das diretrizes foram extraídos primariamente de várias diretrizes e painéis nacionais de tratamento para transtornos depressivos, bem como de metanálises e revisões sobre a eficácia dos antidepressivos e outras intervenções de tratamento biológico identificadas por uma busca no banco de dados MEDLINE e Cochrane Library. A literatura identificada foi avaliada quanto à força das evidências sobre sua eficácia e, então, categorizada em quatro níveis de evidências (A a D. Esta primeira parte das diretrizes abrange definição, classificação, epidemiologia e evolução dos transtornos depressivos unipolares, bem como tratamento das fases aguda e de manutenção. As diretrizes se referem primariamente ao tratamento biológico (incluindo antidepressivos, outros medicamentos psicofarmacológicos e hormonais, eletroconvulsoterapia, fototerapia, estratégias terapêuticas complementares e novas de adultos jovens e também, embora em menor grau, de crianças, adolescentes e adultos idosos.These practice guidelines for the biological treatment of unipolar depressive disorders were developed by an international Task Force of the World Federation of Societies of Biological Psychiatry (WFSBP. The goal for developing these guidelines was to systematically review all available evidence pertaining to the

  12. El nuevo aspecto de la Revista Peruana de Biología / La CI+T y nuestra parte

    Directory of Open Access Journals (Sweden)

    Leonardo Romero

    2006-10-01

    Full Text Available Con el volumen 13 iniciamos una serie de cambios en la Revista Peruana de Biología. Estos cambios se relacionan a la búsqueda de economía del espacio y la mejor presentación preparándonos para el crecimiento futuro. Esperamos así tener la capacidad de incrementar la cantidad de artículos por número de la revista de una manera económica. El más visible de los cambios se refiere al tamaño y a la diagramación. Pasamos del tama- ño menudo (184 x 261 mm al tamaño A4 (210 x 297 mm; la diferencia de costos entre ambas es pequeña y la ganancia en espacio es significativa, además permite la exposición de una adecuada área para figuras. Otro cambio se refiere a la tipografía, pasamos de un texto en Time Roman 10 a Garamond 10, esta última es una letra menuda que permite ahorrar espacio y resalta las letras cursivas. También dejamos las variedades de letras para utilizar la Arial 10 en títulos, resúmenes, leyendas y la Book Antiqua para las tablas.

  13. Pulp-dentin biology in restorative dentistry. Part 4: Dental caries--characteristics of lesions and pulpal reactions.

    Science.gov (United States)

    Bjørndal, L; Mjör, I A

    2001-10-01

    The infectious disease dental caries results in lesions that may affect enamel, dentin, pulp, and cementum. If a caries lesion has progressed to the stage at which it requires restorative intervention, it is important that the clinician understand the tissue changes in the dentin that are likely to have taken place during lesion development. Until the present, no major distinction between the restorative treatment of active (rapidly progressing) and arrested (slowly progressing) lesions has been made, despite the fact that the two conditions exhibit major differences in tissue changes in the pulp-dentin complex. Intratubular changes and tertiary dentin formation will affect the outcome of the restorative treatment. In unaffected dentin and in rapidly progressing lesions, permeable tubules persist, and when the preparation of carious teeth results in the opening of unaffected dentin, greater care must be taken in all phases of the restorative procedures than if the dentin is impermeable. An active, deep lesion can be changed to an arrested lesion by a two-step excavation approach. Optimal assessment of the prevailing clinical conditions can only be made on the basis of thorough knowledge of the biology of the pulp-dentin organ.

  14. Evaluation of polyphenolic fraction isolated from aerial parts of Tribulus pterocarpus on biological properties of blood platelets in vitro.

    Science.gov (United States)

    Olas, Beata; Morel, Agnieszka; Hamed, Arafa I; Oleszek, Wieslaw; Stochmal, Anna

    2013-01-01

    The antiplatelet and antioxidative activity of polyphenolic fraction isolated from aerial parts of Tribulus pterocarpus in blood platelets stimulated by thrombin was studied. Thrombin as a strong physiological agonist induces the enzymatic peroxidation of endogenous arachidonic acid, the formation of different reactive oxygen species, including superoxide anion radicals ([Formula: see text](·)) and the platelet aggregation. Therefore, the aim of our study was to assess if the polyphenolic fraction from aerial parts of T. pterocarpus may change the biological properties of blood platelets activated by thrombin. We used cytochrome c reduction method to test the ability of this fraction to change [Formula: see text](·) generation in platelets. Arachidonic acid metabolism was measured by the level of thiobarbituric acid reactive substances (TBARS) and by the production of 8-epi-prostaglandin (8-EPI) F(2). Moreover, we determined the effects of the fraction on blood platelet aggregation induced by thrombin. We observed that the polyphenolic fraction from T. pterocarpus reduced [Formula: see text](·), 8-EPI and TBARS production in these cells. The ability of the fraction to decrease the [Formula: see text](·) generation in blood platelets supports the importance of free radicals in platelet functions, including aggregation process. This study may suggest that the tested plant fraction might be a good candidate for protecting blood platelets against changes of their biological functions, which may be associated with the pathogenesis of different cardiovascular disorders.

  15. DNA Assembly in 3D Printed Fluidics.

    Directory of Open Access Journals (Sweden)

    William G Patrick

    Full Text Available The process of connecting genetic parts-DNA assembly-is a foundational technology for synthetic biology. Microfluidics present an attractive solution for minimizing use of costly reagents, enabling multiplexed reactions, and automating protocols by integrating multiple protocol steps. However, microfluidics fabrication and operation can be expensive and requires expertise, limiting access to the technology. With advances in commodity digital fabrication tools, it is now possible to directly print fluidic devices and supporting hardware. 3D printed micro- and millifluidic devices are inexpensive, easy to make and quick to produce. We demonstrate Golden Gate DNA assembly in 3D-printed fluidics with reaction volumes as small as 490 nL, channel widths as fine as 220 microns, and per unit part costs ranging from $0.61 to $5.71. A 3D-printed syringe pump with an accompanying programmable software interface was designed and fabricated to operate the devices. Quick turnaround and inexpensive materials allowed for rapid exploration of device parameters, demonstrating a manufacturing paradigm for designing and fabricating hardware for synthetic biology.

  16. Dynamic nanoparticle assemblies.

    Science.gov (United States)

    Wang, Libing; Xu, Liguang; Kuang, Hua; Xu, Chuanlai; Kotov, Nicholas A

    2012-11-20

    a molecule from atoms. Finer classification of NP assemblies in accord with established conventions in the field may include different size dimensionalities: discrete assemblies (artificial molecules) and one-dimensional (spaced chains), two-dimensional (sheets), and three-dimensional (superlattices, twisted structures) assemblies. Notably, these dimensional attributes must be regarded as primarily topological in nature because all of these superstructures can acquire complex three-dimensional shapes. We discuss three primary strategies used to prepare NP superstructures: (1) anisotropy-based assemblies utilizing either intrinsic force field anisotropy around NPs or external anisotropy associated with templates or applied fields, (2) assembly methods utilizing uniform NPs with isotropic interactions, and (3) methods based on mutual recognition of biomolecules, such as DNA and antigen-antibody interactions. We consider optical, electronic, and magnetic properties of dynamic superstructures, focusing primarily on multiparticle effects in NP superstructures as represented by surface plasmon resonance, NP-NP charge transport, and multibody magnetization. Unique properties of NP superstructures are being applied to biosensing, drug delivery, and nanoelectronics. For both Class 1 and Class 2 dynamic assemblies, biosensing is the most dominant and well-developed area of dynamic nanostructures being successfully transitioned into practice. We can foresee the rapid development of dynamic NP assemblies toward applications in harvesting of dissipated energy, photonics, and electronics. The final part of this Account is devoted to the fundamental questions facing dynamic assemblies of NPs in the future.

  17. Physicochemical and biological properties of self-assembled antisense/poly(amidoamine dendrimer nanoparticles: the effect of dendrimer generation and charge ratio

    Directory of Open Access Journals (Sweden)

    Alireza Nomani

    2010-05-01

    Full Text Available Alireza Nomani1,6, Ismaeil Haririan1,5, Ramin Rahimnia2,4, Shamileh Fouladdel2, Tarane Gazori1, Rassoul Dinarvand1, Yadollah Omidi3, Ebrahim Azizi2,41Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; 2Molecular Research Lab, Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; 3Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; 4Department of Medical Biotechnology, School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran, Iran; 5Biomaterials Research Center (BRC Tehran, Iran; 6Department of Pharmaceutics, Faculty of Pharmacy, Zanjan University of Medical Sciences, Zanjan, IranAbstract: To gain a deeper understanding of the physicochemical phenomenon of self-assembled nanoparticles of different generations and ratios of poly (amidoamine dendrimer (PAMAM dendrimer and a short-stranded DNA (antisense oligonucleotide, multiple methods were used to characterize these nanoparticles including photon correlation spectroscopy (PCS; zeta potential measurement; and atomic force microscopy (AFM. PCS and AFM results revealed that, in contrast to larger molecules of DNA, smaller molecules produce more heterodisperse and large nanoparticles when they are condensed with a cationic dendrimer. AFM images also showed that such nanoparticles were spherical. The stability of the antisense content of the nanoparticles was investigated over different charge ratios using polyacrylamide gel electrophoresis. It was clear from such analyses that much more than charge neutrality point was required to obtain stable nanoparticles. For cell uptake, self-assembled nanoparticles were prepared with PAMAM G5 and 5’-FITC labeled antisense and the uptake experiment was carried out in T47D cell culture. This investigation also shows that the cytotoxicity of the nanoparticles was

  18. Synthesis, biological evaluation, and docking studies of new 2-furylbenzimidazoles as anti-angiogenic agents: part II.

    Science.gov (United States)

    Temirak, Ahmed; Shaker, Yasser M; Ragab, Fatma A F; Ali, Mamdouh M; Soliman, Salwa M; Mortier, Jeremie; Wolber, Gerhard; Ali, Hamed I; El Diwani, Hoda I

    2014-04-01

    The 2-(5-methyl-2-furyl)-1H-benzimidazole moiety has shown promising activity against vascular endothelial growth factor (VEGF)-induced angiogenesis. In part I of this study, we have synthesized new analogs and tested their anti-angiogenic potentials. Here, we continue our previous study with different new analogs. Some compounds show promising cytotoxic activity against the human breast cancer cell line MCF-7, with IC50 in the range of 7.80-13.90 µg/mL, and exhibited remarkable in vitro inhibition against VEGF in the MCF-7 cancer cell line, with 95-98% of inhibition in comparison to tamoxifen as reference (IC50: 8.00 µg/mL, % of inhibition = 98%). Additionally, a molecular docking study was carried out to gain insight into plausible binding modes and to understand the structure-activity relationships of the synthesized compounds.

  19. Development of drug loaded nanoparticles for tumor targeting. Part 1: synthesis, characterization, and biological evaluation in 2D cell cultures

    Science.gov (United States)

    El-Dakdouki, Mohammad H.; Puré, Ellen; Huang, Xuefei

    2013-04-01

    Nanoparticles (NPs) are being extensively studied as carriers for drug delivery, but they often have limited penetration inside tumors. We envision that by targeting an endocytic receptor on the cell surface, the uptake of NPs can be significantly enhanced through receptor mediated endocytosis. In addition, if the receptor is recycled to the cell surface, the NP cargo can be transported out of the cells, which is then taken up by neighboring cells thus enhancing solid tumor penetration. To validate our hypothesis, in the first of two articles, we report the synthesis of doxorubicin (DOX)-loaded, hyaluronan (HA) coated silica nanoparticles (SNPs) containing a highly fluorescent core to target CD44, a receptor expressed on the cancer cell surface. HA was conjugated onto amine-functionalized SNPs prepared through an oil-water microemulsion method. The immobilization of the cytotoxic drug DOX was achieved through an acid sensitive hydrazone linkage. The NPs were fully characterized by transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential measurements, thermogravimetric analysis (TGA), UV-vis absorbance, and nuclear magnetic resonance (NMR). Initial biological evaluation experiments demonstrated that compared to ligand-free SNPs, the uptake of HA-SNPs by the CD44-expressing SKOV-3 ovarian cancer cells was significantly enhanced when evaluated in the 2D monolayer cell culture. Mechanistic studies suggested that cellular uptake of HA-SNPs was mainly through CD44 mediated endocytosis. HA-SNPs with immobilized DOX were endocytosed efficiently by the SKOV-3 cells as well. The enhanced tumor penetration and drug delivery properties of HA-SNPs will be evaluated in 3D tumor models in the subsequent paper.Nanoparticles (NPs) are being extensively studied as carriers for drug delivery, but they often have limited penetration inside tumors. We envision that by targeting an endocytic receptor on the cell surface, the uptake of NPs can be

  20. Seismic behaviour of fuel assembly

    Energy Technology Data Exchange (ETDEWEB)

    Song, Heuy Gap; Jhung, Myung Jo [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1993-11-01

    A general approach for the dynamic time-history analysis of the reactor core is presented in this paper as a part of the fuel assembly qualification program. Several detailed core models are set up to reflect the placement of the fuel assemblies within the core shroud. Peak horizontal responses are obtained for each model for the motions induced from earthquake. The dynamic responses such as fuel assembly shear force, bending moment and displacement, and spacer grid impact loads are carefully investigated. Also, the sensitivity responses are obtained for the earthquake motions and the fuel assembly non-linear response characteristics are discussed. (Author) 9 refs., 24 figs., 1 tab.

  1. Synthesis, molecular docking and biological evaluation of 1-phenylsulphonyl-2-(1-methylindol-3-yl)-benzimidazole derivatives as novel potential tubulin assembling inhibitors.

    Science.gov (United States)

    Wang, Yan-Ting; Cai, Xun-Chao; Shi, Tian-Qi; Zhang, Ya-Liang; Wang, Zhong-Chang; Liu, Chang-Hong; Zhu, Hai-Liang

    2016-12-29

    A series of new 1-phenylsulphonyl-2-(1-methylindol-3-yl)-benzimidazole derivatives were designed, synthesized and evaluated as potential inhibitors of tubulin polymerization and anthropic cancer cell lines. Among them, compound 33 displayed the most potent tubulin polymerization inhibitory activity in vitro (IC50  = 1.41 μM) and strong antiproliferative activities against A549, Hela, HepG2 and MCF-7 cell lines in vitro with GI50 value of 1.6, 2.7, 2.9 and 4.3 μM, respectively, comparable with the positive control colchicine (GI50 value of 4.1, 7.2, 9.5 and 14.5 μM, respectively) and CA-4 (GI50 value of 2.2, 4.3, 6.4 and 11.4 μM, respectively). Simultaneously, we evaluated that compound 33 could effectively induce apoptosis of A549 associated with G2/M phase cell cycle arrest. Immunofluorescence microscopy also clearly indicated compound 33 a potent antimicrotubule agent. Docking simulation showed that compound 33 could bind tightly with the colchicine-binding site and act as a tubulin inhibitor. Three-dimensional-QSAR model was also built to provide more pharmacophore understanding that could be used to design new agents with more potent tubulin assembling inhibitory activity in the future.

  2. 基于部位检测和子结构组合的行人检测方法%Pedestrian Detection Method Based on Part Detector and Substructure Assemble

    Institute of Scientific and Technical Information of China (English)

    胡斌; 王生进; 丁晓青

    2009-01-01

    We presented a pedestrian detection method based on part detector and substructure assemble which can be used for driving assistant system or video surveillance system.Firstly we used the head classifier to search the whole image in order to get the ROI(Region of Interesting).Then in each ROI five part detectors including head, torso, leg, left arm and right arm were used individually.Finally we verified the detection result through part detector assemble method based on substructure.Experiments on different database show that our method has high performance in detec-ting pedestrians with numerous poses and partial occlusion in cluttered background.%提出了一种基于部位检测和子结构组合的、可用于辅助驾驶或视频监控系统中行人检测的方法.首先使用头部分类器在整幅图像中检测,得到感兴趣区域;然后在每个感兴趣区域内使用头部、躯干、腿部以及左臂和右臂5个人体部位检测器分别检测并使用基于子结构的检测组合方法对部位检测结果进行组合,以得到最终结果.在不同数据库上的实验结果表明,本方法可以有效地用于移动或静止摄像机所拍摄的视频图像中的多姿态及部分遮挡的行人检测.

  3. The effect of post-sintering treatments on the fatigue and biological behavior of Ti-6Al-4V ELI parts made by selective laser melting.

    Science.gov (United States)

    Benedetti, M; Torresani, E; Leoni, M; Fontanari, V; Bandini, M; Pederzolli, C; Potrich, C

    2017-03-28

    Fatigue resistance and biocompatibility are key parameters for the successful implantation of hard-tissue prostheses, which nowadays are more and more frequently manufactured by selective laser melting (SLM). For this purpose, the present paper is aimed at investigating the effect of post-sintering treatments on the fatigue behavior and biological properties of Ti samples produced by SLM. After the building process, all samples are heat treated to achieve a complete stress relief. The remaining ones are tribofinished with the aim of reducing the surface roughness of the as-sintered condition. Part of the tribofinished samples are then subjected to one of the following post-sintering treatments: (i) shot peening, (ii) hot isostatic pressing (HIP), and (iii) electropolishing. It is found that shot peening and HIP are the most effective treatments to improve the high and the very-high cycle fatigue resistance, respectively. At the same time, they preserve the good biocompatibility ensured by the biomedical Titanium Grade 23.

  4. Simple one step synthesis of nonionic dithiol surfactants and their self-assembling with silver nanoparticles: Characterization, surface properties, biological activity

    Energy Technology Data Exchange (ETDEWEB)

    Abd-Elaal, Ali A., E-mail: ali_ashour5@yahoo.com; Tawfik, Salah M.; Shaban, Samy M.

    2015-07-01

    Graphical abstract: - Highlights: • Nonionic dithiol surfactants were synthesized by simple one step esterification. • The surface activity of the synthesized dithiol surfactants showed high tendency toward adsorption and micellization. • The nanostructure of the synthesized nonionic dithiol surfactants with silver nanoparticles was prepared. • The silver nanoparticles enhanced the biological activity of the synthesized dithiol surfactants. - Abstract: Simple esterification of 2-mercaptoacetic acid and polyethylene glycol with different molecular weights was done to form the desired nonionic dithiol surfactants. The chemical structures of synthesized thiol surfactants were confirmed using FT-IR and {sup 1}H NMR spectra. The surface activity of the synthesized surfactants was determined by measurement of the surface tension at different temperatures. The surface activity measurements showed their high tendency towards adsorption and micellization. The thermodynamic parameters of micellization (ΔG{sub mic}, ΔH{sub mic} and ΔS{sub mic}) and adsorption (ΔG{sub ads}, ΔG{sub ads} and ΔS{sub ads}) showed their tendency toward adsorption at the interfaces and also micellization in the bulk of their solutions. The nanostructure of the synthesized nonionic dithiol surfactants with silver nanoparticles was prepared and investigated using UV and TEM techniques. Screening tests of the synthesized dithiol surfactants and their nanostructure with silver nanoparticles, against gram positive bacteria (Bacillus subtilis and Microccus luteus), gram negative bacteria (Escherichia coli and Bordatella pertussis) and fungi (Aspergillus niger and Candida albicans) showed that they are highly active biocides. The presence of silver nanoparticles enhancement the biological activities of the individual synthesized nonionic dithiol surfactants.

  5. Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler

    Science.gov (United States)

    Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel

    2017-01-01

    This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called digital materials. We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.

  6. Sabot assembly

    Energy Technology Data Exchange (ETDEWEB)

    Bzorgi, Fariborz

    2016-11-08

    A sabot assembly includes a projectile and a housing dimensioned and configured for receiving the projectile. An air pressure cavity having a cavity diameter is disposed between a front end and a rear end of the housing. Air intake nozzles are in fluid communication with the air pressure cavity and each has a nozzle diameter less than the cavity diameter. In operation, air flows through the plurality of air intake nozzles and into the air pressure cavity upon firing of the projectile from a gun barrel to pressurize the air pressure cavity for assisting in separation of the housing from the projectile upon the sabot assembly exiting the gun barrel.

  7. The assembly of C. elegans lamins into macroscopic fibers.

    Science.gov (United States)

    Zingerman-Koladko, Irena; Khayat, Maayan; Harapin, Jan; Shoseyov, Oded; Gruenbaum, Yosef; Salman, Ahmad; Medalia, Ohad; Ben-Harush, Kfir

    2016-10-01

    Intermediate filament (IF) proteins are known mainly by their propensity to form viscoelastic filamentous networks within cells. In addition, IF-proteins are essential parts of various biological materials, such as horn and hagfish slime threads, which exhibit a range of mechanical properties from hard to elastic. These properties and their self-assembly nature made IF-proteins attractive building blocks for biomimetic and biological materials in diverse applications. Here we show that a type V IF-protein, the Caenorhabditis elegans nuclear lamin (Ce-lamin), is a promising building block for protein-based fibers. Electron cryo-tomography of vitrified sections enabled us to depict the higher ordered assembly of the Ce-lamin into macroscopic fibers through the creation of paracrystalline fibers, which are prominent in vitro structures of lamins. The lamin fibers respond to tensile force as other IF-protein-based fibers, i.e., hagfish slime threads, and possess unique mechanical properties that may potentially be used in certain applications. The self-assembly nature of lamin proteins into a filamentous structure, which is further assembled into a complex network, can be easily modulated. This knowledge may lead to a better understanding of the relationship in IF-proteins-based fibers and materials, between their hierarchical structures and their mechanical properties.

  8. Simple one step synthesis of nonionic dithiol surfactants and their self-assembling with silver nanoparticles: Characterization, surface properties, biological activity

    Science.gov (United States)

    Abd-Elaal, Ali A.; Tawfik, Salah M.; Shaban, Samy M.

    2015-07-01

    Simple esterification of 2-mercaptoacetic acid and polyethylene glycol with different molecular weights was done to form the desired nonionic dithiol surfactants. The chemical structures of synthesized thiol surfactants were confirmed using FT-IR and 1H NMR spectra. The surface activity of the synthesized surfactants was determined by measurement of the surface tension at different temperatures. The surface activity measurements showed their high tendency towards adsorption and micellization. The thermodynamic parameters of micellization (ΔGmic, ΔHmic and ΔSmic) and adsorption (ΔGads, ΔGads and ΔSads) showed their tendency toward adsorption at the interfaces and also micellization in the bulk of their solutions. The nanostructure of the synthesized nonionic dithiol surfactants with silver nanoparticles was prepared and investigated using UV and TEM techniques. Screening tests of the synthesized dithiol surfactants and their nanostructure with silver nanoparticles, against gram positive bacteria (Bacillus subtilis and Microccus luteus), gram negative bacteria (Escherichia coli and Bordatella pertussis) and fungi (Aspergillus niger and Candida albicans) showed that they are highly active biocides. The presence of silver nanoparticles enhancement the biological activities of the individual synthesized nonionic dithiol surfactants.

  9. Synthetic Biology with Cytochromes P450 Using Photosynthetic Chassis

    DEFF Research Database (Denmark)

    Gnanasekaran, Thiyagarajan

    Synthetic biology is a rapidly growing engineering discipline in biology. It aims at building novel biological systems that do not exist in nature by selecting the interchangeable standardized biological parts that are already available in the nature, and assembling them in a specific order. Today......, this modern field of synthetic biology is completely dependent on the nature of the chassis - the host organisms - for its endeavor. Of all the chassis, photosynthetic organisms such as cyanobacteria and plants gains special attention due to the remarkable amount of sunlight that is striking the Earth......’s atmosphere and anthropogenic carbon dioxide (CO2) increase in the atmosphere. Hence, tapping into photosynthesis for synthetic biology endeavor is very rational, and for future, it has a huge potential for the industrial production of fuels and high value bioactive compounds in a sustainable way. Most...

  10. Dynamics of assembly production flow

    CERN Document Server

    Ezaki, Takahiro; Nishinari, Katsuhiro

    2015-01-01

    Despite recent developments in management theory, maintaining a manufacturing schedule remains difficult because of production delays and fluctuations in demand and supply of materials. The response of manufacturing systems to such disruptions to dynamic behavior has been rarely studied. To capture these responses, we investigate a process that models the assembly of parts into end products. The complete assembly process is represented by a directed tree, where the smallest parts are injected at leaves and the end products are removed at the root. A discrete assembly process, represented by a node on the network, integrates parts, which are then sent to the next downstream node as a single part. The model exhibits some intriguing phenomena, including overstock cascade, phase transition in terms of demand and supply fluctuations, nonmonotonic distribution of stockout in the network, and the formation of a stockout path and stockout chains. Surprisingly, these rich phenomena result from only the nature of distr...

  11. Assembly Sequence Planning for Mechanical Products

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A method for assembly sequence planning is proposed in this paper. First, two methods for assembly sequence planning are compared, which are indirect method and direct method. Then, the limits of the previous assembly planning system are pointed out. On the basis of indirect method, an improved method for assembly sequence planning is put forward. This method is composed of four parts, which are assembly modeling for products, assembly sequence representing, assembly sequence planning, and evaluation and optimization. The assembly model is established by human machine interaction, and the assembly model contains components' information and the assembly relation among the components. The assembly sequence planning is based on the breaking up of the assembly model. And/or graph is used to represent assembly sequence set. Every component which satisfies the disassembly condition is recorded as a node of an and/or graph. After the disassembly sequence and/or graph is generated, heuristic algorithm - AO* algorithm is used to search the disassembly sequence and/or graph, and the optimum assembly sequence planning is realized. This method is proved to be effective in a prototype system which is a sub-project of a state 863/CIMS research project of China - ‘Concurrent Engineering’.

  12. Dump assembly

    Science.gov (United States)

    Goldmann, Louis H.

    1986-01-01

    A dump assembly having a fixed conduit and a rotatable conduit provided with overlapping plates, respectively, at their adjacent ends. The plates are formed with openings, respectively, normally offset from each other to block flow. The other end of the rotatable conduit is provided with means for securing the open end of a filled container thereto. Rotation of the rotatable conduit raises and inverts the container to empty the contents while concurrently aligning the conduit openings to permit flow of material therethrough.

  13. Molecular motor assembly of a biomimetic system

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Active biological molecules and functional structures can be fabricated into a bio-mimetic system by using molecular assembly method. Such materials can be used for the drug delivery, disease diagnosis and therapy, and new nanodevice construction.

  14. Uracil Excision for Assembly of Complex Pathways

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Nielsen, Morten Thrane; Kim, Se Hyeuk

    2015-01-01

    Despite decreasing prices on synthetic DNA constructs, higher-order assembly of PCR-generated DNA continues to be an important exercise in molecular and synthetic biology. Simplicity and robustness are attractive features met by the uracil excision DNA assembly method, which is one of the most in...

  15. Assembly delay line pulse generators

    CERN Document Server

    1971-01-01

    Assembly of six of the ten delay line pulse generators that will power the ten kicker magnet modules. One modulator part contains two pulse generators. Capacitors, inductances, and voltage dividers are in the oil tank on the left. Triggered high-pressure spark gap switches are on the platforms on the right. High voltage pulse cables to the kicker magnet emerge under the spark gaps. In the centre background are the assembled master gaps.

  16. BEILING HUANENG BUILDING ROOF CONSTRUCTION GLOBAL SLIP ASSEMBLY PARTS%北京华能大厦屋盖散件拼装整体滑移施工技术

    Institute of Scientific and Technical Information of China (English)

    耿爱贤; 刘丙宇; 刘英勇; 程军伟

    2011-01-01

    华能大厦中庭屋盖钢结构是三向网格单层柱面网壳结构.安装时结合现场实际情况并从技术经济角度综合考虑,采用塔式起重机将散件吊装到屋顶上进行拼装,然后将拼装好的单元体通过滑轨牵引到指定位置.在液压同步滑移过程中,测量人员通过测量仪器配合测量点位移的监测,以及专业技术人员对滑移过程中液压器、液压泵站、计算机同步控制系统、传感检测系统等的监控,保证了安装的精度及施工安全.%The Atrium Huaneng Building is a three-way steel mesh roof reticulated shell structures. The actual Situation with on -site installation, technical and economic point of view from the comprehensive consideration, the use of tower crane will be lifting the roof on the parts assembled, and then through the slide assembly unit body good traction to the specified location. Slippage in the hydraulic synchronization process, by measuring the person with the measurements by the displacement measuring instruments, and professional and technical personnel for monitoring the process of hydraulic control on the slip, pump stations, computer synchronization control system, sensor detection systems, monitoring to ensure accuracy of the installation and construction safety.

  17. BioFNet: biological functional network database for analysis and synthesis of biological systems.

    Science.gov (United States)

    Kurata, Hiroyuki; Maeda, Kazuhiro; Onaka, Toshikazu; Takata, Takenori

    2014-09-01

    In synthetic biology and systems biology, a bottom-up approach can be used to construct a complex, modular, hierarchical structure of biological networks. To analyze or design such networks, it is critical to understand the relationship between network structure and function, the mechanism through which biological parts or biomolecules are assembled into building blocks or functional networks. A functional network is defined as a subnetwork of biomolecules that performs a particular function. Understanding the mechanism of building functional networks would help develop a methodology for analyzing the structure of large-scale networks and design a robust biological circuit to perform a target function. We propose a biological functional network database, named BioFNet, which can cover the whole cell at the level of molecular interactions. The BioFNet takes an advantage in implementing the simulation program for the mathematical models of the functional networks, visualizing the simulated results. It presents a sound basis for rational design of biochemical networks and for understanding how functional networks are assembled to create complex high-level functions, which would reveal design principles underlying molecular architectures.

  18. Assembling consumption

    DEFF Research Database (Denmark)

    Assembling Consumption marks a definitive step in the institutionalisation of qualitative business research. By gathering leading scholars and educators who study markets, marketing and consumption through the lenses of philosophy, sociology and anthropology, this book clarifies and applies...... the investigative tools offered by assemblage theory, actor-network theory and non-representational theory. Clear theoretical explanation and methodological innovation, alongside empirical applications of these emerging frameworks will offer readers new and refreshing perspectives on consumer culture and market...... societies. This is an essential reading for both seasoned scholars and advanced students of markets, economies and social forms of consumption....

  19. Minimus: a fast, lightweight genome assembler

    Directory of Open Access Journals (Sweden)

    Salzberg Steven L

    2007-02-01

    Full Text Available Abstract Background Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. Results We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. Conclusion We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.

  20. BASIC: A Simple and Accurate Modular DNA Assembly Method.

    Science.gov (United States)

    Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

    2017-01-01

    Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

  1. A Robust Workflow for Native Mass Spectrometric Analysis of Affinity-Isolated Endogenous Protein Assemblies.

    Science.gov (United States)

    Olinares, Paul Dominic B; Dunn, Amelia D; Padovan, Júlio C; Fernandez-Martinez, Javier; Rout, Michael P; Chait, Brian T

    2016-03-01

    The central players in most cellular events are assemblies of macromolecules. Structural and functional characterization of these assemblies requires knowledge of their subunit stoichiometry and intersubunit connectivity. One of the most direct means for acquiring such information is so-called "native mass spectrometry (MS)", wherein the masses of the intact assemblies and parts thereof are accurately determined. It is of particular interest to apply native MS to the study of endogenous protein assemblies-i.e., those wherein the component proteins are expressed at endogenous levels in their natural functional states, rather than the overexpressed (sometimes partial) constructs commonly employed in classical structural studies, whose assembly can introduce stoichiometry artifacts and other unwanted effects. To date, the application of native MS to the elucidation of endogenous protein complexes has been limited by the difficulty in obtaining pristine cell-derived assemblies at sufficiently high concentrations for effective analysis. Here, to address this challenge, we present a robust workflow that couples rapid and efficient affinity isolation of endogenous protein complexes with a sensitive native MS readout. The resulting workflow has the potential to provide a wealth of data on the stoichiometry and intersubunit connectivity of endogenous protein assemblies-information that is key to successful integrative structural elucidation of biological systems.

  2. General Assembly

    CERN Multimedia

    Staff Association

    2015-01-01

    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : 1- Adoption de l’ordre du jour. 2- Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. 3- Présentation et approbation du rapport d’activités 2014. 4- Présentation et approbation du rapport financier 2014. 5- Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. 6- Programme 2015. 7- Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. 8- Pas de modifications aux Statuts de l'Association du personnel proposée. 9- Élections des membres de la Commission é...

  3. General Assembly

    CERN Multimedia

    Staff Association

    2016-01-01

    Mardi 5 avril à 11 h 00 BE Auditorium Meyrin (6-2-024) Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 5 mai 2015. Présentation et approbation du rapport d’activités 2015. Présentation et approbation du rapport financier 2015. Présentation et approbation du rapport des vérificateurs aux comptes pour 2015. Programme de travail 2016. Présentation et approbation du projet de budget 2016 Approbation du taux de cotisation pour 2017. Modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commissio...

  4. General assembly

    CERN Multimedia

    Staff Association

    2015-01-01

    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. Présentation et approbation du rapport d’activités 2014. Présentation et approbation du rapport financier 2014. Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. Programme 2015. Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. Pas de modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commission électorale. &am...

  5. Self-assembled polyhydroxy fatty acids vesicles: a mechanism for plant cutin synthesis.

    Science.gov (United States)

    Heredia-Guerrero, José A; Benítez, José J; Heredia, Antonio

    2008-03-01

    Despite its biological importance, the mechanism of formation of cutin, the polymeric matrix of plant cuticles, has not yet been fully clarified. Here, for the first time, we show the participation in the process of lipid vesicles formed by the self-assembly of endogenous polyhydroxy fatty acids. The accumulation and fusion of these vesicles (cutinsomes) at the outer part of epidermal cell wall is proposed as the mechanism for early cuticle formation.

  6. Recent development of peptide self-assembly

    Institute of Scientific and Technical Information of China (English)

    Xiubo Zhao; Fang Pan; Jian R. Lu

    2008-01-01

    Amino acids are the building blocks to build peptides and proteins. Recent development in peptide synthesis has however enabled us to mimic this natural process by preparing various long and short peptides possessing different conformations and biological functions. The self-assembly of short designed peptides into molecular nanostructures is becoming a growing interest in nanobiotechnology. Self-assembled peptides exhibit several attractive features for applications in tissue regeneration, drug delivery, biological surface engineering as well as in food science, cosmetic industry and antibiotics. The aim of this review is to introduce the readers to a number of representative studies on peptide self-assembly.

  7. Metagenomic Assembly: Overview, Challenges and Applications

    Science.gov (United States)

    Ghurye, Jay S.; Cepeda-Espinoza, Victoria; Pop, Mihai

    2016-01-01

    Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems. PMID:27698619

  8. Biology Notes.

    Science.gov (United States)

    School Science Review, 1984

    1984-01-01

    Presents information on the teaching of nutrition (including new information relating to many current O-level syllabi) and part 16 of a reading list for A- and S-level biology. Also includes a note on using earthworms as a source of material for teaching meiosis. (JN)

  9. Interfacing Self-Assembled Nanostructures with Biology

    DEFF Research Database (Denmark)

    Vinther, Mathias

    DNA nanoteknologi har gennem de seneste to ̊artier gennemg ̊aet en forblø↵ende udvikling. Brugen af DNA til bottom-up fabrikation af selvsamlende nanopartikler har vist sig uhyre succes- fuld. Teknologien har s ̊aledes været i stand til at producere nanostrukturer af højere strukturel kompleksite...

  10. Biological Assembly of Hybrid Inorganic Nanomaterials (Preprint)

    Science.gov (United States)

    2007-03-01

    this structure is the peptide interface which features a specific sequence (GGLGPAGGCG) that is cleaved by the protease collagenase [18]. So...peptide functionalized gold nanoparticle to mineralize germania nanoshells around gold [20]. CO-ENCAPSULAnON VIA BIOSILIFICATION Alternative

  11. Chemical synthetic biology: a mini-review

    Directory of Open Access Journals (Sweden)

    Cristiano eChiarabelli

    2013-09-01

    Full Text Available Chemical synthetic biology (CSB is a branch of synthetic biology (SB oriented towards the synthesis of chemical structures alternative to those present in nature. Whereas SB combines biology and engineering with the aim of synthesizing biological structures or life forms that do not exist in nature – often based on genome manipulation, CSB uses and assembles biological parts, synthetic or not, to create new and alternative structures. A short epistemological note will introduce the theoretical concepts related to these fields, whereas the text will be largely devoted to introduce and comment two main projects of CSB, carried out in our laboratory in the recent years.The Never Born Biopolymers (NBB project deals with the construction and the screening of RNA and peptide sequences that are not present in nature, whereas the Minimal Cell project focuses on the construction of semi-synthetic compartments (usually liposomes containing the minimal and sufficient number of components to perform the basic function of a biological cell.These two topics are extremely important for both the general understanding of biology in terms of function, organization and development, and for applied biotechnology.

  12. RESEARCH OF MOVEMENT NAVIGATION BASED ON ASSEMBLY CONSTRAINT RECOGNITION

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The requirements and features of virtual assembly movement navigator are analyzed to help operators flexibly manipulate virtual objects, precisely locate or assemble virtual parts in virtual environment. With the degree-of-freedom analysis, the assembly constraint hierarchical model is constructed and the system's constraints are built dynamically. Thus, all objects in virtual environment can be located reasonally by the navigator. Moreover, the assembly constraint recognition in the process of assembly and movement correction is also discussed.

  13. In silico assembly and nanomechanical characterization of carbon nanotube buckypaper.

    Science.gov (United States)

    Cranford, Steven W; Buehler, Markus J

    2010-07-01

    Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.

  14. Synthetic self-assembled models with biomimetic functions

    NARCIS (Netherlands)

    Fiammengo, Roberto; Crego-Calama, Mercedes; Reinhoudt, David N.

    2001-01-01

    Self-assembly can be considered a powerful tool in the hand of chemists for the understanding, modeling and mimicking of biological systems. The possibility of reproducing biological functions in synthetic systems obtained by self-assembly is envisioned as a modest but very important step towards th

  15. Diretrizes da Federação Mundial das Sociedades de Psiquiatria Biológica para o tratamento biológico da esquizofrenia. Parte 2: tratamento de longo prazo World Federation of Societies of Biological Psychiatry (WFSBP guidelines for biological treatment of schizophrenia. Part 2: long-term treatment

    Directory of Open Access Journals (Sweden)

    Peter Falkai

    2006-01-01

    Full Text Available Estas diretrizes para o tratamento biológico da esquizofrenia foram desenvolvidas pela Força-Tarefa da Federação Mundial das Sociedades de Psiquiatria Biológica (World Federation of Societies of Biological Psychiatry, WFSBP. As metas fixadas durante o desenvolvimento destas diretrizes foi a revisão sistemática de todas as evidências disponíveis referentes ao tratamento da esquizofrenia, tanto no âmbito clínico como no científico, e o estabelecimento de um consenso sobre as principais recomendações para a prática psiquiátrica. Estas diretrizes são destinadas a todos os médicos que atendem e tratam de pacientes portadores de esquizofrenia. Os dados usados para desenvolver estas diretrizes foram extraídos primariamente de vários painéis e diretrizes nacionais para o tratamento da esquizofrenia, assim como de metanálises, revisões e estudos clínicos randomizados sobre a eficácia do tratamento farmacológico e de outras intervenções terapêuticas biológicas, identificadas por uma busca nas bases de dados MedLine e na Biblioteca Cochrane. A literatura identificada foi avaliada quanto à solidez das evidências a favor da eficácia de determinada intervenção, sendo, então, categorizada em quatro níveis de evidência (de A a D. A segunda parte das diretrizes abrange o tratamento de longo prazo, bem como o controle dos efeitos colaterais relevantes. Essas diretrizes são primariamente relacionadas ao tratamento biológico de adultos esquizofrênicos, incluindo medicação antipsicótica, outras opções de tratamento farmacológico, eletroconvulsoterapia, estratégias terapêuticas recentes e complementares.These guidelines for the biological treatment of schizophrenia were developed by an international Task Force of the World Federation of Societies of Biological Psychiatry (WFSBP. The goal during the development of these guidelines was to review systematically all available evidence pertaining to the treatment of

  16. Diretrizes da Federação Mundial das Sociedades de Psiquiatria Biológica para o tratamento biológico da esquizofrenia. Parte 1: tratamento agudo World Federation of Societies of Biological Psychiatry (WFSBP guidelines for biological treatment of schizophrenia. Part 1: acute treatment

    Directory of Open Access Journals (Sweden)

    Peter Falkai

    2006-01-01

    Full Text Available Estas diretrizes para o tratamento biológico da esquizofrenia foram desenvolvidas pela Força-Tarefa da Federação Mundial das Sociedades de Psiquiatria Biológica (World Federation of Societies of Biological Psychiatry, WFSBP. A meta fixada durante o desenvolvimento destas diretrizes foi rever sistematicamente todas as evidências disponíveis referentes ao tratamento da esquizofrenia, tanto no âmbito clínico como científico, e chegar a um consenso sobre as principais recomendações para a prática psiquiátrica. Estas diretrizes são destinadas a todos os médicos que atendem e tratam de pacientes portadores de esquizofrenia. Os dados usados para desenvolver estas diretrizes foram extraídos primariamente de vários painéis e diretrizes nacionais de tratamento para esquizofrenia, assim como de metanálises, revisões e estudos clínicos randomizados sobre a eficácia do tratamento farmacológico e de outras intervenções terapêuticas biológicas, identificadas por uma busca nas bases de dados MedLine e Biblioteca Cochrane. A literatura identificada foi avaliada no que diz respeito à solidez das evidências a favor da eficácia de uma dada intervenção e, então, categorizada em quatro níveis de evidências (de A a D. A primeira parte das diretrizes abrange a definição da doença, sua classificação, a epidemiologia e o curso da esquizofrenia, assim como o manejo terapêutico de fase aguda. Estas diretrizes são primariamente relacionadas ao tratamento biológico de adultos esquizofrênicos, incluindo medicação antipsicótica, outras opções de tratamento farmacológico, terapia eletroconvulsiva, estratégias terapêuticas recentes e complementares.These guidelines for the biological treatment of schizophrenia were developed by an international Task Force of the World Federation of Societies of Biological Psychiatry (WFSBP. The goal during the development of these guidelines was to review systematically all available evidence

  17. Chemical reactions directed Peptide self-assembly.

    Science.gov (United States)

    Rasale, Dnyaneshwar B; Das, Apurba K

    2015-05-13

    Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly.

  18. Workload analyse of assembling process

    Science.gov (United States)

    Ghenghea, L. D.

    2015-11-01

    The workload is the most important indicator for managers responsible of industrial technological processes no matter if these are automated, mechanized or simply manual in each case, machines or workers will be in the focus of workload measurements. The paper deals with workload analyses made to a most part manual assembling technology for roller bearings assembling process, executed in a big company, with integrated bearings manufacturing processes. In this analyses the delay sample technique have been used to identify and divide all bearing assemblers activities, to get information about time parts from 480 minutes day work time that workers allow to each activity. The developed study shows some ways to increase the process productivity without supplementary investments and also indicated the process automation could be the solution to gain maximum productivity.

  19. The A, C, G, and T of Genome Assembly

    Directory of Open Access Journals (Sweden)

    Bilal Wajid

    2016-01-01

    Full Text Available Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

  20. Construction of YBS Critical Assembly

    Institute of Scientific and Technical Information of China (English)

    ZHOU; Qi; LIANG; Shu-hong; ZHU; Qing-fu; ZHANG; Wei; YANG; Li-jun; QUAN; Yan-hui

    2015-01-01

    Supported by the XDA program of CAS,the YBS critical assembly has been constructed for the experimental research of the coupling and influence characteristics of spallation target and reactor in ADS system.This work consists of two parts:one is the conversion of the reactor hall and control room,and the other manufacture,installation and commissioning of the critical

  1. Dynamics of assembly production flow

    Science.gov (United States)

    Ezaki, Takahiro; Yanagisawa, Daichi; Nishinari, Katsuhiro

    2015-06-01

    Despite recent developments in management theory, maintaining a manufacturing schedule remains difficult because of production delays and fluctuations in demand and supply of materials. The response of manufacturing systems to such disruptions to dynamic behavior has been rarely studied. To capture these responses, we investigate a process that models the assembly of parts into end products. The complete assembly process is represented by a directed tree, where the smallest parts are injected at leaves and the end products are removed at the root. A discrete assembly process, represented by a node on the network, integrates parts, which are then sent to the next downstream node as a single part. The model exhibits some intriguing phenomena, including overstock cascade, phase transition in terms of demand and supply fluctuations, nonmonotonic distribution of stockout in the network, and the formation of a stockout path and stockout chains. Surprisingly, these rich phenomena result from only the nature of distributed assembly processes. From a physical perspective, these phenomena provide insight into delay dynamics and inventory distributions in large-scale manufacturing systems.

  2. Flowering and pollen value of selected species of umbelliferous family - Umbelliferae Juss. (Apiaceae Lindl.) in Lublin region. Part 1. Biology and abundance of flowering

    OpenAIRE

    Anna Wróblewska

    2013-01-01

    Investigations of the biology of flowering and pollen value of seven species of Umbelliferae family were carried out in natural seats of Lublin region in 1978-1980. Aegopodium podagraria L.,Angelica silvestris L., Anthriscus silvestris L. (Hoffm.), Chaerophyllum aromaticum L., Eryngium planum L., Herac1eum sibiricum L., Pastinaca sativa L. were examined. This paper shows results of studies of the biology of flowering and abundance of flowering. The examined species started their flowering in ...

  3. CT Performance Evaluation Using Multi Material Assemblies

    DEFF Research Database (Denmark)

    Stolfi, Alessandro; De Chiffre, Leonardo

    2015-01-01

    This paper concerns an investigation of the accuracy of Computed Tomography measurements using multi-material assemblies. In this study, assemblies involving similar densities for elementary parts were considered. The investigation includes dimensional and geometrical measurements of two 10 mm hi...

  4. Bioinspired assembly of small molecules in cell milieu.

    Science.gov (United States)

    Wang, Huaimin; Feng, Zhaoqianqi; Xu, Bing

    2017-03-30

    Self-assembly, the autonomous organization of components to form patterns or structures, is a prevalent process in nature at all scales. Particularly, biological systems offer remarkable examples of diverse structures (as well as building blocks) and processes resulting from self-assembly. The exploration of bioinspired assemblies not only allows for mimicking the structures of living systems, but it also leads to functions for applications in different fields that benefit humans. In the last several decades, efforts on understanding and controlling self-assembly of small molecules have produced a large library of candidates for developing the biomedical applications of assemblies of small molecules. Moreover, recent findings in biology have provided new insights on the assemblies of small molecules to modulate essential cellular processes (such as apoptosis). These observations indicate that the self-assembly of small molecules, as multifaceted entities and processes to interact with multiple proteins, can have profound biological impacts on cells. In this review, we illustrate that the generation of assemblies of small molecules in cell milieu with their interactions with multiple cellular proteins for regulating cellular processes can result in primary phenotypes, thus providing a fundamentally new molecular approach for controlling cell behavior. By discussing the correlation between molecular assemblies in nature and the assemblies of small molecules in cell milieu, illustrating the functions of the assemblies of small molecules, and summarizing some guiding principles, we hope this review will stimulate more molecular scientists to explore the bioinspired self-assembly of small molecules in cell milieu.

  5. Improvability of assembly systems I: Problem formulation and performance evaluation

    Directory of Open Access Journals (Sweden)

    S.-Y. Chiang

    2000-01-01

    Full Text Available This work develops improvability theory for assembly systems. It consists of two parts. Part I includes the problem formulation and the analysis technique. Part II presents the so-called improvability indicators and a case study.

  6. Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes

    Science.gov (United States)

    Shen, Hsin-Hui; Belousoff, Matthew J.; Noinaj, Nicholas; Lu, Jingxiong; Holt, Stephen A.; Tan, Khershing; Selkrig, Joel; Webb, Chaille T.; Buchanan, Susan K.; Martin, Lisandra L.; Lithgow, Trevor

    2015-01-01

    In biological membranes, various protein secretion devices function as nanomachines, and measuring the internal movements of their component parts is a major technological challenge. The translocation assembly module (the TAM) is a nanomachine required for virulence of bacterial pathogens. We have reconstituted a membrane containing the TAM onto a gold surface for characterization by Quartz Crystal Microbalance with Dissipation (QCM-D) and Magnetic Contrast Neutron Reflectrometry (MCNR). The MCNR studies provided structural resolution down to 1Å, enabling accurate measurement of protein domains projecting from the membrane layer. Here, we show that dynamic movements within the TamA component of the TAM are initiated in the presence of a substrate protein, Ag43, and that these movements recapitulate an initial stage in membrane protein assembly. The reconstituted system provides a powerful new means to study molecular movements in biological membranes, and the technology is widely applicable to studying the dynamics of diverse cellular nanomachines. PMID:25341963

  7. COMPUTER-AIDED BLOCK ASSEMBLY PROCESS PLANNING IN SHIPBUILD-ING BASED ON RULE-REASONING

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhiying; LI Zhen; JIANG Zhibin

    2008-01-01

    Computer-aided block assembly process planning based on rule-reasoning are developed in order to improve the assembly efficiency and implement the automated block assembly process planning generation in shipbuilding. First, weighted directed liaison graph (WDLG) is proposed to represent the model of block assembly process according to the characteristics of assembly relation, and edge list (EL) is used to describe assembly sequences. Shapes and assembly attributes of block parts are analyzed to determine the assembly position and matched parts of parts used frequently. Then, a series of assembly rules are generalized, and assembly sequences for block are obtained by means of rule reasoning. Final, a prototype system of computer-aided block assembly process planning is built. The system has been tested on actual block, and the results were found to be quite efficiency. Meanwhile, the fundament for the automation of block assembly process generation and integration with other systems is established.

  8. The PLOS ONE synthetic biology collection: six years and counting.

    Science.gov (United States)

    Peccoud, Jean; Isalan, Mark

    2012-01-01

    Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community.

  9. Silk: molecular organization and control of assembly.

    Science.gov (United States)

    Valluzzi, Regina; Winkler, Stefan; Wilson, Donna; Kaplan, David L

    2002-02-28

    The interface between the science and engineering of biology and materials is an area of growing interest. One of the goals of this field is to utilize biological synthesis and processing of polymers as a route to gain insight into topics such as molecular recognition, self-assembly and the formation of materials with well-defined architectures. The biological processes involved in polymer synthesis and assembly can offer important information on fundamental interactions involved in the formation of complex material architectures, as well as practical knowledge into new and important materials related to biomaterial uses and tissue engineering needs. Classic approaches in biology, including genetic engineering, controlled microbial physiology and enzymatic synthesis, are prototypical methods used to control polymer structure and chemistry, including stereoselectivity and regioselectivity, to degrees unattainable using traditional synthetic chemistry. This type of control can lead to detailed and systematic studies of the formation of the structural hierarchy in materials and the subsequent biological responses to these materials.

  10. Scaffold oriented synthesis. Part 4: design, synthesis and biological evaluation of novel 5-substituted indazoles as potent and selective kinase inhibitors employing heterocycle forming and multicomponent reactions.

    Science.gov (United States)

    Akritopoulou-Zanze, Irini; Wakefield, Brian D; Gasiecki, Alan; Kalvin, Douglas; Johnson, Eric F; Kovar, Peter; Djuric, Stevan W

    2011-03-01

    We report the synthesis and biological evaluation of 5-substituted indazoles as kinase inhibitors. The compounds were synthesized in a parallel synthesis fashion from readily available starting materials employing heterocycle forming and multicomponent reactions and were evaluated against a panel of kinase assays. Potent inhibitors were identified for Gsk3β, Rock2, and Egfr.

  11. Probe tip heating assembly

    Science.gov (United States)

    Schmitz, Roger William; Oh, Yunje

    2016-10-25

    A heating assembly configured for use in mechanical testing at a scale of microns or less. The heating assembly includes a probe tip assembly configured for coupling with a transducer of the mechanical testing system. The probe tip assembly includes a probe tip heater system having a heating element, a probe tip coupled with the probe tip heater system, and a heater socket assembly. The heater socket assembly, in one example, includes a yoke and a heater interface that form a socket within the heater socket assembly. The probe tip heater system, coupled with the probe tip, is slidably received and clamped within the socket.

  12. Crystallogenesis of biological macromolecules. Biological, microgravity and other physicochemical aspects

    NARCIS (Netherlands)

    Giege, R; Drenth, J; Ducruix, A; McPherson, A; Saenger, W

    1995-01-01

    After an historical introduction and justification of the importance of proteins (as well as other macromolecules or macromolecular assemblies of biological origin) in modern biology but also in physics, this review presents the state of the field of macromolecular crystallogenesis. The basic questi

  13. Newnes electronics assembly handbook

    CERN Document Server

    Brindley, Keith

    2013-01-01

    Newnes Electronics Assembly Handbook: Techniques, Standards and Quality Assurance focuses on the aspects of electronic assembling. The handbook first looks at the printed circuit board (PCB). Base materials, basic mechanical properties, cleaning of assemblies, design, and PCB manufacturing processes are then explained. The text also discusses surface mounted assemblies and packaging of electromechanical assemblies, as well as the soldering process. Requirements for the soldering process; solderability and protective coatings; cleaning of PCBs; and mass solder/component reflow soldering are des

  14. Algorithms for Automated DNA Assembly

    Science.gov (United States)

    2010-01-01

    Published online 23 March 2010 Nucleic Acids Research , 2010, Vol. 38, No. 8 2607–2616 doi:10.1093/nar/gkq165 The Author(s) 2010. Published by Oxford...composite part Pcon.RFP is also called an ‘intermediate part’ since it is constructed as an intermediate step in assembling the 2608 Nucleic Acids Research , 2010...in A–C. We assume part cd is already present in the part library. Nucleic Acids Research , 2010, Vol. 38, No. 8 2609 at M edical Library on S eptem ber

  15. Mixed Reality-based Interactive Technology for Aircraft Cabin Assembly

    Institute of Scientific and Technical Information of China (English)

    LI Shiqi; PENG Tao; WANG Junfeng; XU Chi

    2009-01-01

    Due to the narrowness of space and the complexity of structure, the assembly of aircraft cabin has become one of the major bottlenecks in the whole manufacturing process. To solve the problem, at the beginning of aircraft design, the different stages of the lifecycle of aircraft must be thought about, which include the trial manufacture, assembly, maintenance, recycling and destruction of the product. Recently, thanks to the development of the virtual reality and augmented reality, some low-cost and fast solutions are found for the product assembly. This paper presents a mixed reality-based interactive technology for the aircraft cabin assembly, which can enhance the efficiency of the assemblage in a virtual environment in terms of vision, information and operation. In the mixed reality-based assembly environment, the physical scene can be obtained by a camera and then generated by a computer. The virtual parts, the features of visual assembly, the navigation information, the physical parts and the physical assembly environment will be mixed and presented in the same assembly scene. The mixed or the augmented information will provide some assembling information as a detailed assembly instruction in the mixed reality-based assembly environment. Constraint proxy and its match rules help to reconstruct and visualize the restriction relationship among different parts, and to avoid the complex calculation of constraint's match. Finally, a desktop prototype system of virtual assembly has been built to assist the assembly verification and training with the virtual hand.

  16. Diretrizes da World Federation of Societies of Biological Psychiatry (WFSBP para tratamento biológico de transtornos depressivos unipolares, 2ª parte: tratamento de manutenção do transtorno depressivo maior e tratamento dos transtornos depressivos crônicos e das depressões subliminares World Federation of Societies of Biological Psychiatry (WFSBP Guidelines for biological treatment of unipolar depressive disorders, part 2: maintenance treatment of major depressive disorder and treatment of chronic depressive disorders and subthreshold depressions

    Directory of Open Access Journals (Sweden)

    Michael Bauer

    2009-01-01

    Full Text Available Estas diretrizes práticas para o tratamento biológico de transtornos depressivos unipolares foram desenvolvidas por uma Força-Tarefa internacional da Federação Mundial de Sociedades de Psiquiatria Biológica (WFSBP. O objetivo ao desenvolver tais diretrizes foi rever sistematicamente todas as evidências existentes referentes ao tratamento de transtornos depressivos unipolares e produzir uma série de recomendações práticas com significado clínico e científico, baseadas nas evidências existentes. Têm como objetivo seu uso por todos os médicos que atendam e tratem pacientes com essas afecções. Os dados usados para o desenvolvimento das diretrizes foram extraídos primariamente de várias diretrizes e painéis nacionais de tratamento para transtornos depressivos, bem como de metanálises e revisões sobre a eficácia dos antidepressivos e outras intervenções de tratamento biológico identificadas por uma busca no banco de dados MEDLINE e Cochrane Library. A literatura identificada foi avaliada quanto à força das evidências sobre sua eficácia e, então, categorizada em quatro níveis de evidências (A a D. Esta primeira parte das diretrizes abrange definição, classificação, epidemiologia e evolução dos transtornos depressivos unipolares, bem como tratamento das fases aguda e de manutenção. As diretrizes se referem primariamente ao tratamento biológico (incluindo antidepressivos, outros medicamentos psicofarmacológicos e hormonais, eletroconvulsoterapia, fototerapia, estratégias terapêuticas complementares e novas de adultos jovens e também, embora em menor grau, de crianças, adolescentes e adultos idosos.These practice guidelines for the biological treatment of unipolar depressive disorders were developed by an international Task Force of the World Federation of Societies of Biological Psychiatry (WFSBP. The goal for developing these guidelines was to systematically review all available evidence pertaining to the

  17. Passive micro-assembly of modular, hot embossed, polymer microfluidic devices using exact constraint design

    Science.gov (United States)

    You, Byoung Hee; Chen, Pin-Chuan; Park, Daniel S.; Park, Sunggook; Nikitopoulos, Dimitris E.; Soper, Steven A.; Murphy, Michael C.

    2009-12-01

    Low-cost microfluidic platforms have the potential to change accepted practices in many fields, including biology and medicine, in the near future. Micro-assembly of molded polymer microfluidic devices is one approach to cost-effective mass production of modular, microfluidic instruments. Polymer, passive alignment structures were used to precisely assemble molded polymer components to prevent infinitesimal motions and minimize the misalignment between assembled components and devices. The motion and constraint of the assemblies were analyzed using screw theory to identify combinations of passive alignment structures that would provide exact constraint of all degrees of freedom of the two mating parts without over-constraint. One option identified by kinematic analysis was a set of three v-groove and hemisphere-tipped pin joints, which are well known from precision engineering and suitable for microfabrication. To validate the passive alignment scheme, brass mold inserts containing alignment structures were micro-milled and used to hot emboss components in polycarbonate (PC). Dimensional and location variations of prototype alignment structures were measured to quantify the difference between the as-designed and actual dimensions and the locations of the alignment structures. The dimensional variation was 0.2-3% less than the designed dimensions and the location variation was 0.7% less. The alignment accuracy of an assembly was characterized by measuring the mismatch and vertical variation between molded alignment standards embossed on each pair of mating plates. With molded, polymer alignment structures the mean mismatch and mean vertical variation were as low as 13 ± 3 µm in the lateral plane along the x- and y-axes and -6 ± 15 µm with respect to the nominal value of 107 µm. This micro-assembly technology is applicable to the integration of all microsystems including the interconnection of microfluidic devices, the assembly of hybrid microsystems and the

  18. Biologic Treatments for Sports Injuries II Think Tank-Current Concepts, Future Research, and Barriers to Advancement, Part 2: Rotator Cuff.

    Science.gov (United States)

    Murray, Iain R; LaPrade, Robert F; Musahl, Volker; Geeslin, Andrew G; Zlotnicki, Jason P; Mann, Barton J; Petrigliano, Frank A

    2016-03-01

    Rotator cuff tears are common and result in considerable morbidity. Tears within the tendon substance or at its insertion into the humeral head represent a considerable clinical challenge because of the hostile local environment that precludes healing. Tears often progress without intervention, and current surgical treatments are inadequate. Although surgical implants, instrumentation, and techniques have improved, healing rates have not improved, and a high failure rate remains for large and massive rotator cuff tears. The use of biologic adjuvants that contribute to a regenerative microenvironment have great potential for improving healing rates and function after surgery. This article presents a review of current and emerging biologic approaches to augment rotator cuff tendon and muscle regeneration focusing on the scientific rationale, preclinical, and clinical evidence for efficacy, areas for future research, and current barriers to advancement and implementation.

  19. Automatic Identification of Digital Label Assembly Drawings of Mechanical Parts Based on Computer Vision Technology%基于计算机视觉技术的机械零件装配图数字标号的自动识别

    Institute of Scientific and Technical Information of China (English)

    江能兴

    2011-01-01

    In order to realize precisely the automatic identification of numeric characters in the assembly drawings of mechanical parts, the technology of Open Computer Vision libraries (OpenCV) are developed. This paper not only introduces the basic framework of OpenCV and its typical application areas, also, it compares and analyses the numeric characters in the assembly drawings of mechanical parts, which has great significance to the improvement on the current development in the area of the automatic identification of digital label assembly drawings of mechanical parts.%为精准快速地对机械零件装配图中的数字字符进行自动识别,提出一种基于开源计算机视觉库OpenCV的模板匹配方法.本文介绍OpenCV的基本框架、典型运用领域和利用OpenCV开发库对机械零件装配图中的数字字符进行自动识别的比较分析,该项工作对改进目前对机械图进行人工数字识别的现状具有重要的意义.

  20. Scaffold oriented synthesis. Part 3: design, synthesis and biological evaluation of novel 5-substituted indazoles as potent and selective kinase inhibitors employing [2+3] cycloadditions.

    Science.gov (United States)

    Akritopoulou-Zanze, Irini; Wakefield, Brian D; Gasiecki, Alan; Kalvin, Douglas; Johnson, Eric F; Kovar, Peter; Djuric, Stevan W

    2011-03-01

    We report the synthesis and biological evaluation of 5-substituted indazoles and amino indazoles as kinase inhibitors. The compounds were synthesized in a parallel synthesis fashion from readily available starting materials employing [2+3] cycloaddition reactions and were evaluated against a panel of kinase assays. Potent inhibitors were identified for numerous kinases such as Rock2, Gsk3β, Aurora2 and Jak2.

  1. Impact of river overflowing on trace element contamination of volcanic soils in south Italy: Part II. Soil biological and biochemical properties in relation to trace element speciation

    Energy Technology Data Exchange (ETDEWEB)

    D' Ascoli, R. [Dipartimento di Scienze Ambientali, Seconda Universita degli Studi di Napoli, via Vivaldi 43, 81100 Caserta (Italy)]. E-mail: rosaria.dascoli@unina2.it; Rao, M.A. [Dipartimento di Scienze del Suolo, della Pianta e dell' Ambiente, Universita degli Studi di Napoli Federico II, Via Universita 100, 80055 Portici (Italy)]. E-mail: maria.rao@unina.it; Adamo, P. [Dipartimento di Scienze del Suolo, della Pianta e dell' Ambiente, Universita degli Studi di Napoli Federico II, Via Universita 100, 80055 Portici (Italy)]. E-mail: adamo@unina.it; Renella, G. [Dipartimento di Scienza del Suolo e Nutrizione della Pianta, Universita degli Studi di Firenze, P.le delle Cascine 28, 50144 Firenze (Italy)]. E-mail: giancarlo.renella@unifi.it; Landi, L. [Dipartimento di Scienza del Suolo e Nutrizione della Pianta, Universita degli Studi di Firenze, P.le delle Cascine 28, 50144 Firenze (Italy)]. E-mail: loretta.landi@unifi.it; Rutigliano, F.A. [Dipartimento di Scienze Ambientali, Seconda Universita degli Studi di Napoli, via Vivaldi 43, 81100 Caserta (Italy)]. E-mail: floraa.rutigliano@unina2.it; Terribile, F. [Dipartimento di Scienze del Suolo, della Pianta e dell' Ambiente, Universita degli Studi di Napoli Federico II, Via Universita 100, 80055 Portici (Italy)]. E-mail: terribil@unina.it; Gianfreda, L. [Dipartimento di Scienze del Suolo, della Pianta e dell' Ambiente, Universita degli Studi di Napoli Federico II, Via Universita 100, 80055 Portici (Italy)]. E-mail: liliana.gianfreda@unina.it

    2006-11-15

    The effect of heavy metal contamination on biological and biochemical properties of Italian volcanic soils was evaluated in a multidisciplinary study, involving pedoenvironmental, micromorphological, physical, chemical, biological and biochemical analyses. Soils affected by recurring river overflowing, with Cr(III)-contaminated water and sediments, and a non-flooded control soil were analysed for microbial biomass, total and active fungal mycelium, enzyme activities (i.e., FDA hydrolase, dehydrogenase, {beta}-glucosidase, urease, arylsulphatase, acid phosphatase) and bacterial diversity (DGGE characterisation). Biological and biochemical data were related with both total and selected fractions of Cr and Cu (the latter deriving from agricultural chemical products) as well as with total and extractable organic C. The growth and activity of soil microbial community were influenced by soil organic C content rather than Cu or Cr contents. In fact, positive correlations between all studied parameters and organic C content were found. On the contrary, negative correlations were observed only between total fungal mycelium, dehydrogenase, arylsulphatase and acid phosphatase activities and only one Cr fraction (the soluble, exchangeable and carbonate bound). However, total Cr content negatively affected the eubacterial diversity but it did not determine changes in soil activity, probably because of the redundancy of functions within species of soil microbial community. On the other hand, expressing biological and biochemical parameters per unit of total organic C, Cu pollution negatively influenced microbial biomass, fungal mycelium and several enzyme activities, confirming soil organic matter is able to mask the negative effects of Cu on microbial community. - In studied soils organic C content resulted the principal factor influencing growth and activity of microbial community, with Cu and Cr contents having a lower relevance.

  2. Integrated risk assessment for WFD ecological status classification applied to Llobregat river basin (Spain). Part I-Fuzzy approach to aggregate biological indicators.

    Science.gov (United States)

    Gottardo, S; Semenzin, E; Giove, S; Zabeo, A; Critto, A; de Zwart, D; Ginebreda, A; Marcomini, A

    2011-10-15

    Water Framework Directive (WFD) requirements and recommendations for Ecological Status (ES) classification of surface water bodies do not address all issues that Member States have to face in the implementation process, such as selection of appropriate stressor-specific environmental indicators, definition of class boundaries, aggregation of heterogeneous data and information and uncertainty evaluation. In this context the "One-Out, All-Out" (OOAO) principle is the suggested approach to lead the entire classification procedure and ensure conservative results. In order to support water managers in achieving a more comprehensive and realistic evaluation of ES, an Integrated Risk Assessment (IRA) methodology was developed. It is based on the Weight of Evidence approach and implements a Fuzzy Inference System in order to hierarchically aggregate a set of environmental indicators, which are grouped into five Lines of Evidence (i.e. Biology, Chemistry, Ecotoxicology, Physico-chemistry and Hydromorphology). The whole IRA methodology has been implemented as an individual module into a freeware GIS (Geographic Information System)-based Decision Support System (DSS), named MODELKEY DSS. The paper focuses on the conceptual and mathematical procedure underlying the evaluation of the most complex Line of Evidence, i.e. Biology, which identifies the biological communities that are potentially at risk and the stressors that are most likely responsible for the observed alterations. The results obtained from testing the procedure through application of the MODELKEY DSS to the Llobregat case study are reported and discussed.

  3. Biologic Treatments for Sports Injuries II Think Tank-Current Concepts, Future Research, and Barriers to Advancement, Part 3: Articular Cartilage.

    Science.gov (United States)

    Zlotnicki, Jason P; Geeslin, Andrew G; Murray, Iain R; Petrigliano, Frank A; LaPrade, Robert F; Mann, Barton J; Musahl, Volker

    2016-04-01

    Focal chondral defects of the articular surface are a common occurrence in the field of orthopaedics. These isolated cartilage injuries, if not repaired surgically with restoration of articular congruency, may have a high rate of progression to posttraumatic osteoarthritis, resulting in significant morbidity and loss of function in the young, active patient. Both isolated and global joint disease are a difficult entity to treat in the clinical setting given the high amount of stress on weightbearing joints and the limited healing potential of native articular cartilage. Recently, clinical interest has focused on the use of biologically active compounds and surgical techniques to regenerate native cartilage to the articular surface, with the goal of restoring normal joint health and overall function. This article presents a review of the current biologic therapies, as discussed at the 2015 American Orthopaedic Society for Sports Medicine (AOSSM) Biologics Think Tank, that are used in the treatment of focal cartilage deficiencies. For each of these emerging therapies, the theories for application, the present clinical evidence, and specific areas for future research are explored, with focus on the barriers currently faced by clinicians in advancing the success of these therapies in the clinical setting.

  4. Systematic Review of Breast Cancer Biology in Developing Countries (Part 1: Africa, the Middle East, Eastern Europe, Mexico, the Caribbean and South America

    Directory of Open Access Journals (Sweden)

    Andrew G Hill

    2011-05-01

    Full Text Available There has been no systematic appraisal of ethnicity-based variations in breast cancer (BC biology amongst women from developing countries. A qualitative systematic review was conducted of breast cancer size, stage, grade, histological type, extra-mammary involvement, hormone receptor status as well as patient demographics. This review includes patients from Africa, the Middle East, Eastern Europe, Mexico, the Caribbean and South America. BC in these regions present at an earlier age with large aggressive tumours. Distant metastases are frequently present at the time of diagnosis. African women have a higher frequency of triple negative tumours. Over half of Middle Eastern women have lymph node involvement at the time of diagnosis. Despite experiencing a lower incidence compared to the Ashkenazi Jewish population, Palestinian women have poorer five-year survival outcomes. The majority of women from Mexico and South America have stage two or three disease whilst over sixty percent of women from Eastern Europe have either stage one or stage two disease. The biological characteristics of BC in the Caribbean cannot be fully assessed due to a paucity of data from the region. BC amongst the developing world is characterised by an early peak age of onset with aggressive biological characteristics. Strategies that improve breast cancer awareness, address amenable risk factors and improve early detection are essential.

  5. Systematic Review of Breast Cancer Biology in Developing Countries (Part 1): Africa, the Middle East, Eastern Europe, Mexico, the Caribbean and South America

    Energy Technology Data Exchange (ETDEWEB)

    Bhikoo, Riyaz, E-mail: riyazbhikoo@gmail.com; Srinivasa, Sanket; Yu, Tzu-Chieh [Department of Surgery, South Auckland Clinical School, University of Auckland, Auckland 1640 (New Zealand); Moss, David [Department of Surgery, Middlemore Hospital, Auckland 1640 (New Zealand); Hill, Andrew G [Department of Surgery, South Auckland Clinical School, University of Auckland, Auckland 1640 (New Zealand)

    2011-05-13

    There has been no systematic appraisal of ethnicity-based variations in breast cancer (BC) biology amongst women from developing countries. A qualitative systematic review was conducted of breast cancer size, stage, grade, histological type, extra-mammary involvement, hormone receptor status as well as patient demographics. This review includes patients from Africa, the Middle East, Eastern Europe, Mexico, the Caribbean and South America. BC in these regions present at an earlier age with large aggressive tumours. Distant metastases are frequently present at the time of diagnosis. African women have a higher frequency of triple negative tumours. Over half of Middle Eastern women have lymph node involvement at the time of diagnosis. Despite experiencing a lower incidence compared to the Ashkenazi Jewish population, Palestinian women have poorer five-year survival outcomes. The majority of women from Mexico and South America have stage two or three disease whilst over sixty percent of women from Eastern Europe have either stage one or stage two disease. The biological characteristics of BC in the Caribbean cannot be fully assessed due to a paucity of data from the region. BC amongst the developing world is characterised by an early peak age of onset with aggressive biological characteristics. Strategies that improve breast cancer awareness, address amenable risk factors and improve early detection are essential.

  6. Error Analysis of Robotic Assembly System Based on Screw Theory

    Institute of Scientific and Technical Information of China (English)

    韩卫军; 费燕琼; 赵锡芳

    2003-01-01

    Assembly errors have great influence on assembly quality in robotic assembly systems. Error analysis is directed to the propagations and accumula-tions of various errors and their effect on assembly success.Using the screw coordinates, assembly errors are represented as "error twist", the extremely compact expression. According to the law of screw composition, relative position and orientation errors of mating parts are computed and the necessary condition of assembly success is concluded. A new simple method for measuring assembly errors is also proposed based on the transformation law of a screw.Because of the compact representation of error, the model presented for error analysis can be applied to various part- mating types and especially useful for error analysis of complexity assembly.

  7. Biological long-term observation of air pollution - lichen mapping as part of the environmental monitoring Esslingen/Altbach (Germany) 1983-1998

    Energy Technology Data Exchange (ETDEWEB)

    Bartholmess, H.

    2002-07-01

    In the area surrounding the Altbach/Deizisau power station, an environmental monitoring programme was installed in 1983 for a period of 5 years, using biological indicators and augmented by immission measurements and soil analyses. The proximate cause was the granting of approval under immission-control law for the building of a new heat- and power station on the site of Altbach/Deizisau in 1981. The programme continued on voluntary basis until 1998, always adjusted to current questions in air pollution control strategy. (orig.)

  8. Reversibly assembled cellular composite materials.

    Science.gov (United States)

    Cheung, Kenneth C; Gershenfeld, Neil

    2013-09-13

    We introduce composite materials made by reversibly assembling a three-dimensional lattice of mass-produced carbon fiber-reinforced polymer composite parts with integrated mechanical interlocking connections. The resulting cellular composite materials can respond as an elastic solid with an extremely large measured modulus for an ultralight material (12.3 megapascals at a density of 7.2 milligrams per cubic centimeter). These materials offer a hierarchical decomposition in modeling, with bulk properties that can be predicted from component measurements and deformation modes that can be determined by the placement of part types. Because site locations are locally constrained, structures can be produced in a relative assembly process that merges desirable features of fiber composites, cellular materials, and additive manufacturing.

  9. U1-RNP and Toll-like receptors in the pathogenesis of mixed connective tissue diseasePart II. Endosomal TLRs and their biological significance in the pathogenesis of mixed connective tissue disease.

    Science.gov (United States)

    Paradowska-Gorycka, Agnieszka

    2015-01-01

    Mixed connective tissue disease (MCTD) is a chronic autoimmune immunopathological disease of unknown etiology, which is characterized by the presence of various clinical symptoms and the presence of autoantibodies against U1-RNP particles. The U1-RNP component engages immune cells and their receptors in a complex network of interactions that ultimately lead to autoimmunity, inflammation, and tissue injury. The anti-U1-RNP autoantibodies form an immune complex with self-RNA, present in MCTD serum, which can act as endosomal Toll-like receptor (TLR) ligands. Inhibition of TLRs by nucleic acids is a promising area of research for the development of novel therapeutic strategies against pathogenic infection, tumorigenesis and autoimmunity. In this review we summarize current knowledge of endogenous TLRs and discuss their biological significance in the pathogenesis of MCTD. In part I we described the structure, biological function and significance of the U1-RNP complex in MCTD.

  10. Flowering and pollen value of selected species of umbelliferous family - Umbelliferae Juss. (Apiaceae Lindl. in Lublin region. Part 1. Biology and abundance of flowering

    Directory of Open Access Journals (Sweden)

    Anna Wróblewska

    2013-12-01

    Full Text Available Investigations of the biology of flowering and pollen value of seven species of Umbelliferae family were carried out in natural seats of Lublin region in 1978-1980. Aegopodium podagraria L.,Angelica silvestris L., Anthriscus silvestris L. (Hoffm., Chaerophyllum aromaticum L., Eryngium planum L., Herac1eum sibiricum L., Pastinaca sativa L. were examined. This paper shows results of studies of the biology of flowering and abundance of flowering. The examined species started their flowering in the following chronological order: Anthriscus silvestris, Aegopodium podagraria, Pastinaca sativa, Chaerophyllum aromaticum, Heracleum sibiricum, Eryngium planum, Angelica silvestris. The period of time of flowering lasts 3-5 weeks. Both bisexual and male flowers were found in the inflorescences. The number of flowers produced by a single plant were as follows: Pastinaca sativa 5390-6354, Angelica silvestris 3408-4944, Chaerophyllum aromaticum 3972-4532, Anthriscus silvestris 3438-4374, Aegopodium podagraria 1915-2033, Heracleum sibiricum 1626-1908, Eryngium planum 1185-1420.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-31

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

  12. Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part II: from genes to networks: tissue engineering from the viewpoint of systems biology and network science.

    Science.gov (United States)

    Lenas, Petros; Moos, Malcolm; Luyten, Frank P

    2009-12-01

    The field of tissue engineering is moving toward a new concept of "in vitro biomimetics of in vivo tissue development." In Part I of this series, we proposed a theoretical framework integrating the concepts of developmental biology with those of process design to provide the rules for the design of biomimetic processes. We named this methodology "developmental engineering" to emphasize that it is not the tissue but the process of in vitro tissue development that has to be engineered. To formulate the process design rules in a rigorous way that will allow a computational design, we should refer to mathematical methods to model the biological process taking place in vitro. Tissue functions cannot be attributed to individual molecules but rather to complex interactions between the numerous components of a cell and interactions between cells in a tissue that form a network. For tissue engineering to advance to the level of a technologically driven discipline amenable to well-established principles of process engineering, a scientifically rigorous formulation is needed of the general design rules so that the behavior of networks of genes, proteins, or cells that govern the unfolding of developmental processes could be related to the design parameters. Now that sufficient experimental data exist to construct plausible mathematical models of many biological control circuits, explicit hypotheses can be evaluated using computational approaches to facilitate process design. Recent progress in systems biology has shown that the empirical concepts of developmental biology that we used in Part I to extract the rules of biomimetic process design can be expressed in rigorous mathematical terms. This allows the accurate characterization of manufacturing processes in tissue engineering as well as the properties of the artificial tissues themselves. In addition, network science has recently shown that the behavior of biological networks strongly depends on their topology and has

  13. Assembly planning at the micro scale

    Energy Technology Data Exchange (ETDEWEB)

    Feddema, J.T.; Xavier, P.; Brown, R.

    1998-05-14

    This paper investigates a new aspect of fine motion planning for the micro domain. As parts approach 1--10 {micro}m or less in outside dimensions, interactive forces such as van der Waals and electrostatic forces become major factors which greatly change the assembly sequence and path plans. It has been experimentally shown that assembly plans in the micro domain are not reversible, motions required to pick up a part are not the reverse of motions required to release a part. This paper develops the mathematics required to determine the goal regions for pick up, holding, and release of a micro-sphere being handled by a rectangular tool.

  14. Polymer Directed Protein Assemblies

    NARCIS (Netherlands)

    van Rijn, Patrick

    2013-01-01

    Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e. g., virus particles. Viruses are a multi-protein assembly of which the morphology is

  15. Part 1. Assessment of carcinogenicity and biologic responses in rats after lifetime inhalation of new-technology diesel exhaust in the ACES bioassay.

    Science.gov (United States)

    McDonald, Jacob D; Doyle-Eisele, Melanie; Seagrave, JeanClare; Gigliotti, Andrew P; Chow, Judith; Zielinska, Barbara; Mauderly, Joe L; Seilkop, Steven K; Miller, Rodney A

    2015-01-01

    The Health Effects Institute and its partners conceived and funded a program to characterize the emissions from heavy-duty diesel engines compliant with the 2007 and 2010 on-road emissions standards in the United States and to evaluate indicators of lung toxicity in rats and mice exposed repeatedly to 2007-compliant new-technology diesel exhaust (NTDE*). The a priori hypothesis of this Advanced Collaborative Emissions Study (ACES) was that 2007-compliant on-road diesel emissions "... will not cause an increase in tumor formation or substantial toxic effects in rats and mice at the highest concentration of exhaust that can be used ... although some biological effects may occur." This hypothesis was tested at the Lovelace Respiratory Research Institute (LRRI) by exposing rats by chronic inhalation as a carcinogenicity bioassay. Indicators of pulmonary toxicity in rats were measured after 1, 3, 12, 24, and 28-30 months of exposure. Similar indicators of pulmonary toxicity were measured in mice, as an interspecies comparison of the effects of subchronic exposure, after 1 and 3 months of exposure. A previous HEI report (Mauderly and McDonald 2012) described the operation of the engine and exposure systems and the characteristics of the exposure atmospheres during system commissioning. Another HEI report described the biologic responses in mice and rats after subchronic exposure to NTDE (McDonald et al. 2012). The primary motivation for the present chronic study was to evaluate the effects of NTDE in rats in the context of previous studies that had shown neoplastic lung lesions in rats exposed chronically to traditional technology diesel exhaust (TDE) (i.e., exhaust from diesel engines built before the 2007 U.S. requirements went into effect). The hypothesis was largely based on the marked reduction of diesel particulate matter (DPM) in NTDE compared with emissions from older diesel engine and fuel technologies, although other emissions were also reduced. The DPM

  16. Variability and connectivity of plaice populations from the Eastern North Sea to the Baltic Sea, part II. Biological evidence of population mixing

    DEFF Research Database (Denmark)

    Ulrich, Clara; Hansen, Jakob Hemmer; Boje, Jesper

    2016-01-01

    A multi-disciplinary study was conducted to clarify stock identity and connectivity patterns in the populations of European plaice (Pleuronectes platessa) in the Skagerrak-Kattegat transition area between the Eastern North Sea and the Baltic Sea. Five independent biological studies were carried out...... in parallel. Genetic markers suggested the existence of different genetic populations in the transition area. Growth backcalculation with otoliths resulted in significant although limited differences in growth rates between North Sea and Skagerrak, indicating weak differentiation or important mixing....... Hydrogeographical drift modelling suggested that some North Sea juveniles could settle along the coast line of the Skagerrak and the Kattegat. Tagging data suggested that both juveniles and adult fish from the North Sea perform feeding migrations into Skagerrak in summer/autumn. Finally, survey data suggested...

  17. Applications of Recombinant DNA Technology in Gastrointestinal Medicine and Hepatology: Basic Paradigms of Molecular Cell Biology. Part A: Eukaryotic Gene Structure and DNA Replication

    Directory of Open Access Journals (Sweden)

    Gary E Wild

    2000-01-01

    Full Text Available Progress in the basic sciences of cell and molecular biology has provided an exciting dimension that has translated into clinically relevant information in every medical subspecialty. Importantly, the application of recombinant DNA technology has played a major role in unravelling the intricacies related to the molecular pathophysiology of disease. This series of review articles constitutes a framework for the integration of the database of new information into the core knowledge base of concepts related to the pathogenesis of gastrointestinal disorders and liver disease. The goal of this series of three articles is to review the basic principles of eukaryotic gene expression. The first article examines the role of DNA in directing the flow of genetic information in eukaryotic cells.

  18. Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Dwayne; Schadt, Christopher; Miller, Lance; Phelps, Tommy; Brown, S. D.; Arkin, Adam; Hazen, Terry; Drake, Megin; Yang, Z.K.; Podar, Mircea

    2010-05-17

    One of the largest experimental gaps is between the simplicity of pure cultures and the complexity of open environmental systems, particularly in metal-contaminated areas. These microbial communities form ecosystem foundations, drive biogeochemical processes, and are relevant for biotechnology and bioremediation. A model, metal-reducing microbial community was constructed as either syntrophic or competitive to study microbial cell to cell interactions, cell signaling and competition for resources. The microbial community was comprised of the metal-reducing Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens PCA. Additionally, Methanococcus maripaludis S2 was added to study complete carbon reduction and maintain a low hydrogen partial pressure for syntrophism to occur. Further, considerable work has been published on D. vulgaris and the D. vulgaris/ Mc. maripaludis co-culture both with and without stress. We are extending this work by conducting the same stress conditions on the model community. Additionally, this comprehensive investigation includes physiological and metabolic analyses as well as specially designed mRNA microarrays with the genes for all three organisms on one slide so as to follow gene expression changes in the various cultivation conditions as well as being comparable to the co- and individual cultures. Further, state-of -the-art comprehensive AMT tag proteomics allows for these comparisons at the protein level for a systems biology assessment of a model, metal-reducing microbial community. Preliminary data revealed that lactate oxidation by D. vulgaris was sufficient to support both G. sulfurreducens and M. maripaludis via the excretion of H2 and acetate. Fumarate was utilized by G. sulfurreducens and reduced to succinate since neither of the other two organisms can reduce fumarate. Methane was quantified, suggesting acetate and H2 concentrations were sufficient for M. maripaludis. Steady state community cultivation will allow for

  19. A Generation Method of Mechanical Assembly Drawing in CAD

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    This paper supplies a generation method of mechanical assembly drawing in CAD. By means of the programs of Auto Lisp, the method which based on AutoCAD may complete profiling the parts, forming parts graphic base, calculation of removing hidden line, and establishing assembly drawing.

  20. Parallel Assembly of LIGA Components

    Energy Technology Data Exchange (ETDEWEB)

    Christenson, T.R.; Feddema, J.T.

    1999-03-04

    In this paper, a prototype robotic workcell for the parallel assembly of LIGA components is described. A Cartesian robot is used to press 386 and 485 micron diameter pins into a LIGA substrate and then place a 3-inch diameter wafer with LIGA gears onto the pins. Upward and downward looking microscopes are used to locate holes in the LIGA substrate, pins to be pressed in the holes, and gears to be placed on the pins. This vision system can locate parts within 3 microns, while the Cartesian manipulator can place the parts within 0.4 microns.

  1. Sensor mount assemblies and sensor assemblies

    Science.gov (United States)

    Miller, David H [Redondo Beach, CA

    2012-04-10

    Sensor mount assemblies and sensor assemblies are provided. In an embodiment, by way of example only, a sensor mount assembly includes a busbar, a main body, a backing surface, and a first finger. The busbar has a first end and a second end. The main body is overmolded onto the busbar. The backing surface extends radially outwardly relative to the main body. The first finger extends axially from the backing surface, and the first finger has a first end, a second end, and a tooth. The first end of the first finger is disposed on the backing surface, and the tooth is formed on the second end of the first finger.

  2. Molecular assembly in natural and engineered systems

    CERN Document Server

    Howorka, Stefan

    2011-01-01

    This volume explores some of the most exciting recent advances in basic research on molecular assembly in natural and engineered systems and how this knowledge is leading to advances in the various fields.* This series provides a forum for discussion of new discoveries, approaches, and ideas * Contributions from leading scholars and industry experts * Reference guide for researchers involved in molecular biology and related fields

  3. SolidWorks 2011 Assemblies Bible

    CERN Document Server

    Lombard, Matt

    2011-01-01

    A fan of the SolidWorks Bible, but want more detail on assemblies? Here you go. SolidWorks fans have long sought more detail on SolidWorks topics, and now you have it. We took our popular SolidWorks Bible, divided it into two books (SolidWorks 2011 Assemblies Bible and SolidWorks 2011 Parts Bible) and packed each new book with a host of items from your wish lists, such as more extensive coverage of the basics, additional tutorials, and expanded coverage of topics largely ignored by other books. This SolidWorks 2011 Assemblies Bible shows you how to organize parts data to create assemblies or s

  4. Soldering in electronics assembly

    CERN Document Server

    Judd, Mike

    2013-01-01

    Soldering in Electronics Assembly discusses several concerns in soldering of electronic assemblies. The book is comprised of nine chapters that tackle different areas in electronic assembly soldering. Chapter 1 discusses the soldering process itself, while Chapter 2 covers the electronic assemblies. Chapter 3 talks about solders and Chapter 4 deals with flux. The text also tackles the CS and SC soldering process. The cleaning of soldered assemblies, solder quality, and standards and specifications are also discussed. The book will be of great use to professionals who deal with electronic assem

  5. Metabolites from nematophagous fungi and nematicidal natural products from fungi as alternatives for biological control. Part II: metabolites from nematophagous basidiomycetes and non-nematophagous fungi.

    Science.gov (United States)

    Degenkolb, Thomas; Vilcinskas, Andreas

    2016-05-01

    In this second section of a two-part mini-review article, we introduce 101 further nematicidal and non-nematicidal secondary metabolites biosynthesized by nematophagous basidiomycetes or non-nematophagous ascomycetes and basidiomycetes. Several of these compounds have promising nematicidal activity and deserve further and more detailed analysis. Thermolides A and B, omphalotins, ophiobolins, bursaphelocides A and B, illinitone A, pseudohalonectrins A and B, dichomitin B, and caryopsomycins A-C are excellent candidates or lead compounds for the development of biocontrol strategies for phytopathogenic nematodes. Paraherquamides, clonostachydiol, and nafuredins offer promising leads for the development of formulations against the intestinal nematodes of ruminants.

  6. A trait-based approach for examining microbial community assembly

    Science.gov (United States)

    Prest, T. L.; Nemergut, D.

    2015-12-01

    Microorganisms regulate all of Earth's major biogeochemical cycles and an understanding of how microbial communities assemble is a key part in evaluating controls over many types of ecosystem processes. Rapid advances in technology and bioinformatics have led to a better appreciation for the variation in microbial community structure in time and space. Yet, advances in theory are necessary to make sense of these data and allow us to generate unifying hypotheses about the causes and consequences of patterns in microbial biodiversity and what they mean for ecosystem function. Here, I will present a metaanalysis of microbial community assembly from a variety of successional and post-disturbance systems. Our analysis shows various distinct patterns in community assembly, and the potential importance of nutrients and dispersal in shaping microbial community beta diversity in these systems. We also used a trait-based approach to generate hypotheses about the mechanisms driving patterns of microbial community assembly and the implications for function. Our work reveals the importance of rRNA operon copy number as a community aggregated trait in helping to reconcile differences in community dynamics between distinct types of successional and disturbed systems. Specifically, our results demonstrate that decreases in average copy number can be a common feature of communities across various drivers of ecological succession, supporting a transition from an r-selected to a K-selected community. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, from cells to populations and communities, and has implications for both ecology and evolution. Trait-based approaches are an important next step to generate and test hypotheses about the forces structuring microbial communities and the subsequent consequences for ecosystem function.

  7. Marine biology

    Energy Technology Data Exchange (ETDEWEB)

    Thurman, H.V.; Webber, H.H.

    1984-01-01

    This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the nature of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index.

  8. Mechanical Self-Assembly Science and Applications

    CERN Document Server

    2013-01-01

    Mechanical Self-Assembly: Science and Applications introduces a novel category of self-assembly driven by mechanical forces. This book discusses self-assembly in various types of small material structures including thin films, surfaces, and micro- and nano-wires, as well as the practice's potential application in micro and nanoelectronics, MEMS/NEMS, and biomedical engineering. The mechanical self-assembly process is inherently quick, simple, and cost-effective, as well as accessible to a large number of materials, such as curved surfaces for forming three-dimensional small structures. Mechanical self-assembly is complementary to, and sometimes offer advantages over, the traditional micro- and nano-fabrication. This book also: Presents a highly original aspect of the science of self-assembly Describes the novel methods of mechanical assembly used to fabricate a variety of new three-dimensional material structures in simple and cost-effective ways Provides simple insights to a number of biological systems and ...

  9. Chemical composition and biological evaluation of the volatile constituents from the aerial parts of Nephrolepis exaltata (L.) and Nephrolepis cordifolia (L.) C. Presl grown in Egypt.

    Science.gov (United States)

    El-Tantawy, Mona E; Shams, Manal M; Afifi, Manal S

    2016-01-01

    The essential oil from the aerial parts of Nephrolepis exaltata and Nephrolepis cordifolia obtained by hydro-distillation were analyzed by gas chromatography/ mass spectrometry. The essential oils exhibited potential antibacterial and antifungal activities against a majority of the selected microorganisms. NEA oil showed promising cytotoxicity in breast, colon and lung carcinoma cells. The results presented indicate that NEA oil could be useful alternative for the treatment of dermatophytosis. Comparative investigation of hydro-distilled volatile constituents from aerial parts (A) of Nephrolepis exaltata (NE) and Nephrolepis cordifolia (NC) (Family Nephrolepidaceae) was carried out. Gas chromatography/mass spectrometry revealed that oils differ in composition and percentages of components. Oxygenated compounds were dominant in NEA and NCA. 2,4-Hexadien-1-ol (16.1%), nonanal (14.4%), β-Ionone (6.7%) and thymol (2.7%) were predominant in NEA. β-Ionone (8.0%), eugenol (7.2%) and anethol (4.6%) were the main constituents in NCA. Volatile samples were screened for their antibacterial and antifungal activities using agar diffusion method and minimum inhibitory concentrations. The cytotoxic activity was evaluated using viability assay in breast (MCF-7), colon (HCT-116) and lung carcinoma (A-549) cells by the MTT assay. The results revealed that NEA oil exhibited potential antimicrobial activity against most of the tested organisms and showed promising cytotoxicity.

  10. Long-read sequence assembly of the gorilla genome

    Science.gov (United States)

    Gordon, David; Huddleston, John; Chaisson, Mark J. P.; Hill, Christopher M.; Kronenberg, Zev N.; Munson, Katherine M.; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, LaDeana W.; Dunn, Christopher; Baker, Carl; Armstrong, Joel; Diekhans, Mark; Paten, Benedict; Shendure, Jay; Wilson, Richard K.; Haussler, David; Chin, Chen-Shan; Eichler, Evan E.

    2016-01-01

    Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome. PMID:27034376

  11. Design, synthesis and biological evaluation of novel 4-alkapolyenylpyrrolo[1,2-a]quinoxalines as antileishmanial agents--part III.

    Science.gov (United States)

    Ronga, Luisa; Del Favero, Marco; Cohen, Anita; Soum, Claire; Le Pape, Patrice; Savrimoutou, Solène; Pinaud, Noël; Mullié, Catherine; Daulouede, Sylvie; Vincendeau, Philippe; Farvacques, Natacha; Agnamey, Patrice; Pagniez, Fabrice; Hutter, Sébastien; Azas, Nadine; Sonnet, Pascal; Guillon, Jean

    2014-06-23

    A series of new 4-alkapolyenylpyrrolo[1,2-a]quinoxaline derivatives, original and structural analogues of alkaloid chimanine B and of previously described 4-alkenylpyrrolo[1,2-a]quinoxalines, was synthesized in good yields using efficient palladium-catalyzed Suzuki-Miyaura cross-coupling reactions. These new compounds were tested for in vitro antiparasitic activity upon three Leishmania spp. strains. Biological results showed activity against the promastigote forms of L. major, L. mexicana and L. donovani with IC50 ranging from 1.2 to 14.7 μM. In attempting to investigate if our pyrrolo[1,2-a]quinoxaline derivatives are broad-spectrum antiprotozoal compounds activities toward one Trypanosoma brucei brucei strain and the W2 and 3D7 Plasmodium falciparum strains were also investigated. In parallel, the in vitro cytotoxicity of these molecules was assessed on the murine J774 and human HepG2 cell lines. Structure-activity relationships of these new synthetic compounds are here discussed.

  12. Variability and connectivity of plaice populations from the Eastern North Sea to the Baltic Sea, part II. Biological evidence of population mixing

    Science.gov (United States)

    Ulrich, Clara; Hemmer-Hansen, Jakob; Boje, Jesper; Christensen, Asbjørn; Hüssy, Karin; Sun, Hailu; Clausen, Lotte Worsøe

    2017-02-01

    A multi-disciplinary study was conducted to clarify stock identity and connectivity patterns in the populations of European plaice (Pleuronectes platessa) in the Skagerrak-Kattegat transition area between the Eastern North Sea and the Baltic Sea. Five independent biological studies were carried out in parallel. Genetic markers suggested the existence of different genetic populations in the transition area. Growth backcalculation with otoliths resulted in significant although limited differences in growth rates between North Sea and Skagerrak, indicating weak differentiation or important mixing. Hydrogeographical drift modelling suggested that some North Sea juveniles could settle along the coast line of the Skagerrak and the Kattegat. Tagging data suggested that both juveniles and adult fish from the North Sea perform feeding migrations into Skagerrak in summer/autumn. Finally, survey data suggested that Skagerrak also belongs to the area distribution of North Sea plaice. The outcomes of the individual studies were then combined into an overall synthesis. The existence of some resident components was evidenced, but it was also demonstrated that North Sea plaice migrate for feeding into Skagerrak and might constitute a large share of the catches in this area. The mixing of different populations within a management area has implications for stock assessment and management. Choice must be made to either lump or split the populations, and the feasibility and constraints of both options are discussed. The outcomes of this work have directly influenced the management decisions in 2015.

  13. Fused heterocycles bearing bridgehead nitrogen as potent HIV-1 NNRTIs. Part 4: design, synthesis and biological evaluation of novel imidazo[1,2-a]pyrazines.

    Science.gov (United States)

    Huang, Boshi; Liang, Xin; Li, Cuicui; Chen, Wenmin; Liu, Tao; Li, Xiao; Sun, Yueyue; Fu, Lu; Liu, Huiqing; De Clercq, Erik; Pannecouque, Christophe; Zhan, Peng; Liu, Xinyong

    2015-03-26

    Through a structure-guided core-refining approach, a series of novel imidazo[1,2-a]pyrazine derivatives were designed, synthesized and evaluated as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Biological results of antiviral assay in MT-4 cell cultures showed that 12 target compounds displayed moderate activities against wild-type (wt) HIV-1 strain (IIIB) with EC50 values ranging from 0.26 μM to 19 μM. Among them, 4a and 5a were found to be the two most active analogues possessing EC50 values of 0.26 μM and 0.32 μM respectively, comparable to delavirdine (DLV, EC50 = 0.54 μM) and nevirapine (NVP, EC50 = 0.31 μM) in a cell-based assay. Additionally, 9 compounds showed RT inhibitory activity superior to that of NVP. Moreover, some predicted drug-like properties of representative compounds 4a and 5a, as well as the structure-activity relationship (SAR) analysis were discussed in detail. The binding mode of compound 4a was investigated by molecular simulation studies.

  14. Nickel-quinolones interaction. Part 5-Biological evaluation of nickel(II) complexes with first-, second- and third-generation quinolones.

    Science.gov (United States)

    Skyrianou, Kalliopi C; Perdih, Franc; Papadopoulos, Athanasios N; Turel, Iztok; Kessissoglou, Dimitris P; Psomas, George

    2011-10-01

    The nickel(II) complexes with the quinolone antibacterial agents oxolinic acid, flumequine, enrofloxacin and sparfloxacin in the presence of the N,N'-donor heterocyclic ligand 2,2'-bipyridylamine have been synthesized and characterized. The quinolones act as bidentate ligands coordinated to Ni(II) ion through the pyridone oxygen and a carboxylato oxygen. The crystal structure of [(2,2'-bipyridylamine)bis(sparfloxacinato)nickel(II)] has been determined by X-ray crystallography. UV study of the interaction of the complexes with calf-thymus DNA (CT DNA) has shown that they bind to CT DNA with [(2,2'-bipyridylamine)bis(flumequinato)nickel(II)] exhibiting the highest binding constant to CT DNA. The cyclic voltammograms of the complexes have shown that in the presence of CT DNA the complexes can bind to CT DNA by the intercalative binding mode which has also been verified by DNA solution viscosity measurements. Competitive study with ethidium bromide (EB) has shown that the complexes can displace the DNA-bound EB indicating that they bind to DNA in strong competition with EB. The complexes exhibit good binding propensity to human or bovine serum albumin protein having relatively high binding constant values. The biological properties of the [Ni(quinolonato)(2)(2,2'-bipyridylamine)] complexes have been evaluated in comparison to the previously reported Ni(II) quinolone complexes [Ni(quinolonato)(2)(H(2)O)(2)], [Ni(quinolonato)(2)(2,2'-bipyridine)] and [Ni(quinolonato)(2)(1,10-phenanthroline)]. The quinolones and their Ni(II) complexes have been tested for their antioxidant and free radical scavenging activity. They have been also tested in vitro for their inhibitory activity against soybean lipoxygenase.

  15. Large Pelagics Biological Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Large Pelagics Biological Survey (LPBS) collects additional length and weight information and body parts such as otoliths, caudal vertebrae, dorsal spines, and...

  16. Virus Assemblies as Templates for Nanocircuits

    Energy Technology Data Exchange (ETDEWEB)

    James N Culver; Michael T Harris

    2011-08-31

    The goals of this project were directed at the identification and characterization of bio-mineralization processes and patterning methods for the development of nano scale materials and structures with novel energy and conductive traits. This project utilized a simple plant virus as a model template to investigate methods to attach and coat metals and other inorganic compounds onto biologically based nanotemplates. Accomplishments include: the development of robust biological nanotemplates with enhanced inorganic coating activities; novel coating strategies that allow for the deposition of a continuous inorganic layer onto a bio-nanotemplate even in the absence of a reducing agent; three-dimensional patterning methods for the assemble of nano-featured high aspect ratio surfaces and the demonstrated use of these surfaces in enhancing battery and energy storage applications. Combined results from this project have significantly advanced our understanding and ability to utilize the unique self-assembly properties of biologically based molecules to produce novel materials at the nanoscale level.

  17. Finishing of the cold mass assembly

    CERN Multimedia

    Maximilien Brice

    2001-01-01

    Photo 1 The connection-side end of the active part assembly. This view shows the electrical connections between the poles and the curved bus ended with flanges for the connection with the protection diode. Photo 2 The connection-side end of the active part assembly. This view shows the electrical connections between the poles, the auxiliary bus bars and the instrumentation wires. Photo 3 Lyre-side end of the active part assembly. One can see the mechanical support of the corretor magnets that are to be installed around the cold bore tubes. Photo 4 General view of the finishing station showing the special supporting structures (blue and yellow structures) needed for the geometric measurements and for the alignment operations. Around the magnet, there are datum points (on the tripodes) needed to build up the coordinates system for the measurements.

  18. Linear Logic for Meaning Assembly

    CERN Document Server

    Dalrymple, M; Pereira, F C N; Saraswat, V; Dalrymple, Mary; Lamping, John; Pereira, Fernando; Saraswat, Vijay

    1995-01-01

    Semantic theories of natural language associate meanings with utterances by providing meanings for lexical items and rules for determining the meaning of larger units given the meanings of their parts. Meanings are often assumed to combine via function application, which works well when constituent structure trees are used to guide semantic composition. However, we believe that the functional structure of Lexical-Functional Grammar is best used to provide the syntactic information necessary for constraining derivations of meaning in a cross-linguistically uniform format. It has been difficult, however, to reconcile this approach with the combination of meanings by function application. In contrast to compositional approaches, we present a deductive approach to assembling meanings, based on reasoning with constraints, which meshes well with the unordered nature of information in the functional structure. Our use of linear logic as a `glue' for assembling meanings allows for a coherent treatment of the LFG requ...

  19. A facile and green strategy for the synthesis of Au, Ag and Au-Ag alloy nanoparticles using aerial parts of R. hypocrateriformis extract and their biological evaluation.

    Science.gov (United States)

    Godipurge, S S; Yallappa, S; Biradar, Naveen J; Biradar, J S; Dhananjaya, B L; Hegde, Gajanan; Jagadish, K; Hegde, Gurumurthy

    2016-12-01

    A facile and green strategy is reported here to synthesize gold (Au), silver (Ag) and gold-silver (Au-Ag) alloy nanoparticles (NPs) through bio-reduction reactions of aqueous corresponding metal precursors mediated by extracts of aerial parts of R. hypocrateriformis, which act as both reducing and stabilizing agents, under microwave irradiation. UV-vis spectrophotometer, XRD, FT-IR, FESEM/TEM, TGA and EDAX analysis were used to characterize the obtained NPs. The formation of NPs is evident from their surface plasmon resonance peak observed at λmax=∼550, 450 and 500nm for Au, Ag and Au-Ag alloy NPs respectively. XRD pattern revealed that fcc structure, while FT-IR spectra signify the presence of phytochemicals adsorbed on NPs. Such a biofunctionalized NPs were characterized by their weight loss, 30% due to thermal degradation of plant phytochemicals observed in TG analysis. The spherical shape of Au, Ag and Au-Ag alloy NPs (∼10-50nm) is observed by FE-SEM/TEM images. EDAX analysis confirms the expected elemental composition. Moreover, these NPs showed enhanced antimicrobial, antioxidant, and anticancer activities, though it is more pronounced for Au-Ag alloy NPs, which is due to the combining effect of phytochemicals, Au and Ag metals. Thus, the biosynthesized NPs could be applied as effective growth inhibitors for various biomedical applications.

  20. Metabolites from nematophagous fungi and nematicidal natural products from fungi as an alternative for biological control. Part I: metabolites from nematophagous ascomycetes.

    Science.gov (United States)

    Degenkolb, Thomas; Vilcinskas, Andreas

    2016-05-01

    Plant-parasitic nematodes are estimated to cause global annual losses of more than US$ 100 billion. The number of registered nematicides has declined substantially over the last 25 years due to concerns about their non-specific mechanisms of action and hence their potential toxicity and likelihood to cause environmental damage. Environmentally beneficial and inexpensive alternatives to chemicals, which do not affect vertebrates, crops, and other non-target organisms, are therefore urgently required. Nematophagous fungi are natural antagonists of nematode parasites, and these offer an ecophysiological source of novel biocontrol strategies. In this first section of a two-part review article, we discuss 83 nematicidal and non-nematicidal primary and secondary metabolites found in nematophagous ascomycetes. Some of these substances exhibit nematicidal activities, namely oligosporon, 4',5'-dihydrooligosporon, talathermophilins A and B, phomalactone, aurovertins D and F, paeciloxazine, a pyridine carboxylic acid derivative, and leucinostatins. Blumenol A acts as a nematode attractant. Other substances, such as arthrosporols and paganins, play a decisive role in the life cycle of the producers, regulating the formation of reproductive or trapping organs. We conclude by considering the potential applications of these beneficial organisms in plant protection strategies.

  1. Artful interfaces within biological materials

    Directory of Open Access Journals (Sweden)

    John W.C. Dunlop

    2011-03-01

    Full Text Available Biological materials have a wide range of mechanical properties matching their biological function. This is achieved via complex structural hierarchies, spanning many length scales, arising from the assembly of different sized building blocks during growth. The interfaces between these building blocks can increase resistance to fracture, join materials of different character, make them deform more easily and provide motility. While they represent only a tiny fraction of the overall volume, interfaces are essential for the integrity and function of the overall tissue. Understanding their construction principles, often based on specialized molecular assemblies, may change our current thinking about composite materials.

  2. Nanopropulsion by biocatalytic self-assembly.

    Science.gov (United States)

    Leckie, Joy; Hope, Alexander; Hughes, Meghan; Debnath, Sisir; Fleming, Scott; Wark, Alastair W; Ulijn, Rein V; Haw, Mark D

    2014-09-23

    A number of organisms and organelles are capable of self-propulsion at the micro- and nanoscales. Production of simple man-made mimics of biological transportation systems may prove relevant to achieving movement in artificial cells and nano/micronscale robotics that may be of biological and nanotechnological importance. We demonstrate the propulsion of particles based on catalytically controlled molecular self-assembly and fiber formation at the particle surface. Specifically, phosphatase enzymes (acting as the engine) are conjugated to a quantum dot (the vehicle), and are subsequently exposed to micellar aggregates (fuel) that upon biocatalytic dephosphorylation undergo fibrillar self-assembly, which in turn causes propulsion. The motion of individual enzyme/quantum dot conjugates is followed directly using fluorescence microscopy. While overall movement remains random, the enzyme-conjugates exhibit significantly faster transport in the presence of the fiber forming system, compared to controls without fuel, a non-self-assembling substrate, or a substrate which assembles into spherical, rather than fibrous structures upon enzymatic dephosphorylation. When increasing the concentration of the fiber-forming fuel, the speed of the conjugates increases compared to non-self-assembling substrate, although directionality remains random.

  3. Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

    Science.gov (United States)

    Currin, Andrew; Jervis, Adrian J.; Rattray, Nicholas J. W.; Swainston, Neil; Yan, Cunyu; Breitling, Rainer

    2016-01-01

    Covering: 2000 to 2016 Progress 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

  4. SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Cavaleiro, Mafalda; Rennig, Maja

    2016-01-01

    DNA vectors serve to maintain and select recombinant DNA in cell factories, and as design complexity increases, there is a greater need for well-characterized parts and methods for their assembly. Standards in synthetic biology are top priority, but standardizing molecular cloning contrasts...... flexibility, and different researchers prefer and master different molecular technologies. Here, we describe a new, highly versatile and automatable standard “SEVA linkers” for vector exchange. SEVA linkers enable backbone swapping with 20 combinations of classical enzymatic restriction/ligation, Gibson...... to the synthetic biology community....

  5. Dynamic self-assembly of 'living' polymeric chains

    Science.gov (United States)

    Deng, Binghui; Shi, Yunfeng

    2017-01-01

    We report a dynamic self-assembly system of 'living' polymeric chains sustained by chemistry using reactive molecular dynamics simulations. The linear polymeric chains consist of self-assembled nanoparticles connected by metastable linker molecules. As such, the polymeric chains, once assembled, undergo spontaneous dissociation driven by thermodynamics. However, with a continuous supply of linker molecules and the stored chemical energy therein, the polymeric chains can survive and maintain a steady state averaged chain length. These dynamically self-assembled polymeric chains are analogous to biological systems that both are thermodynamically metastable, yet dynamically stable upon continuous influx of matter and energy.

  6. ex vivo DNA assembly

    Directory of Open Access Journals (Sweden)

    Adam B Fisher

    2013-10-01

    Full Text Available Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.

  7. Target Assembly Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Target Assembly Facility integrates new armor concepts into actual armored vehicles. Featuring the capability ofmachining and cutting radioactive materials, it...

  8. Self-assembly of colloidal surfactants

    Science.gov (United States)

    Kegel, Willem

    2012-02-01

    We developed colloidal dumbbells with a rough and a smooth part, based on a method reported in Ref. [1]. Specific attraction between the smooth parts occurs upon addition of non-adsorbing polymers of appropriate size. We present the first results in terms of the assemblies that emerge in these systems. [4pt] [1] D.J. Kraft, W.S. Vlug, C.M. van Kats, A. van Blaaderen, A. Imhof and W.K. Kegel, Self-assembly of colloids with liquid protrusions, J. Am. Chem. Soc. 131, 1182, (2009)

  9. All biology is computational biology

    Science.gov (United States)

    2017-01-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science. PMID:28278152

  10. 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

  11. Rationally engineering natural protein assemblies in nanobiotechnology.

    Science.gov (United States)

    Howorka, Stefan

    2011-08-01

    Multimeric protein assemblies are essential components in viruses, bacteria, eukaryotic cells, and organisms where they act as cytoskeletal scaffold, storage containers, or for directional transport. The bottom-up structures can be exploited in nanobiotechnology by harnessing their built-in properties and combining them with new functional modules. This review summarizes the design principles of natural protein assemblies, highlights recent progress in their structural elucidation, and shows how rational engineering can create new biomaterials for applications in vaccine development, biocatalysis, materials science, and synthetic biology.

  12. Assembly design system based on engineering connection

    Science.gov (United States)

    Yin, Wensheng

    2016-12-01

    An assembly design system is an important part of computer-aided design systems, which are important tools for realizing product concept design. The traditional assembly design system does not record the connection information of production on the engineering layer; consequently, the upstream design idea cannot be fully used in the downstream design. An assembly design model based on the relationship of engineering connection is presented. In this model, all nodes are divided into two categories: The component and the connection. Moreover, the product is constructed on the basis of the connection relationship of the components. The model is an And/Or graph and has the ability to record all assembly schemes. This model records only the connection information that has engineering application value in the product design. In addition, this model can significantly reduce the number of combinations, and is very favorable for the assembly sequence planning in the downstream. The system contains a connection knowledge system that can be mapped to the connection node, and the connection knowledge obtained in practice can be returned to the knowledge system. Finally, VC++ 6.0 is used to develop a prototype system called Connect-based Assembly Planning (CAP). The relationship between the CAP system and the commercial assembly design system is also established.

  13. Mitochondrial ribosome assembly in health and disease.

    Science.gov (United States)

    De Silva, Dasmanthie; Tu, Ya-Ting; Amunts, Alexey; Fontanesi, Flavia; Barrientos, Antoni

    2015-01-01

    The ribosome is a structurally and functionally conserved macromolecular machine universally responsible for catalyzing protein synthesis. Within eukaryotic cells, mitochondria contain their own ribosomes (mitoribosomes), which synthesize a handful of proteins, all essential for the biogenesis of the oxidative phosphorylation system. High-resolution cryo-EM structures of the yeast, porcine and human mitoribosomal subunits and of the entire human mitoribosome have uncovered a wealth of new information to illustrate their evolutionary divergence from their bacterial ancestors and their adaptation to synthesis of highly hydrophobic membrane proteins. With such structural data becoming available, one of the most important remaining questions is that of the mitoribosome assembly pathway and factors involved. The regulation of mitoribosome biogenesis is paramount to mitochondrial respiration, and thus to cell viability, growth and differentiation. Moreover, mutations affecting the rRNA and protein components produce severe human mitochondrial disorders. Despite its biological and biomedical significance, knowledge on mitoribosome biogenesis and its deviations from the much-studied bacterial ribosome assembly processes is scarce, especially the order of rRNA processing and assembly events and the regulatory factors required to achieve fully functional particles. This article focuses on summarizing the current available information on mitoribosome assembly pathway, factors that form the mitoribosome assembly machinery, and the effect of defective mitoribosome assembly on human health.

  14. A systems study of the waste management system in Gothenburg. Part of the project: Thermal and biological waste treatment in a systems perspective; Systemstudie Avfall i Goeteborg. Delprojekt i Termisk och biologisk avfallsbehandling i ett systemperspektiv

    Energy Technology Data Exchange (ETDEWEB)

    Bisaillon, Mattias; Sundberg, Johan; Haraldsson, Maarten; Norrman Eriksson, Ola

    2010-07-01

    The purpose of the project A system study of waste management in Gothenburg is to evaluate new waste treatment options for municipal and industrial waste from a system perspective. The project has been carried out as a part of the project Thermal and biological waste treatment in a systems perspective - WR21. The focus is set to the waste and district heating system in Gothenburg. The project has been running for 2,5 years with an active group consisting of persons from Renova, Kretsloppskontoret, Goeteborg Energi, Gryaab and Profu. The work on development of models and of methods of handling strategic questions within the field has gone back and forth within the group. This report focuses on presenting the final results from the project, which means that the process in which we've excluded several treatment options and scenarios are only briefly described

  15. Spacer conformation in biologically active molecules. Part 2. Structure and conformation of 4-[2-(diphenylmethylamino)ethyl]-1-(2-methoxyphenyl) piperazine and its diphenylmethoxy analog—potential 5-HT 1A receptor ligands

    Science.gov (United States)

    Karolak-Wojciechowska, J.; Fruziński, A.; Czylkowski, R.; Paluchowska, M. H.; Mokrosz, M. J.

    2003-09-01

    As a part of studies on biologically active molecule structures with aliphatic linking chain, the structures of 4-[2-diphenylmethylamino)ethyl]-1-(2-methoxyphenyl)piperazine dihydrochloride ( 1) and 4-[2-diphenylmethoxy)ethyl]-1-(2-methoxyphenyl)piperazine fumarate ( 2) have been reported. In both compounds, four atomic non-all-carbons linking chains (N)C-C-X-C are present. The conformation of that linking spacer depends on the nature of the X-atom. The preferred conformation for chain with XNH has been found to be fully extended while for that with XO—the bend one. It was confirmed by conformational calculations (strain energy distribution and random search) and crystallographic data, including statistics from CCDC.

  16. Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits.

    Science.gov (United States)

    Harbage, David; Kondev, Jané

    2016-07-01

    Self-assembling filamentous structures made of protein subunits are ubiquitous in cell biology. These structures are often highly dynamic, with subunits in a continuous state of flux, binding to and falling off of filaments. In spite of this constant turnover of their molecular parts, many cellular structures seem to maintain a well-defined size over time, which is often required for their proper functioning. One widely discussed mechanism of size regulation involves the cell maintaining a finite pool of protein subunits available for assembly. This finite pool mechanism can control the length of a single filament by having assembly proceed until the pool of free subunits is depleted to the point when assembly and disassembly are balanced. Still, this leaves open the question of whether the same mechanism can provide size control for multiple filamentous structures that are assembled from a common pool of protein subunits, as is often the case in cells. We address this question by solving the steady-state master equation governing the stochastic assembly and disassembly of multifilament structures made from a shared finite pool of subunits. We find that, while the total number of subunits within a multifilament structure is well-defined, individual filaments within the structure have a wide, power-law distribution of lengths. We also compute the phase diagram for two multifilament structures competing for the same pool of subunits and identify conditions for coexistence when both have a well-defined size. These predictions can be tested in cell experiments in which the size of the subunit pool or the number of filament nucleators is tuned.

  17. Perspective: Geometrically frustrated assemblies

    Science.gov (United States)

    Grason, Gregory M.

    2016-09-01

    This perspective will overview an emerging paradigm for self-organized soft materials, geometrically frustrated assemblies, where interactions between self-assembling elements (e.g., particles, macromolecules, proteins) favor local packing motifs that are incompatible with uniform global order in the assembly. This classification applies to a broad range of material assemblies including self-twisting protein filament bundles, amyloid fibers, chiral smectics and membranes, particle-coated droplets, curved protein shells, and phase-separated lipid vesicles. In assemblies, geometric frustration leads to a host of anomalous structural and thermodynamic properties, including heterogeneous and internally stressed equilibrium structures, self-limiting assembly, and topological defects in the equilibrium assembly structures. The purpose of this perspective is to (1) highlight the unifying principles and consequences of geometric frustration in soft matter assemblies; (2) classify the known distinct modes of frustration and review corresponding experimental examples; and (3) describe outstanding questions not yet addressed about the unique properties and behaviors of this broad class of systems.

  18. Extending reference assembly models

    DEFF Research Database (Denmark)

    Church, Deanna M.; Schneider, Valerie A.; Steinberg, Karyn Meltz;

    2015-01-01

    The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles. However, the models and analysis assumptions that underlie the current assembly need revising to fully represent human sequence diversity. Improved analysis tools...

  19. Assembly of primary cilia

    DEFF Research Database (Denmark)

    Pedersen, Lotte B; Veland, Iben R; Schrøder, Jacob M

    2008-01-01

    in primary cilia assembly or function have been associated with a panoply of disorders and diseases, including polycystic kidney disease, left-right asymmetry defects, hydrocephalus, and Bardet Biedl Syndrome. Here we provide an up-to-date review focused on the molecular mechanisms involved in the assembly...

  20. Research overview on vibration damping of mistuned bladed disk assemblies

    Directory of Open Access Journals (Sweden)

    Liang ZHANG

    2016-04-01

    Full Text Available Bladed disk assemblies are very important parts in auto engine and gas turbine, and is widely used in practical engineering. The mistuning existing commonly in the bladed disk assemblies can destroy the vibration characteristics of the bladed disk assemblies, which is one of the reasons for the high cycle fatigue failure of bladed disk assemblies, so it is necessary to research how to reduce the vibration of the bladed disk assemblies. On the basis of the review of relevant research at home and abroad, the mistuning vibration mechanism of the bladed disk assemblies is introduced, and the main technical methods of the vibration damping of bladed disk assemblies are reviewed, such as artificially active mistuning, collision damping, friction damping and optimization of the blade position. Some future research directions are presented.

  1. 3D Assembly Group Analysis for Cognitive Automation

    Directory of Open Access Journals (Sweden)

    Christian Brecher

    2012-01-01

    Full Text Available A concept that allows the cognitive automation of robotic assembly processes is introduced. An assembly cell comprised of two robots was designed to verify the concept. For the purpose of validation a customer-defined part group consisting of Hubelino bricks is assembled. One of the key aspects for this process is the verification of the assembly group. Hence a software component was designed that utilizes the Microsoft Kinect to perceive both depth and color data in the assembly area. This information is used to determine the current state of the assembly group and is compared to a CAD model for validation purposes. In order to efficiently resolve erroneous situations, the results are interactively accessible to a human expert. The implications for an industrial application are demonstrated by transferring the developed concepts to an assembly scenario for switch-cabinet systems.

  2. Expanding coordination chemistry from protein to protein assembly.

    Science.gov (United States)

    Sanghamitra, Nusrat J M; Ueno, Takafumi

    2013-05-14

    Bioinorganic chemistry is of growing importance in the fields of nanomaterial science and biotechnology. Coordination of metals by biological systems is a crucial step in intricate enzymatic reactions such as photosynthesis, nitrogen fixation and biomineralization. Although such systems employ protein assemblies as molecular scaffolds, the important roles of protein assemblies in coordination chemistry have not been systematically investigated and characterized. Many researchers are joining the field of bioinorganic chemistry to investigate the inorganic chemistry of protein assemblies. This area is emerging as an important next-generation research field in bioinorganic chemistry. This article reviews recent progress in rational design of protein assemblies in coordination chemistry for integration of catalytic reactions using metal complexes, preparation of mineral biomimetics, and mechanistic investigations of biomineralization processes with protein assemblies. The unique chemical properties of protein assemblies in the form of cages, tubes, and crystals are described in this review.

  3. Operon Gene Order Is Optimized for Ordered Protein Complex Assembly.

    Science.gov (United States)

    Wells, Jonathan N; Bergendahl, L Therese; Marsh, Joseph A

    2016-02-02

    The assembly of heteromeric protein complexes is an inherently stochastic process in which multiple genes are expressed separately into proteins, which must then somehow find each other within the cell. Here, we considered one of the ways by which prokaryotic organisms have attempted to maximize the efficiency of protein complex assembly: the organization of subunit-encoding genes into operons. Using structure-based assembly predictions, we show that operon gene order has been optimized to match the order in which protein subunits assemble. Exceptions to this are almost entirely highly expressed proteins for which assembly is less stochastic and for which precisely ordered translation offers less benefit. Overall, these results show that ordered protein complex assembly pathways are of significant biological importance and represent a major evolutionary constraint on operon gene organization.

  4. The determinism and boundedness of self-assembling structures

    CERN Document Server

    Tesoro, S

    2016-01-01

    Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Among the most important of these properties are whether the self-assembly is deterministic or nondeterministic, and whether it is bound or unbound. The former tells us whether the same set of building blocks always generates the same structure, and the latter whether it grows indefinitely. These properties are highly relevant in the context of protein structures, as the difference between deterministic protein self-assembly and nondeterministic protein aggregation is central to a number of diseases. Here we introduce a graph-based approach that can determine, with a few restrictions, whether a set of self-assembly building blocks is deterministic or nondeterministic, and whether it is bound or unbound. We apply this methodology to a previously studied lattice self-assembly model and discuss generalisatio...

  5. Assembly: a resource for assembled genomes at NCBI.

    Science.gov (United States)

    Kitts, Paul A; Church, Deanna M; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D; Pruitt, Kim D; Kimchi, Avi

    2016-01-04

    The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site.

  6. Constrained space camera assembly

    Science.gov (United States)

    Heckendorn, Frank M.; Anderson, Erin K.; Robinson, Casandra W.; Haynes, Harriet B.

    1999-01-01

    A constrained space camera assembly which is intended to be lowered through a hole into a tank, a borehole or another cavity. The assembly includes a generally cylindrical chamber comprising a head and a body and a wiring-carrying conduit extending from the chamber. Means are included in the chamber for rotating the body about the head without breaking an airtight seal formed therebetween. The assembly may be pressurized and accompanied with a pressure sensing means for sensing if a breach has occurred in the assembly. In one embodiment, two cameras, separated from their respective lenses, are installed on a mounting apparatus disposed in the chamber. The mounting apparatus includes means allowing both longitudinal and lateral movement of the cameras. Moving the cameras longitudinally focuses the cameras, and moving the cameras laterally away from one another effectively converges the cameras so that close objects can be viewed. The assembly further includes means for moving lenses of different magnification forward of the cameras.

  7. Self-assembling and self-limiting monolayer deposition

    Science.gov (United States)

    Foest, Rüdiger; Schmidt, Martin; Gargouri, Hassan

    2014-02-01

    Effects of spatial ordering of molecules on surfaces are commonly utilized to deposit ultra-thin films with a thickness of a few nm. In this review paper, several methods are discussed, that are distinguished from other thin film deposition processes by exactly these effects that lead to self-assembling and self-limiting layer growth and eventually to coatings with unique and fascinating properties and applications in micro-electronics, optics, chemistry, or biology. Traditional methods for the formation of self-assembled films of ordered organic molecules, such as the Langmuir-Blodgett technique along with thermal atomic layer deposition (ALD) of inorganic molecules are evaluated. The overview is complemented by more recent developments for the deposition of organic or hybrid films by molecular layer deposition. Particular attention is given to plasma assisted techniques, either as a preparative, supplementary step or as inherent part of the deposition as in plasma enhanced ALD or plasma assisted, repeated grafting deposition. The different methods are compared and their film formation mechanisms along with their advantages are presented from the perspective of a plasma scientist. The paper contains lists of established film compounds and a collection of the relevant literature is provided for further reading.

  8. Research on Key Technologies of Unit-Based CNC Machine Tool Assembly Design

    Directory of Open Access Journals (Sweden)

    Zhongqi Sheng

    2014-01-01

    Full Text Available Assembly is the part that produces the maximum workload and consumed time during product design and manufacturing process. CNC machine tool is the key basic equipment in manufacturing industry and research on assembly design technologies of CNC machine tool has theoretical significance and practical value. This study established a simplified ASRG for CNC machine tool. The connection between parts, semantic information of transmission, and geometric constraint information were quantified to assembly connection strength to depict the assembling difficulty level. The transmissibility based on trust relationship was applied on the assembly connection strength. Assembly unit partition based on assembly connection strength was conducted, and interferential assembly units were identified and revised. The assembly sequence planning and optimization of parts in each assembly unit and between assembly units was conducted using genetic algorithm. With certain type of high speed CNC turning center, as an example, this paper explored into the assembly modeling, assembly unit partition, and assembly sequence planning and optimization and realized the optimized assembly sequence of headstock of CNC machine tool.

  9. On computational properties of gene assembly in ciliates

    Directory of Open Access Journals (Sweden)

    Vladimir Rogojin

    2010-11-01

    Full Text Available Gene assembly in stichotrichous ciliates happening during sexual reproduction is one of the most involved DNA manipulation processes occurring in biology. This biological process is of high interest from the computational and mathematical points of view due to its close analogy with such concepts and notions in theoretical computer science as permutation and linked list sorting and string rewriting. Studies on computational properties of gene assembly in ciliates represent a good example of interdisciplinary research contributing to both computer science and biology. We review here a number of general results related both to the development of different computational methods enhancing our understanding on the nature of gene assembly, as well as to the development of new biologically motivated computational and mathematical models and paradigms. Those paradigms contribute in particular to combinatorics, formal languages and computability theories.

  10. Finishing of the cold mass assembly

    CERN Multimedia

    Maximilien Brice

    2001-01-01

    Photo 1 Zoom of the lyre-side end of the active part assembly. The extremity of the shrinking cylinder has been bevelled in view of welding the end cover. Photo 2 General view of the finishing station showing the special supporting structures (blue and yellow structures) needed for the geometric measurements and for the alignment operations. Photo 3 Zoom of the lyre-side end of the active part assembly. One can also see the auxiliary bus bars needed to power the corrector magnets that are installed in the dipole cold mass assembly. Photo 4 Technicians are putting in order the instrumentation wires. The prototype magnets were equipped with numerous sensors to monitor key parameters during the performance tests at cold conditions.

  11. Plant synthetic biology.

    Science.gov (United States)

    Liu, Wusheng; Stewart, C Neal

    2015-05-01

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

  12. 精密微小型零件自动装配系统显微机器视觉的照明自动优化%Automatic Illumination of Microscopic Machine Vision Optimization for Precision Miniature Parts Automatic Assembly System

    Institute of Scientific and Technical Information of China (English)

    张习文; 王晓东; 罗怡; 滕霖; 陈亮

    2012-01-01

    In order to always obtain the optimal images of parts in the assembly process, the problem of automatic optimization of microscopic vision illumination intensity was investigated. To realize the illumination of parts edges and surface detail, the illumination automatic control system based on coaxial and ring light source was developed. The illumination optimize performance of four types of image quality evaluation function was compared and analyzed, the image quality evaluation methods based on Roberts gradient sum function was proposed and applied in developed assembly systems. The results show that the process of illumination optimization is fast and accurate, the contrast of the target edge is significantly enhanced and the parts recognition error is eliminated after illumination optimization. Moreover, the precision automatic assembly requirements of miniature parts can be met.%为了在微小型零件装配过程中始终获得质量最佳的零件图像,对显微视觉照明光强的自动优化问题进行了研究.为实现对零件的轮廓边缘与表面细节的照明,基于同轴光源与环形光源开发了照明自动控制系统.对比分析了四种图像质量评价函数的照明优化性能,提出了基于Roberts梯度和函数的图像质量评测方法,并应用于研制的装配系统.装配实验结果表明,光强优化过程快速准确,光强优化后目标边缘的对比度显著增强,消除了零件误识别现象,满足微小型零件高精度装配自动化的要求.

  13. Advanced DNA assembly technologies in drug discovery.

    Science.gov (United States)

    Tsvetanova, Billyana; Peng, Lansha; Liang, Xiquan; Li, Ke; Hammond, Linda; Peterson, Todd C; Katzen, Federico

    2012-05-01

    Recombinant DNA technologies have had a fundamental impact on drug discovery. The continuous emergence of unique gene assembly techniques resulted in the generation of a variety of therapeutic reagents such as vaccines, cancer treatment molecules and regenerative medicine precursors. With the advent of synthetic biology there is a growing need for precise and concerted assembly of multiple DNA fragments of various sizes, including chromosomes. In this article, we summarize the highlights of the recombinant DNA technology since its inception in the early 1970s, emphasizing on the most recent advances, and underscoring their principles, advantages and shortcomings. Current and prior cloning trends are discussed in the context of sequence requirements and scars left behind. Our opinion is that despite the remarkable progress that has enabled the generation and manipulation of very large DNA sequences, a better understanding of the cell's natural circuits is needed in order to fully exploit the current state-of-the-art gene assembly technologies.

  14. Biological physics and synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Filhol, J.M.; Chavanne, J. [European Synchrotron Radiation Facility, 38 - Grenoble (France); Weckert, E. [Hasylab at Desy, Hamburg (Germany)] [and others

    2001-07-01

    This conference deals with the applications of synchrotron radiation to current problems in biology and medicine. Seven sessions take stock on the subject: sources and detectors; inelastic scattering and dynamics; muscle diffraction; reaction mechanisms; macromolecular assemblies; medical applications; imaging and spectroscopy. The document presents the papers abstracts. (A.L.B.)

  15. Fibrillin: from microfibril assembly to biomechanical function.

    Science.gov (United States)

    Kielty, Cay M; Baldock, Clair; Lee, David; Rock, Matthew J; Ashworth, Jane L; Shuttleworth, C Adrian

    2002-02-28

    Fibrillins form the structural framework of a unique and essential class of extracellular microfibrils that endow dynamic connective tissues with long-range elasticity. Their biological importance is emphasized by the linkage of fibrillin mutations to Marfan syndrome and related connective tissue disorders, which are associated with severe cardiovascular, ocular and skeletal defects. These microfibrils have a complex ultrastructure and it has proved a major challenge both to define their structural organization and to relate it to their biological function. However, new approaches have at last begun to reveal important insights into their molecular assembly, structural organization and biomechanical properties. This paper describes the current understanding of the molecular assembly of fibrillin molecules, the alignment of fibrillin molecules within microfibrils and the unique elastomeric properties of microfibrils.

  16. Modular assembled space telescope

    Science.gov (United States)

    Feinberg, Lee D.; Budinoff, Jason; MacEwen, Howard; Matthews, Gary; Postman, Marc

    2013-09-01

    We present a new approach to building a modular segmented space telescope that greatly leverages the heritage of the Hubble Space Telescope and the James Webb Space Telescope. The modular design in which mirror segments are assembled into identical panels allows for economies of scale and for efficient space assembly that make a 20-m aperture approach cost effective. This assembly approach can leverage NASA's future capabilities and has the power to excite the public's imagination. We discuss the science drivers, basic architecture, technology, and leveraged NASA infrastructure, concluding with a proposed plan for going forward.

  17. DC source assemblies

    Science.gov (United States)

    Campbell, Jeremy B; Newson, Steve

    2013-02-26

    Embodiments of DC source assemblies of power inverter systems of the type suitable for deployment in a vehicle having an electrically grounded chassis are provided. An embodiment of a DC source assembly comprises a housing, a DC source disposed within the housing, a first terminal, and a second terminal. The DC source also comprises a first capacitor having a first electrode electrically coupled to the housing, and a second electrode electrically coupled to the first terminal. The DC source assembly further comprises a second capacitor having a first electrode electrically coupled to the housing, and a second electrode electrically coupled to the second terminal.

  18. Plant and Animal Gravitational Biology. Part 2

    Science.gov (United States)

    1997-01-01

    Session WA2 includes short reports concerning: (1) The Asymmetrical Growth of Otoliths in Fish Affected by Altered Gravity and Causes Kinetosis; (2) Neurobiological Responses of Fish to Altered Gravity conditions: A Review; (3) An Age-Dependent Sensitivity of the Roll-Induced Vestibulocular Reflex to Hypergravity Exposure of Several Days in an Amphibian (Xenopus Laevis); (4) Mechanically-Induced Membrane Wounding During Parabolic Flight; and (5) Erythropoietin Stimulates Increased F Cell Numbers in Bone Marrow Cultures Established in Gravity and Microgravity Conditions.

  19. Engineering microbes with synthetic biology frameworks.

    Science.gov (United States)

    Leonard, Effendi; Nielsen, David; Solomon, Kevin; Prather, Kristala Jones

    2008-12-01

    Typically, the outcome of biologically engineered unit operations cannot be controlled a priori due to the incorporation of ad hoc design into complex natural systems. To mitigate this problem, synthetic biology presents a systematic approach to standardizing biological components for the purpose of increasing their programmability and robustness when assembled with the aim to achieve novel biological functions. A complex engineered biological system using only standardized biological components is yet to exist. Nevertheless, current attempts to create and to implement modular, standardized biological components pave the way for the future creation of highly predictable artificial biological systems. Although synthetic biology frameworks can be applied to any biological engineering endeavor, this article will focus on providing a brief overview of advances in the field and its recent utilization for the engineering of microbes.

  20. Designing Assemblies Of Plates

    Science.gov (United States)

    Williams, F. W.; Kennedy, D.; Butler, R.; Aston, G.; Anderson, M. S.

    1992-01-01

    VICONOPT calculates vibrations and instabilities of assemblies of prismatic plates. Designed for efficient, accurate analysis of buckling and vibration, and for optimum design of panels of composite materials. Written in FORTRAN 77.

  1. Self-assembly of smallest magnetic particles.

    Science.gov (United States)

    Mehdizadeh Taheri, Sara; Michaelis, Maria; Friedrich, Thomas; Förster, Beate; Drechsler, Markus; Römer, Florian M; Bösecke, Peter; Narayanan, Theyencheri; Weber, Birgit; Rehberg, Ingo; Rosenfeldt, Sabine; Förster, Stephan

    2015-11-24

    The assembly of tiny magnetic particles in external magnetic fields is important for many applications ranging from data storage to medical technologies. The development of ever smaller magnetic structures is restricted by a size limit, where the particles are just barely magnetic. For such particles we report the discovery of a kind of solution assembly hitherto unobserved, to our knowledge. The fact that the assembly occurs in solution is very relevant for applications, where magnetic nanoparticles are either solution-processed or are used in liquid biological environments. Induced by an external magnetic field, nanocubes spontaneously assemble into 1D chains, 2D monolayer sheets, and large 3D cuboids with almost perfect internal ordering. The self-assembly of the nanocubes can be elucidated considering the dipole-dipole interaction of small superparamagnetic particles. Complex 3D geometrical arrangements of the nanodipoles are obtained under the assumption that the orientation of magnetization is freely adjustable within the superlattice and tends to minimize the binding energy. On that basis the magnetic moment of the cuboids can be explained.

  2. Biological computation

    CERN Document Server

    Lamm, Ehud

    2011-01-01

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

  3. RESEARCH OF GUIDANCE TECHNOLOGY FOR ASSEMBLY MODELING IN VIRTUAL ENVIRONMENT

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Technology of movement and knowledge guidance in virtual assembly is presented. The designer can move the mechanical part precisely under the movement guidance. The movement guidance is implemented based on constraint recognition and assembly degree of freedom analysis. A multi-hierarchy knowledge base is built to represent the assembly knowledge and information. The virtual assembly system judges the requirement of the designer based on the context of design task and searches for the useful knowledge and information, which can be provided to the designer in a natural way.

  4. Automated Sequencing and Subassembly Detection in Automobile Body Assembly Planning

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The choice of the sequence in which parts or subass em blies are put together in the mechanical assembly of a product can drastical ly affect the efficiency of the assembly process. Unlike metal cutting operation s where computer aided system have been available for some 15 to 25 years to hel p manufacturing engineers in generating cutting sequences and NC programs, the m ajority of assembly planning tasks in automobile body design is still manually p erformed by assembly designers according to their pa...

  5. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  6. Nestedness across biological scales

    Science.gov (United States)

    Marquitti, Flavia M. D.; Raimundo, Rafael L. G.; Sebastián-González, Esther; Coltri, Patricia P.; Perez, S. Ivan; Brandt, Débora Y. C.; Nunes, Kelly; Daura-Jorge, Fábio G.; Floeter, Sergio R.; Guimarães, Paulo R.

    2017-01-01

    Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness

  7. Human Assisted Assembly Processes

    Energy Technology Data Exchange (ETDEWEB)

    CALTON,TERRI L.; PETERS,RALPH R.

    2000-01-01

    Automatic assembly sequencing and visualization tools are valuable in determining the best assembly sequences, but without Human Factors and Figure Models (HFFMs) it is difficult to evaluate or visualize human interaction. In industry, accelerating technological advances and shorter market windows have forced companies to turn to an agile manufacturing paradigm. This trend has promoted computerized automation of product design and manufacturing processes, such as automated assembly planning. However, all automated assembly planning software tools assume that the individual components fly into their assembled configuration and generate what appear to be a perfectly valid operations, but in reality the operations cannot physically be carried out by a human. Similarly, human figure modeling algorithms may indicate that assembly operations are not feasible and consequently force design modifications; however, if they had the capability to quickly generate alternative assembly sequences, they might have identified a feasible solution. To solve this problem HFFMs must be integrated with automated assembly planning to allow engineers to verify that assembly operations are possible and to see ways to make the designs even better. Factories will very likely put humans and robots together in cooperative environments to meet the demands for customized products, for purposes including robotic and automated assembly. For robots to work harmoniously within an integrated environment with humans the robots must have cooperative operational skills. For example, in a human only environment, humans may tolerate collisions with one another if they did not cause much pain. This level of tolerance may or may not apply to robot-human environments. Humans expect that robots will be able to operate and navigate in their environments without collisions or interference. The ability to accomplish this is linked to the sensing capabilities available. Current work in the field of cooperative

  8. Biology of Nanobots

    Science.gov (United States)

    Duan, Wentao; Pavlick, Ryan; Sen, Ayusman

    2013-12-01

    One of the more interesting recent discoveries has been the ability to design nano/microbots which catalytically harness the chemical energy in their environment to move autonomously. Their potential applications include delivery of materials, self-assembly of superstructures, and roving sensors. One emergent area of research is the study of their collective behavior and how they emulate living systems. The aim of this chapter is to describe the "biology" of nanobots, summarizing the fundamentals physics behind their motion and how the bots interact with each other to initiate complex emergent behavior.

  9. Molecular Recognition Directed Self-Assembly of Supramolecular Polymers

    Science.gov (United States)

    1994-06-30

    demonstrated that various substituted gallic acid derivatives can be used to constmict exo-receptors with a tapered shape. "Tihis paper will review...understood self-assembled biological system [3ab.5]. Therefore, we believe it provides an ideal model to be used for the understanding of the principles...governing the self-assembly of synthetic supraimolecular architectures. Synthetic Strategy Used In The Design Of TMV-Like Supramolecular Architectures fl

  10. Mathematical and numerical challenges in living biological materials

    Science.gov (United States)

    Forest, M. Gregory; Vasquez, Paula A.

    2013-10-01

    The proclaimed Century of Biology is rapidly leading to the realization of how starkly different and more complex biological materials are than the materials that underpinned the industrial and technological revolution. These differences arise, in part, because biological matter exhibits both viscous and elastic behavior. Moreover, this behavior varies across the frequency, wavelength and amplitude spectrum of forcing. This broadclass of responsesin biological matter requires multiple frequency-dependent functions to specify material behavior, instead of a discrete set of parameters that relate to either viscosity or elasticity. This complexity prevails even if the biological matter is assumed to be spatially homogeneous, which is rarely true. However, very little progress has been made on the characterization of heterogeneity and how to build that information into constitutive laws and predictive models. In addition, most biological matter is non-stationary, which motivates the term "living". Biomaterials typically are in an active state in order to perform certain functions, and they often are modified or replenished on the basis of external stimuli. It has become popular in materials engineering to try to duplicate some of the functionality of biomaterials, e.g., a lot of effort has gone into the design of self-assembling, self-healing and shape shifting materials. These distinguishing features of biomaterials require significantly more degrees of freedom than traditional composites and many of the molecular species and their roles in functionality have yet to be determined. A typical biological material includes small molecule biochemical species that react and diffuse within larger species. These large molecular weightspecies provide the primary structural and biophysical properties of the material. The small molecule binding and unbinding kinetics serves to modulate material properties, and typical small molecule production and release are governed by

  11. 78 FR 43817 - Distribution of Reference Biological Standards and Biological Preparations

    Science.gov (United States)

    2013-07-22

    ... HUMAN SERVICES 42 CFR Part 7 RIN 0920-AA53 Distribution of Reference Biological Standards and Biological... sections of its regulations titled ``Distribution of Reference Biological Standards and Biological... section states that HHS/CDC may prepare any biological product described under section 351 of the...

  12. Combining supramolecular chemistry with biology.

    Science.gov (United States)

    Uhlenheuer, Dana A; Petkau, Katja; Brunsveld, Luc

    2010-08-01

    Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.

  13. Theory of meiotic spindle assembly

    Science.gov (United States)

    Furthauer, Sebastian; Foster, Peter; Needleman, Daniel; Shelley, Michael

    2016-11-01

    The meiotic spindle is a biological structure that self assembles from the intracellular medium to separate chromosomes during meiosis. It consists of filamentous microtubule (MT) proteins that interact through the fluid in which they are suspended and via the associated molecules that orchestrate their behavior. We aim to understand how the interplay between fluid medium, MTs, and regulatory proteins allows this material to self-organize into the spindle's highly stereotyped shape. To this end we develop a continuum model that treats the spindle as an active liquid crystal with MT turnover. In this active material, molecular motors, such as dyneins which collect MT minus ends and kinesins which slide MTs past each other, generate active fluid and material stresses. Moreover nucleator proteins that are advected with and transported along MTs control the nucleation and depolymerization of MTs. This theory captures the growth process of meiotic spindles, their shapes, and the essential features of many perturbation experiments. It thus provides a framework to think about the physics of this complex biological suspension.

  14. Photovoltaic self-assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Lavin, Judith; Kemp, Richard Alan; Stewart, Constantine A.

    2010-10-01

    This late-start LDRD was focused on the application of chemical principles of self-assembly on the ordering and placement of photovoltaic cells in a module. The drive for this chemical-based self-assembly stems from the escalating prices in the 'pick-and-place' technology currently used in the MEMS industries as the size of chips decreases. The chemical self-assembly principles are well-known on a molecular scale in other material science systems but to date had not been applied to the assembly of cells in a photovoltaic array or module. We explored several types of chemical-based self-assembly techniques, including gold-thiol interactions, liquid polymer binding, and hydrophobic-hydrophilic interactions designed to array both Si and GaAs PV chips onto a substrate. Additional research was focused on the modification of PV cells in an effort to gain control over the facial directionality of the cells in a solvent-based environment. Despite being a small footprint research project worked on for only a short time, the technical results and scientific accomplishments were significant and could prove to be enabling technology in the disruptive advancement of the microelectronic photovoltaics industry.

  15. Part Transportation Improvement in Warehouse of an Automotive Factory

    Science.gov (United States)

    Choojan, Tiwapom; Chutima, Parames

    2016-05-01

    This research is focus on the problems cause the assembly line stop in a Japanese automotive manufacturer in Thailand. The problem arose from not being able to supply parts to the assembly line in time and supplying wrong parts to the assembly line. Methods to resolve these problems involved the followings: 1) design new tag labels, 2) improve operations method and 3) redesign the parts storage layout and supply routes. The result showed that the time for transferring parts from the warehouse to the preparing area and the overlapped routes were reduced. Moreover, the supply accuracy from the preparation area to the assembly line was improved.

  16. Pulse detonation assembly and hybrid engine

    Science.gov (United States)

    Rasheed, Adam (Inventor); Dean, Anthony John (Inventor); Vandervort, Christian Lee (Inventor)

    2010-01-01

    A pulse detonation (PD) assembly includes a number of PD chambers adapted to expel respective detonation product streams and a number of barriers disposed between respective pairs of PD chambers. The barriers define, at least in part, a number of sectors that contain at least one PD chamber. A hybrid engine includes a number of PD chambers and barriers. The hybrid engine further includes a turbine assembly having at least one turbine stage, being in flow communication with the PD chambers and being configured to be at least partially driven by the detonation product streams. A segmented hybrid engine includes a number of PD chambers and segments configured to receive and direct the detonation product streams from respective PD chambers. The segmented hybrid engine further includes a turbine assembly configured to be at least partially driven by the detonation product streams.

  17. [Biological weapons].

    Science.gov (United States)

    Kerwat, K; Becker, S; Wulf, H; Densow, D

    2010-08-01

    Biological weapons are weapons of mass destruction that use pathogens (bacteria, viruses) or the toxins produced by them to target living organisms or to contaminate non-living substances. In the past, biological warfare has been repeatedly used. Anthrax, plague and smallpox are regarded as the most dangerous biological weapons by various institutions. Nowadays it seems quite unlikely that biological warfare will be employed in any military campaigns. However, the possibility remains that biological weapons may be used in acts of bioterrorism. In addition all diseases caused by biological weapons may also occur naturally or as a result of a laboratory accident. Risk assessment with regard to biological danger often proves to be difficult. In this context, an early identification of a potentially dangerous situation through experts is essential to limit the degree of damage.

  18. Force-controlled robotic assembly processes of rigid and flexible objects methodologies and applications

    CERN Document Server

    Ghalyan, Ibrahim Fahad Jasim

    2016-01-01

    This book provides comprehensive and integrated approaches for rigid and flexible object assembly. It presents comparison studies with the available force-guided robotic processes and covers contact-state modeling, scheme control strategies, and position searching algorithms. Further, it includes experimental validations for different assembly situations, including those for the assembly of industrial parts taken from the automotive industry. .

  19. In vitro kinetochore assembly

    Science.gov (United States)

    Miell, Matthew D D; Straight, Aaron F

    2016-01-01

    The kinetochore is the primary site of interaction between chromosomes and microtubules of the mitotic spindle during chromosome segregation. The kinetochore is a complex of more than 100 proteins that transiently assemble during mitosis at a single defined region on each chromosome, known as the centromere. Kinetochore assembly and activity must be tightly regulated to ensure proper microtubule interaction and faithful chromosome segregation because perturbation of kinetochores often results in aneuploidy and cell lethality. As such, cell free and reconstituted systems to analyze kinetochore formation and function are invaluable in probing the biochemical activities of kinetochores. In vitro approaches to studying kinetochores have enabled the manipulation of kinetochore protein structure, function, interactions and regulation that are not possible in cells. Here we outline a cell-free approach for the assembly of centromeres and recruitment of functional kinetochores that enables their manipulation and analysis. PMID:27193846

  20. Assembling Sustainable Territories

    DEFF Research Database (Denmark)

    Vandergeest, Peter; Ponte, Stefano; Bush, Simon

    2015-01-01

    The authors show how certification assembles ‘sustainable’ territories through a complex layering of regulatory authority in which both government and nongovernment entities claim rule-making authority, sometimes working together, sometimes in parallel, sometimes competitively. It is argued...... that territorialisation is accomplished not just through (re)defining bounded space, but more broadly through the assembling of four elements: space, subjects, objects, and expertise. Four case studies of sustainability certification in seafood are analyzed to show that ‘green gabbing’ is not necessarily the central...... dynamic in assembling sustainable territories, and that certification always involves state agencies in determining how the key elements that comprise it are defined. Whereas some state agencies have been suspicious of sustainability certification, others have embraced it or even used it to extend...

  1. Power module assembly

    Science.gov (United States)

    Campbell, Jeremy B [Torrance, CA; Newson, Steve [Redondo Beach, CA

    2011-11-15

    A power module assembly of the type suitable for deployment in a vehicular power inverter, wherein the power inverter has a grounded chassis, is provided. The power module assembly comprises a conductive base layer electrically coupled to the chassis, an insulating layer disposed on the conductive base layer, a first conductive node disposed on the insulating layer, a second conductive node disposed on the insulating layer, wherein the first and second conductive nodes are electrically isolated from each other. The power module assembly also comprises a first capacitor having a first electrode electrically connected to the conductive base layer, and a second electrode electrically connected to the first conductive node, and further comprises a second capacitor having a first electrode electrically connected to the conductive base layer, and a second electrode electrically connected to the second conductive node.

  2. Blade attachment assembly

    Science.gov (United States)

    Garcia-Crespo, Andres Jose; Delvaux, John McConnell; Miller, Diane Patricia

    2016-05-03

    An assembly and method for affixing a turbomachine rotor blade to a rotor wheel are disclosed. In an embodiment, an adaptor member is provided disposed between the blade and the rotor wheel, the adaptor member including an adaptor attachment slot that is complementary to the blade attachment member, and an adaptor attachment member that is complementary to the rotor wheel attachment slot. A coverplate is provided, having a coverplate attachment member that is complementary to the rotor wheel attachment slot, and a hook for engaging the adaptor member. When assembled, the coverplate member matingly engages with the adaptor member, and retains the blade in the adaptor member, and the assembly in the rotor wheel.

  3. Integrated magnetic transformer assembly

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to an integrated magnetics transformer assembly comprising a first magnetically permeable core forming a first substantially closed magnetic flux path and a second magnetically permeable core forming a second substantially closed magnetic flux path. A first input...... inductor winding is wound around a first predetermined segment of the first magnetically permeable core and a second input inductor winding is wound around a first predetermined segment of the second magnetically permeable core. The integrated magnetics transformer assembly further comprises a first output......-winding of the first output inductor winding and the first half-winding of the second output inductor winding are configured to produce aligned, i.e. in the same direction, magnetic fluxes through the first substantially closed magnetic flux path. The integrated magnetics transformer assembly is well- suited for use...

  4. Pressure effects on lipids and bio-membrane assemblies

    Directory of Open Access Journals (Sweden)

    Nicholas J. Brooks

    2014-11-01

    Full Text Available Membranes are amongst the most important biological structures; they maintain the fundamental integrity of cells, compartmentalize regions within them and play an active role in a wide range of cellular processes. Pressure can play a key role in probing the structure and dynamics of membrane assemblies, and is also critical to the biology and adaptation of deep-sea organisms. This article presents an overview of the effect of pressure on the mesostructure of lipid membranes, bilayer organization and lipid–protein assemblies. It also summarizes recent developments in high-pressure structural instrumentation suitable for experiments on membranes.

  5. Self assembling proteins

    Science.gov (United States)

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  6. Low inductance connector assembly

    Science.gov (United States)

    Holbrook, Meghan Ann; Carlson, Douglas S

    2013-07-09

    A busbar connector assembly for coupling first and second terminals on a two-terminal device to first and second contacts on a power module is provided. The first terminal resides proximate the first contact and the second terminal resides proximate the second contact. The assembly comprises a first bridge having a first end configured to be electrically coupled to the first terminal, and a second end configured to be electrically coupled to the second contact, and a second bridge substantially overlapping the first bridge and having a first end electrically coupled to the first contact, and a second end electrically coupled to the second terminal.

  7. Solar central receiver heliostat reflector assembly

    Science.gov (United States)

    Horton, Richard H.; Zdeb, John J.

    1980-01-01

    A heliostat reflector assembly for a solar central receiver system comprises a light-weight, readily assemblable frame which supports a sheet of stretchable reflective material and includes mechanism for selectively applying tension to and positioning the sheet to stretch it to optical flatness. The frame is mounted on and supported by a pipe pedestal assembly that, in turn, is installed in the ground. The frame is controllably driven in a predetermined way by a light-weight drive system so as to be angularly adjustable in both elevation and azimuth to track the sun and efficiently continuously reflect the sun's rays to a focal zone, i.e. central receiver, which forms part of a solar energy utilization system, such as a solar energy fueled electrical power generation system. The frame may include a built-in system for testing for optical flatness of the reflector. The preferable geometric configuration of the reflector is octagonal; however, it may be other shapes, such as hexagonal, pentagonal or square. Several different embodiments of means for tensioning and positioning the reflector to achieve optical flatness are disclosed. The reflector assembly is based on the stretch frame concept which provides an extremely light-weight, simple, low-cost reflector assembly that may be driven for positioning and tracking by a light-weight, inexpensive drive system.

  8. Challenging Students' Intuitions--The Influence of a Tangible Model of Virus Assembly on Students' Conceptual Reasoning about the Process of Self-Assembly

    Science.gov (United States)

    Larsson, Caroline; Tibell, Lena A.

    2015-01-01

    A well-ordered biological complex can be formed by the random motion of its components, i.e. self-assemble. This is a concept that incorporates issues that may contradict students' everyday experiences and intuitions. In previous studies, we have shown that a tangible model of virus self-assembly, used in a group exercise, helps students to grasp…

  9. Combinatorial Models for Assembly and Decomposition of Products

    Directory of Open Access Journals (Sweden)

    A. N. Bojko

    2015-01-01

    Full Text Available The paper discusses the most popular combinatorial models that are used for the synthesis of design solutions at the stage of the assembly process flow preparation. It shows that while assembling the product the relations of parts can be represented as a structure of preferences, which is formed on the basis of objective design restrictions put in at the stage of the product design. This structure is a binary preference relation pre-order. Its symmetrical part is equivalence and describes the entry of parts into the assembly unit. The asymmetric part is a partial order. It specifies part- ordering time in in the course of the assembly process. The structure of preferences is a minimal description of the restrictions and constraints in the assembly process. It can serve as a source for generating multiple assembly sequences of a product and its components, which are allowed by design. This multiplicity increases the likelihood of rational choice under uncertainty, unpredictable changes in the properties of technological or industrial systems.Incomplete dominance relation gives grounds for further examination and better understanding of the project situation. Operation field of the study is limited to a set of disparate elements of the partial order. Different strategies for processing the disparate elements may be offered, e.g. selection of the most informative pairs, comparison of which foremost linearizes the original partial order.

  10. Study of electronic made-to-measure for clothing based on body parts assembly technology%基于人体部件模板组装的服装量身定制技术研究

    Institute of Scientific and Technical Information of China (English)

    石秀金; 孙莉; 李继云; 施霞萍; 陈家训

    2009-01-01

    通过采集人体样本数据,形成人体部件模板系列,根据客户提供的不同类型体形特征数据文件,提取出对应人体特征数据,生成个性化的三维虚拟人体模型,并最终生成个性化服装原型衣片.依照上述技术路线,设计了原型系统的架构,给出了功能结构,最后实现了原型系统.原型系统的运行结果表明,技术路线正确,系统方案合理,有助于推广电子化量身定制(eMTM)应用.%The human body parts template series were formed through gathering the sample data of human body. The personal 3-dimensional virtual human body model was generated by extracting the feature data of the corresponding human body from different types of body shape data files provided by the customer, and then personal prototype garment chips were achieved. According to the technical route above, the architecture of the prototype system was designed, the function structure was provided, and then the prototype system was realized finally. The operation results of the prototype system show that the technical route is right, and the system scheme is reasonable, can help to popularize the application of electronic Made to Measure (eMTM).

  11. An Interactive Assembly Process Planner

    Institute of Scientific and Technical Information of China (English)

    廖华飞; 张林鍹; 肖田元; 曾理; 古月

    2004-01-01

    This paper describes the implementation and performance of the virtual assembly support system (VASS), a new system that can provide designers and assembly process engineers with a simulation and visualization environment where they can evaluate the assemblability/disassemblability of products, and thereby use a computer to intuitively create assembly plans and interactively generate assembly process charts. Subassembly planning and assembly priority reasoning techniques were utilized to find heuristic information to improve the efficiency of assembly process planning. Tool planning was implemented to consider tool requirements in the product design stage. New methods were developed to reduce the computation amount involved in interference checking. As an important feature of the VASS, human interaction was integrated into the whole process of assembly process planning, extending the power of computer reasoning by including human expertise, resulting in better assembly plans and better designs.

  12. Fire resistant PV shingle assembly

    Science.gov (United States)

    Lenox, Carl J.

    2012-10-02

    A fire resistant PV shingle assembly includes a PV assembly, including PV body, a fire shield and a connection member connecting the fire shield below the PV body, and a support and inter-engagement assembly. The support and inter-engagement assembly is mounted to the PV assembly and comprises a vertical support element, supporting the PV assembly above a support surface, an upper interlock element, positioned towards the upper PV edge, and a lower interlock element, positioned towards the lower PV edge. The upper interlock element of one PV shingle assembly is inter-engageable with the lower interlock element of an adjacent PV shingle assembly. In some embodiments the PV shingle assembly may comprise a ventilation path below the PV body. The PV body may be slidably mounted to the connection member to facilitate removal of the PV body.

  13. Self assembly of interlocked architectures

    CERN Document Server

    Schergna, S

    2002-01-01

    An area of great interest is the synthesis and characterisation of molecules possessing moving parts, with the goal that they can act as 'molecular machine' carrying out tasks that molecules with fixed conventional architectures cannot do. Rotaxanes and catenanes (mechanically interlocked architectures) represent one approach toward achieving these aims as their component wheels and / or threads are connected together but can still move, in certain, controlled directions. This thesis focused on the study of structural rigidity and the preorganisation of thread binding sites as factors of major influence on template efficiency in the synthesis of hydrogen bond assembled supramolecular structures (rotaxanes and catenanes). Chapter One gives a brief outline of the common synthetic approaches to interlocked architectures (catenanes and rotaxanes) that are now being developed to address the problems outlined above. Chapter Two and Chapter Three concerns the synthesis of novel amide-based rotaxanes containing vario...

  14. Three-dimensional bioprinting using self-assembling scalable scaffold-free “tissue strands” as a new bioink

    Science.gov (United States)

    Yu, Yin; Moncal, Kazim K.; Li, Jianqiang; Peng, Weijie; Rivero, Iris; Martin, James A.; Ozbolat, Ibrahim T.

    2016-01-01

    Recent advances in bioprinting have granted tissue engineers the ability to assemble biomaterials, cells, and signaling molecules into anatomically relevant functional tissues or organ parts. Scaffold-free fabrication has recently attracted a great deal of interest due to the ability to recapitulate tissue biology by using self-assembly, which mimics the embryonic development process. Despite several attempts, bioprinting of scale-up tissues at clinically-relevant dimensions with closely recapitulated tissue biology and functionality is still a major roadblock. Here, we fabricate and engineer scaffold-free scalable tissue strands as a novel bioink material for robotic-assisted bioprinting technologies. Compare to 400 μm-thick tissue spheroids bioprinted in a liquid delivery medium into confining molds, near 8 cm-long tissue strands with rapid fusion and self-assemble capabilities are bioprinted in solid form for the first time without any need for a scaffold or a mold support or a liquid delivery medium, and facilitated native-like scale-up tissues. The prominent approach has been verified using cartilage strands as building units to bioprint articular cartilage tissue. PMID:27346373

  15. HPC-MAQ : A PARALLEL SHORT-READ REFERENCE ASSEMBLER

    Directory of Open Access Journals (Sweden)

    Veeram Venkata Siva Prasad

    2011-07-01

    Full Text Available Bioinformatics and computational biology are rooted in life sciences as well as computer and information sciences and technologies. Bioinformatics applies principles of information sciences and technologies to make the vast, diverse, and complex life sciences data more understandable and useful. Computational biology uses mathematical and computational approaches to address theoretical and experimental questions in biology. Short read sequence assembly is one of the most important steps in the analysis of biological data. There are many open source software’s available for short read sequence assembly where MAQ is one such popularly used software by the research community. In general, biological data sets generated by next generation sequencers are very huge and massive which requires tremendous amount of computational resources. The algorithm used for the short read sequence assembly is NP Hard which is computationally expensive and time consuming. Also MAQ is single threaded software which doesn't use the power of multi core and distributed computing and it doesn't scale. In this paper we report HPC-MAQ which addresses the NP-Hard related challenges of genome reference assembly and enables MAQ parallel and scalable through Hadoop which is a software framework for distributed computing.

  16. A Method for Designing Assembly Tolerance Networks of Mechanical Assemblies

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2012-01-01

    Full Text Available When designing mechanical assemblies, assembly tolerance design is an important issue which must be seriously considered by designers. Assembly tolerances reflect functional requirements of assembling, which can be used to control assembling qualities and production costs. This paper proposes a new method for designing assembly tolerance networks of mechanical assemblies. The method establishes the assembly structure tree model of an assembly based on its product structure tree model. On this basis, assembly information model and assembly relation model are set up based on polychromatic sets (PS theory. According to the two models, the systems of location relation equations and interference relation equations are established. Then, using methods of topologically related surfaces (TTRS theory and variational geometric constraints (VGC theory, three VGC reasoning matrices are constructed. According to corresponding relations between VGCs and assembly tolerance types, the reasoning matrices of tolerance types are also established by using contour matrices of PS. Finally, an exemplary product is used to construct its assembly tolerance networks and meanwhile to verify the feasibility and effectiveness of the proposed method.

  17. Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

    Science.gov (United States)

    Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

    2011-01-01

    Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome

  18. SSME component assembly and life management expert system

    Science.gov (United States)

    Ali, M.; Dietz, W. E.; Ferber, H. J.

    1989-01-01

    The space shuttle utilizes several rocket engine systems, all of which must function with a high degree of reliability for successful mission completion. The space shuttle main engine (SSME) is by far the most complex of the rocket engine systems and is designed to be reusable. The reusability of spacecraft systems introduces many problems related to testing, reliability, and logistics. Components must be assembled from parts inventories in a manner which will most effectively utilize the available parts. Assembly must be scheduled to efficiently utilize available assembly benches while still maintaining flight schedules. Assembled components must be assigned to as many contiguous flights as possible, to minimize component changes. Each component must undergo a rigorous testing program prior to flight. In addition, testing and assembly of flight engines and components must be done in conjunction with the assembly and testing of developmental engines and components. The development, testing, manufacture, and flight assignments of the engine fleet involves the satisfaction of many logistical and operational requirements, subject to many constraints. The purpose of the SSME Component Assembly and Life Management Expert System (CALMES) is to assist the engine assembly and scheduling process, and to insure that these activities utilize available resources as efficiently as possible.

  19. Liaison concatenation – A method to obtain feasible assembly sequences from 3D-CAD product

    Indian Academy of Sciences (India)

    M V A Raju Bahubalendruni; Bibhuti Bhusan Biswal

    2016-01-01

    Selection of optimized assembly sequence from the available feasible assembly sequences is significantly essential to achieve cost-effective manufacturing process. To achieve this, at the outset, generation of feasible assembly sequences with topological, geometrical, precedence and stability conditions should be generated. The increase of part count in a product results huge number of assembly sequences, the Liaison matrix/Liaison graph generated based on the connections between the assembly components eliminates nonpossible assembly sequences at the initial phase. There exist methods namely cut-set method to eliminate the non-possible assembly sequences using liaison graph. In this paper a new approach to eliminate the non-possible assembly sequences based on liaisons is described and the correctness of the methodology is illustrated with an example. The methodology to obtain the feasible assembly sequences is also briefly described and presented. An algorithm to interface with the CAD environment is described briefly.

  20. Triggered self-assembly of magnetic nanoparticles

    Science.gov (United States)

    Ye, L.; Pearson, T.; Cordeau, Y.; Mefford, O. T.; Crawford, T. M.

    2016-03-01

    Colloidal magnetic nanoparticles are candidates for application in biology, medicine and nanomanufac-turing. Understanding how these particles interact collectively in fluids, especially how they assemble and aggregate under external magnetic fields, is critical for high quality, safe, and reliable deployment of these particles. Here, by applying magnetic forces that vary strongly over the same length scale as the colloidal stabilizing force and then varying this colloidal repulsion, we can trigger self-assembly of these nanoparticles into parallel line patterns on the surface of a disk drive medium. Localized within nanometers of the medium surface, this effect is strongly dependent on the ionic properties of the colloidal fluid but at a level too small to cause bulk colloidal aggregation. We use real-time optical diffraction to monitor the dynamics of self-assembly, detecting local colloidal changes with greatly enhanced sensitivity compared with conventional light scattering. Simulations predict the triggering but not the dynamics, especially at short measurement times. Beyond using spatially-varying magnetic forces to balance interactions and drive assembly in magnetic nanoparticles, future measurements leveraging the sensitivity of this approach could identify novel colloidal effects that impact real-world applications of these nanoparticles.

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

    Directory of Open Access Journals (Sweden)

    Ya-Tang Yang

    2016-10-01

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

  2. Self-Assembled DNA Templated Nano-wires and Circuits

    Science.gov (United States)

    Braun, Erez

    2000-03-01

    The realization that conventional microelectronics is approaching its miniaturization limits has motivated the search for an alternative route based on self-assembled nanometer-scale electronics. We have recently proposed a new approach based on the hybridization of biological and electronic materials (Braun E., Eichen Y., Sivan U. and Ben-Yoseph G., Nature 391, 775 (1998)). The concept relies on a two-step self-assembly process. The inherent molecular recognition capabilities of DNA molecules are first utilized to construct a network that serves as a template for the subsequent assembly of electronic materials into a circuit. The utilization of DNA and its associated enzymatic machinery enables: (a) self-assembly of complex substrates, (b) specific molecular addresses for the localization of electronic materials (e.g., gold colloids) by standard molecular biology techniques, (c) interdevice wiring and (d) bridging the microscopic structures to the macroscopic world. The self-assembly of nanometer scale electronics relies on two complementary developments. First, the ability to convert DNA molecules into thin conductive wires and second, the self-assembly of complex extended DNA templates. Our progress in these two directions will be presented. Regarding the first issue, a physical process resulting in condensation of gold colloids onto DNA molecules enables the assembly of thin gold wires (around 100-200 A wide) having, in principle, unlimited extensions. The second issue is developed in the context of recombinant DNA which allows the self-assembly of precise molecular junctions and networks. Specifically, we use RecA protein, which is the main protein responsible for genetic recombination in E. Coli bacteria, to construct DNA junctions at pre-designed addresses (sequences) on the molecules. The integration of these processes allows advancing nanometer-scale electronics. A realistic fabrication scheme for a room-temperature single-electron transistor

  3. Metaphase Spindle Assembly

    Directory of Open Access Journals (Sweden)

    Tarun M. Kapoor

    2017-02-01

    Full Text Available A microtubule-based bipolar spindle is required for error-free chromosome segregation during cell division. In this review I discuss the molecular mechanisms required for the assembly of this dynamic micrometer-scale structure in animal cells.

  4. Dump valve assembly

    Science.gov (United States)

    Owen, T.J.

    1984-01-01

    A dump valve assembly comprising a body having a bore defined by a tapered wall and a truncated spherical valve member adapted to seat along a spherical surface portion thereof against said tapered wall. Means are provided for pivoting said valve member between a closed position engagable with said tapered wall and an open position disengaged therefrom.

  5. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2010-01-01

    Tuesday 20 April at 10.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 12 May 2009 Presentation and approval of the Activity Report 2009 Presentation and approval of the Financial Report 2009 Presentation and approval of the Auditors Report 2009 Programme for 2010 Presentation et and approval of the draft budget and subscription rate 2010 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may require t...

  6. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2011-01-01

    Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation et and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly ma...

  7. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2011-01-01

    Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may r...

  8. Supramolecular Assemblies in Photosynthesis

    Science.gov (United States)

    Wrachtrup, J.; Tietz, C.; Jelezko, F.; Gerken, U.; Schuler, S.; Götze, B.; Volkmer, A.

    2002-10-01

    The photosynthetic apparatus contains a wealth of supramolecular assemblies that are optimized for charge and energy transfer. Various techniques have been applied to investigate these functions that rely on the electronic interaction among pigment molecules. In this contribution we will present single-molecule studies of pigment protein complexes. They reveal new information about electronic interactions between chlorophyll molecules in light harvesting complexes.

  9. Turbomachine blade assembly

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Crespo, Andres Jose

    2016-11-01

    Embodiments of the present disclosure include a system comprising a turbomachine blade assembly having a blade portion, a shank portion, and a mounting portion, wherein the blade portion, the shank portion, and the mounting portion comprise a first plurality of plies extending from a tip of the airfoil to a base of the dovetail.

  10. America's Assembly Line

    DEFF Research Database (Denmark)

    Nye, David Edwin

    A social history of the assembly line, invented in 1913. Both praised as a boon to consumers and as a curse for workers, it has been satirized, imitated, and celebrated for 100 years. It has inspired fiction, comedy, cafeteria layouts, and suburban housing. It transformed industrial labor...

  11. Industrial Assembly Cases

    DEFF Research Database (Denmark)

    Ellekilde, Lars-Peter; Buch, Jacob Pørksen; Iversen, Thorbjørn Mosekjær;

    This technical report presents 13 different industrial assembly tasks, which are composed of 70 different operations. The report is written to provide an overview and do as such not contain product specific information such as object weights, dimensions etc. The operations are classified into a set...

  12. Assembling Sustainable Territories

    DEFF Research Database (Denmark)

    Vandergeest, Peter; Ponte, Stefano; Bush, Simon

    2015-01-01

    that territorialisation is accomplished not just through (re)defining bounded space, but more broadly through the assembling of four elements: space, subjects, objects, and expertise. Four case studies of sustainability certification in seafood are analyzed to show that ‘green gabbing’ is not necessarily the central...

  13. Data assimilation in a coupled physical-biogeochemical model of the California Current System using an incremental lognormal 4-dimensional variational approach: Part 2-Joint physical and biological data assimilation twin experiments

    Science.gov (United States)

    Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2016-10-01

    Coupled physical and biological data assimilation is performed within the California Current System using model twin experiments. The initial condition of physical and biological variables is estimated using the four-dimensional variational (4DVar) method under the Gaussian and lognormal error distributions assumption, respectively. Errors are assumed to be independent, yet variables are coupled by assimilation through model dynamics. Using a nutrient-phytoplankton-zooplankton-detritus (NPZD) model coupled to an ocean circulation model (the Regional Ocean Modeling System, ROMS), the coupled data assimilation procedure is evaluated by comparing results to experiments with no assimilation and with assimilation of physical data and biological data separately. Independent assimilation of physical (biological) data reduces the root-mean-squared error (RMSE) of physical (biological) state variables by more than 56% (43%). However, the improvement in biological (physical) state variables is less than 7% (13%). In contrast, coupled data assimilation improves both physical and biological components by 57% and 49%, respectively. Coupled data assimilation shows robust performance with varied observational errors, resulting in significantly smaller RMSEs compared to the free run. It still produces the estimation of observed variables better than that from the free run even with the physical and biological model error, but leads to higher RMSEs for unobserved variables. A series of twin experiments illustrates that coupled physical and biological 4DVar assimilation is computationally efficient and practical, capable of providing the reliable estimation of the coupled system with the same and ready to be examined in a realistic configuration.

  14. Design Concepts in Set Parts Supply Implementation

    Directory of Open Access Journals (Sweden)

    Suhartini Mohd Jainury

    2013-10-01

    Full Text Available The increasing number of parts variants on an assembly line requires an improvement for a cost efficient and flexible parts supply system. For that reason, the Set Parts Supply (SPS system was introduced by Toyota as a new material handling system for supplying parts in sets based on the kitting concept. In this study, we investigate the consideration of design concepts in SPS implementation at one of Malaysia’s automotive manufacturers through a case study in a mixed-model assembly line that contains many parts to be assembled to the car body. From our case study, we found that the design of the ‘parts only’ or minomi concept on the component racks contributes to the elimination of waste; mura, muri and muda. Finally, we present the lean approach in the minomi concepts that used in designing the component racks.

  15. Development of a virtual manufacturing assembly simulation system

    Directory of Open Access Journals (Sweden)

    Abdulrahman M Al-Ahmari

    2016-03-01

    Full Text Available Assembly operations are a key component of modern manufacturing systems. Designing, planning, and conducting assembly operations represent an important part of the cost of a product. Virtual reality provides an efficient and cost-effective solution to manufacturing design, planning, and prototyping. Still there are certain issues (such as data translation, integration of various hardware and software systems, and real-time collision detection faced while applying this advanced technology to the assembly domain. For example, existing works focus on using virtual reality systems and environments mainly to design new products and to plan for assembly. Little focus has been given to develop virtual reality environments that contribute to train operators on assembly operations and to bridge the gap between design and implementation/execution of assembly. Therefore, the research work presented in this article focuses on developing a fully functional virtual manufacturing assembly simulation system that solves the issues related to virtual reality environments. The proposed system uses a virtual environment to create an interactive workbench that can be used for evaluating assembly decisions and training assembly operations. It is a comprehensive system that provides visual, auditory, tactile, as well as force feedback. The system works successfully even with large components.

  16. Thermodynamics of Biological Processes

    Science.gov (United States)

    Garcia, Hernan G.; Kondev, Jane; Orme, Nigel; Theriot, Julie A.; Phillips, Rob

    2012-01-01

    There is a long and rich tradition of using ideas from both equilibrium thermodynamics and its microscopic partner theory of equilibrium statistical mechanics. In this chapter, we provide some background on the origins of the seemingly unreasonable effectiveness of ideas from both thermodynamics and statistical mechanics in biology. After making a description of these foundational issues, we turn to a series of case studies primarily focused on binding that are intended to illustrate the broad biological reach of equilibrium thinking in biology. These case studies include ligand-gated ion channels, thermodynamic models of transcription, and recent applications to the problem of bacterial chemotaxis. As part of the description of these case studies, we explore a number of different uses of the famed Monod–Wyman–Changeux (MWC) model as a generic tool for providing a mathematical characterization of two-state systems. These case studies should provide a template for tailoring equilibrium ideas to other problems of biological interest. PMID:21333788

  17. Membrane biology: fission behind BARs.

    Science.gov (United States)

    Haucke, Volker

    2012-06-05

    Membrane bending is accomplished in part by amphipathic helix insertion into the bilayer and the assembly of BAR domain scaffolds preparing the membrane for fission. Two recent studies highlight the roles of amphipathic helices and BAR scaffolds in membrane fission and establish the structural basis of membrane bending by the N-BAR protein endophilin.

  18. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

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

  19. Geometric design of part feeders

    NARCIS (Netherlands)

    Berretty, R.-P.M.

    2001-01-01

    This thesis presents solutions for problems derived from industrial assembly and robotic manipulation. The basic tasks in a factory are manufacturing the parts, and combining them into the desired product. In automating these tasks, we want to use robot manipulators that require little or no h

  20. The Robust Assembly of Small Symmetric Nanoshells.

    Science.gov (United States)

    Wagner, Jef; Zandi, Roya

    2015-09-01

    Highly symmetric nanoshells are found in many biological systems, such as clathrin cages and viral shells. Many studies have shown that symmetric shells appear in nature as a result of the free-energy minimization of a generic interaction between their constituent subunits. We examine the physical basis for the formation of symmetric shells, and by using a minimal model, demonstrate that these structures can readily grow from the irreversible addition of identical subunits. Our model of nanoshell assembly shows that the spontaneous curvature regulates the size of the shell while the mechanical properties of the subunit determine the symmetry of the assembled structure. Understanding the minimum requirements for the formation of closed nanoshells is a necessary step toward engineering of nanocontainers, which will have far-reaching impact in both material science and medicine.

  1. 49 CFR 583.6 - Procedure for determining U.S./Canadian parts content.

    Science.gov (United States)

    2010-10-01

    ..., gasoline, oil, blackout, phosphate rinse, windshield washer fluid, fasteners, tire assembly fluid, rivets.... (1) For items of equipment received at the final assembly point, the value is the price paid by the... the final assembly point (but not as part of final assembly), the value is the fair market price...

  2. Computational biology

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  3. Amphiphiles Self-Assembly: Basic Concepts and Future Perspectives of Supramolecular Approaches

    Directory of Open Access Journals (Sweden)

    Domenico Lombardo

    2015-01-01

    Full Text Available Amphiphiles are synthetic or natural molecules with the ability to self-assemble into a wide variety of structures including micelles, vesicles, nanotubes, nanofibers, and lamellae. Self-assembly processes of amphiphiles have been widely used to mimic biological systems, such as assembly of lipids and proteins, while their integrated actions allow the performance of highly specific cellular functions which has paved a way for bottom-up bionanotechnology. While amphiphiles self-assembly has attracted considerable attention for decades due to their extensive applications in material science, drug and gene delivery, recent developments in nanoscience stimulated the combination of the simple approaches of amphiphile assembly with the advanced concept of supramolecular self-assembly for the development of more complex, hierarchical nanostructures. Introduction of stimulus responsive supramolecular amphiphile assembly-disassembly processes provides particularly novel approaches for impacting bionanotechnology applications. Leading examples of these novel self-assembly processes can be found, in fact, in biosystems where assemblies of different amphiphilic macrocomponents and their integrated actions allow the performance of highly specific biological functions. In this perspective, we summarize in this tutorial review the basic concept and recent research on self-assembly of traditional amphiphilic molecules (such as surfactants, amphiphile-like polymers, or lipids and more recent concepts of supramolecular amphiphiles assembly which have become increasingly important in emerging nanotechnology.

  4. Optical Space Telescope Assembly Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Optical Space Telescope Assembly (OSTA) task is to demonstrate the technology readiness of assembling large space telescopes on orbit in 2015. This task is an...

  5. X-Ray Assembler Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — Federal regulations require that an assembler who installs one or more certified components of a diagnostic x-ray system submit a report of assembly. This database...

  6. The Promises of Biology and the Biology of Promises

    DEFF Research Database (Denmark)

    Lee, Jieun

    2015-01-01

    commitments with differently imagined futures. I argue that promises are constitutive of the stem cell biology, rather than being derivative of it. Since the biological concept of stem cells is predicated on the future that they promise, the biological life of stem cells is inextricably intertwined...... patients’ bodies in anticipation of materializing the promises of stem cell biology, they are produced as a new form of biovaluable. The promises of biology move beyond the closed circuit of scientific knowledge production, and proliferate in the speculative marketplaces of promises. Part II looks at how...... of technologized biology and biological time can appear promising with the backdrop of the imagined intransigence of social, political, and economic order in the Korean society....

  7. Issues in Biological Shape Modelling

    DEFF Research Database (Denmark)

    Hilger, Klaus Baggesen

    This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape or appear......This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape...

  8. 3D vision assisted flexible robotic assembly of machine components

    Science.gov (United States)

    Ogun, Philips S.; Usman, Zahid; Dharmaraj, Karthick; Jackson, Michael R.

    2015-12-01

    Robotic assembly systems either make use of expensive fixtures to hold components in predefined locations, or the poses of the components are determined using various machine vision techniques. Vision-guided assembly robots can handle subtle variations in geometries and poses of parts. Therefore, they provide greater flexibility than the use of fixtures. However, the currently established vision-guided assembly systems use 2D vision, which is limited to three degrees of freedom. The work reported in this paper is focused on flexible automated assembly of clearance fit machine components using 3D vision. The recognition and the estimation of the poses of the components are achieved by matching their CAD models with the acquired point cloud data of the scene. Experimental results obtained from a robot demonstrating the assembly of a set of rings on a shaft show that the developed system is not only reliable and accurate, but also fast enough for industrial deployment.

  9. Low inductance busbar assembly

    Science.gov (United States)

    Holbrook, Meghan Ann

    2010-09-21

    A busbar assembly for electrically coupling first and second busbars to first and second contacts, respectively, on a power module is provided. The assembly comprises a first terminal integrally formed with the first busbar, a second terminal integrally formed with the second busbar and overlapping the first terminal, a first bridge electrode having a first tab electrically coupled to the first terminal and overlapping the first and second terminals, and a second tab electrically coupled to the first contact, a second bridge electrode having a third tab electrically coupled to the second terminal, and overlapping the first and second terminals and the first tab, and a fourth tab electrically coupled to the second contact, and a fastener configured to couple the first tab to the first terminal, and the third tab to the second terminal.

  10. Biological Oceanography

    Science.gov (United States)

    Dyhrman, Sonya

    2004-10-01

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

  11. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

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

  12. Synthetic biology: ethical ramifications 2009.

    Science.gov (United States)

    Rabinow, Paul; Bennett, Gaymon

    2009-12-01

    During 2007 and 2008 synthetic biology moved from the manifesto stage to research programs. As of 2009, synthetic biology is ramifying; to ramify means to produce differentiated trajectories from previous determinations. From its inception, most of the players in synthetic biology agreed on the need for (a) rationalized design and construction of new biological parts, devices, and systems as well as (b) the re-design of natural biological systems for specified purposes, and that (c) the versatility of designed biological systems makes them suitable to address such challenges as renewable energy, the production of inexpensive drugs, and environmental remediation, as well as providing a catalyst for further growth of biotechnology. What is understood by these goals, however, is diverse. Those assorted understandings are currently contributing to different ramifications of synthetic biology. The Berkeley Human Practices Lab, led by Paul Rabinow, is currently devoting its efforts to documenting and analyzing these ramifications as they emerge.

  13. Fourth Doctoral Student Assembly

    CERN Multimedia

    Ingrid Haug

    2016-01-01

    On 10 May, over 130 PhD students and their supervisors, from both CERN and partner universities, gathered for the 4th Doctoral Student Assembly in the Council Chamber.   The assembly was followed by a poster session, at which eighteen doctoral students presented the outcome of their scientific work. The CERN Doctoral Student Programme currently hosts just over 200 students in applied physics, engineering, computing and science communication/education. The programme has been in place since 1985. It enables students to do their research at CERN for a maximum of three years and to work on a PhD thesis, which they defend at their University. The programme is steered by the TSC committee, which holds two selection committees per year, in June and December. The Doctoral Student Assembly was opened by the Director-General, Fabiola Gianotti, who stressed the importance of the programme in the scientific environment at CERN, emphasising that there is no more rewarding activity than lear...

  14. OH Module Assembly Stand

    Energy Technology Data Exchange (ETDEWEB)

    Bolan, P.J.; /Fermilab

    1990-10-16

    There is an OR module assembly stand in use at IB4. This design has been approved by safety, as presented by Mike Foley, and has been successfully used. Another one is needed at the D-zero assembly building, but some modifications need to be made. This report will show that the new modified design is at least as strong, if not stronger, than the older IB4 design in every aspect. Since the weight distribution of the OR modules on the sling is indeterminate, this report compares three cases of support for the entire assembly: the lowest two beams only, the lowest four beams only, and all six beams. In each of these cases, the new design is stronger than the old design in maximum allowable weight. The ability of the the cradle to support the weight is also shown. For all of the failure conditions except for two, the cradle is stronger than the beams that it supports. In the two excepted situations, the calculated limit of the cradle is less than the beams it supports. This is because no credit is taken for the sling and strongback, which in reality will relieve much of the horizontal load.

  15. IAHS Third Scientific Assembly

    Science.gov (United States)

    The International Association of Hydrological Sciences (IAHS) convened its Third Scientific Assembly in Baltimore, Md., May 10-19, 1989. The Assembly was attended by about 450 scientists and engineers. The attendance was highest from the U.S., as could be expected; 37 were from Canada; 22 each, Netherlands and United Kingdom; 14, Italy; 12, China; 10, Federal Republic of Germany; 8 each from France, the Republic of South Africa, and Switzerland; 7, Austria; 6 each, Finland and Japan; others were scattered among the remainder of 48 countries total.one of the cosponsors and also handled business matters for the Assembly. Other cosponsors included the International Association of Meteorology and Atmospheric Physics (IAMAP), United Nations Environmental Program (UNEP), United Nations Educational, Scientific, and Cultural Organization (UNESCO), World Meteorological Organization (WMO), and U.K. Overseas Development Authority (ODA). U.S. federal agencies serving as cosponsors included the Environmental Protection Agency, National Aeronautics and Space Administration, National Science Foundation, National Weather Service, Department of Agriculture, Department of State, and U.S. Geological Survey.

  16. Ordinary General Assembly

    CERN Multimedia

    Association du personnel

    2010-01-01

    Tuesday 20 April at 10.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 12 May 2009 Presentation and approval of the Activity Report 2009 Presentation and approval of the Financial Report 2009 Presentation and approval of the Auditors Report 2009 Programme for 2010 Presentation et and approval of the draft budget and subscription rate 2010 Modifications to the statutes of the association Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda...

  17. SCT Barrel Assembly Complete

    CERN Multimedia

    L. Batchelor

    As reported in the April 2005 issue of the ATLAS eNews, the first of the four Semiconductor Tracker (SCT) barrels, complete with modules and services, arrived safely at CERN in January of 2005. In the months since January, the other three completed barrels arrived as well, and integration of the four barrels into the entire barrel assembly commenced at CERN, in the SR1 building on the ATLAS experimental site, in July. Assembly was completed on schedule in September, with the addition of the innermost layer to the 4-barrel assembly. Work is now underway to seal the barrel thermal enclosure. This is necessary in order to enclose the silicon tracker in a nitrogen atmosphere and provide it with faraday-cage protection, and is a delicate and complicated task: 352 silicon module powertapes, 352 readout-fibre bundles, and over 400 Detector Control System sensors must be carefully sealed into the thermal enclosure bulkhead. The team is currently verifying the integrity of the low mass cooling system, which must be d...

  18. Effect of the effective parts of Salvia chinensis of the biological behaviors on vascular endothelial cells%石见穿有效部位对血管内皮细胞生物学行为的影响

    Institute of Scientific and Technical Information of China (English)

    权雯; 钱晓萍; 刘宝瑞; 胡静; 杨阳; 李茹恬; 禹立霞

    2013-01-01

    Objective:To investigate the effects of the effective parts of Salvia chinensis of the biological behaviors of vascular endothelial cells.Methods:Human umbilical vein endothelial cells (HUVECs) were cultured primarily in vitro.The MTT assay was used to observe the effect of the effective parts of Salvia chinensis on HUVECs and human lung carcinoma A549 cell.Transwell cabin test and tube formation assay were used to observe the effect of the effective parts of Salvia chinensis on the migration and tube formation ability of HUVECs.Results:3.125-25μg/ml chloroform and ethyl acetate extract from Salvia chinensis treated in HUVEC 48h,the proliferation inhibition rate was 17.36% to 53.08%,from 9.53% to 31.36%.Acting on sensitive cell lines of human lung cancer A549 proliferation inhibition rate of 7.10% to 31.18%,2.24% to 21.69%,both were significantly different in cytotoxicity (P=0.001).3.125-25μg/ml chloroform and ethyl acetate extract from Salvia chinensis treated the HUVECs 12h migration inhibition rates were 5.39% and 57.38%,1.92% to 37.37% ;3.75μg/ml to 25μg/ml trichloromethane extraction part from Salvia chinensis for 24h HUVEC tube formation number reduced,and the lumen was not complete,the same concentration Iwami wear ethyl acetate extract weak inhibition.Conclusion:The trichloromethane extraction part from Salvia chinensis inhibit endothelial cell proliferation,migration and tube formation was significantly better than the ethyl acetate extract for the Salvia chinensis to play a major site of action of anti-angiogenic.%目的:探讨石见穿氯仿及乙酸乙酯部位在体外对血管内皮细胞生物学行为的影响.方法:培养人脐静脉内皮细胞(HUVEC)至3-6代,采用MTT实验、Transwell小室迁移实验、体外小管形成实验观察石见穿氯仿及乙酸乙酯部位对HUVECs体外增殖、迁移、小管形成能力的影响.结果:3.125-25μg/ml的石见穿氯仿部位及乙酸乙酯部位作用于HUVEC 48h

  19. Self-assembly drugs: from micelles to nanomedicine.

    Science.gov (United States)

    Messina, Paula V; Besada-Porto, Jose Miguel; Ruso, Juan M

    2014-03-01

    Self-assembly has fascinated many scientists over the past few decades. Rapid advances and widespread interest in the study of this subject has led to the synthesis of an ever-increasing number of elegant and intricate functional structures with sizes that approach nano- and mesoscopic dimensions. Today, it has grown into a mature field of modern science whose interfaces with many disciplines have provided invaluable opportunities for crossing boundaries for scientists seeking to design novel molecular materials exhibiting unusual properties, and for researchers investigating the structure and function of biomolecules. Consequently, self-assembly transcends the traditional divisional boundaries of science and represents a highly interdisciplinary field including nanotechnology and nanomedicine. Basically, self-assembly focuses on a wide range of discrete molecules or molecular assemblies and uses physical transformations to achieve its goals. In this Review, we present a comprehensive overview of the advances in the field of drug self-assembly and discuss in detail the synthesis, self-assembly behavior, and physical properties as well as applications. We refer the reader to past reviews dealing with colloidal molecules and colloidal self-assembly. In the first part, we will discuss, compare, and link the various bioinformatic procedures: Molecular Dynamics and Quantitative Structure Activity Relationship. The second section deals with the self-assembly behavior in more detail, in which we focus on several experimental techniques, selected according to the depth of knowledge obtained. The last part will review the advances in drug-protein assembly. Nature provides many examples of proteins that form their substrate binding sites by bringing together the component pieces in a process of self-assembly. We will focus in the understanding of physical properties and applications developing thereof.

  20. Foldit Biology

    Science.gov (United States)

    2015-07-31

    Report 8/1/2013-7/31/2015 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Foldit Biology NOOO 14-13-C-0221 Sb. GRANT NUMBER N/A Sc. PROGRAM ELEMENT...Include area code) Unclassified Unclassified Unclassified (206) 616-2660 Zoran Popović Foldit Biology (Task 1, 2, 3, 4) Final Report...Period Covered by the Report August 1, 2013 – July 31, 2015 Date of Report: July 31, 2015 Project Title: Foldit Biology Contract Number: N00014-13

  1. Biological Systems, Energy Sources, and Biology Teaching. Biology and Human Welfare.

    Science.gov (United States)

    Tribe, Michael; Pritchard, Alan J.

    This five-chapter document (part of a series on biology and human welfare) focuses on biological systems as energy sources and on the teaching of this subject area. Chapter 1 discusses various topics related to energy and ecology, including biomass, photosynthesis and world energy balances, energy flow through ecosystems, and others. Chapter 2…

  2. Light-structured colloidal assemblies

    Science.gov (United States)

    Aubret, Antoine; Mena, Youssef; Ramananarivo, Sophie; Sacanna, Stefano; Palacci, Jeremie; Palacci lab Team; Sacanna lab Team

    2016-11-01

    Self-propelled particles (SPP) are a key tool since they are of relative simplicity as compared to biological micro-entities and provide a higher level of control. They can convert an energy source into motion and work, and exhibit surprising non-equilibrium behavior. In our work, we focus on the manipulation of colloids using light. We exploit osmotic and phoretic effects to act on single and ensemble of colloids. The key mechanism relies on the photocatalytic decomposition of hydrogen peroxide using hematite, which triggers the motion of colloids around it when illuminated. We use hematite particles and particles with photocatalytic inclusions (i.e. SPP). We first show that the interactions between hematite and colloidal tracers can be tuned by adjusting the chemical environment. Furthermore, we report a phototaxic behavior (migration in light gradient) of the particles. From this, we explore the effect of spatio-temporal modulation of the light to control the motion of colloids at the single particle level, and to generate self-assembled colloidal structures through time and space. The so-formed structures are maintained by phoretic and hydrodynamic forces resulting from the motion of each particles. Ultimately, a dynamic light modulation may be a route for the creation of active colloidal motion on a collective scale through the synchronization of the individual motions of SPP. This work is supported by NSF CAREER DMR 1554724.

  3. MALDI-imaging enables direct observation of kinetic and thermodynamic products of mixed peptide fiber assembly.

    Science.gov (United States)

    Medini, Karima; West, Brandi; Williams, David E; Brimble, Margaret A; Gerrard, Juliet A

    2017-02-04

    Controlling the self-assembly of multicomponent systems provides a key to designing new materials and understanding the molecular complexity of biology. Here, we demonstrate the first use of MALDI-imaging to characterize a multicomponent self-assembling peptide fiber. Observations of mixed peptide systems over time demonstrate how simple sequence variation can change the balance between kinetic and thermodynamic products.

  4. Carbohydrate nanotechnology: hierarchical assembly using nature's other information carrying biopolymers.

    Science.gov (United States)

    Han, Xu; Zheng, Yeting; Munro, Catherine J; Ji, Yiwen; Braunschweig, Adam B

    2015-08-01

    Despite their central role in directing some of the most complex biological processes, carbohydrates--nature's other information carrying biopolymer--have been largely ignored as building blocks for synthetic hierarchical assemblies. The non-stoichiometric binding and astronomical diversity characteristic of carbohydrates could lead to tantalizingly complex assembly algorithms, but these attributes simultaneously increase the difficulty of preparing carbohydrate assemblies and anticipating their behavior. Convergences in biotechnology, nanotechnology, polymer chemistry, surface science, and supramolecular chemistry have led to many recent important breakthroughs in glycan microarrays and synthetic carbohydrate receptors, where the idiosyncrasies of carbohydrate structure and binding are increasingly considered. We hope to inspire more researchers to consider carbohydrate structure, diversity, and binding as attractive tools for constructing synthetic hierarchical assemblies.

  5. Structure, dynamics, assembly, and evolution of protein complexes.

    Science.gov (United States)

    Marsh, Joseph A; Teichmann, Sarah A

    2015-01-01

    The assembly of individual proteins into functional complexes is fundamental to nearly all biological processes. In recent decades, many thousands of homomeric and heteromeric protein complex structures have been determined, greatly improving our understanding of the fundamental principles that control symmetric and asymmetric quaternary structure organization. Furthermore, our conception of protein complexes has moved beyond static representations to include dynamic aspects of quaternary structure, including conformational changes upon binding, multistep ordered assembly pathways, and structural fluctuations occurring within fully assembled complexes. Finally, major advances have been made in our understanding of protein complex evolution, both in reconstructing evolutionary histories of specific complexes and in elucidating general mechanisms that explain how quaternary structure tends to evolve. The evolution of quaternary structure occurs via changes in self-assembly state or through the gain or loss of protein subunits, and these processes can be driven by both adaptive and nonadaptive influences.

  6. Methodological studies on the VVER-440 control assembly calculations

    Energy Technology Data Exchange (ETDEWEB)

    Hordosy, G.; Kereszturi, A.; Maraczy, C. [KFKI Atomic Energy Research Institute, Budapest (Hungary)

    1995-12-31

    The control assembly regions of VVER-440 reactors are represented by 2-group albedo matrices in the global calculations of the KARATE code system. Some methodological aspects of calculating albedo matrices with the COLA transport code are presented. Illustrations are given how these matrices depend on the relevant parameters describing the boron steel and steel regions of the control assemblies. The calculation of the response matrix for a node consisting of two parts filled with different materials is discussed.

  7. Immune and Genetic Algorithm Based Assembly Sequence Planning

    Institute of Scientific and Technical Information of China (English)

    YANG Jian-guo; LI Bei-zhi; YU Lei; JIN Yu-song

    2004-01-01

    In this paper an assembly sequence planning model inspired by natural immune and genetic algorithm (ASPIG) based on the part degrees of freedom matrix (PDFM) is proposed, and a proto system - DSFAS based on the ASPIG is introduced to solve assembly sequence problem. The concept and generation of PDFM and DSFAS are also discussed. DSFAS can prevent premature convergence, and promote population diversity, and can accelerate the learning and convergence speed in behavior evolution problem.

  8. Biological, chemical and other data collected in the North Atlantic Ocean on the WEATHERBIRD II cruises UNKNOWN as part of the EDDIES project from 2004-06-24 to 2005-08-25 (NODC Accession 0081718)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — PI: Nick Bates of: Bermuda Biological Station for Research (BBSR) dataset: Niskin bottle and CTD data; nutrients, oxygen, DIC, POC, PON platform: R/V Weatherbird II...

  9. Physical and biological data collected with CDT, fluorometer, and SeaSoar aboard the ship WECOMA as part of Global Ocean Ecosystem Dynamics (GLOBEC) in the North Pacific Ocean from May 30 to June 16 2000 (NODC Accession 0000986)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical and biological data collected with CDT, fluorometer, and SeaSoar aboard the ship WECOMA in the North Pacific Ocean from May 30 to June 16 2000. These data...

  10. Chemical and biological data collected as part of the CArbon Retention In A Colored Ocean (CARIACO) program in the Cariaco Basin off the coast of Venezuela, May 23, 2005 - November 11, 2006 (NODC Accession 0038513)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Chemical and biological data were collected using bottle casts on the continental shelf of Venezuela from the HERMANO GINES from May 23, 2005 to November 11, 2006....

  11. Chemical and biological data collected as part of the CArbon Retention In A Colored Ocean (CARIACO) program in the Cariaco Basin off the coast of Venezuela, January 17, 2005 - January 16, 2006 (NODC Accession 0013170)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Chemical and biological data were collected using bottle casts on the continental shelf of Venezuela from the HERMANO GINES from January 17, 2005 to January 16,...

  12. Biological data collected in the North Atlantic Ocean on the OCEANUS cruises WB0409, WB0413, WB0506, and WB0508 as part of the EDDIES project from 2004-06-24 to 2005-08-24 (NODC Accession 0086459)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — PI: Nick Bates of: Bermuda Biological Station for Research (BBSR) dataset: Primary Production data platform: R/V Weatherbird II Methodology: see Chapter 18: Primary...

  13. Precharacterization Report for Instrumented Fuel Assembly (IFA)-527

    Energy Technology Data Exchange (ETDEWEB)

    Cunningham, M. E.; Bradley, E. R.; Daniel, J. L.; Davis, N. C.; Lanning, D. D.; Williford, R. E.

    1981-07-01

    This report is a resource document covering the rationale, design, fabrication, and preirradiation characterization of instrumented fuel assembly (IFA)-527. This assembly is being irradiated in the Halden Boiling Water Reactor (HBWR) in Norway as part of the Experimental Support and Development of Single-Rod Fuel Codes Program conducted by Pacific Northwest laboratory (PNL) and sponsored by the Fuel Behavior Research Branch of the U.S. Nuclear Regulatory Commission (NRC). Data from this assembly will be used to better understand light water reactor (LWR) fuel behavior under normal operating conditions.

  14. Product Assembly Cost Estimation Based on Artificial Neural Networks

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper proposes a method for assembly cost estimation in actual manufacture during the design phase using artificial neural networks (ANN). It can support the de signers in cost effectiveness, then help to control the total cost. The method was used in the assembly cost estimation of the crucial parts of some railway stock products. As a compari son, we use the linear regression (LR) model in the same field. The result shows that ANN model performs better than the LR model in assembly cost estimation.

  15. Design and testing of a synthetic biology framework for genetic engineering of Corynebacterium glutamicum

    Directory of Open Access Journals (Sweden)

    Ravasi Pablo

    2012-11-01

    Full Text Available Abstract Background Synthetic biology approaches can make a significant contribution to the advance of metabolic engineering by reducing the development time of recombinant organisms. However, most of synthetic biology tools have been developed for Escherichia coli. Here we provide a platform for rapid engineering of C. glutamicum, a microorganism of great industrial interest. This bacteria, used for decades for the fermentative production of amino acids, has recently been developed as a host for the production of several economically important compounds including metabolites and recombinant proteins because of its higher capacity of secretion compared to traditional bacterial hosts like E. coli. Thus, the development of modern molecular platforms may significantly contribute to establish C. glutamicum as a robust and versatile microbial factory. Results A plasmid based platform named pTGR was created where all the genetic components are flanked by unique restriction sites to both facilitate the evaluation of regulatory sequences and the assembly of constructs for the expression of multiple genes. The approach was validated by using reporter genes to test promoters, ribosome binding sites, and for the assembly of dual gene operons and gene clusters containing two transcriptional units. Combinatorial assembly of promoter (tac, cspB and sod and RBS (lacZ, cspB and sod elements with different strengths conferred clear differential gene expression of two reporter genes, eGFP and mCherry, thus allowing transcriptional “fine-tuning”of multiple genes. In addition, the platform allowed the rapid assembly of operons and genes clusters for co-expression of heterologous genes, a feature that may assist metabolic pathway engineering. Conclusions We anticipate that the pTGR platform will contribute to explore the potential of novel parts to regulate gene expression, and to facilitate the assembly of genetic circuits for metabolic engineering of C

  16. Maximum shields: the assembly and function of the bacterial spore coat.

    Science.gov (United States)

    Driks, Adam

    2002-06-01

    Spores produced by bacilli and clostridia are surrounded by a multilayered protein shell called the coat. As the armor-like appearance of the coat suggests, this structure, along with others within the spore, confers the remarkable resistance properties that make Bacillus anthracis spores such potent biological weapons. Here, I review recent studies of coat assembly in the model organism Bacillus subtilis, and explore the implications of these findings for coat assembly in B. anthracis and for defense against biological weapons.

  17. Volcano ecology: Disturbance characteristics and assembly of biological communities

    Science.gov (United States)

    Volcanic eruptions are powerful expressions of Earth’s geophysical forces which have shaped and influenced ecological systems since the earliest days of life. The study of the interactions of volcanoes and ecosystems, termed volcano ecology, focuses on the ecological responses of organisms and biolo...

  18. The TileCal Barrel Test Assembly

    CERN Multimedia

    Leitner, R

    On 30th October, the mechanics test assembly of the central barrel of the ATLAS tile hadronic calorimeter was completed in building 185. It started on 23rd June and is the second wheel for the Tilecal completely assembled this year. The ATLAS engineers and technicians are quick: instead of the 27 weeks initially foreseen for assembling the central barrel of the tile hadronic calorimeter (Tilecal) in building 185, they inserted the last of the 64 modules on 30th October after only 19 weeks. In part, this was due to the experience gained in the dry run assembly of the first extended barrel, produced in Spain, in spring this year (see Bulletin 23/2003); however, the central barrel is twice as long - and twice as heavy. With a length of 6.4 metres, an outer diameter of 8.5 metres and an inner diameter of 4.5 metres, the object weight is 1300 tonnes. The whole barrel cylinder is supported by the stainless steel support structure weighing only 27 tons. The barrel also has to have the right shape: over the whole 8...

  19. Examination of the regulatory frameworks applicable to biologic drugs (including stem cells and their progeny) in Europe, the U.S., and Australia: part I--a method of manual documentary analysis.

    Science.gov (United States)

    Ilic, Nina; Savic, Snezana; Siegel, Evan; Atkinson, Kerry; Tasic, Ljiljana

    2012-12-01

    Recent development of a wide range of regulatory standards applicable to production and use of tissues, cells, and other biologics (or biologicals), as advanced therapies, indicates considerable interest in the regulation of these products. The objective of this study was to analyze and compare high-tier documents within the Australian, European, and U.S. biologic drug regulatory environments using qualitative methodology. Cohort 1 of the selected 18 high-tier regulatory documents from the European Medicines Agency (EMA), the U.S. Food and Drug Administration (FDA), and the Therapeutic Goods Administration (TGA) regulatory frameworks were subject to a manual documentary analysis. These documents were consistent with the legal requirements for manufacturing and use of biologic drugs in humans and fall into six different categories. Manual analysis included a terminology search. The occurrence, frequency, and interchangeable use of different terms and phrases were recorded in the manual documentary analysis. Despite obvious differences, manual documentary analysis revealed certain consistency in use of terminology across analyzed frameworks. Phrase search frequencies have shown less uniformity than the search of terms. Overall, the EMA framework's documents referred to "medicinal products" and "marketing authorization(s)," the FDA documents discussed "drug(s)" or "biologic(s)," and the TGA documents referred to "biological(s)." Although high-tier documents often use different terminology they share concepts and themes. Documents originating from the same source have more conjunction in their terminology although they belong to different frameworks (i.e., Good Clinical Practice requirements based on the Declaration of Helsinki, 1964). Automated (software-based) documentary analysis should be obtained for the conceptual and relational analysis.

  20. Molecular assembly on two-dimensional materials

    Science.gov (United States)

    Kumar, Avijit; Banerjee, Kaustuv; Liljeroth, Peter

    2017-02-01

    Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional (2D) materials is a developing field driven by the interest in functionalization of 2D materials in order to tune their electronic properties. This has resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy. The review covers three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moiré pattern present on 2D materials grown on substrates. We also see that modification of intermolecular interactions and molecule–substrate interactions influences the assembly drastically and that 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moiré pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled, acceptor and donor type, organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from atomically thin crystals, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging

  1. The renaissance of developmental biology.

    Science.gov (United States)

    St Johnston, Daniel

    2015-05-01

    Since its heyday in the 1980s and 90s, the field of developmental biology has gone into decline; in part because it has been eclipsed by the rise of genomics and stem cell biology, and in part because it has seemed less pertinent in an era with so much focus on translational impact. In this essay, I argue that recent progress in genome-wide analyses and stem cell research, coupled with technological advances in imaging and genome editing, have created the conditions for the renaissance of a new wave of developmental biology with greater translational relevance.

  2. Plant mitochondrial Complex I composition and assembly: A review.

    Science.gov (United States)

    Subrahmanian, Nitya; Remacle, Claire; Hamel, Patrice Paul

    2016-07-01

    In the mitochondrial inner membrane, oxidative phosphorylation generates ATP via the operation of several multimeric enzymes. The proton-pumping Complex I (NADH:ubiquinone oxidoreductase) is the first and most complicated enzyme required in this process. Complex I is an L-shaped enzyme consisting of more than 40 subunits, one FMN molecule and eight Fe-S clusters. In recent years, genetic and proteomic analyses of Complex I mutants in various model systems, including plants, have provided valuable insights into the assembly of this multimeric enzyme. Assisted by a number of key players, referred to as "assembly factors", the assembly of Complex I takes place in a sequential and modular manner. Although a number of factors have been identified, their precise function in mediating Complex I assembly still remains to be elucidated. This review summarizes our current knowledge of plant Complex I composition and assembly derived from studies in plant model systems such as Arabidopsis thaliana and Chlamydomonas reinhardtii. Plant Complex I is highly conserved and comprises a significant number of subunits also present in mammalian and fungal Complexes I. Plant Complex I also contains additional subunits absent from the mammalian and fungal counterpart, whose function in enzyme activity and assembly is not clearly understood. While 14 assembly factors have been identified for human Complex I, only two proteins, namely GLDH and INDH, have been established as bona fide assembly factors for plant Complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.

  3. Unraveling the complexity of mitochondrial complex I assembly: A dynamic process.

    Science.gov (United States)

    Sánchez-Caballero, Laura; Guerrero-Castillo, Sergio; Nijtmans, Leo

    2016-07-01

    Mammalian complex I is composed of 44 different subunits and its assembly requires at least 13 specific assembly factors. Proper function of the mitochondrial respiratory chain enzyme is of crucial importance for cell survival due to its major participation in energy production and cell signaling. Complex I assembly depends on the coordination of several crucial processes that need to be tightly interconnected and orchestrated by a number of assembly factors. The understanding of complex I assembly evolved from simple sequential concept to the more sophisticated modular assembly model describing a convoluted process. According to this model, the different modules assemble independently and associate afterwards with each other to form the final enzyme. In this review, we aim to unravel the complexity of complex I assembly and provide the latest insights in this fundamental and fascinating process. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.

  4. High precision optomechanical assembly using threads as mechanical reference

    Science.gov (United States)

    Lamontagne, Frédéric; Desnoyers, Nichola; Bergeron, Guy; Cantin, Mario

    2016-09-01

    A convenient method to assemble optomechanical components is to use threaded interface. For example, lenses are often secured inside barrels using threaded rings. In other cases, multiple optical sub-assemblies such as lens barrels can be threaded to each other. Threads have the advantage to provide a simple assembly method, to be easy to manufacture, and to offer a compact mechanical design. On the other hand, threads are not considered to provide accurate centering between parts because of the assembly clearance between the inner and outer threads. For that reason, threads are often used in conjunction with precision cylindrical surfaces to limit the radial clearance between the parts to be centered. Therefore, tight manufacturing tolerances are needed on these pilot diameters, which affect the cost of the optical assembly. This paper presents a new optomechanical approach that uses threads as mechanical reference. This innovative method relies on geometric principles to auto-center parts to each other with a very low centering error that is usually less than 5 μm. The method allows to auto-center an optical group in a main barrel, to perform an axial adjustment of an optical group inside a main barrel, and to perform stacking of multiple barrels. In conjunction with the lens auto-centering method that also used threads as a mechanical reference, this novel solution opens new possibilities to realize a variety of different high precision optomechanical assemblies at lower cost.

  5. Programmed assembly of nanoscale structures using peptoids.

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Jianhua (University of the Pacific, Stockton, CA); Russell, Scott (California State University, Stanislaus, Turlock, CA); Morishetti, Kiran (University of the Pacific, Stockton, CA); Robinson, David B.; Zuckermann, Ronald N. (Lawrence Berkeley National Laboratory, Berkeley, CA); Buffleben, George M.; Hjelm, Rex P. (Los Alamos National Laboratory, Los Alamos, NM); Kent, Michael Stuart (Sandia National Laboratories, Albuquerque, NM)

    2011-02-01

    Sequence-specific polymers are the basis of the most promising approaches to bottom-up programmed assembly of nanoscale materials. Examples include artificial peptides and nucleic acids. Another class is oligo(N-functional glycine)s, also known as peptoids, which permit greater sidegroup diversity and conformational control, and can be easier to synthesize and purify. We have developed a set of peptoids that can be used to make inorganic nanoparticles more compatible with biological sequence-specific polymers so that they can be incorporated into nucleic acid or other biologically based nanostructures. Peptoids offer degrees of modularity, versatility, and predictability that equal or exceed other sequence-specific polymers, allowing for rational design of oligomers for a specific purpose. This degree of control will be essential to the development of arbitrarily designed nanoscale structures.

  6. Biological and medical sensor technologies

    CERN Document Server

    Iniewski, Krzysztof

    2012-01-01

    Biological and Medical Sensor Technologies presents contributions from top experts who explore the development and implementation of sensors for various applications used in medicine and biology. Edited by a pioneer in the area of advanced semiconductor materials, the book is divided into two sections. The first part covers sensors for biological applications. Topics include: Advanced sensing and communication in the biological world DNA-derivative architectures for long-wavelength bio-sensing Label-free silicon photonics Quartz crystal microbalance-based biosensors Lab-on-chip technologies fo

  7. Biomimetics applied to centering in micro-assembly

    DEFF Research Database (Denmark)

    Shu, L.H.; Lenau, Torben Anker; Hansen, Hans Nørgaard;

    2003-01-01

    This paper describes the application of a biomimetic search method to develop ideas for centering objects in micro-assembly. Biomimetics involves the imitation of biological phenomena to solve problems. An obstacle to the use of biomimetics in engineering is knowledge of biological phenomena...... that is relevant to the problem at hand. The method described here starts with an engineering problem, and then systematically searches for analogous biological phenomena using functional keywords. This method is illustrated by finding and using analogies for the problem of positioning and centering objects during...

  8. Spatially confined assembly of nanoparticles.

    Science.gov (United States)

    Jiang, Lin; Chen, Xiaodong; Lu, Nan; Chi, Lifeng

    2014-10-21

    The ability to assemble NPs into ordered structures that are expected to yield collective physical or chemical properties has afforded new and exciting opportunities in the field of nanotechnology. Among the various configurations of nanoparticle assemblies, two-dimensional (2D) NP patterns and one-dimensional (1D) NP arrays on surfaces are regarded as the ideal assembly configurations for many technological devices, for example, solar cells, magnetic memory, switching devices, and sensing devices, due to their unique transport phenomena and the cooperative properties of NPs in assemblies. To realize the potential applications of NP assemblies, especially in nanodevice-related applications, certain key issues must still be resolved, for example, ordering and alignment, manipulating and positioning in nanodevices, and multicomponent or hierarchical structures of NP assemblies for device integration. Additionally, the assembly of NPs with high precision and high levels of integration and uniformity for devices with scaled-down dimensions has become a key and challenging issue. Two-dimensional NP patterns and 1D NP arrays are obtained using traditional lithography techniques (top-down strategies) or interfacial assembly techniques (bottom-up strategies). However, a formidable challenge that persists is the controllable assembly of NPs in desired locations over large areas with high precision and high levels of integration. The difficulty of this assembly is due to the low efficiency of small features over large areas in lithography techniques or the inevitable structural defects that occur during the assembly process. The combination of self-assembly strategies with existing nanofabrication techniques could potentially provide effective and distinctive solutions for fabricating NPs with precise position control and high resolution. Furthermore, the synergistic combination of spatially mediated interactions between nanoparticles and prestructures on surfaces may play

  9. Multivalent Protein Assembly Using Monovalent Self-Assembling Building Blocks

    Directory of Open Access Journals (Sweden)

    Katja Petkau-Milroy

    2013-10-01

    Full Text Available Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard to streptavidin. Next to tetravalent streptavidin, monovalent streptavidin was used to study the protein assembly along the supramolecular polymer in detail without the interference of cross-linking. Upon self-assembly of the monovalent biotinylated discotics, multivalent proteins can be assembled along the supramolecular polymer. The concentration of discotics, which influences the length of the final polymers at the same time dictates the amount of assembled proteins.

  10. Failure of granular assemblies

    OpenAIRE

    Welker, Philipp

    2011-01-01

    This work investigates granular assemblies subjected to increasing external forces in the quasi-static limit. In this limit, the system’s evolution depends on static properties of the system, but is independent of the particles’ inertia. At the failure, which occurs at a certain value of the external forces, the particles’ motions increase quickly. In this thesis, the properties of granular systems during the weakening process and at the failure are investigated with the Discrete Element Meth...

  11. [Biologics in SLE].

    Science.gov (United States)

    Karonitsch, Thomas; Aringer, Martin

    2015-01-01

    Biologics have become indispensable in the last decade in the treatment of the more common rheumatic diseases. For treating systemic lupus erythematodes (SLE), B-cell depletion, albeit off-label, has been a well-accepted strategy in severe and refractory disease. Unexpectedly, however, the results of the first randomized controlled rituximab trials in SLE were negative. New trials with improved study protocols are ongoing, which should resolve this issue. In 2012, with the approval of belimumab, SLE finally entered the era of approved biological therapies. The anti-Blys/BAFF antibody belimumab showed prevention of SLE flares, glucocorticoid sparing, and significant improvement in the quality of life of SLE patients, in part by drastically reducing immune complex mediated fatigue. Positive reports on further targeting approaches give hope that additional biological agents will be available for SLE therapy soon.

  12. Biomolecular decision-making process for self assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Osbourn, Gordon Cecil

    2005-01-01

    The brain is often identified with decision-making processes in the biological world. In fact, single cells, single macromolecules (proteins) and populations of molecules also make simple decisions. These decision processes are essential to survival and to the biological self-assembly and self-repair processes that we seek to emulate. How do these tiny systems make effective decisions? How do they make decisions in concert with a cooperative network of other molecules or cells? How can we emulate the decision-making behaviors of small-scale biological systems to program and self-assemble microsystems? This LDRD supported research to answer these questions. Our work included modeling and simulation of protein populations to help us understand, mimic, and categorize molecular decision-making mechanisms that nonequilibrium systems can exhibit. This work is an early step towards mimicking such nanoscale and microscale biomolecular decision-making processes in inorganic systems.

  13. Cooperativity governs the size and structure of biological interfaces.

    Science.gov (United States)

    Qin, Zhao; Buehler, Markus J

    2012-11-15

    Interfaces, defined as the surface of interactions between two parts of a system at a discontinuity, are very widely found in nature. While it is known that the specific structure of an interface plays an important role in defining its properties, it is less clear whether or not there exist universal scaling laws that govern the structural evolution of a very broad range of natural interfaces. Here we show that cooperativity of interacting elements, leading to great strength at low material use, is a key concept that governs the structural evolution of many natural interfaces. We demonstrate this concept for the cases of β-sheet proteins in spider silk, gecko feet, legs of caterpillars, and self-assembling of penguins into huddles, which range in scales from the submolecular to the macroscopic level. A general model is proposed that explains the size and structure of biological interfaces from a fundamental point of view.

  14. Fixture Variation Diagnosis of Compliant Assembly Using Sensitivity Matrix

    Institute of Scientific and Technical Information of China (English)

    YU Kui-gang; JIN Sun; LAI Xin-min

    2009-01-01

    An automotive body is composed of compliant sheet metal parts. Fast and exactly diagnosing variation sources is very important when assembly variations happen. This paper proposes a diagnosis method of multi fixture variations based on the variation model of compliant sheet metal assembly. The assembly variation model is obtained by using the method of influence coefficients (MIC) and considering the manufacturing variations of compliant parts and multi fixture variations. The measurement point variations induced by part manufacturing variations are firstly removed from the measurement data. The variation patterns of multi fixture variations are constructed by column vectors of fixture variation sensitivity matrix. This method is proved to be feasible for exactly diagnosing the fixture variations and has higher diagnosis efficiency than designated component analysis (DCA).

  15. Biological preconcentrator

    Science.gov (United States)

    Manginell, Ronald P.; Bunker, Bruce C.; Huber, Dale L.

    2008-09-09

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

  16. Engineering Cellular Photocomposite Materials Using Convective Assembly

    Directory of Open Access Journals (Sweden)

    Orlin D. Velev

    2013-05-01

    Full Text Available Fabricating industrial-scale photoreactive composite materials containing living cells, requires a deposition strategy that unifies colloid science and cell biology. Convective assembly can rapidly deposit suspended particles, including whole cells and waterborne latex polymer particles into thin (<10 µm thick, organized films with engineered adhesion, composition, thickness, and particle packing. These highly ordered composites can stabilize the diverse functions of photosynthetic cells for use as biophotoabsorbers, as artificial leaves for hydrogen or oxygen evolution, carbon dioxide assimilation, and add self-cleaning capabilities for releasing or digesting surface contaminants. This paper reviews the non-biological convective assembly literature, with an emphasis on how the method can be modified to deposit living cells starting from a batch process to its current state as a continuous process capable of fabricating larger multi-layer biocomposite coatings from diverse particle suspensions. Further development of this method will help solve the challenges of engineering multi-layered cellular photocomposite materials with high reactivity, stability, and robustness by clarifying how process, substrate, and particle parameters affect coating microstructure. We also describe how these methods can be used to selectively immobilize photosynthetic cells to create biomimetic leaves and compare these biocomposite coatings to other cellular encapsulation systems.

  17. Ultra-Precise Assembly of Micro-Electromechanical Systems (MEMS) Components

    Energy Technology Data Exchange (ETDEWEB)

    Feddema, J.T.; Simon, R.; Polosky, M.; Christenson, T.

    1999-04-01

    This report summarizes a three year effort to develop an automated microassembly workcell for the assembly of LIGA (Lithography Galvonoforming Abforming) parts. Over the last several years, Sandia has developed processes for producing surface machined silicon and LIGA parts for use in weapons surety devices. Some of these parts have outside dimensions as small as 100 micron, and most all have submicron tolerances. Parts this small and precise are extremely difficult to assembly by hand. Therefore, in this project, we investigated the technologies required to develop a robotic workcell to assembly these parts. In particular, we concentrated on micro-grippers, visual servoing, micro-assembly planning, and parallel assembly. Three different micro-grippers were tested: a pneumatic probe, a thermally actuated polysilicon tweezer, and a LIGA fabricated tweezer. Visual servoing was used to accuracy position two parts relative to one another. Fourier optics methods were used to generate synthetic microscope images from CAD drawings. These synthetic images are used off-line to test image processing routines under varying magnifications and depths of field. They also provide reference image features which are used to visually servo the part to the desired position. We also investigated a new aspect of fine motion planning for the micro-domain. As parts approach 1-10 {micro}m or less in outside dimensions, interactive forces such as van der Waals and electrostatic forces become major factors which greatly change the assembly sequence and path plans. We developed the mathematics required to determine the goal regions for pick up, holding, and release of a micro-sphere being handled by a rectangular tool. Finally, we implemented and tested the ability to assemble an array of LIGA parts attached to two 3 inch diameter wafers. In this way, hundreds of parts can be assembled in parallel rather than assembling each part individually.

  18. Finishing of the cold mass assembly

    CERN Multimedia

    Patrice Loïez

    2001-01-01

    Photo 1 Technicians are putting in order the instrumentation wires. The prototype magnets were equipped with numerous sensors to monitor key parameters during the performance tests at cold conditions. Photo 2 The cold mass assembly is resting on special supports in order to allow the finishing operations. Technicians are putting in order the instrumentation wires. The prototype magnets were equipped with numerous sensors to monitor key parameters during the performance tests at cold conditions. Photo 3 View of the lyre-side end of the active part assembly. The extremity of the shrinking cylinder has been bevelled in view of welding the end cover. Photo 4 General view of the finishing station showing the special supporting structures (blue and yellow structures) needed for the geometric measurements and for the alignment operations. One can also see the light building surrounding the finishing station, which purpose is to isolate the laser measuring machines from disturbances. Photo 5 The extremity of the shri...

  19. Milli-Biology

    Science.gov (United States)

    2011-10-30

    inefficient at low RPM because power is wasted as heat in the coils, requiring gearing at low RPM, and power is required to maintain static position...soldering to join metal parts, epoxy to join the heat -sensitive permanent magnets, and screws to reversibly fasten subassemblies that might require...aerospace, and heliostat pointing for solar power. These are now transitioning to commercial development. The milli-biology workflow for coded

  20. 9 CFR 114.4 - Identification of biological products.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Identification of biological products... REQUIREMENTS FOR BIOLOGICAL PRODUCTS § 114.4 Identification of biological products. Suitable tags or labels of... biological products, all component parts to be combined to form a biological product, all......

  1. Progress of EMBarrel assembly

    CERN Multimedia

    Chalifour, M

    2002-01-01

    The assembly of the sixteen "M" modules into a vertical axis cylinder has been achieved last Friday, completing the first wheel of the Electromagnetic Barrel Calorimeter (see picture). With this, an important milestone in the construction of the ATLAS detector has been reached. Future steps are the rotation of the cylinder axis into horizontal position, in order to integrate the presamplers and heat exchangers by the end of October. The transportation of the wheel and its insertion into the cryostat is the next major milestone, and is planned for the beginning of 2003. The construction of the modules (the so-called "P" modules) of the second wheel is ongoing at Saclay, Annecy and CERN, and will be completed in the coming months. The assembly of the second wheel should start at CERN in February, and its insertion in the cryostat is scheduled for June 2003. This achievement is the result of a successful collaboration of all institutes involved in the construction of the EM Barrel, namely Annecy, Saclay and CE...

  2. Microchannel heat sink assembly

    Science.gov (United States)

    Bonde, Wayne L.; Contolini, Robert J.

    1992-01-01

    The present invention provides a microchannel heat sink with a thermal range from cryogenic temperatures to several hundred degrees centigrade. The heat sink can be used with a variety of fluids, such as cryogenic or corrosive fluids, and can be operated at a high pressure. The heat sink comprises a microchannel layer preferably formed of silicon, and a manifold layer preferably formed of glass. The manifold layer comprises an inlet groove and outlet groove which define an inlet manifold and an outlet manifold. The inlet manifold delivers coolant to the inlet section of the microchannels, and the outlet manifold receives coolant from the outlet section of the microchannels. In one embodiment, the manifold layer comprises an inlet hole extending through the manifold layer to the inlet manifold, and an outlet hole extending through the manifold layer to the outlet manifold. Coolant is supplied to the heat sink through a conduit assembly connected to the heat sink. A resilient seal, such as a gasket or an O-ring, is disposed between the conduit and the hole in the heat sink in order to provide a watetight seal. In other embodiments, the conduit assembly may comprise a metal tube which is connected to the heat sink by a soft solder. In still other embodiments, the heat sink may comprise inlet and outlet nipples. The present invention has application in supercomputers, integrated circuits and other electronic devices, and is suitable for cooling materials to superconducting temperatures.

  3. ULTRASONIC ASSEMBLY [REVIEW

    Directory of Open Access Journals (Sweden)

    PORAV Viorica

    2015-05-01

    Full Text Available The paper exposes the possibility of machine producesers to optimize the costs of clothes assembling. Ultrasonic systems being frequently utilized have many advantages on semi products of synthetic textile and technical textile. First of all, sewing – cutting process can be accomplished under high speeds and rate of losses can be minimized. Cutting seal applications are frequently used for underwear and sportswear. Slicing and unit cutting machines, as well as portable sealing machines are available for labeling sector. Products such as bag, pocket and cover can be sewed in a seamless manner for promotion purposes. All objects in terms of accessories are obtained in same standard. Our quilting machines are preferred in worldwide due to its threadless, high quality sealing. An alternative to the classic sewing assembly, with thread and needles is ultrasonic seaming. In ultrasonic welding, there are no connective bolts, nails, soldering materials, or adhesives necessary to bind the materials together. Ultrasonic is defined as acoustic frequencies above the range audible to the human ear. Ultrasonic frequencies are administered to the fabric from the sonotrode of bonding machine. The high frequency and powerful energy produced, when is release in one special environment, the ultrasound heating this environment. The ability to ultrasonic weld textiles and films depend on their thermoplastic contents and the desired end results. The paper defines the weld ability of more common textiles and films. The welding refers to all types of bonding and sealing, as in point bonding of fabric, or continuous sealing of film.

  4. ANNUAL GENERAL ASSEMBLY

    CERN Multimedia

    2001-01-01

    All members and beneficiaries of the Pension Fund are invited to attend the Annual General Asssembly to be held in the CERN Auditorium on Wednesday 3 October 2001 at 14.30 hrs The Agenda comprises:   Opening Remarks (P. Levaux) Some aspects of risk in a pension fund (C. Cuénoud) Annual Report 2000: Presentation and results (C. Cuénoud) Copies of the Report are available from divisional secretariats. Results of the actuarial reviews (G. Maurin) Questions from members and beneficiaries Persons wishing to ask questions are encouraged to submit them, where possible, in writing in advance, addressed to Mr C. Cuénoud, Administrator of the Fund. Conclusions (P. Levaux) As usual, participants are invited to drinks after the assembly. NB The minutes of the 2000 General Assembly are available from the Administration of the Fund (tel. + 41 22 767 91 94; e-mail Graziella.Praire@cern.ch) The English version will be published next week.

  5. 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.

  6. Artificial metalloenzymes constructed from hierarchically-assembled proteins.

    Science.gov (United States)

    Ueno, Takafumi; Tabe, Hiroyasu; Tanaka, Yuya

    2013-08-01

    The design of artificial metalloenzymes has become an important topic in biological chemistry and inorganic chemistry due to the potential applications of artificial metalloenzymes in nanoscience and biotechnology. One of the general methods used to produce artificially metalloenzymes involves the encapsulation of non-natural metal cofactors within protein scaffolds. This method has been used in the construction of small artificial metalloproteins with high activity and selectivity. However, the important roles of protein assemblies have not yet been systematically investigated in this field, even though natural enzymatic systems employ protein assemblies as molecular scaffolds for elaborate enzymatic reactions. In recent years, the above-mentioned general strategy has been applied to functionalize protein assemblies such as protein cages and protein crystals. These assembled structures form confined interior environments, which can be used to accommodate metal complex catalysts and to prepare metal nanoparticles. The development of artificial metalloenzymes with hierarchically-assembled proteins would enable us to provide powerful tools for industrial and biological applications. In this Focus Review, we discuss the most significant recent research in this field as well as future directions.

  7. Selecting Operations for Assembler Encoding

    Directory of Open Access Journals (Sweden)

    Tomasz Praczyk

    2010-04-01

    Full Text Available Assembler Encoding is a neuro-evolutionary method in which a neural network is represented in the form of a simple program called Assembler Encoding Program. The task of the program is to create the so-called Network Definition Matrix which maintains all the information necessary to construct the network. To generate Assembler Encoding Programs and the subsequent neural networks evolutionary techniques are used.
    The performance of Assembler Encoding strongly depends on operations used in Assembler Encoding Programs. To select the most effective operations, experiments in the optimization and the predator-prey problem were carried out. In the experiments, Assembler Encoding Programs equipped with different types of operations were tested. The results of the tests are presented at the end of the paper.

  8. DHS Internship Summary-Crystal Assembly at Different Length Scales

    Energy Technology Data Exchange (ETDEWEB)

    Mishchenko, L

    2009-08-06

    I was part of a project in which in situ atomic force microscopy (AFM) was used to monitor growth and dissolution of atomic and colloidal crystals. At both length scales, the chemical environment of the system greatly altered crystal growth and dissolution. Calcium phosphate was used as a model system for atomic crystals. A dissolution-reprecipitation reaction was observed in this first system, involving the conversion of brushite (DCPD) to octacalcium phosphate (OCP). In the second system, polymeric colloidal crystals were dissolved in an ionic solvent, revealing the underlying structure of the crystal. The dissolved crystal was then regrown through an evaporative step method. Recently, we have also found that colloids can be reversibly deposited in situ onto an ITO (indium tin oxide) substrate via an electrochemistry setup. The overall goal of this project was to develop an understanding of the mechanisms that control crystallization and order, so that these might be controlled during material synthesis. Controlled assembly of materials over a range of length scales from molecules to nanoparticles to colloids is critical for designing new materials. In particular, developing materials for sensor applications with tailorable properties and long range order is important. In this work, we examine two of these length scales: small molecule crystallization of calcium phosphate (whose crystal phases include DCPD, OCP, and HAP) and colloidal crystallization of Poly(methyl methacrylate) beads. Atomic Force Microscopy is ideal for this line of work because it allows for the possibility of observing non-conducting samples in fluid during growth with high resolution ({approx} 10 nm). In fact, during atomic crystal growth one can observe changes in atomic steps, and with colloidal crystals, one can monitor the individual building blocks of the crystal. Colloids and atoms crystallize under the influence of different forces acting at different length scales as seen in Table 1

  9. Biology Education Research: Lessons and Future Directions

    Science.gov (United States)

    Singer, Susan R.; Nielsen, Natalie R.; Schweingruber, Heidi A.

    2013-01-01

    Biologists have long been concerned about the quality of undergraduate biology education. Over time, however, biology faculty members have begun to study increasingly sophisticated questions about teaching and learning in the discipline. These scholars, often called biology education researchers, are part of a growing field of inquiry called…

  10. 9 CFR 311.39 - Biological residues.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Biological residues. 311.39 Section... Biological residues. Carcasses, organs, or other parts of carcasses of livestock shall be condemned if it is determined that they are adulterated because of the presence of any biological residues....

  11. Biology-Derived Algorithms in Engineering Optimization

    CERN Document Server

    Yang, Xin-She

    2010-01-01

    Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural evolution and biological activities, and these biologically inspired computations include genetic algorithms, neural networks, cellular automata, and other algorithms.

  12. Coded nanoscale self-assembly

    Indian Academy of Sciences (India)

    Prathyush Samineni; Debabrata Goswami

    2008-12-01

    We demonstrate coded self-assembly in nanostructures using the code seeded at the component level through computer simulations. Defects or cavities occur in all natural assembly processes including crystallization and our simulations capture this essential aspect under surface minimization constraints for self-assembly. Our bottom-up approach to nanostructures would provide a new dimension towards nanofabrication and better understanding of defects and crystallization process.

  13. Next-generation transcriptome assembly

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey A.; Wang, Zhong

    2011-09-01

    Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.

  14. Rocket Assembly and Checkout Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Integrates, tests, and calibrates scientific instruments flown on sounding rocket payloads. The scientific instruments are assembled on an optical bench;...

  15. Moisture Research - Optimizing Wall Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Arena, Lois [Consortium for Advanced Residential Buildings (CARB), Norwalk, CT (United States); Mantha, Pallavi [Consortium for Advanced Residential Buildings (CARB), Norwalk, CT (United States)

    2013-05-01

    In this project, the Consortium for Advanced Residential Buildings (CARB) team evaluated several different configurations of wall assemblies to determine the accuracy of moisture modeling and make recommendations to ensure durable, efficient assemblies. WUFI and THERM were used to model the hygrothermal and heat transfer characteristics of these walls. Wall assemblies evaluated included code minimum walls using spray foam insulation and fiberglass batts, high R-value walls at least 12 in. thick (R-40 and R-60 assemblies), and brick walls with interior insulation.

  16. Multi-position photovoltaic assembly

    Science.gov (United States)

    Dinwoodie, Thomas L.

    2003-03-18

    The invention is directed to a PV assembly, for use on a support surface, comprising a base, a PV module, a multi-position module support assembly, securing the module to the base at shipping and inclined-use angles, a deflector, a multi-position deflector support securing the deflector to the base at deflector shipping and deflector inclined-use angles, the module and deflector having opposed edges defining a gap therebetween. The invention permits transport of the PV assemblies in a relatively compact form, thus lowering shipping costs, while facilitating installation of the PV assemblies with the PV module at the proper inclination.

  17. Biology Notes.

    Science.gov (United States)

    School Science Review, 1981

    1981-01-01

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

  18. (Biological dosimetry)

    Energy Technology Data Exchange (ETDEWEB)

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  19. Marine Biology

    Science.gov (United States)

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

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

  20. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

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

  1. Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. Part 7: structure-activity studies of bicyclic 2-pyridone-containing peptidomimetics.

    Science.gov (United States)

    Dragovich, Peter S; Prins, Thomas J; Zhou, Ru; Johnson, Theodore O; Brown, Edward L; Maldonado, Fausto C; Fuhrman, Shella A; Zalman, Leora S; Patick, Amy K; Matthews, David A; Hou, Xinjun; Meador, James W; Ferre, Rose Ann; Worland, Stephen T

    2002-03-11

    The structure-based design, chemical synthesis, and biological evaluation of bicyclic 2-pyridone-containing human rhinovirus (HRV) 3C protease (3CP) inhibitors are described. An optimized compound is shown to exhibit antiviral activity when tested against a variety of HRV serotypes (EC(50)'s ranging from 0.037 to 0.162 microM).

  2. Spanish evidence-based guidelines on the treatment of psoriasis with biologic agents, 2013. Part 1: on efficacy and choice of treatment. Spanish Psoriasis Group of the Spanish Academy of Dermatology and Venereology.

    Science.gov (United States)

    Puig, L; Carrascosa, J M; Carretero, G; de la Cueva, P; Lafuente-Urrez, R F; Belinchón, I; Sánchez-Regaña, M; García-Bustínduy, M; Ribera, M; Alsina, M; Ferrándiz, C; Fonseca, E; García-Patos, V; Herrera, E; López-Estebaranz, J L; Marrón, S E; Moreno, J C; Notario, J; Rivera, R; Rodriguez-Cerdeira, C; Romero, A; Ruiz-Villaverde, R; Taberner, R; Vidal, D

    2013-10-01

    Biologic therapy is a well-established strategy for managing moderate and severe psoriasis. Nevertheless, the high cost of such therapy, the relatively short span of clinical experience with biologics, and the abundance of literature now available on these agents have made evidence-based and consensus-based clinical guidelines necessary. The ideal goal of psoriasis treatment is to achieve complete or nearly complete clearing of lesions and to maintain it over time. Failing that ideal, the goal would be to reduce involvement to localized lesions that can be controlled with topical therapy. Although current evidence allows us to directly or indirectly compare the efficacy or risk of primary or secondary failure of available biologics based on objective outcomes, clinical trial findings cannot be directly translated to routine practice. As a result, the prescribing physician must tailor the treatment regimen to the individual patient. This update of the clinical practice guidelines issued by the Spanish Academy of Dermatology and Venereology (AEDV) on biologic therapy for psoriasis incorporates information from the most recent publications on this topic.

  3. Implementation of a robotic flexible assembly system

    Science.gov (United States)

    Benton, Ronald C.

    1987-01-01

    As part of the Intelligent Task Automation program, a team developed enabling technologies for programmable, sensory controlled manipulation in unstructured environments. These technologies include 2-D/3-D vision sensing and understanding, force sensing and high speed force control, 2.5-D vision alignment and control, and multiple processor architectures. The subsequent design of a flexible, programmable, sensor controlled robotic assembly system for small electromechanical devices is described using these technologies and ongoing implementation and integration efforts. Using vision, the system picks parts dumped randomly in a tray. Using vision and force control, it performs high speed part mating, in-process monitoring/verification of expected results and autonomous recovery from some errors. It is programmed off line with semiautomatic action planning.

  4. A Practical Approach for Integrating Automatically Designed Fixtures with Automated Assembly Planning

    Energy Technology Data Exchange (ETDEWEB)

    Calton, Terri L.; Peters, Ralph R.

    1999-07-20

    This paper presents a practical approach for integrating automatically designed fixtures with automated assembly planning. Product assembly problems vary widely; here the focus is on assemblies that are characterized by a single base part to which a number of smaller parts and subassemblies are attached. This method starts with three-dimension at CAD descriptions of an assembly whose assembly tasks require a fixture to hold the base part. It then combines algorithms that automatically design assembly pallets to hold the base part with algorithms that automatically generate assembly sequences. The designed fixtures rigidly constrain and locate the part, obey task constraints, are robust to part shape variations, are easy to load, and are economical to produce. The algorithm is guaranteed to find the global optimum solution that satisfies these and other pragmatic conditions. The assembly planner consists of four main elements: a user interface, a constraint system, a search engine, and an animation module. The planner expresses all constraints at a sequencing level, specifying orders and conditions on part mating operations in a number of ways. Fast replanning enables an interactive plan-view-constrain-replan cycle that aids in constrain discovery and documentation. The combined algorithms guarantee that the fixture will hold the base part without interfering with any of the assembly operations. This paper presents an overview of the planners, the integration approach, and the results of the integrated algorithms applied to several practical manufacturing problems. For these problems initial high-quality fixture designs and assembly sequences are generated in a matter of minutes with global optimum solutions identified in just over an hour.

  5. Biomolecular Assembly of Gold Nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Micheel, Christine Marya [Univ. of California, Berkeley, CA (United States)

    2005-05-20

    Over the past ten years, methods have been developed to construct discrete nanostructures using nanocrystals and biomolecules. While these frequently consist of gold nanocrystals and DNA, semiconductor nanocrystals as well as antibodies and enzymes have also been used. One example of discrete nanostructures is dimers of gold nanocrystals linked together with complementary DNA. This type of nanostructure is also known as a nanocrystal molecule. Discrete nanostructures of this kind have a number of potential applications, from highly parallel self-assembly of electronics components and rapid read-out of DNA computations to biological imaging and a variety of bioassays. My research focused in three main areas. The first area, the refinement of electrophoresis as a purification and characterization method, included application of agarose gel electrophoresis to the purification of discrete gold nanocrystal/DNA conjugates and nanocrystal molecules, as well as development of a more detailed understanding of the hydrodynamic behavior of these materials in gels. The second area, the development of methods for quantitative analysis of transmission electron microscope data, used computer programs written to find pair correlations as well as higher order correlations. With these programs, it is possible to reliably locate and measure nanocrystal molecules in TEM images. The final area of research explored the use of DNA ligase in the formation of nanocrystal molecules. Synthesis of dimers of gold particles linked with a single strand of DNA possible through the use of DNA ligase opens the possibility for amplification of nanostructures in a manner similar to polymerase chain reaction. These three areas are discussed in the context of the work in the Alivisatos group, as well as the field as a whole.

  6. Self-assembly of flagellin on Au(111) surfaces.

    Science.gov (United States)

    González Orive, Alejandro; Pissinis, Diego E; Diaz, Carolina; Miñán, Alejandro; Benítez, Guillermo A; Rubert, Aldo; Daza Millone, Antonieta; Rumbo, Martin; Hernández Creus, Alberto; Salvarezza, Roberto C; Schilardi, Patricia L

    2014-11-01

    The adsorption of flagellin monomers from Pseudomonas fluorescens on Au(111) has been studied by Atomic Force Microscopy (AFM), Scanning Tunneling Microscopy (STM), X-ray Photoelectron Spectroscopy (XPS), Surface Plasmon Resonance (SPR), and electrochemical techniques. Results show that flagellin monomers spontaneously self-assemble forming a monolayer thick protein film bounded to the Au surface by the more hydrophobic subunit and exposed to the environment the hydrophilic subunit. The films are conductive and allow allocation of electrochemically active cytochrome C. The self-assembled films could be used as biological platforms to build 3D complex molecular structures on planar metal surfaces and to functionalize metal nanoparticles.

  7. Hyper bio assembler for 3D cellular systems

    CERN Document Server

    Arai, Fumihito; Yamato, Masayuki

    2015-01-01

    Hyper Bio Assembler for Cellular Systems is the first book to present a new methodology for measuring and separating target cells at high speed and constructing 3D cellular systems in vitro. This book represents a valuable resource for biologists, biophysicists and robotic engineers, as well as researchers interested in this new frontier area, offering a better understanding of the measurement, separation, assembly, analysis and synthesis of complex biological tissue, and of the medical applications of these technologies. This book is the outcome of the new academic fields of the Ministry of Education, Culture, Sports, Science and Technology’s Grant-in-Aid for Scientific Research in Japan.

  8. Directional Self-assembly in Archaerhodopsin-Reconstituted Phospholipid Liposomes

    Institute of Scientific and Technical Information of China (English)

    吴佳; 黄力; 刘坚; 明明; 李庆国; 丁建东

    2005-01-01

    This paper reports, for the first time, that Archaerhodopsin-4 (AR4) could be reconstituted into phospholipid liposomes by self-assembly. AR4 is a new membrane protein isolated from halobacteria H.sp. xz515 in a salt lake of Tibet, China. This is a bacteriorhodopsin (bR) like protein, function as a light-driven proton pump. Experimental measurements verified that similar to bR, AR not only remains its biological activity in pmteoliposome, but also keeps a preferred orientation in self-assembly.

  9. Multilayer Thin Films Sequential Assembly of Nanocomposite Materials

    CERN Document Server

    Decher, Gero

    2012-01-01

    This second, comprehensive edition of the pioneering book in this field has been completely revised and extended, now stretching to two volumes. The result is a comprehensive summary of layer-by-layer assembled, truly hybrid nanomaterials and thin films, covering organic, inorganic, colloidal, macromolecular and biological components, plus the assembly of nanoscale films derived from them on surfaces. Praise for the first edition: "... highly recommended to anyone interested in the field... and to scientists and researchers active in materials development..." –Polymer News With contri

  10. Cilium assembly and disassembly

    Science.gov (United States)

    2016-01-01

    The primary cilium is an antenna-like, immotile organelle present on most types of mammalian cells, which interprets extracellular signals that regulate growth and development. Although once considered a vestigial organelle, the primary cilium is now the focus of considerable interest. We now know that ciliary defects lead to a panoply of human diseases, termed ciliopathies, and the loss of this organelle may be an early signature event during oncogenic transformation. Ciliopathies include numerous seemingly unrelated developmental syndromes, with involvement of the retina, kidney, liver, pancreas, skeletal system and brain. Recent studies have begun to clarify the key mechanisms that link cilium assembly and disassembly to the cell cycle, and suggest new possibilities for therapeutic intervention. PMID:27350441

  11. Photovoltaic cell assembly

    Science.gov (United States)

    Beavis, Leonard C.; Panitz, Janda K. G.; Sharp, Donald J.

    1990-01-01

    A photovoltaic assembly for converting high intensity solar radiation into lectrical energy in which a solar cell is separated from a heat sink by a thin layer of a composite material which has excellent dielectric properties and good thermal conductivity. This composite material is a thin film of porous Al.sub.2 O.sub.3 in which the pores have been substantially filled with an electrophoretically-deposited layer of a styrene-acrylate resin. This composite provides electrical breakdown strengths greater than that of a layer consisting essentially of Al.sub.2 O.sub.3 and has a higher thermal conductivity than a layer of styrene-acrylate alone.

  12. Fluid cooled electrical assembly

    Science.gov (United States)

    Rinehart, Lawrence E.; Romero, Guillermo L.

    2007-02-06

    A heat producing, fluid cooled assembly that includes a housing made of liquid-impermeable material, which defines a fluid inlet and a fluid outlet and an opening. Also included is an electrical package having a set of semiconductor electrical devices supported on a substrate and the second major surface is a heat sink adapted to express heat generated from the electrical apparatus and wherein the second major surface defines a rim that is fit to the opening. Further, the housing is constructed so that as fluid travels from the fluid inlet to the fluid outlet it is constrained to flow past the opening thereby placing the fluid in contact with the heat sink.

  13. Developmental self-assembly of a DNA tetrahedron.

    Science.gov (United States)

    Sadowski, John P; Calvert, Colby R; Zhang, David Yu; Pierce, Niles A; Yin, Peng

    2014-04-22

    Kinetically controlled isothermal growth is fundamental to biological development, yet it remains challenging to rationally design molecular systems that self-assemble isothermally into complex geometries via prescribed assembly and disassembly pathways. By exploiting the programmable chemistry of base pairing, sophisticated spatial and temporal control have been demonstrated in DNA self-assembly, but largely as separate pursuits. By integrating temporal with spatial control, here we demonstrate the "developmental" self-assembly of a DNA tetrahedron, where a prescriptive molecular program orchestrates the kinetic pathways by which DNA molecules isothermally self-assemble into a well-defined three-dimensional wireframe geometry. In this reaction, nine DNA reactants initially coexist metastably, but upon catalysis by a DNA initiator molecule, navigate 24 individually characterizable intermediate states via prescribed assembly pathways, organized both in series and in parallel, to arrive at the tetrahedral final product. In contrast to previous work on dynamic DNA nanotechnology, this developmental program coordinates growth of ringed substructures into a three-dimensional wireframe superstructure, taking a step toward the goal of kinetically controlled isothermal growth of complex three-dimensional geometries.

  14. Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments.

    Science.gov (United States)

    Lee, Kyung-Ho; Kim, Dong-Myung

    2013-11-01

    Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms.

  15. A Versatile Microfluidic Device for Automating Synthetic Biology.

    Science.gov (United States)

    Shih, Steve C C; Goyal, Garima; Kim, Peter W; Koutsoubelis, Nicolas; Keasling, Jay D; Adams, Paul D; Hillson, Nathan J; Singh, Anup K

    2015-10-16

    New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.

  16. Preliminary physical, nutrients, biological, meteorological, and other data from bottle casts, CTD casts, ADCP casts, moored current meters, and meteorological sensors from the GYRE from as part of the Texas-Louisiana Shelf Circulation and Transport Processes Study (LATEX PART A) from 04 November 1992 to 05 August 1994 (NODC Accession 9500054)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Preliminary physical, nutrients, biological, meteorological, and other data from bottle casts, CTD casts, ADCP casts, and meteorological sensors from the GYRE from...

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

    DEFF Research Database (Denmark)

    Borodina, Irina; Li, Mingji

    2015-01-01

    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...... 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.......-of-concept chemicals have been made in yeast, only a very small fraction of those has reached commercial-scale production so far. The limiting factor is the high research cost associated with the development of a robust cell factory that can produce the desired chemical at high titer, rate, and yield. Synthetic...

  18. Improving Robotic Assembly of Planar High Energy Density Targets

    Science.gov (United States)

    Dudt, D.; Carlson, L.; Alexander, N.; Boehm, K.

    2016-10-01

    Increased quantities of planar assemblies for high energy density targets are needed with higher shot rates being implemented at facilities such as the National Ignition Facility and the Matter in Extreme Conditions station of the Linac Coherent Light Source. To meet this growing demand, robotics are used to reduce assembly time. This project studies how machine vision and force feedback systems can be used to improve the quantity and quality of planar target assemblies. Vision-guided robotics can identify and locate parts, reducing laborious manual loading of parts into precision pallets and associated teaching of locations. On-board automated inspection can measure part pickup offsets to correct part drop-off placement into target assemblies. Force feedback systems can detect pickup locations and apply consistent force to produce more uniform glue bond thickness, thus improving the performance of the targets. System designs and performance evaluations will be presented. Work supported in part by the US DOE under the Science Undergraduate Laboratory Internships Program (SULI) and ICF Target Fabrication DE-NA0001808.

  19. Quantum Effects in Biology

    Science.gov (United States)

    Mohseni, Masoud; Omar, Yasser; Engel, Gregory S.; Plenio, Martin B.

    2014-08-01

    List of contributors; Preface; Part I. Introduction: 1. Quantum biology: introduction Graham R. Fleming and Gregory D. Scholes; 2. Open quantum system approaches to biological systems Alireza Shabani, Masoud Mohseni, Seogjoo Jang, Akihito Ishizaki, Martin Plenio, Patrick Rebentrost, Alàn Aspuru-Guzik, Jianshu Cao, Seth Lloyd and Robert Silbey; 3. Generalized Förster resonance energy transfer Seogjoo Jang, Hoda Hossein-Nejad and Gregory D. Scholes; 4. Multidimensional electronic spectroscopy Tomáš Mančal; Part II. Quantum Effects in Bacterial Photosynthetic Energy Transfer: 5. Structure, function, and quantum dynamics of pigment protein complexes Ioan Kosztin and Klaus Schulten; 6. Direct observation of quantum coherence Gregory S. Engel; 7. Environment-assisted quantum transport Masoud Mohseni, Alàn Aspuru-Guzik, Patrick Rebentrost, Alireza Shabani, Seth Lloyd, Susana F. Huelga and Martin B. Plenio; Part III. Quantum Effects in Higher Organisms and Applications: 8. Excitation energy transfer in higher plants Elisabet Romero, Vladimir I. Novoderezhkin and Rienk van Grondelle; 9. Electron transfer in proteins Spiros S. Skourtis; 10. A chemical compass for bird navigation Ilia A. Solov'yov, Thorsten Ritz, Klaus Schulten and Peter J. Hore; 11. Quantum biology of retinal Klaus Schulten and Shigehiko Hayashi; 12. Quantum vibrational effects on sense of smell A. M. Stoneham, L. Turin, J. C. Brookes and A. P. Horsfield; 13. A perspective on possible manifestations of entanglement in biological systems Hans J. Briegel and Sandu Popescu; 14. Design and applications of bio-inspired quantum materials Mohan Sarovar, Dörthe M. Eisele and K. Birgitta Whaley; 15. Coherent excitons in carbon nanotubes Leonas Valkunas and Darius Abramavicius; Glossary; References; Index.

  20. Identification based on facial parts

    Directory of Open Access Journals (Sweden)

    Stevanov Zorica

    2007-01-01

    Full Text Available Two opposing views dominate face identification literature, one suggesting that the face is processed as a whole and another suggesting analysis based on parts. Our research tried to establish which of these two is the dominant strategy and our results fell in the direction of analysis based on parts. The faces were covered with a mask and the participants were uncovering different parts, one at the time, in an attempt to identify a person. Already at the level of a single facial feature, such as mouth or eye and top of the nose, some observers were capable to establish the identity of a familiar face. Identification is exceptionally successful when a small assembly of facial parts is visible, such as eye, eyebrow and the top of the nose. Some facial parts are not very informative on their own but do enhance recognition when given as a part of such an assembly. Novel finding here is importance of the top of the nose for the face identification. Additionally observers have a preference toward the left side of the face. Typically subjects view the elements in the following order: left eye, left eyebrow, right eye, lips, region between the eyes, right eyebrow, region between the eyebrows, left check, right cheek. When observers are not in a position to see eyes, eyebrows or top of the nose, they go for lips first and then region between the eyebrows, region between the eyes, left check, right cheek and finally chin.