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Sample records for biological part assembly

  1. Asmparts: assembly of biological model parts.

    PubMed

    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. Asmparts: assembly of biological model parts

    PubMed Central

    Rodrigo, Guillermo; Carrera, Javier

    2008-01-01

    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. PMID:19003441

  3. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts

    PubMed Central

    Yang, Kun; Stracquadanio, Giovanni; Luo, Jingchuan; Boeke, Jef D.; Bader, Joel S.

    2016-01-01

    Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: joel.bader@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26568632

  4. 2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts

    PubMed Central

    2013-01-01

    There is growing demand for robust DNA assembly strategies to quickly and accurately fabricate genetic circuits for synthetic biology. One application of this technology is reconstitution of multi-gene assemblies. Here, we integrate a new software tool chain with 2ab assembly and show that it is robust enough to generate 528 distinct composite parts with an error-free success rate of 96%. Finally, we discuss our findings in the context of its implications for biosafety and biosecurity. PMID:23305072

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

    SciTech Connect

    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.

  6. Unique nucleotide sequence (UNS)-guided assembly of repetitive DNA parts for synthetic biology applications

    PubMed Central

    Torella, Joseph P.; Lienert, Florian; Boehm, Christian R.; Chen, Jan-Hung; Way, Jeffrey C.; Silver, Pamela A.

    2016-01-01

    Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts and 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 that 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 days. If the DNA parts must be generated from scratch, an additional 2–5 days are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques. PMID:25101822

  7. CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology.

    PubMed

    Iverson, Sonya V; Haddock, Traci L; Beal, Jacob; Densmore, Douglas M

    2016-01-15

    Multipart and modular DNA part libraries and assembly standards have become common tools in synthetic biology since the publication of the Gibson and Golden Gate assembly methods, yet no multipart modular library exists for use in bacterial systems. Building upon the existing MoClo assembly framework, we have developed a publicly available collection of modular DNA parts and enhanced MoClo protocols to enable rapid one-pot, multipart assembly, combinatorial design, and expression tuning in Escherichia coli. The Cross-disciplinary Integration of Design Automation Research lab (CIDAR) MoClo Library is openly available and contains promoters, ribosomal binding sites, coding sequence, terminators, vectors, and a set of fluorescent control plasmids. Optimized protocols reduce reaction time and cost by >80% from that of previously published protocols. PMID:26479688

  8. Method of forming and assembly of parts

    DOEpatents

    Ripley, Edward B.

    2010-12-28

    A method of assembling two or more parts together that may be metal, ceramic, metal and ceramic parts, or parts that have different CTE. Individual parts are formed and sintered from particles that leave a network of interconnecting porosity in each sintered part. The separate parts are assembled together and then a fill material is infiltrated into the assembled, sintered parts using a method such as capillary action, gravity, and/or pressure. The assembly is then cured to yield a bonded and fully or near-fully dense part that has the desired physical and mechanical properties for the part's intended purpose. Structural strength may be added to the parts by the inclusion of fibrous materials.

  9. Magnetic self-assembly of small parts

    NASA Astrophysics Data System (ADS)

    Shetye, Sheetal B.

    Modern society's propensity for miniaturized end-user products is compelling electronic manufacturers to assemble and package different micro-scale, multi-technology components in more efficient and cost-effective manners. As the size of the components gets smaller, issues such as part sticking and alignment precision create challenges that slow the throughput of conventional robotic pick-n-place systems. As an alternative, various self-assembly approaches have been proposed to manipulate micro to millimeter scale components in a parallel fashion without human or robotic intervention. In this dissertation, magnetic self-assembly (MSA) is demonstrated as a highly efficient, completely parallel process for assembly of millimeter scale components. MSA is achieved by integrating permanent micromagnets onto component bonding surfaces using wafer-level microfabrication processes. Embedded bonded powder methods are used for fabrication of the magnets. The magnets are then magnetized using pulse magnetization methods, and the wafers are then singulated to form individual components. When the components are randomly mixed together, self-assembly occurs when the intermagnetic forces overcome the mixing forces. Analytical and finite element methods (FEM) are used to study the force interactions between the micromagnets. The multifunctional aspects of MSA are presented through demonstration of part-to-part and part-to-substrate assembly of 1 mm x 1mm x 0.5 mm silicon components. Part-to-part assembly is demonstrated by batch assembly of free-floating parts in a liquid environment with the assembly yield of different magnetic patterns varying from 88% to 90% in 20 s. Part-to-substrate assembly is demonstrated by assembling an ordered array onto a fixed substrate in a dry environment with the assembly yield varying from 86% to 99%. In both cases, diverse magnetic shapes/patterns are used to control the alignment and angular orientation of the components. A mathematical model is

  10. Directed Assembly of Biological Polymers

    NASA Astrophysics Data System (ADS)

    Miller, Aline

    2009-03-01

    The self-assembly of polypeptides into beta-sheet rich nanofibrils has attracted considerable attention in recent years to both understand amyloidgenesis and for their potential biomaterials applications. This self-assembly process is generic to all proteins where fibrillation is typically induced under harsh conditions of low pH and/or high temperature, which are of course not suitable for biomaterials applications. Here we will outline the method developed in our laboratory to create thermo-reversible fibrillar hydrogels from aqueous solutions of a series of proteins by adding a reductant. Proteins studied include beta-lactoglobulin, ovalbimum, lysozyme and bovine serum albimum; all contain an increasing number of disulfide bridges that are disrupted by the reductant. Such disruption destabilises the native state of the protein and this allows us to form transparent, self-supporting hydrogels under physiological conditions. The potential to control and manipulate the gel properties, including mechanical strength and structure (fibre diameter and mesh size of hydrogel) has been explored by varying the protein (consequently the number of disulfide bridges), protein concentration, reductant concentration and ionic strength of the matrix. Our results will be presented here and similarities and differences highlighted. Furthermore we will present both our 2- and 3-dimensional cell culture experiments that show the gel matrix promotes both fibroblast and chondrocyte cell spreading, attachment and proliferation; indicating our hydrogels gels are biocompatible and they can provide a viable support for different cell types.

  11. Indentured Parts List Maintenance and Part Assembly Capture Tool - IMPACT

    NASA Technical Reports Server (NTRS)

    Jain, Bobby; Morris, Jill; Sharpe, Kelly

    2004-01-01

    Johnson Space Center's (JSC's) indentured parts list (IPL) maintenance and parts assembly capture tool (IMPACT) is an easy-to-use graphical interface for viewing and maintaining the complex assembly hierarchies of large databases. IMPACT, already in use at JSC to support the International Space Station (ISS), queries, updates, modifies, and views data in IPL and associated resource data, functions that it can also perform, with modification, for any large commercial database. By enabling its users to efficiently view and manipulate IPL hierarchical data, IMPACT performs a function unlike that of any other tool. Through IMPACT, users will achieve results quickly, efficiently, and cost effectively.

  12. PaperClip: A Simple Method for Flexible Multi-Part DNA Assembly.

    PubMed

    Trubitsyna, Maryia; Liu, Chao-Kuo; Salinas, Alejandro; Elfick, Alistair; French, Christopher E

    2017-01-01

    Joining DNA sequences to create linear and circular constructs is a basic requirement in molecular biology. Here we describe PaperClip, a recently developed method, which enables assembly of multiple DNA sequences in one reaction in a combinatorial manner. In contrast to other homology-based multi-part assembly methods currently available, PaperClip allows assembly of a given set of parts in any order without requiring specific single-use oligonucleotides for each assembly order. PMID:27671936

  13. Shape Remodeling Assemblies in Biologically Inspired Materials

    NASA Astrophysics Data System (ADS)

    Safinya, Cyrus

    2013-03-01

    Much of our research is inspired by, and directed at, understanding the formation of novel structures (both relatively static and highly dynamic) with distinct shapes and morphologies observed in charged biological systems. The structures, in turn, often correlate to specific functions. For example, charged nanoscale tubules and rods and their assemblies are of interest in a range of applications, including as templates for hierarchical nanostructures, encapsulation systems, and biosensors. A series of studies will be described on charged biological assemblies exhibiting ``molecularly-triggered'' dynamical shape changes. In particular, we will focus on protein and lipid based nanotubule formation through small molecule stimuli-induced shape remodeling events. The systems include invertible protein nanotubes from two-state tubulin-protein building blocks and lipid nanotubes and nanorods from curvature stabilizing lipids (mimicking membrane curvature generating proteins). Funded by DOE-BES grant number DOE-DE-FG02-06ER46314 (protein and lipid assembly, lipid synthesis, structure-function) and NSF-DMR-1101900 (phase behavior).

  14. The biological microprocessor, or how to build a computer with biological parts.

    PubMed

    Moe-Behrens, Gerd Hg

    2013-01-01

    Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.

  15. The biological microprocessor, or how to build a computer with biological parts

    PubMed Central

    Moe-Behrens, Gerd HG

    2013-01-01

    Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system. PMID:24688733

  16. The Structural Biology of HIV Assembly

    PubMed Central

    Ganser-Pornillos, Barbie; Yeager, Mark; Sundquist, Wesley I.

    2009-01-01

    HIV assembly and replication proceed through formation of morphologically distinct immature and mature viral capsids that are organized by the Gag polyprotein (immature) and by the fully processed CA protein (mature). The Gag polyprotein is composed of three folded polypeptides (MA, CA, and NC) and three smaller peptides (SP1, SP2, and p6) that function together to coordinate membrane binding and Gag-Gag lattice interactions in immature virions. Following budding, HIV maturation is initiated by proteolytic processing of Gag, which induces conformational changes in the CA domain and results in assembly of the distinctive conical capsid. Retroviral capsids are organized following the principles of fullerene cones, and the hexagonal CA lattice is stabilized by three distinct interfaces. Recently identified inhibitors of viral maturation act by disrupting the final stage of Gag processing, or by inhibiting formation of a critical intermolecular CA-CA interface in the mature capsid. Following release into a new host cell, the capsid disassembles and host cell factors can potently restrict this stage of retroviral replication. Here, we review the structures of immature and mature HIV virions, focusing on recent studies that have defined the global organization of the immature Gag lattice, identified sites likely to undergo conformational changes during maturation, revealed the molecular structure of the mature capsid lattice, demonstrated that capsid architectures are conserved, identified the first capsid assembly inhibitors, and begun to uncover the remarkable biology of the mature capsid. PMID:18406133

  17. Liquid crystal assemblies in biologically inspired systems

    PubMed Central

    Safinya, Cyrus R.; Deek, Joanna; Beck, Roy; Jones, Jayna B.; Leal, Cecilia; Ewert, Kai K.; Li, Youli

    2013-01-01

    In this paper, which is part of a collection in honor of Noel Clark's remarkable career on liquid crystal and soft matter research, we present examples of biologically inspired systems, which form liquid crystal (LC) phases with their LC nature impacting biological function in cells or being important in biomedical applications. One area focuses on understanding network and bundle formation of cytoskeletal polyampholytes (filamentous-actin, microtubules, and neurofilaments). Here, we describe studies on neurofilaments (NFs), the intermediate filaments of neurons, which form open network nematic liquid crystal hydrogels in axons. Synchrotron small-angle-x-ray scattering studies of NF-protein dilution experiments and NF hydrogels subjected to osmotic stress show that neurofilament networks are stabilized by competing long-range repulsion and attractions mediated by the neurofilament's polyampholytic sidearms. The attractions are present both at very large interfilament spacings, in the weak sidearm-interpenetrating regime, and at smaller interfilament spacings, in the strong sidearm-interpenetrating regime. A second series of experiments will describe the structure and properties of cationic liposomes (CLs) complexed with nucleic acids (NAs). CL-NA complexes form liquid crystalline phases, which interact in a structure-dependent manner with cellular membranes enabling the design of complexes for efficient delivery of nucleic acid (DNA, RNA) in therapeutic applications. PMID:24558293

  18. Self-assembling hybrid diamond-biological quantum devices

    NASA Astrophysics Data System (ADS)

    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.

  19. Method of forming and assembly of metal and ceramic parts

    DOEpatents

    Ripley, Edward B

    2014-04-22

    A method of forming and assembling at least two parts together that may be metal, ceramic, or a combination of metal and ceramic parts. Such parts may have different CTE. Individual parts that are formed and sintered from particles leave a network of interconnecting porosity in each sintered part. The separate parts are assembled together and then a fill material is infiltrated into the assembled parts using a method such as capillary action, gravity, and/or pressure. The assembly is then cured to yield a bonded and fully or near-fully dense part that has the desired physical and mechanical properties for the part's intended purpose. Structural strength may be added to the parts by the inclusion of fibrous materials.

  20. Method of forming and assembly of metal parts and ceramic parts

    DOEpatents

    Ripley, Edward B.

    2011-11-22

    A method of forming and assembling at least two parts together that may be metal, ceramic, or a combination of metal and ceramic parts. Such parts may have different CTE. Individual parts that are formed and sintered from particles leave a network of interconnecting porosity in each sintered part. The separate parts are assembled together and then a fill material is infiltrated into the assembled parts using a method such as capillary action, gravity, and/or pressure. The assembly is then cured to yield a bonded and fully or near-fully dense part that has the desired physical and mechanical properties for the part's intended purpose. Structural strength may be added to the parts by the inclusion of fibrous materials.

  1. Rigidity analysis of protein biological assemblies and periodic crystal structures

    PubMed Central

    2013-01-01

    Background We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu. Results We provide two types of results: on biological assemblies and on crystals. We found that when only isolated subchains are considered, structural and functional information may be missed. Indeed, the rigidity of biological assemblies is sometimes dependent on the count and placement of hydrogen bonds and other interactions among the individual subchains of the biological unit. Similarly, the rigidity of small crystals may be affected by the interactions between atoms belonging to different unit cells. We have analyzed a dataset of approximately 300 proteins, from which we generated 982 crystals (some of which are biological assemblies). We identified two types of behaviors. (a) Some crystals and/or biological assemblies will aggregate into rigid bodies that span multiple unit cells/asymmetric units. Some of them create substantially larger rigid cluster in the crystal/biological assembly form, while in other cases, the aggregation has a smaller effect just at the interface between the units. (b) In other cases, the rigidity properties of the asymmetric units are retained, because the rigid bodies did not combine. We also identified two interesting cases where rigidity analysis may be correlated with the functional behavior of the protein. This type of information, identified here for the first time, depends critically on the ability to create crystals and biological assemblies

  2. In situ TEM of biological assemblies in liquid.

    PubMed

    Dukes, Madeline J; Gilmore, Brian L; Tanner, Justin R; McDonald, Sarah M; Kelly, Deborah F

    2013-12-30

    Researchers regularly use Transmission Electron Microscopes (TEMs) to examine biological entities and to assess new materials. Here, we describe an additional application for these instruments- viewing viral assemblies in a liquid environment. This exciting and novel method of visualizing biological structures utilizes a recently developed microfluidic-based specimen holder. Our video article demonstrates how to assemble and use a microfluidic holder to image liquid specimens within a TEM. In particular, we use simian rotavirus double-layered particles (DLPs) as our model system. We also describe steps to coat the surface of the liquid chamber with affinity biofilms that tether DLPs to the viewing window. This permits us to image assemblies in a manner that is suitable for 3D structure determination. Thus, we present a first glimpse of subviral particles in a native liquid environment.

  3. In situ TEM of Biological Assemblies in Liquid

    PubMed Central

    McDonald, Sarah M.; Kelly, Deborah F.

    2013-01-01

    Researchers regularly use Transmission Electron Microscopes (TEMs) to examine biological entities and to assess new materials. Here, we describe an additional application for these instruments- viewing viral assemblies in a liquid environment. This exciting and novel method of visualizing biological structures utilizes a recently developed microfluidic-based specimen holder. Our video article demonstrates how to assemble and use a microfluidic holder to image liquid specimens within a TEM. In particular, we use simian rotavirus double-layered particles (DLPs) as our model system. We also describe steps to coat the surface of the liquid chamber with affinity biofilms that tether DLPs to the viewing window. This permits us to image assemblies in a manner that is suitable for 3D structure determination. Thus, we present a first glimpse of subviral particles in a native liquid environment. PMID:24429390

  4. Precise Truss Assembly using Commodity Parts and Low Precision Welding

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

    We describe an Intelligent Precision Jigging Robot (IPJR), which allows high precision assembly of commodity parts with low-precision bonding. We present preliminary experiments in 2D that are motivated by the problem of assembling a space telescope optical bench on orbit using inexpensive, stock hardware and low-precision welding. An IPJR is a robot that acts as the precise "jigging", holding parts of a local 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 (in this case, 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. We report the challenges of designing the IPJR hardware and software, analyze the error in assembly, document the test results over several experiments including a large-scale ring structure, and describe future work to implement the IPJR in 3D and with micron precision.

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

    NASA Technical Reports Server (NTRS)

    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.

  6. Biologically controlled synthesis and assembly of magnetite nanoparticles.

    PubMed

    Bennet, Mathieu; Bertinetti, Luca; Neely, Robert K; Schertel, Andreas; Körnig, André; Flors, Cristina; Müller, Frank D; Schüler, Dirk; Klumpp, Stefan; Faivre, Damien

    2015-01-01

    Magnetite nanoparticles have size- and shape-dependent magnetic properties. In addition, assemblies of magnetite nanoparticles forming one-dimensional nanostructures have magnetic properties distinct from zero-dimensional or non-organized materials due to strong uniaxial shape anisotropy. However, assemblies of free-standing magnetic nanoparticles tend to collapse and form closed-ring structures rather than chains in order to minimize their energy. Magnetotactic bacteria, ubiquitous microorganisms, have the capability to mineralize magnetite nanoparticles, the so-called magnetosomes, and to direct their assembly in stable chains via biological macromolecules. In this contribution, the synthesis and assembly of biological magnetite to obtain functional magnetic dipoles in magnetotactic bacteria are presented, with a focus on the assembly. We present tomographic reconstructions based on cryo-FIB sectioning and SEM imaging of a magnetotactic bacterium to exemplify that the magnetosome chain is indeed a paradigm of a 1D magnetic nanostructure, based on the assembly of several individual particles. We show that the biological forces are a major player in the formation of the magnetosome chain. Finally, we demonstrate by super resolution fluorescence microscopy that MamK, a protein of the actin family necessary to form the chain backbone in the bacteria, forms a bundle of filaments that are not only found in the vicinity of the magnetosome chain but are widespread within the cytoplasm, illustrating the dynamic localization of the protein within the cells. These very simple microorganisms have thus much to teach us with regards to controlling the design of functional 1D magnetic nanoassembly.

  7. Diversity in virus assembly: biology makes things complicated

    NASA Astrophysics Data System (ADS)

    Zlotnick, Adam

    2008-03-01

    Icosahedral viruses have an elegance of geometry that implies a general path of assembly. However, structure alone provides insufficient information. Cowpea Chlorotic Mottle Virus (CCMV), an important system for studying virus assembly, consists of 90 coat protein (CP) homodimers condensed around an RNA genome. The crystal structure (Speir et al, 1995) reveals that assembly causes burial of hydrophobic surface and formation of β hexamers, the intertwining of N-termini of the CPs surrounding a quasi-sixfold. This structural view leads to reasonable and erroneous predictions: (i) CCMV capsids are extremely stable, and (ii) β hexamer formation is critical to assembly. Experimentally, we have found that capsids are based on a network of extremely weak (4-5 kT) pairwise interactions and that pentamer formation is the critical step in assembly kinetics. Because of the fragility of CP-Cp interaction, we can redirect assembly to generate and dissociate tubular nanostructures. The dynamic behavior of CCMV reflects the requirements and peculiarities of an evolved biological system; it does not necessarily reflect the behavior predicted from a more static picture of the virus.

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

    ERIC Educational Resources Information Center

    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…

  9. Mining Environmental Plasmids for Synthetic Biology Parts and Devices.

    PubMed

    Martínez-García, Esteban; Benedetti, Ilaria; Hueso, Angeles; De Lorenzo, Víctor

    2015-02-01

    The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include inter alia origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties. PMID:26104565

  10. Assembly of hair bundles, an amazing problem for cell biology

    PubMed Central

    Barr-Gillespie, Peter-G.

    2015-01-01

    The hair bundle—the sensory organelle of inner-ear hair cells of vertebrates—exemplifies the ability of a cell to assemble complex, elegant structures. Proper construction of the bundle is required for proper mechanotransduction in response to external forces and to transmit information about sound and movement. Bundles contain tightly controlled numbers of actin-filled stereocilia, which are arranged in defined rows of precise heights. Indeed, many deafness mutations that disable hair-cell cytoskeletal proteins also disrupt bundles. Bundle assembly is a tractable problem in molecular and cellular systems biology; the sequence of structural changes in stereocilia is known, and a modest number of proteins may be involved. PMID:26229154

  11. Directed self-assembly, genomic assembly complexity and the formation of biological structure, or, what are the genes for nacre?

    PubMed

    Cartwright, Julyan H E

    2016-03-13

    Biology uses dynamical mechanisms of self-organization and self-assembly of materials, but it also choreographs and directs these processes. The difference between abiotic self-assembly and a biological process is rather like the difference between setting up and running an experiment to make a material remotely compared with doing it in one's own laboratory: with a remote experiment-say on the International Space Station-everything must be set up beforehand to let the experiment run 'hands off', but in the laboratory one can intervene at any point in a 'hands-on' approach. It is clear that the latter process, of directed self-assembly, can allow much more complicated experiments and produce far more complex structures than self-assembly alone. This control over self-assembly in biology is exercised at certain key waypoints along a trajectory and the process may be quantified in terms of the genomic assembly complexity of a biomaterial.

  12. Directed self-assembly, genomic assembly complexity and the formation of biological structure, or, what are the genes for nacre?

    PubMed

    Cartwright, Julyan H E

    2016-03-13

    Biology uses dynamical mechanisms of self-organization and self-assembly of materials, but it also choreographs and directs these processes. The difference between abiotic self-assembly and a biological process is rather like the difference between setting up and running an experiment to make a material remotely compared with doing it in one's own laboratory: with a remote experiment-say on the International Space Station-everything must be set up beforehand to let the experiment run 'hands off', but in the laboratory one can intervene at any point in a 'hands-on' approach. It is clear that the latter process, of directed self-assembly, can allow much more complicated experiments and produce far more complex structures than self-assembly alone. This control over self-assembly in biology is exercised at certain key waypoints along a trajectory and the process may be quantified in terms of the genomic assembly complexity of a biomaterial. PMID:26857670

  13. FLOAT OPERATED RADIAL GATE HOIST ASSEMBLY LIST OF PARTS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FLOAT OPERATED RADIAL GATE HOIST ASSEMBLY - LIST OF PARTS - BASE-CRANK. WASTEWAY NO. 1. WELLTON-MOHAWK CANAL - STA. 99+23.50. United States Department of the Interior, Bureau of Reclamation; Gila Project, Arizona, Wellton-Mohawk Division. Drawing No. 50-D-2511, dated May 3, 1949, Denver Colorado. Sheet 1 of 2 - Wellton-Mohawk Irrigation System, Wasteway No. 1, Wellton-Mohawk Canal, North side of Wellton-Mohawk Canal, bounded by Gila River to North & the Union Pacific Railroad & Gila Mountains to south, Wellton, Yuma County, AZ

  14. Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

    PubMed Central

    Bilitchenko, Lesia; Liu, Adam; Cheung, Sherine; Weeding, Emma; Xia, Bing; Leguia, Mariana; Anderson, J. Christopher; Densmore, Douglas

    2011-01-01

    Background Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. Results We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. Conclusions Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly. PMID:21559524

  15. Part identification in robotic assembly using vision system

    NASA Astrophysics Data System (ADS)

    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.

  16. Peptide Self-Assembly for Crafting Functional Biological Materials

    PubMed Central

    Matson, John B.; Zha, R. Helen; Stupp, Samuel I.

    2011-01-01

    Self-assembling, peptide-based scaffolds are frontrunners in the search for biomaterials with widespread impact in regenerative medicine. The inherent biocompatibility and cell signaling capabilities of peptides, in combination with control of secondary structure, has led to the development of a broad range of functional materials with potential for many novel therapies. More recently, membranes formed through complexation of peptide nanostructures with natural biopolymers have led to the development of hierarchically-structured constructs with potentially far-reaching applications in biology and medicine. In this review, we highlight recent advances in peptide-based gels and membranes, including work from our group and others. Specifically, we discuss the application of peptide-based materials in the regeneration of bone and enamel, cartilage, and the central nervous system, as well as the transplantation of islets, wound-healing, cardiovascular therapies, and treatment of erectile dysfunction after prostatectomy PMID:22125413

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

    PubMed

    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.

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

    PubMed

    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. PMID:26171760

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

    NASA Astrophysics Data System (ADS)

    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

  20. 76 FR 41669 - Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-15

    ..., Continuous Flow Passenger Oxygen Mask Assembly, Part Numbers 174006-( ), 174080-( ), 174085-( ), 174095... assemblies. This AD was prompted by a report that several oxygen mask assemblies with broken in-line flow... indicators of the oxygen mask assembly from fracturing and separating, which could inhibit oxygen flow to...

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

    PubMed

    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.

  2. Electrophoretic separator for purifying biologicals, part 1

    NASA Technical Reports Server (NTRS)

    Mccreight, L. R.

    1978-01-01

    A program to develop an engineering model of an electrophoretic separator for purifying biologicals is summarized. An extensive mathematical modeling study and numerous ground based tests were included. Focus was placed on developing an actual electrophoretic separator of the continuous flow type, configured and suitable for flight testing as a space processing applications rocket payload.

  3. GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology.

    PubMed

    Sarrion-Perdigones, Alejandro; Vazquez-Vilar, Marta; Palací, Jorge; Castelijns, Bas; Forment, Javier; Ziarsolo, Peio; Blanca, José; Granell, Antonio; Orzaez, Diego

    2013-07-01

    Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene structures at the DNA level while enabling the exchange of genetic building blocks among plant bioengineers. Here, we describe GoldenBraid 2.0 (GB2.0), a comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GB2.0 relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GB2.0 toolkit offers an evergrowing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc. Use of the GB2.0 framework is facilitated by a number of Web resources that include a publicly available database, tutorials, and a software package that provides in silico simulations and laboratory protocols for GB2.0 part domestication and multigene engineering. In short, GB2.0 provides a framework to exchange both information and physical DNA elements among bioengineers to help implement plant synthetic biology projects. PMID:23669743

  4. GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology.

    PubMed

    Sarrion-Perdigones, Alejandro; Vazquez-Vilar, Marta; Palací, Jorge; Castelijns, Bas; Forment, Javier; Ziarsolo, Peio; Blanca, José; Granell, Antonio; Orzaez, Diego

    2013-07-01

    Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene structures at the DNA level while enabling the exchange of genetic building blocks among plant bioengineers. Here, we describe GoldenBraid 2.0 (GB2.0), a comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GB2.0 relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GB2.0 toolkit offers an evergrowing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc. Use of the GB2.0 framework is facilitated by a number of Web resources that include a publicly available database, tutorials, and a software package that provides in silico simulations and laboratory protocols for GB2.0 part domestication and multigene engineering. In short, GB2.0 provides a framework to exchange both information and physical DNA elements among bioengineers to help implement plant synthetic biology projects.

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

    PubMed

    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. Plant and Animal Gravitational Biology. Part 1

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Session TA2 includes short reports covering: (1) The Interaction of Microgravity and Ethylene on Soybean Growth and Metabolism; (2) Structure and G-Sensitivity of Root Statocytes under Different Mass Acceleration; (3) Extracellular Production of Taxanes on Cell Surfaces in Simulated Microgravity and Hypergravity; (4) Current Problems of Space Cell Phytobiology; (5) Biological Consequences of Microgravity-Induced Alterations in Water Metabolism of Plant Cells; (6) Localization of Calcium Ions in Chlorella Cells Under Clinorotation; (7) Changes of Fatty Acids Content of Plant Cell Plasma Membranes under Altered Gravity; (8) Simulation of Gravity by Non-Symmetrical Vibrations and Ultrasound; and (9) Response to Simulated weightlessness of In Vitro Cultures of Differentiated Epithelial Follicular Cells from Thyroid.

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

    DOEpatents

    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.

  8. Toward scalable parts families for predictable design of biological circuits.

    PubMed

    Lucks, Julius B; Qi, Lei; Whitaker, Weston R; Arkin, Adam P

    2008-12-01

    Our current ability to engineer biological circuits is hindered by design cycles that are costly in terms of time and money, with constructs failing to operate as desired, or evolving away from the desired function once deployed. Synthetic biologists seek to understand biological design principles and use them to create technologies that increase the efficiency of the genetic engineering design cycle. Central to the approach is the creation of biological parts--encapsulated functions that can be composited together to create new pathways with predictable behaviors. We define five desirable characteristics of biological parts--independence, reliability, tunability, orthogonality and composability, and review studies of small natural and synthetic biological circuits that provide insights into each of these characteristics. We propose that the creation of appropriate sets of families of parts with these properties is a prerequisite for efficient, predictable engineering of new function in cells and will enable a large increase in the sophistication of genetic engineering applications. PMID:18983935

  9. A unified convention for biological assemblies with helical symmetry

    SciTech Connect

    Tsai, Chung-Jung; Nussinov, Ruth

    2011-08-01

    A new representation of helical structure by four parameters, [n{sub 1}, n{sub 2}, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam. Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems, respectively. The unification suggests that a new helical description with only four parameters [n{sub 1}, n{sub 2}, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.

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

    PubMed

    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.

  11. Biology coming full circle: Joining the whole and the parts

    PubMed Central

    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. PMID:25583953

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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

  14. Controlled Assembly of Viral Surface Proteins into Biological Nanoparticles

    NASA Astrophysics Data System (ADS)

    Nakatani-Webster, Eri

    In recent years, therapeutic use of engineered particles on the 1-1,000 nm scale has gained popularity; these nanoparticles have been developed for use in drug delivery, gene therapy, vaccine preparation, and diagnostics. Often, viral proteins are utilized in the design of such species, and outlined here are completed studies on the in vitro assembly of nanoparticles derived from two very different viral systems. The incorporation of the human immunodeficiency virus (HIV) envelope glycoprotein precursor gp160 into phospholipid bilayer nanodiscs is discussed as a potential platform for vaccine design; efforts were successful, however yield currently limits the practical application of this approach. The utility of bacteriophage lambda procapsids and virus-like particles in therapeutic nanoparticle design is also outlined, as are efforts toward the structural and thermodynamic characterization of a urea-triggered capsid maturation event. It is demonstrated that lambda virus-like particles can be assembled from purified capsid and scaffolding proteins, and that these particles undergo urea-triggered maturation and in vitro decoration protein addition similar to that seen in lambda procapsids. The studies on lambda provided materials for the further development of nanoparticles potentially useful in a clinical setting, as well as shedding light on critical viral assembly and maturation events as they may take place in vivo.

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed

    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.

  17. 16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY... Gravity for Drop Assembly ER10MR98.010...

  18. 16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY... Gravity for Drop Assembly ER10MR98.010...

  19. 16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY... Gravity for Drop Assembly ER10MR98.010...

  20. 16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY... Gravity for Drop Assembly ER10MR98.010...

  1. 16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY... Gravity for Drop Assembly ER10MR98.010...

  2. Directed self-assembly defectivity assessment. Part II

    NASA Astrophysics Data System (ADS)

    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.

  3. Automated selection of synthetic biology parts for genetic regulatory networks.

    PubMed

    Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron; Densmore, Douglas; Beal, Jacob

    2012-08-17

    Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal matching, and part matching. Feature matching ensures that the mapping satisfies the regulatory relationships in the abstract design. Signal matching ensures that the expression levels of functional units are compatible. Finally, part matching finds a DNA part sequence that can implement the design. Our software tool MatchMaker implements these three steps. PMID:23651287

  4. Weak Polyelectrolyte-Clay Assemblies: Physical Mechanisms of Biological Response

    NASA Astrophysics Data System (ADS)

    Sukhishvili, Svetlana; Pavlukhina, Svetlana; Zhuk, Iryna

    2014-03-01

    We report on a highly efficient, non-leachable antibacterial coating, consisting of an ultrathin nanocomposite hydrogel capable of hosting, protecting and delivering antibiofilm agents in response to bacterial infection. Constructed using layer-by-layer (LbL) deposition of clay nanoplatelets and a weak polyelectrolyte and loaded with an antimicrobial agent (AmA), the coatings was highly resistant to colonization by Staphylococcus aureus. The high antibiofilm activity of the coating results from a combination of highly localized, bacteria-triggered AmA release and hydrogel swelling, as well as retention of AmA by clay nanoplatelets. We discuss the dependence of rheological and swelling properties of weak polyelectrolyte-clay assemblies on film thickness, clay platelet orientation and environmental pH.

  5. Biologically Inspired Strategy for the Assembly of Viral Building Blocks with Controlled Dimensions

    NASA Astrophysics Data System (ADS)

    Rego, Jennifer M.

    I demonstrate the assembly of nanoscale viral building blocks of controlled lengths using a biologically motivated strategy. To achieve this I exploit the simple assembly mechanism of Tobacco mosaic virus (TMV), whose length is solely governed by the length of its genomic mRNA, using both the wildtype and genetically engineered (displaying cysteine residues) forms of the virus. The observed lengths of the viral building blocks correlate well with the expected lengths. Additionally, I demonstrate the assembly of viral building blocks of controlled length derived from the genetically engineered form of TMV displaying cysteine groups, which signifies that the mutation does not affect viral building block assembly. Next, I examine the application of WT viral building blocks as individual components for the assembly of 1 dimensional nanoarrays via biotin-streptavidin binding. Finally, I examine the application of genetically engineered 1cys viral building blocks as a biological template for the synthesis of metal nanoparticles, functionalization by small molecules and a component of a vertically patterned template. I envision that the biologically inspired assembly strategy to design and construct viral building blocks of controlled dimensions together with the applications explored could be employed to fabricate well-controlled nanoarchitectures and hybrid nanomaterials for a wide variety of applications.

  6. Building DNA nanostructures for molecular computation, templated assembly, and biological applications.

    PubMed

    Rangnekar, Abhijit; LaBean, Thomas H

    2014-06-17

    CONSPECTUS: DNA is a critical biomolecule well-known for its roles in biology and genetics. Moreover, its double-helical structure and the Watson-Crick pairing of its bases make DNA structurally predictable. This predictability enables design and synthesis of artificial DNA nanostructures by suitable programming of the base sequences of DNA strands. Since the advent of the field of DNA nanotechnology in 1982, a variety of DNA nanostructures have been designed and used for numerous applications. In this Account, we discuss the progress made by our lab which has contributed toward the overall advancement of the field. Tile-based DNA nanostructures are an integral part of structural DNA nanotechnology. These structures are formed using several short, chemically synthesized DNA strands by programming their base sequences so that they self-assemble into desired constructs. Design and assembly of several DNA tiles will be discussed in this Account. Tiles include, for example, TX tiles with three parallel, coplanar duplexes, 4 × 4 cross-tiles with four arms, and weave-tiles with weave-like architecture. Another category of tiles we will present involve multiple parallel duplexes that assemble to form closed tubular structures. All of these tile types have been used to form micrometer-scale one- and two-dimensional arrays and lattices. Origami-based structures constitute another category where a long single-stranded DNA scaffold is folded into desired shapes by association with multiple short staple strands. This Account will describe the efforts by our lab in devising new strategies to improve the maximum size of origami structures. The various DNA nanostructures detailed here have been used in a wide variety of different applications. This Account will discuss the use of DNA tiles for logical computation, encoding information as molecular barcodes, and functionalization for patterning of other nanoscale organic and inorganic materials. Consequently, we have used DNA

  7. DNA assembly of nanoparticle superstructures for controlled biological delivery and elimination

    NASA Astrophysics Data System (ADS)

    Chou, Leo Y. T.; Zagorovsky, Kyryl; Chan, Warren C. W.

    2014-02-01

    The assembly of nanomaterials using DNA can produce complex nanostructures, but the biological applications of these structures remain unexplored. Here, we describe the use of DNA to control the biological delivery and elimination of inorganic nanoparticles by organizing them into colloidal superstructures. The individual nanoparticles serve as building blocks, whose size, surface chemistry and assembly architecture dictate the overall superstructure design. These superstructures interact with cells and tissues as a function of their design, but subsequently degrade into building blocks that can escape biological sequestration. We demonstrate that this strategy reduces nanoparticle retention by macrophages and improves their in vivo tumour accumulation and whole-body elimination. Superstructures can be further functionalized to carry and protect imaging or therapeutic agents against enzymatic degradation. These results suggest a different strategy to engineer nanostructure interactions with biological systems and highlight new directions in the design of biodegradable and multifunctional nanomedicine.

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

    PubMed Central

    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

    2015-01-01

    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. PMID:25956650

  9. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

    PubMed Central

    Hillier, LaDeana W.; Zody, Michael C.; Goldstein, Steve; She, Xinwe; Bult, Carol J.; Agarwala, Richa; Cherry, Joshua L.; DiCuccio, Michael; Hlavina, Wratko; Kapustin, Yuri; Meric, Peter; Maglott, Donna; Birtle, Zoë; Marques, Ana C.; Graves, Tina; Zhou, Shiguo; Teague, Brian; Potamousis, Konstantinos; Churas, Christopher; Place, Michael; Herschleb, Jill; Runnheim, Ron; Forrest, Daniel; Amos-Landgraf, James; Schwartz, David C.; Cheng, Ze; Lindblad-Toh, Kerstin; Eichler, Evan E.; Ponting, Chris P.

    2009-01-01

    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. PMID:19468303

  10. The Didactics of Biology. A Selected Bibliography for 1979. Part I [and] Part II.

    ERIC Educational Resources Information Center

    Altmann, Antonin, Ed.; Lipertova, Pavla, Ed.

    Selected articles on various aspects of biology teaching published in 1979 have been annotated in this two-part bibliography. Entries from 18 journals representing 11 different countries are presented according to a topic area classification scheme listed in the table of contents. Countries represented include: Australia; Bulgaria; Czechoslovakia;…

  11. Evolving together: the biology of symbiosis, part 1

    PubMed Central

    2000-01-01

    Symbioses, prolonged associations between organisms often widely separated phylogenetically, are more common in biology than we once thought and have been neglected as a phenomenon worthy of study on its own merits. Extending along a dynamic continuum from antagonistic to cooperative and often involving elements of both antagonism and mutualism, symbioses involve pathogens, commensals, and mutualists interacting in myriad ways over the evolutionary history of the involved “partners.” In this first of 2 parts, some remarkable examples of symbiosis will be explored, from the coral-algal symbiosis and nitrogen fixation to the great diversity of dietary specializations enabled by the gastrointestinal microbiota of animals. PMID:16389385

  12. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

    NASA Astrophysics Data System (ADS)

    Ruder, Warren C.; Hsu, Chia-Pei D.; Edelman, Brent D.; Schwartz, Russell; LeDuc, Philip R.

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe3O4) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures.

  13. DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature

    PubMed Central

    Nowak, Robert M.; Wojtowicz-Krawiec, Anna; Plucienniczak, Andrzej

    2015-01-01

    Artificial gene synthesis requires consideration of nucleotide sequence development as well as long DNA molecule assembly protocols. The nucleotide sequence of the molecule must meet many conditions including particular preferences of the host organism for certain codons, avoidance of specific regulatory subsequences, and a lack of secondary structures that inhibit expression. The chemical synthesis of DNA molecule has limitations in terms of strand length; thus, the creation of artificial genes requires the assembly of long DNA molecules from shorter fragments. In the approach presented, the algorithm and the computer program address both tasks: developing the optimal nucleotide sequence to encode a given peptide for a given host organism and determining the long DNA assembly protocol. These tasks are closely connected; a change in codon usage may lead to changes in the optimal assembly protocol, and the lack of a simple assembly protocol may be addressed by changing the nucleotide sequence. The computer program presented in this study was tested with real data from an experiment in a wet biological laboratory to synthesize a peptide. The benefit of the presented algorithm and its application is the shorter time, compared to polymerase cycling assembly, needed to produce a ready synthetic gene. PMID:25629047

  14. Assembling new technologies at the interface of materials science and biology

    NASA Astrophysics Data System (ADS)

    Stendahl, John C.

    Molecular self-assembly can be used to construct advanced materials by taking cues from nature and harnessing noncovalent interactions. This bottom-up approach affords molecular level precision that can cultivate pathways to improved materials function. The graduate research presented in this thesis integrates molecular self-assembly with traditional concepts in chemistry and materials science, with the ultimate goal of developing innovative solutions in technology and medicine. In the field of polymer engineering, self-assembly was used to create supramolecular nanoribbons that, when incorporated into polystyrene, modify its microstructure and significantly enhance its toughness and ductility. In medicine, self-assembly was used to create ordered, chemically functional materials to improve interactions with cells and other constituents of the biological environment. One system that was investigated is based on a triblock molecule in which cholesterol is connected to a lysine dendron by a flexible oligo-(L-lactic acid) spacer. These molecules self-assemble into polar surface coatings on fibrous poly(L-lactic acid) scaffolds that improve the scaffold's wettability and increase its retention of cells during seeding. Another self-assembling system that was investigated for biomedical applications is a family of molecules referred to as peptide amphiphiles (PA's). PA's consist of hydrophobic alkyl tails connected to short, hydrophilic peptides that incorporate biological signaling epitopes. These molecules spontaneously assemble into networks of well-defined nanofibers in aqueous environments, with the signaling epitopes presented in high density on the nanofiber exteriors. Nanofiber assembly is triggered by charge screening on the peptides and is able to produce self-supporting gels in concentrations of less than 1.0 wt.-%. The assembly process and mechanical properties of PA gels was investigated in detail with vibrational spectroscopy and oscillatory rheology. PA

  15. Self-Assembled Fluorescent Nanoparticles from π-Conjugated Small Molecules: En Route to Biological Applications.

    PubMed

    Schill, Jurgen; Schenning, Albertus P H J; Brunsveld, Luc

    2015-07-01

    Since the development of supramolecular chemical biology, self-organised nano-architectures have been widely explored in a variety of biomedical applications. Functionalized synthetic molecules with the ability of non-covalent assembly in an aqueous environment are typically able to interact with biological systems and are therefore especially interesting for their use in theranostics. Nanostructures based on π-conjugated oligomers are particularly promising as theranostic platforms as they bear outstanding photophysical properties as well as drug loading capabilities. This Feature Article provides an overview on the recent advances in the self-assembly of intrinsically fluorescent nanoparticles from π-conjugated small molecules such as fluorene or perylene based chromophores for biomedical applications.

  16. 16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FLAMMABLE FABRICS ACT REGULATIONS STANDARD FOR THE FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt. 1633,...

  17. 16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FLAMMABLE FABRICS ACT REGULATIONS STANDARD FOR THE FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt.1633,...

  18. 16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FLAMMABLE FABRICS ACT REGULATIONS STANDARD FOR THE FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt.1633,...

  19. 16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FLAMMABLE FABRICS ACT REGULATIONS STANDARD FOR THE FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt.1633,...

  20. 16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FLAMMABLE FABRICS ACT REGULATIONS STANDARD FOR THE FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt. 1633,...

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

    PubMed Central

    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

  2. Supramolecular disassembly of facially amphiphilic dendrimer assemblies in response to physical, chemical, and biological stimuli.

    PubMed

    Raghupathi, Krishna R; Guo, Jing; Munkhbat, Oyuntuya; Rangadurai, Poornima; Thayumanavan, S

    2014-07-15

    CONSPECTUS: Supramolecular assemblies formed from spontaneous self-assembly of amphiphilic macromolecules are explored as biomimetic architectures and for applications in areas such as sensing, drug delivery, and diagnostics. Macromolecular assemblies are usually preferred, compared with their simpler small molecule counterparts, due to their low critical aggregate concentrations (CAC) and high thermodynamic stability. This Account focuses on the structural and functional aspects of assemblies formed from dendrimers, specifically facially amphiphilic dendrons that form micelle or inverse micelle type supramolecular assemblies depending on the nature of the solvent medium. The micelle type assemblies formed from facially amphiphilic dendrons sequester hydrophobic guest molecules in their interiors. The stability of these assemblies is dependent on the relative compatibility of the hydrophilic and hydrophobic functionalities with water, often referred to as hydrophilic-lipophilic balance (HLB). Disruption of the HLB, using an external stimulus, could lead to disassembly of the aggregates, which can then be utilized to cause an actuation event, such as guest molecule release. Studying these possibilities has led to (i) a robust and general strategy for stimulus-induced disassembly and molecular release and (ii) the introduction of a new approach to protein-responsive supramolecular disassembly. The latter strategy provides a particularly novel avenue for impacting biomedical applications. Most of the stimuli-sensitive supramolecular assemblies have been designed to be responsive to factors such pH, temperature, and redox conditions. The reason for this interest stems from the fact that certain disease microenvironments have aberrations in these factors. However, these variations are the secondary imbalances in biology. Imbalances in protein activity are the primary reasons for most, if not all, human pathology. There have been no robust strategies in stimulus

  3. Supramolecular disassembly of facially amphiphilic dendrimer assemblies in response to physical, chemical, and biological stimuli.

    PubMed

    Raghupathi, Krishna R; Guo, Jing; Munkhbat, Oyuntuya; Rangadurai, Poornima; Thayumanavan, S

    2014-07-15

    CONSPECTUS: Supramolecular assemblies formed from spontaneous self-assembly of amphiphilic macromolecules are explored as biomimetic architectures and for applications in areas such as sensing, drug delivery, and diagnostics. Macromolecular assemblies are usually preferred, compared with their simpler small molecule counterparts, due to their low critical aggregate concentrations (CAC) and high thermodynamic stability. This Account focuses on the structural and functional aspects of assemblies formed from dendrimers, specifically facially amphiphilic dendrons that form micelle or inverse micelle type supramolecular assemblies depending on the nature of the solvent medium. The micelle type assemblies formed from facially amphiphilic dendrons sequester hydrophobic guest molecules in their interiors. The stability of these assemblies is dependent on the relative compatibility of the hydrophilic and hydrophobic functionalities with water, often referred to as hydrophilic-lipophilic balance (HLB). Disruption of the HLB, using an external stimulus, could lead to disassembly of the aggregates, which can then be utilized to cause an actuation event, such as guest molecule release. Studying these possibilities has led to (i) a robust and general strategy for stimulus-induced disassembly and molecular release and (ii) the introduction of a new approach to protein-responsive supramolecular disassembly. The latter strategy provides a particularly novel avenue for impacting biomedical applications. Most of the stimuli-sensitive supramolecular assemblies have been designed to be responsive to factors such pH, temperature, and redox conditions. The reason for this interest stems from the fact that certain disease microenvironments have aberrations in these factors. However, these variations are the secondary imbalances in biology. Imbalances in protein activity are the primary reasons for most, if not all, human pathology. There have been no robust strategies in stimulus

  4. Model-independent electron spin resonance for measuring order of immobile components in a biological assembly.

    PubMed Central

    Burghardt, T P; Thompson, N L

    1985-01-01

    A model-independent description of the angular orientation distribution of elements in an ordered biological assembly is applied to the electron spin resonance (ESR) technique. As in a previous model-independent treatment of fluorescence polarization (Burghardt, T.P., 1984, Biopolymers, 23:2383-2406) the elemental order is described by an angular distribution of molecular frames with one frame fixed in each element of the assembly. The distribution is expanded in a complete orthonormal set of functions. The coefficients of the series expansion (the order parameters) describe the orientation distribution of the elements in the assembly without reference to a model and can be obtained from the observed spectrum. The method establishes the limitations of ESR in detecting order in the assembly by determining which distribution coefficients the technique can detect. A method of determining the order parameters from an ESR spectra, using a set of ESR basis spectra, is developed. We also describe a treatment that incorporates the actual line shape measured from randomly oriented, immobile elements. In this treatment, no model-dependent assumptions about the line shape are required. We have applied the model-independent analysis to ESR spectra from spin-labeled myosin cross-bridges in muscle fibers. The results contain detailed information on the spin-probe angular distribution and differ in interesting ways from previous model-dependent interpretations of the spectra. PMID:2994768

  5. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

    PubMed Central

    Ruder, Warren C.; Hsu, Chia-Pei D.; Edelman, Brent D.; Schwartz, Russell; LeDuc, Philip R.

    2012-01-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe3O4) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures. PMID:22952408

  6. The Dynamics of Microtubule/Motor-Protein Assemblies in Biology and Physics

    NASA Astrophysics Data System (ADS)

    Shelley, Michael J.

    2016-01-01

    Many important processes in the cell are mediated by stiff microtubule polymers and the active motor proteins moving on them. This includes the transport of subcellular structures (nuclei, chromosomes, organelles) and the self-assembly and positioning of the mitotic spindle. Little is understood of these processes, but they present fascinating problems in fluid-structure interactions. Microtubules and motor proteins are also the building blocks of new biosynthetic active suspensions driven by motor-protein activity. These reduced systems can be probed—and modeled—more easily than can the fully biological ones and demonstrate their own aspects of self-assembly and complex dynamics. I review recent work modeling such systems as fluid-structure interaction problems and as multiscale complex fluids.

  7. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid.

    PubMed

    Ruder, Warren C; Hsu, Chia-Pei D; Edelman, Brent D; Schwartz, Russell; Leduc, Philip R

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe(3)O(4)) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures. PMID:22952408

  8. Biological bottom-up assembly of antibody nanotubes on patterned antigen arrays.

    PubMed

    Nuraje, Nurxat; Banerjee, Ipsita A; MacCuspie, Robert I; Yu, Lingtao; Matsui, Hiroshi

    2004-07-01

    Application of biotechnology in nanofabrication has an advantage to produce functional building-block materials that may not have synthetic counterparts. Here we introduced a new type of building block, antibody nanotubes, and demonstrated anchoring them on complementary antigen arrays via antibody-antigen recognition. Biological recognition between the antibody nanotubes and the antigen arrays permitted recognition-driven assembly of ordered nanotube arrays. The array of antigens was written by using the tip of an atomic force microscope (AFM) on alkylthiol self-assembled monolayer (SAM)-coated Au substrates via nanografting. After antigens were immobilized onto the shaved regions of the alkylthiol SAMs with the AFM tip, antibody nanotubes, produced by incubating antibodies in template nanotube solutions, were selectively attached onto the antigen regions. This technique is very useful when multiple building blocks are necessary to address specific locations on substrates because simultaneous immobilization of multiple antibody nanotubes at specific complementary binding positions can be achieved in a single process.

  9. Self-assembly of dendritic dipeptides as a model of chiral selection in primitive biological systems.

    PubMed

    Rosen, Brad M; Roche, Cécile; Percec, Virgil

    2013-01-01

    Biological macromolecules are homochiral, composed of sequences of stereocenters possessing the same repeated absolute configuration. This chapter addresses the mechanism of homochiral selection in polypeptides. In particular, the relationship between the stereochemistry (L or D) of structurally distinct α-amino acids is explored. Through functionalization of Tyr-Xaa dipeptides with self-assembling dendrons, the effect of stereochemical sequence of the dipeptide on the thermodynamics of self-assembly and the resulting structural features can be quantified. The dendritic dipeptide approach effectively isolates the stereochemical information of the shortest sequence of stereochemical information possible in polypeptide, while simultaneously allowing for dendron driven tertiary and quaternary structure formation and subsequent transfer of chiral information from the dipeptide to the dendritic sheath. This approach elucidates a mechanism of selecting a homochiral relationship between dissimilar but neighboring α-amino acids through thermodynamic preference for homochirality in solution-phase and bulk supramolecular helical polymerization. PMID:23306867

  10. Strontium: Part II. Chemistry, Biological Aspects and Applications.

    ERIC Educational Resources Information Center

    Britton, G. C.; Johnson, C. H.

    1987-01-01

    Reviews basic information on the Chemistry of strontium and its compounds. Explains biological aspects of strontium and its pharmaceutical applications. Highlights industrial application of strontium and its components. (ML)

  11. Invasion Ecology and School Biology--Part II.

    ERIC Educational Resources Information Center

    Wells, R. V.

    1981-01-01

    Suggests that invasion biology can supply subject matter for teaching evolution, genetics, ecological relationships, and conservation. Describes flowering and non-flowering plant invaders, vertebrates and invertebrates, and two ecological invasions on the southern coast of England. (JN)

  12. Engineering biological structures of prescribed shape using self-assembling multicellular systems

    PubMed Central

    Jakab, Karoly; Neagu, Adrian; Mironov, Vladimir; Markwald, Roger R.; Forgacs, Gabor

    2004-01-01

    Self-assembly is a fundamental process that drives structural organization in both inanimate and living systems. It is in the course of self-assembly of cells and tissues in early development that the organism and its parts eventually acquire their final shape. Even though developmental patterning through self-assembly is under strict genetic control it is clear that ultimately it is physical mechanisms that bring about the complex structures. Here we show, both experimentally and by using computer simulations, how tissue liquidity can be used to build tissue constructs of prescribed geometry in vitro. Spherical aggregates containing many thousands of cells, which form because of tissue liquidity, were implanted contiguously into biocompatible hydrogels in circular geometry. Depending on the properties of the gel, upon incubation, the aggregates either fused into a toroidal 3D structure or their constituent cells dispersed into the surrounding matrix. The model simulations, which reproduced the experimentally observed shapes, indicate that the control parameter of structure evolution is the aggregate–gel interfacial tension. The model-based analysis also revealed that the observed toroidal structure represents a metastable state of the cellular system, whose lifetime depends on the magnitude of cell–cell and cell–matrix interactions. Thus, these constructs can be made long-lived. We suggest that spherical aggregates composed of organ-specific cells may be used as “bio-ink” in the evolving technology of organ printing. PMID:14981244

  13. Biological stimuli and biomolecules in the assembly and manipulation of nanoscale polymeric particles

    PubMed Central

    Randolph, Lyndsay M.; Chien, Miao-Ping; Gianneschi, Nathan C.

    2013-01-01

    Living systems are replete with complex, stimuli-responsive nanoscale materials and molecular self-assemblies. There is an ever increasing and intense interest within the chemical sciences to understand, mimic and interface with these biological systems utilizing synthetic and/or semi-synthetic tools. Our aim in this review is to give perspective on this emerging field of research by highlighting examples of polymeric nanoparticles and micelles that are prepared utilizing biopolymers together with synthetic polymers for the purpose of developing nanomaterials capable of interacting and responding to biologically relevant stimuli. It is expected that with the merging of evolved biological molecules with synthetic materials, will come the ability to prepare complex, functional devices. A variety of applications will become accessible including self-healing materials, self-replicating systems, biodiagnostic tools, drug targeting materials and autonomous, adaptive sensors. Most importantly, the success of this type of strategy will impact how biomolecules are stabilized and incorporated into synthetic devices and at the same time, will influence how synthetic materials are utilized within biomedical applications. PMID:24353895

  14. River Pollution: Part II. Biological Methods for Assessing Water Quality.

    ERIC Educational Resources Information Center

    Openshaw, Peter

    1984-01-01

    Discusses methods used in the biological assessment of river quality and such indicators of clean and polluted waters as the Trent Biotic Index, Chandler Score System, and species diversity indexes. Includes a summary of a river classification scheme based on quality criteria related to water use. (JN)

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

    PubMed

    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.

  16. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 1: Identifying Proteins Based on Molecular Mass

    ERIC Educational Resources Information Center

    Arnquist, Isaac J.; Beussman, Douglas J.

    2007-01-01

    Biological mass spectrometry is an important analytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. Currently, few hands-on opportunities exist for undergraduate students to learn about this technique. With the 2002 Nobel Prize being awarded, in part, for the development of biological mass…

  17. Multicomponent, Mannich-type assembly process for generating novel, biologically-active 2-arylpiperidines and derivatives

    PubMed Central

    Hardy, Simon; Martin, Stephen F.

    2014-01-01

    A multicomponent, Mannich-type assembly process commencing with commercially available bromobenzaldehydes was sequenced with [3+2] dipolar cycloaddition reactions involving nitrones and azomethine ylides to generate collections of fused, bicyclic scaffolds based on the 2-arylpiperidine subunit. Use of the 4-pentenoyl group, which served both as an activator in the Mannich-type reaction and a readily-cleaved amine protecting group, allowed sub-libraries to be prepared through piperidine N-functionalization and cross-coupling of the aryl bromide. A number of these derivatives displayed biological activities that had not previously been associated with this substructure. Methods were also developed that allowed rapid conversion of these scaffolds to novel, polycyclic dihydroquinazolin-2-ones, 2-imino-1,3-benzothiazinanes, dihydroisoquinolin-3-ones and bridged tetrahydroquinolines. PMID:25267860

  18. Membrane-electrode assembly enhances performance of a microbial fuel cell type biological oxygen demand sensor.

    PubMed

    Kim, Mia; Hyun, Moon Sik; Gadd, Geoffrey M; Kim, Gwang Tae; Lee, Sang-Joon; Kim, Hyung Joo

    2009-04-01

    A membrane-electrode assembly (MEA) was applied to a microbial fuel cell (MFC) type biological oxygen demand (BOD) sensor and the performance of the sensor was assessed. To establish the optimal conditions for MEA fabrication, platinum-catalysed carbon cloth cathodic electrodes were assembled with cation exchange membranes under various temperatures and pressures. By analysing coulombs from the MFCs, it could be determined that the optimal hot-pressing conditions were 120 degrees C and 150 kg cm(-2) for 30 s. When the MEA fabricated under optimal conditions and an air cathode were utilized for the construction of the MFC type BOD sensor, coulombs increased to 4.65 C from 0.52 C and power increased to 69,080 mW m(-3) from 880 mW m(-3) (at a BOD concentration of 200 mg L(-1)), respectively, compared with the conventional MFC lacking a MEA. The increased power improved the performance of the MFC type BOD sensor: sensitivity increased from 1.2 x 10(-3) to 1.8 x 10(-2) C per mg L(-1) of BOD, with good linearity (r2 = 0.97) and over 97% repeatability. We conclude that the MEA can be successfully applied to MFCs to make them highly sensitive BOD sensors.

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

    PubMed

    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.

  20. [Research under reduced gravity. Part I: bases of gravitational biology].

    PubMed

    Volkmann, D; Sievers, A

    1992-02-01

    The orientation of organisms in space and their morphogenesis in relation to the gravitational field of the Earth are the main topics of research in the field of gravitational biology. For more than 100 years clinostats provided the only possibility to simulate physiological weightlessness. In contrast to animals, plants are characterized by intracellular gravireceptors. Nevertheless, there are some indications, e.g., the minimal energy of approx. 10(-18) J triggering a gravity-dependent response, for similar mechanisms of gravity perception. Stretch-activated ion channels might be the common structural basis. PMID:11536493

  1. Application of the Modular Automated Reconfigurable Assembly System (MARAS) concept to adaptable vision gauging and parts feeding

    NASA Technical Reports Server (NTRS)

    By, Andre Bernard; Caron, Ken; Rothenberg, Michael; Sales, Vic

    1994-01-01

    This paper presents the first phase results of a collaborative effort between university researchers and a flexible assembly systems integrator to implement a comprehensive modular approach to flexible assembly automation. This approach, named MARAS (Modular Automated Reconfigurable Assembly System), has been structured to support multiple levels of modularity in terms of both physical components and system control functions. The initial focus of the MARAS development has been on parts gauging and feeding operations for cylinder lock assembly. This phase is nearing completion and has resulted in the development of a highly configurable system for vision gauging functions on a wide range of small components (2 mm to 100 mm in size). The reconfigurable concepts implemented in this adaptive Vision Gauging Module (VGM) are now being extended to applicable aspects of the singulating, selecting, and orienting functions required for the flexible feeding of similar mechanical components and assemblies.

  2. Immunomodulatory effects of macrolide antibiotics - part 1: biological mechanisms.

    PubMed

    Altenburg, J; de Graaff, C S; van der Werf, T S; Boersma, W G

    2011-01-01

    Macrolide antibiotics are well known for their antibacterial and anti-inflammatory properties. This article provides an overview of the biological mechanisms through which macrolides exert this 'double effect'. Their antibacterial effect consists of the inhibition of bacterial protein synthesis, impaired bacterial biofilm synthesis, and the attenuation of other bacterial virulence factors. Apart from these direct antimicrobial effects, macrolides are known for their modulating effect on many components of the human immune system. By influencing the production of cytokines, they have a dampening effect on the proinflammatory response. Furthermore, the majority of cells involved in the immune response are, in one way or another, influenced when macrolide antibiotics are administered. Having such an obvious effect on the various aspects of the immune system, macrolides seem to be exceptionally suited for the treatment of chronic inflammatory diseases.

  3. Evolving together: the biology of symbiosis, part 2

    PubMed Central

    2000-01-01

    Symbiotic trade-offs dominate the world of biology and medicine in colonist-host relationships and between separate, mutually dependent organisms of different species. Infectious and parasitic diseases can be better understood by exploring the dynamic continuum between pathogenicity and mutualism, between antagonism and cooperation—the sliding scale along which microorganisms can move in a moment's notice with a single nucleotide substitution. Organisms practicing piracy or pastoralism may be close genetic relatives. Mergers occur not only between cells but also between genomes; viruses co-opt host genes and in turn insert themselves into host genomes. Separate organisms, from ants to fungi to plants, establish symbiotic ties with each other that bind over deep time, generating much of the diversity we see in nature. PMID:16389348

  4. Amyloids assemble as part of recognizable structures during oogenesis in Xenopus

    PubMed Central

    Hayes, Michael H.

    2016-01-01

    ABSTRACT A hallmark of Alzheimer's, Huntington's and similar diseases is the assembly of proteins into amyloids rather than folding into their native state. There is an increasing appreciation that amyloids, under specific conditions, may be non-pathogenic. Here we show that amyloids form as a normal part of Xenopus oocyte development. Amyloids are detectable in the cytosol and the nucleus using an amyloid binding dye and antibodies that recognize amyloid structure. In the cytosol, yolk platelets are amyloid reactive, as are a number of yet to be characterized particles. In the nucleus, we find particles associated with transcription by RNA polymerase I, II and III and RNA processing contain amyloids. Nuclear amyloids remain intact for hours following isolation; however, RNase treatment rapidly disrupts nuclear amyloids. PMID:27215327

  5. [Topical issues of biological safety under current conditions. Part 2. Conceptual, terminological, and definitive framework of biological safety].

    PubMed

    Onishchenko, G G; Smolenskiĭ, V Iu; Ezhlova, E B; Demina, Iu V; Toporkov, V P; Toporkov, A V; Liapin, M N; Kutyrev, V V

    2013-01-01

    In accordance with the established conceptual base for the up-to-date broad interpretation of biological safety, and IHR (2005), developed is the notional, terminological, and definitive framework, comprising 33 elements. Key item of the nomenclature is the biological safety that is identified as population safety (individual, social, national) from direct and (or) human environment mediated (occupational, socio-economic, geopolitical infrastructures, ecological system) exposures to hazardous biological factors. Ultimate objective of the biological safety provision is to prevent and liquidate aftermaths of emergency situations of biological character either of natural or human origin (anthropogenic) arising from direct and indirect impact of the biological threats to the public health compatible with national and international security hazard. Elaborated terminological framework allows for the construction of self-sufficient semantic content for biological safety provision, subject to formalization in legislative, normative and methodological respects and indicative of improvement as regards organizational and structural-functional groundwork of the Russian Federation National chemical and biological safety system, which is to become topical issue of Part 3.

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

    SciTech Connect

    Durkee, Jr., Joe W.

    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

  7. Collagen oligomers modulate physical and biological properties of three-dimensional self-assembled matrices.

    PubMed

    Bailey, J L; Critser, P J; Whittington, C; Kuske, J L; Yoder, M C; Voytik-Harbin, S L

    2011-02-01

    Elucidation of mechanisms underlying collagen fibril assembly and matrix-induced guidance of cell fate will contribute to the design and expanded use of this biopolymer for research and clinical applications. Here, we define how Type I collagen oligomers affect in-vitro polymerization kinetics as well as fibril microstructure and mechanical properties of formed matrices. Monomers and oligomers were fractionated from acid-solubilized pig skin collagen and used to generate formulations varying in monomer/oligomer content or average polymer molecular weight (AMW). Polymerization half-times decreased with increasing collagen AMW and closely paralleled lag times, indicating that oligomers effectively served as nucleation sites. Furthermore, increasing AMW yielded matrices with increased interfibril branching and had no correlative effect on fibril density or diameter. These microstructure changes increased the stiffness of matrices as evidenced by increases in both shear storage and compressive moduli. Finally, the biological relevance of modulating collagen AMW was evidenced by the ability of cultured endothelial colony forming cells to sense associated changes in matrix physical properties and alter vacuole and capillary-like network formation. This work documents the importance of oligomers as another physiologically-relevant design parameter for development and standardization of polymerizable collagen formulations to be used for cell culture, regenerative medicine, and engineered tissue applications. PMID:20740490

  8. 1994 Baseline biological studies for the Device Assembly Facility at the Nevada Test Site

    SciTech Connect

    Townsend, Y.E.; 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.

  9. Nanoscale assembly in biological systems: from neuronal cytoskeletal proteins to curvature stabilizing lipids.

    PubMed

    Safinya, Cyrus R; Raviv, Uri; Needleman, Daniel J; Zidovska, Alexandra; Choi, Myung Chul; Ojeda-Lopez, Miguel A; Ewert, Kai K; Li, Youli; Miller, Herbert P; Quispe, Joel; Carragher, Bridget; Potter, Clinton S; Kim, Mahn Won; Feinstein, Stuart C; Wilson, Leslie

    2011-05-24

    The review will describe experiments inspired by the rich variety of bundles and networks of interacting microtubules (MT), neurofilaments, and filamentous-actin in neurons where the nature of the interactions, structures, and structure-function correlations remain poorly understood. We describe how three-dimensional (3D) MT bundles and 2D MT bundles may assemble, in cell free systems in the presence of counter-ions, revealing structures not predicted by polyelectrolyte theories. Interestingly, experiments reveal that the neuronal protein tau, an abundant MT-associated-protein in axons, modulates the MT diameter providing insight for the control of geometric parameters in bio- nanotechnology. In another set of experiments we describe lipid-protein-nanotubes, and lipid nano-tubes and rods, resulting from membrane shape evolution processes involving protein templates and curvature stabilizing lipids. Similar membrane shape changes, occurring in cells for the purpose of specific functions, are induced by interactions between membranes and proteins. The biological materials systems described have applications in bio-nanotechnology.

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

    SciTech Connect

    Hjelm, R.P.; Thiyagarajan, P.; Hoffman, A.; Alkan-Onyuksel, H.

    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.

  11. 15 CFR Supplement No. 1 to Part 742 - Nonproliferation of Chemical and Biological Weapons

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 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...

  12. 15 CFR Supplement No. 1 to Part 742 - Nonproliferation of Chemical and Biological Weapons

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 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...

  13. 15 CFR Supplement No. 1 to Part 742 - Nonproliferation of Chemical and Biological Weapons

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 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...

  14. 15 CFR Supplement No. 1 to Part 742 - Nonproliferation of Chemical and Biological Weapons

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 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...

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

    Code of Federal Regulations, 2010 CFR

    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...

  16. TiO2 thin films self-assembled with a partly fluorinated surfactant template.

    PubMed

    Henderson, Mark J; Zimny, Kevin; Blin, Jean-Luc; Delorme, Nicolas; Bardeau, Jean-François; Gibaud, Alain

    2010-01-19

    New TiO(2) films have been self-assembled on solid substrate by dip-coating using TiCl(4) as the titanium source and the partly fluorinated surfactant F(CF(2))(8)C(2)H(4)(OC(2)H(4))(9)OH as the liquid crystal template. By control over the dip-withdrawal speed, film thicknesses from a minimum of 43 nm were produced with rms roughnesses of 0.5-0.7 nm. The films were characterized by X-ray reflectivity, grazing incidence small-angle X-ray scattering, atomic force microscopy, contact angle measurements, and Raman spectroscopy. Their GI-SAXS patterns are characteristic of a 2-D hexagonal structure in which tubular rods of the fluorinated surfactant are packed hexagonally and aligned parallel to the substrate. Reflectivity and contact angle measurements of the as-prepared film indicate that a low-density hydrophilic TiO(2) surface presents to the air. PMID:19754061

  17. 16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height...

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

    SciTech Connect

    Talamo, A.; Gohar, Y.

    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.

  19. Efficient Assembly of DNA Using Yeast Homologous Recombination (YHR).

    PubMed

    Chandran, Sunil; Shapland, Elaine

    2017-01-01

    The assembly of multiple DNA parts into a larger DNA construct is a requirement in most synthetic biology laboratories. Here we describe a method for the efficient, high-throughput, assembly of DNA utilizing the yeast homologous recombination (YHR). The YHR method utilizes overlapping DNA parts that are assembled together by Saccharomyces cerevisiae via homologous recombination between designed overlapping regions. Using this method, we have successfully assembled up to 12 DNA parts in a single reaction. PMID:27671941

  20. The study on large space structure assembly technology: The study on deployable truss structure, part 1

    NASA Astrophysics Data System (ADS)

    1993-03-01

    An overview of the results of the study on large structure assembly technology is presented. The following aspects of the study are outlined: (1) placement and scope of the study; (2) study on large structure assembly technology, establishment of the dimensional requirements for the deployable structure, and extraction of critical elements in deployable structure system technology; (3) design study on critical elements, including study on the deployable structure systems, design study on one dimensional deployable truss structure and element technologies, and study on deployment simulation software and deployment test equipment; (4) planning of the trial production and test program; and (5) WBS (Work Breakdown Structure) for the deployable assembly structure study.

  1. Self-assembly and nanofabrication approaches towards photonics and plasmonics: Part I: Directed assembly of inorganic nanostructures through chemical and biomimetic templating. Part II: Fabrication of plasmon resonant structures for surface-enhanced sensing and fluorescence

    NASA Astrophysics Data System (ADS)

    Zin, Melvin T.

    Applications of inorganic nanostructures in sensing and optoelectronics are limited by the methods currently available to spatially organize them into desired configurations on solid supports. To address these challenges, a method combining "top-down" lithography and "bottom-up" self-assembly was employed to fabricate nanostructured systems using organic, inorganic and biological building blocks. Lithographic techniques, such as electron beam, colloidal and soft lithography, were used to pattern functional organic molecules and genetically engineered peptides on Au, SiO2/Si, mica and glass substrates with feature sizes ranging from sub-100nm to microscale over a large surface area (1--5 cm2). These surfaces present chemical functionalities or biomolecular recognition to direct the self-assembly of Au nanoparticles and CdSe-ZnS core-shell quantum dots into well-defined arrays in a site-specific, parallel manner. In addition to the lateral ordering imposed by these templates, placement of quantum dots on patterned Ag and Au nanostructures was controlled vertically through layer-by-layer assembly of molecular spacers. This allowed the construction of tunable arrays of quantum dots with surface-plasmon-enhanced fluorescence. In addition to the directed self-assembly of inorganic nanostructures, a novel nanofabrication technique was also developed to generate a new class of periodically arrayed plasmon resonant structures with unique topographical characteristics for ultra-sensitive surface-enhanced molecular sensing.

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed

    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.

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

    ERIC Educational Resources Information Center

    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…

  5. GenoLIB: a database of biological parts derived from a library of common plasmid features.

    PubMed

    Adames, Neil R; Wilson, Mandy L; Fang, Gang; Lux, Matthew W; Glick, Benjamin S; Peccoud, Jean

    2015-05-26

    Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes because existing databases of plasmids and features are loosely organized. These databases often lack consistency in the way they identify and describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about the purpose of features. We have analyzed the annotations of a library of ∼2000 widely used plasmids to build a non-redundant database of plasmid features. We looked at the variability of plasmid features, their usage statistics and their distributions by feature type. We segmented the plasmid features by expression hosts. We derived a library of biological parts from the database of plasmid features. The library was formatted using the Synthetic Biology Open Language, an emerging standard developed to better organize libraries of genetic parts to facilitate synthetic biology workflows. As proof, the library was converted into GenoCAD grammar files to allow users to import and customize the library based on the needs of their research projects.

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

    PubMed

    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.

  7. Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging.

    PubMed

    Peck, Evan M; Battles, Paul M; Rice, Douglas R; Roland, Felicia M; Norquest, Kathryn A; Smith, Bradley D

    2016-05-18

    A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  10. NEW DEVELOPMENTS IN LOW TEMPERATURE PHYSICS : Part of the Activity Report to the IUPAP General Assembly

    NASA Astrophysics Data System (ADS)

    Hallock, Bob; Paalanen, Mikko

    2009-03-01

    Below you find part of the Activity Report to the IUPAP General Assembly, October 2008, by the present and previous Chairmen of C5. It provides an overview of the most important and recent developments in low temperature physics, much in line with the program of LT25. For the field of experimental low temperature physics, the ability to conduct research has been damaged by the dramatic increase in the price of liquid helium. In the United States for example, the price of liquid helium has approximately doubled over the past two years. This has led to a reduction in activity in many laboratories as the funding agencies have not quickly increased support in proportion. The increase in price of liquid helium has accelerated interest in the development and use of alternative cooling systems. In particular, pulse tube coolers are now available that will allow cryostats with modest cooling needs to operate dilution refrigerators without the need for repeated refills of liquid helium from external supply sources. Solid helium research has seen a dramatic resurgence. Torsional oscillator experiments have been interpreted to show that solid helium may undergo a transition to a state in which some of the atoms in the container do not follow the motion of the container, e.g. may be 'supersolid'. The observation is robust, but the interpretation is controversial. The shear modulus of solid helium undergoes a similar signature with respect to temperature. Experiments that should be expected to cause helium to flow give conflicting results. Theory predicts that a perfect solid cannot show supersolid behavior, but novel superfluid-like behavior should be seen in various defects that can exist in the solid, and vorticity may play a significant role. And, recently there have been reports of unusual mass decoupling in films of pure 4He on graphite surfaces as well as 3He-4He mixture films on solid hydrogen surfaces. These may be other examples of unusual superfluid-like behavior

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  13. Methods for disassembling, replacing and assembling parts of a steam cooling system for a gas turbine

    DOEpatents

    Wilson, Ian D.; Wesorick, Ronald R.

    2002-01-01

    The steam cooling circuit for a gas turbine includes a bore tube assembly supplying steam to circumferentially spaced radial tubes coupled to supply elbows for transitioning the radial steam flow in an axial direction along steam supply tubes adjacent the rim of the rotor. The supply tubes supply steam to circumferentially spaced manifold segments located on the aft side of the 1-2 spacer for supplying steam to the buckets of the first and second stages. Spent return steam from these buckets flows to a plurality of circumferentially spaced return manifold segments disposed on the forward face of the 1-2 spacer. Crossover tubes couple the steam supply from the steam supply manifold segments through the 1-2 spacer to the buckets of the first stage. Crossover tubes through the 1-2 spacer also return steam from the buckets of the second stage to the return manifold segments. Axially extending return tubes convey spent cooling steam from the return manifold segments to radial tubes via return elbows. The bore tube assembly, radial tubes, elbows, manifold segments and crossover tubes are removable from the turbine rotor and replaceable.

  14. Biomimetic assembly of the [FeFe] hydrogenase: synthetic mimics in a biological shell.

    PubMed

    Apfel, Ulf-Peter; Weigand, Wolfgang

    2013-11-25

    Combining synthetic chemistry and biology: A new method that allows the incorporation of synthetic [FeFe] hydrogenase mimics into the apo-hydrogenase is highlighted. Azadithiolato-functionalized model complexes showed similar activity to wild-type enzymes when implemented into the protein.

  15. Wholes that cause their parts: organic self-reproduction and the reality of biological teleology.

    PubMed

    Teufel, Thomas

    2011-06-01

    A well-rehearsed move among teleological realists in the philosophy of biology is to base the idea of genuinely teleological forms of organic self-reproduction on a type of causality derived from Kant. Teleological realists have long argued for the causal possibility of this form of causality--in which a whole is considered the cause of its parts--as well as formulated a set of teleological criteria of adequacy for it. What is missing, to date, is an account of the mereological principles that govern the envisioned whole-to-part causality. When the latter principles are taken into account, we find that there is no version of whole-to-part causality that is mereologically, causally and teleologically possible all at once, as teleological realism requires. PMID:21486664

  16. Fort Lewis College Indian Tuition Grants: Part II. Legislative Council Report to the Colorado General Assembly.

    ERIC Educational Resources Information Center

    Colorado State General Assembly, Denver. Legislative Council.

    The objective of Part II of the Colorado Legislative Council's Committee on American Indian Enrollment Problems report is to recommend policies and procedures for dealing with American Indian tuitions and Indian education at Fort Lewis College. The committee members worked with the Colorado congressional delegation and representatives of the U.S.…

  17. Simulations of impulsive laser scattering of biological protein assemblies: Application to M13 bacteriophage

    NASA Astrophysics Data System (ADS)

    Dykeman, Eric C.; Benson, Daryn; Tsen, K.-T.; Sankey, Otto F.

    2009-10-01

    We develop a theoretical framework, based on a bond-polarizability model, for simulating the impulsive force experienced on a protein or an assembly of proteins from a pulsed light source by coupling the laser electric field to an atomic distortion. The mechanism is impulsive stimulated Raman scattering (ISRS) where mechanical distortions produce variation in the electronic polarization through atomic displacements similar to vibrational Raman scattering. The magnitude of the impulsive force is determined from the empirical two-body bond-polarizability model and the intensity of the incident light. We apply the method to the M13 bacteriophage protein capsid system by performing several classical molecular-dynamics simulations that include the additional impulsive laser scattering force at various light intensities and pulse widths. The results of the molecular-dynamics simulations are then qualitatively interpreted with a simple harmonic oscillator model driven by ISRS. The intensity of light required to produce damage to the capsid in the simulations was found to be far higher than what was found in recent pulsed laser scattering experiments of M13 phage, suggesting that the observed inactivation of viruses with ultrashort laser pulses involves processes and/or mechanisms not taken into account in the present simulations.

  18. Waterborne firm coating for temporary protection of parts, providing controlled lubrication during assembly

    SciTech Connect

    Hayner, R.E.

    1987-03-03

    This patent describes a protective, emulsified oil in water, dispersible, lubricant coating composition having a pH in the range of about 7.0 to 10, and capable of application and flow on a threaded solid substrate consisting essentially of: A. about 65 to 99% by weight of a composition comprising: (1) about 0.5 to 30 parts by weight of organic wax components having a melting point above 50/sup 0/C, the wax container ester groups; (2) about 0.5 to 6 parts of a surfactant comprising 2 to 8% of carboxylic acid and about 1 to 5% of an amine, the acid and the amine forming a salt providing at least a portion of a surfactant; (3) about 10 to 30 parts of a coupling agent comprising a C/sub 5/-C/sub 30/ liquid hydrocarbon coupling component and a C/sub 2/-C/sub 20/ alcohol in the ratio of between 1:1 and 10:1 by weight respectively, selected from the group consisting of: mineral spirits, kerosene, ethylene glycol ether, butyl cellosolve, diethylene glycol monoethyl ether, ethylene glycol monopropyl ether, propyl cellosolve, ethyl cellosolve, diethylene glycol monoethyl ether, ethylene glycol monoacetate, diethylene glycol monoproprionate, diethylene glycol monoacetate, propylene glycol monoacetate, ethanol, isopropanol and isobutanol; and (4) about 30 to 97 parts of water the sum of all parts being equal to 100; and (B) about 3.5 to 9% total pigment comprising about 0.4 to 4% by weight carbon black.

  19. [Nutrition and biological value of food parts of a trade bivalve mollusk Anadara broughtoni].

    PubMed

    Tabakaeva, O V; Tabakaev, A V

    2015-01-01

    Currently, the human diet includes different new products of seafishing, including non-fish--bivalves and gastropods, holothurias, echinoderms, jellyfishes that demands careful studying of their chemical composition. The purpose of the study was to determine the nutritional and biological value of all soft parts of the burrowing bivalve MOLLUSK Anadara broughtoni from the Far East region. It was established thatfood parts of a bivalve were significantly flooded (water content--73.5-84.2%), with the minimum water content in the adductor and maximum in the mantle. Dry solids are presented by organic (89-93%) and mineral (7-11%) components. Organic components consist of protein (14.6-20.7%), lipids (1.8-2.3%), carbohydrates (2.1-2.6%). The analysis of amino-acid composition of proteins of food parts of the mollusk of Anadara broughtonishowed the presence of all essential amino acids with slight differences in their content depending on the localization of the protein. All edible parts have tryptophan as the limiting amino acid. Muscle proteins have maximum level of lysine, methionine, cysteine, phenylalanine and tyrosine; mantle proteins--leucine, isoleucine and threonine; adductor proteins--valine, phenylalanine, tyrosine, methionine and cysteine. Predominant nonessential amino acids forproteins of all food pieces are glycine, aspartic acid, glutamic acid, arginine. The coefficient of amino-acid score differences of adductor protein (31.7%) is less than the same of cloak by 3.7%. The indicator "biological value" is maximal for adductor (68.3%), but the differenceformuscle is only 0.83%. Mantle proteins are characterized by minimum biological value (64.6%). The coefficient of utility of amino acid composition of protein is maximalfor muscle (57.83%), and values for a cloak and an adductor differ slightly (55.81 and 55.96%). Taurine content in food parts of a mollusk Anadara broughtoni is rather high compared to with other bivalve mollusks of the Far East region

  20. [Nutrition and biological value of food parts of a trade bivalve mollusk Anadara broughtoni].

    PubMed

    Tabakaeva, O V; Tabakaev, A V

    2015-01-01

    Currently, the human diet includes different new products of seafishing, including non-fish--bivalves and gastropods, holothurias, echinoderms, jellyfishes that demands careful studying of their chemical composition. The purpose of the study was to determine the nutritional and biological value of all soft parts of the burrowing bivalve MOLLUSK Anadara broughtoni from the Far East region. It was established thatfood parts of a bivalve were significantly flooded (water content--73.5-84.2%), with the minimum water content in the adductor and maximum in the mantle. Dry solids are presented by organic (89-93%) and mineral (7-11%) components. Organic components consist of protein (14.6-20.7%), lipids (1.8-2.3%), carbohydrates (2.1-2.6%). The analysis of amino-acid composition of proteins of food parts of the mollusk of Anadara broughtonishowed the presence of all essential amino acids with slight differences in their content depending on the localization of the protein. All edible parts have tryptophan as the limiting amino acid. Muscle proteins have maximum level of lysine, methionine, cysteine, phenylalanine and tyrosine; mantle proteins--leucine, isoleucine and threonine; adductor proteins--valine, phenylalanine, tyrosine, methionine and cysteine. Predominant nonessential amino acids forproteins of all food pieces are glycine, aspartic acid, glutamic acid, arginine. The coefficient of amino-acid score differences of adductor protein (31.7%) is less than the same of cloak by 3.7%. The indicator "biological value" is maximal for adductor (68.3%), but the differenceformuscle is only 0.83%. Mantle proteins are characterized by minimum biological value (64.6%). The coefficient of utility of amino acid composition of protein is maximalfor muscle (57.83%), and values for a cloak and an adductor differ slightly (55.81 and 55.96%). Taurine content in food parts of a mollusk Anadara broughtoni is rather high compared to with other bivalve mollusks of the Far East region

  1. Design, synthesis and biological evaluation of novel pyrazoline-containing derivatives as potential tubulin assembling inhibitors.

    PubMed

    Qin, Ya-Juan; Li, Yu-jing; Jiang, Ai-Qin; Yang, Meng-Ru; Zhu, Qi-Zhang; Dong, Hong; Zhu, Hai-Liang

    2015-04-13

    A series of novel pyrazoline-containing derivatives (15-47) has been designed, synthesized and evaluated for their biological activities. Among them, compound 18 displayed the most potent antiproliferative activity against A549, MCF-7 and HepG-2 cells line (IC50 = 0.07 μM, 0.05 μM, 0.03 μM, respectively) and the tubulin polymerization inhibitory activity (IC50 = 1.88 μM), being comparable to CA-4. Furthermore, we also tested that compound 18 was a potent inducer of apoptosis in HepG-2 cells and it had cellular effects typical for microtubule interacting agents, causing accumulation of cells in the G2/M phase of the cell cycle. These studies, along with molecular docking, provided a new molecular scaffold for the further development of antitumor agents that target tubulin.

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

    PubMed

    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.

  3. Magnetic Orientation in Biology:. Virus Structure - Blood Clot Assembly - Cell Guidance

    NASA Astrophysics Data System (ADS)

    Torbet, J.

    2005-07-01

    Our childhood games with permanent magnets leave us with the impression that matter, in general, does not respond to a magnetic field. In reality, virtually everything is subjected to minute forces of attraction, repulsion or orientation. Strong fields combined with better understanding allow us to exploit these effects to tackle biological problems. In particular, the very weak diamagnetic anisotropy associated with individual molecules can give rise to high orientation of well organized structures such as crystals, liquid-crystals, semi-rigid polymers and individual cells. High orientation is often accompanied by better data and superior properties. In some circumstances, such as in crystallization, the orientating torque might induce effects over and above simple orientation. Magnetic field orientation has a number of advantages over other orienting techniques. Drawing or spinning produce fibers and can alter structure or cause damage while template methods invariable work only over a short range. The application of an electric field can cause heating and electrophoresis. In contrast, a magnetic field acts at a distance allowing uniform orientation in bulk and the creation of composites with components having different orientations. The contribution that magnetic orientation has made to a range of biological topics is illustrated by briefly describing a number of examples. For example, it has been a boon to x-ray studies of some non-crystalline filamentous complexes (e.g. fibrin, actin, microtubules, bacterial flagella and filamentous viruses) and is being vigorously exploited in NMR. The blood-clot polymer, fibrin, forms highly oriented gels when polymerized in a strong field and a number of its properties have been elucidated as a result. Magnetically oriented scaffolds of collagen, the major connective tissue protein, and fibrin are being used to study cell contact guidance. Oriented biomaterials might eventually be incorporated into specialized wound

  4. Systematic, spatial imaging of large multimolecular assemblies and the emerging principles of supramolecular order in biological systems

    PubMed Central

    Schubert, Walter

    2013-01-01

    Understanding biological systems at the level of their relational (emergent) molecular properties in functional protein networks relies on imaging methods, able to spatially resolve a tissue or a cell as a giant, non-random, topologically defined collection of interacting supermolecules executing myriads of subcellular mechanisms. Here, the development and findings of parameter-unlimited functional super-resolution microscopy are described—a technology based on the fluorescence imaging cycler (IC) principle capable of co-mapping thousands of distinct biomolecular assemblies at high spatial resolution and differentiation (<40 nm distances). It is shown that the subcellular and transcellular features of such supermolecules can be described at the compositional and constitutional levels; that the spatial connection, relational stoichiometry, and topology of supermolecules generate hitherto unrecognized functional self-segmentation of biological tissues; that hierarchical features, common to thousands of simultaneously imaged supermolecules, can be identified; and how the resulting supramolecular order relates to spatial coding of cellular functionalities in biological systems. A large body of observations with IC molecular systems microscopy collected over 20 years have disclosed principles governed by a law of supramolecular segregation of cellular functionalities. This pervades phenomena, such as exceptional orderliness, functional selectivity, combinatorial and spatial periodicity, and hierarchical organization of large molecular systems, across all species investigated so far. This insight is based on the high degree of specificity, selectivity, and sensitivity of molecular recognition processes for fluorescence imaging beyond the spectral resolution limit, using probe libraries controlled by ICs. © 2013 The Authors. Journal of Molecular Recognition published by John Wiley & Sons, Ltd. PMID:24375580

  5. Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Stepanauskas, Ramunas [Bigelow Laboratory

    2016-07-12

    DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  6. Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Stepanauskas, Ramunas

    2011-10-13

    DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Facile synthesis of AIE-active amphiphilic polymers: Self-assembly and biological imaging applications.

    PubMed

    Long, Zi; Liu, Meiying; Wang, Ke; Deng, Fengjie; Xu, Dazhuang; Liu, Liangji; Wan, Yiqun; Zhang, Xiaoyong; Wei, Yen

    2016-09-01

    In this work, we reported a rather facile method for fabrication of ultrabright, well dispersible and biocompatible fluorescent organic nanoparticles (FONs) with aggregation-induced emission (AIE) properties through combination of esterification and ring-opening reaction. The hydroxyl groups of Pluronic F127 was first reacted with the chloride of trimellitic anhydride chloride (TMAC), and its anhydride groups were further reacted with the amino groups of amino-terminated AIE dye (PhNH2) through ring-opening reaction. The optical properties, biocompatibility as well as cell uptake behavior of these obtained AIE-active nanoparticles (F127-TMAC-PhNH2 FONs) were examined by a series of characterization techniques and assays. We demonstrated that uniform organic nanoparticles with high water dispersibility, strong luminescence and desirable biocompatibility can be facilely obtained, which are promising for biological imaging applications. More importantly, a number of carboxyl groups were introduced into these AIE-active nanoparticles, which can be further utilized for further conjugation reaction and carrying anticancer drugs such as cisplatin. Therefore, the strategy of described in this work should be a simple and useful route for fabrication of multifunctional AIE-active luminescent nanotheranostic systems. PMID:27207057

  8. Bottom-up Assembly of RNA Arrays and Superstructures as Potential Parts in Nanotechnology.

    PubMed

    Shu, Dan; Moll, Wulf-Dieter; Deng, Zhaoxiang; Mao, Chengde; Guo, Peixuan

    2004-09-01

    DNA and protein have been extensively scrutinized for feasibility as parts in nanotechnology, but another natural building block, RNA, has been largely ignored. RNA can be manipulated to form versatile shapes, thus providing an element of adaptability to DNA nanotechnology, which is predominantly based upon a double-helical structure. The DNA-packaging motor of bacterial virus phi29 contains six DNA-packaging RNAs (pRNA), which together form a hexameric ring via loop/loop interaction. Here we report that this pRNA can be redesigned to form a variety of structures and shapes, including twins, tetramers, rods, triangles, and 3D arrays several microns in size via interaction of programmed helical regions and loops. Three dimensional RNA array formation required a defined nucleotide number for twisting of the interactive helix and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH.

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

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal...; MANDATORY MEAT AND POULTRY PRODUCTS INSPECTION AND VOLUNTARY INSPECTION AND CERTIFICATION POULTRY PRODUCTS... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time...

  10. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal...; MANDATORY MEAT AND POULTRY PRODUCTS INSPECTION AND VOLUNTARY INSPECTION AND CERTIFICATION POULTRY PRODUCTS... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time...

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

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal...; MANDATORY MEAT AND POULTRY PRODUCTS INSPECTION AND VOLUNTARY INSPECTION AND CERTIFICATION POULTRY PRODUCTS... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time...

  12. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal...; MANDATORY MEAT AND POULTRY PRODUCTS INSPECTION AND VOLUNTARY INSPECTION AND CERTIFICATION POULTRY PRODUCTS... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time...

  13. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY ORGANIZATION AND TERMINOLOGY... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time...

  14. Supramolecular assembly of biological molecules purified from bovine nerve cells: from microtubule bundles and necklaces to neurofilament networks

    NASA Astrophysics Data System (ADS)

    Needleman, Daniel J.; Jones, Jayna B.; Raviv, Uri; Ojeda-Lopez, Miguel A.; Miller, H. P.; Li, Y.; Wilson, L.; Safinya, C. R.

    2005-11-01

    With the completion of the human genome project, the biosciences community is beginning the daunting task of understanding the structures and functions of a large number of interacting biological macromolecules. Examples include the interacting molecules involved in the process of DNA condensation during the cell cycle, and in the formation of bundles and networks of filamentous actin proteins in cell attachment, motility and cytokinesis. In this proceedings paper we present examples of supramolecular assembly based on proteins derived from the vertebrate nerve cell cytoskeleton. The axonal cytoskeleton in vertebrate neurons provides a rich example of bundles and networks of neurofilaments, microtubules (MTs) and filamentous actin, where the nature of the interactions, structures, and structure-function correlations remains poorly understood. We describe synchrotron x-ray diffraction, electron microscopy, and optical imaging data, in reconstituted protein systems purified from bovine central nervous system, which reveal unexpected structures not predicted by current electrostatic theories of polyelectrolyte bundling, including three-dimensional MT bundles and two-dimensional MT necklaces.

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

    SciTech Connect

    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.

  16. Peptide-directed self-assembly of functionalized polymeric nanoparticles. Part II: effects of nanoparticle composition on assembly behavior and multiple drug loading ability.

    PubMed

    Xiang, Xu; Ding, Xiaochu; Moser, Trevor; Gao, Qi; Shokuhfar, Tolou; Heiden, Patricia A

    2015-04-01

    Peptide-functionalized polymeric nanoparticles were designed and self-assembled into continuous nanoparticle fibers and three-dimensional scaffolds via ionic complementary peptide interaction. Different nanoparticle compositions can be designed to be appropriate for each desired drug, so that the release of each drug is individually controlled and the simultaneous sustainable release of multiple drugs is achieved in a single scaffold. A self-assembled scaffold membrane was incubated with NIH3T3 fibroblast cells in a culture dish that demonstrated non-toxicity and non-inhibition on cell proliferation. This type of nanoparticle scaffold combines the advantages of peptide self-assembly and the versatility of polymeric nanoparticle controlled release systems for tissue engineering.

  17. Qualification Testing of Solid Rocket Booster Diagonal Strut Restraint Cable Assembly Part Number 10176-0031-102/103

    NASA Technical Reports Server (NTRS)

    Malone, T. W.

    2006-01-01

    This Technical Memorandum presents qualification test results for solid rocket booster diagonal strut restraint cable part number 101276-00313-102/103. During flight this assembly is exposed to a range of temperatures. MIL-W-83420 shows the breaking strength of the cable as 798 kg (1,760 lb) at room temperature but does not define cable strength at the maximum temperature to which the cable is exposed during the first 2 min of flight; 669 C (1,236 F). The cable, which can be built from different corrosion resistant steel alloys, may also vary in its chemical, physical, and mechanical properties at temperature. Negative margins of safety were produced by analysis of the cable at temperature using standard knockdown factors. However, MSFC-HDBK-5 allows the use of a less conservative safety factor of 1.4 and knockdown factors verified by testing. Test results allowed a calculated knockdown factor of 0.1892 to be determined for the restraint cables, which provides a minimum breaking strength of 151 kg (333 lb) at 677 C (1,250 F) when combined with the minimum breaking strength of 0.317-cm (0.125- or 1/8-in) diameter, type 1 composition rope.

  18. The synthesis and characterization of self-assembling peptides bearing organic-electronic units for the development of biologically active nanowires

    NASA Astrophysics Data System (ADS)

    Diegelmann, Stephen Robert

    The development of complex self-assembling supramolecular systems derived from single, and sometimes simple, molecules has become an area of vast interest. These molecules are specifically designed to foster favorable intermolecular interactions leading to highly ordered macromolecular assemblies through 'bottom-up' fabrication with size dimensions that are on the order of nanometers to tens of microns. Self-assembling amyloid-like nanostructures provide biologically relevant systems that can be harnessed for the development of novel nanobiomaterials. Amyloid-like materials are composed of well-defined one dimensional (1-D) structures that can be used as scaffolding for controlled organization of organic electronic materials in aqueous environments. We have developed and functionalized a wide array of organic semiconductors and incorporated them into oligopeptides designed to self-assemble into 1-D amyloid-like nanofibers. These nanofibers have internalized intermolecularly delocalized pi-stacked oligothiophenes as well as linearly conjugated polydiacetylene (PDA) polymers running along the nanofiber long axis. These nanofibers can be globally aligned and fabricated into electronic devices that have a high degree of directionally dependent charge mobility. Preliminary experiments have also shown that these materials can be interfaced with biological systems with potential use as electro-active cell culture matrices.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed

    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. PMID:24395353

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

    PubMed

    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.

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

    PubMed

    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.

  3. Thematic mapper flight model preshipment review data package. Volume 4: Appendix. Part D: Focal plane assembly data

    NASA Technical Reports Server (NTRS)

    1982-01-01

    The data obtained for the Band 1 thematic mapper flight full band assembly (P/N 50797) are summarized. The data were collected from half band, post amplifier, and full band acceptance test data records.

  4. Higher -Order Assembly of BRCC36–KIAA0157 Is Required for DUB Activity and Biological Function

    PubMed Central

    Zeqiraj, Elton; Tian, Lei; Piggott, Christopher A.; Pillon, Monica C.; Duffy, Nicole M.; Ceccarelli, Derek F.; Keszei, Alexander F. A.; Lorenzen, Kristina; Kurinov, Igor; Orlicky, Stephen; Gish, Gerald D.; Heck, Albert J.R.; Guarné, Alba; Greenberg, Roger A.; Sicheri, Frank

    2015-01-01

    Summary BRCC36 is a Zn2+ dependent deubiquitinating enzyme (DUB) that hydrolyzes lysine-63-linked ubiquitin chains as part of distinct macromolecular complexes that participate in either interferon signaling or DNA-damage recognition. The MPN+ domain protein BRCC36 associates with pseudo-DUB MPN− proteins KIAA0157 or Abraxas, which are essential for BRCC36 enzymatic activity. To understand the basis for BRCC36 regulation, we have solved the structure of an active BRCC36-KIAA0157 heterodimer and an inactive BRCC36 homodimer. Structural and functional characterizations show how BRCC36 is switched to an active conformation by contacts with KIAA0157. Higher order association of BRCC36 and KIAA0157 into a dimer of heterodimers (super dimers) was required for DUB activity and interaction with targeting proteins SHMT2 and RAP80. These data provide the first explanation of how an inactive pseudo DUB allosterically activates a cognate DUB partner, and implicates super dimerization as a new regulatory mechanism underlying BRCC36 DUB activity, subcellular localization, and biological function. PMID:26344097

  5. Biological materials: Part A. tuning LCST of raft copolymers and gold/copolymer hybrid nanoparticles and Part B. Biobased nanomaterials

    NASA Astrophysics Data System (ADS)

    Chen, Ning

    The research described in this dissertation is comprised of two major parts. The first part studied the effects of asymmetric amphiphilic end groups on the thermo-response of diblock copolymers of (oligo/di(ethylene glycol) methyl ether (meth)acrylates, OEGA/DEGMA) and the hybrid nanoparticles of these copolymers with a gold nanoparticle core. Placing the more hydrophilic end group on the more hydrophilic block significantly increased the cloud point compared to a similar copolymer composition with the end group placement reversed. For a given composition, the cloud point was shifted by as much as 28 °C depending on the placement of end groups. This is a much stronger effect than either changing the hydrophilic/hydrophobic block ratio or replacing the hydrophilic acrylate monomer with the equivalent methacrylate monomer. The temperature range of the coil-globule transition was also altered. Binding these diblock copolymers to a gold core decreased the cloud point by 5-15 °C and narrowed the temperature range of the coil-globule transition. The effects were more pronounced when the gold core was bound to the less hydrophilic block. Given the limited numbers of monomers that are approved safe for in vivo use, employing amphiphilic end group placement is a useful tool to tune a thermo-response without otherwise changing the copolymer composition. The second part of the dissertation investigated the production of value-added nanomaterials from two biorefinery "wastes": lignin and peptidoglycan. Different solvents and spinning methods (melt-, wet-, and electro-spinning) were tested to make lignin/cellulose blended and carbonized fibers. Only electro-spinning yielded fibers having a small enough diameter for efficient carbonization (≤ 5-10 μm), but it was concluded that cellulose was not a suitable binder. Cellulose lignin fibers before carbonization showed up to 90% decrease in moisture uptake compared to pure cellulose. Peptidoglycan (a bacterial cell wall

  6. Apples: content of phenolic compounds vs. variety, part of apple and cultivation model, extraction of phenolic compounds, biological properties.

    PubMed

    Kalinowska, Monika; Bielawska, Aleksandra; Lewandowska-Siwkiewicz, Hanna; Priebe, Waldemar; Lewandowski, Włodzimierz

    2014-11-01

    Apples are among the most popular fruits in the world. They are rich in phenolic compounds, pectin, sugar, macro- and microelements. Applying different extraction techniques it is possible to isolate a particular group of compounds or individual chemicals and then test their biological properties. Many reports point to the antioxidant, antimicrobial, anticancer and many other beneficial effects of apple components that may have potential applications in food, pharmaceutical and cosmetic industries. This paper summarizes and compiles information about apple phenolic compounds, their biological properties with particular emphasis on health-related aspects. The data are reviewed with regard to different apple varieties, part of apple, cultivation model and methods of extraction. PMID:25282014

  7. Apples: content of phenolic compounds vs. variety, part of apple and cultivation model, extraction of phenolic compounds, biological properties.

    PubMed

    Kalinowska, Monika; Bielawska, Aleksandra; Lewandowska-Siwkiewicz, Hanna; Priebe, Waldemar; Lewandowski, Włodzimierz

    2014-11-01

    Apples are among the most popular fruits in the world. They are rich in phenolic compounds, pectin, sugar, macro- and microelements. Applying different extraction techniques it is possible to isolate a particular group of compounds or individual chemicals and then test their biological properties. Many reports point to the antioxidant, antimicrobial, anticancer and many other beneficial effects of apple components that may have potential applications in food, pharmaceutical and cosmetic industries. This paper summarizes and compiles information about apple phenolic compounds, their biological properties with particular emphasis on health-related aspects. The data are reviewed with regard to different apple varieties, part of apple, cultivation model and methods of extraction.

  8. [Topical issues of biological safety under current conditions. Part 3. Scientific provision for the national regulation of the biological safety framework in its broad interpretation].

    PubMed

    Onishchenko, G G; Smolensky, V Yu; Ezhlova, E B; Demina, Yu V; Toporkov, V P; Toporkov, A V; Lyapin, M N; Kutyrev, V V

    2014-01-01

    Consequent of investigation concerned with biological safety (BS) framework development in its broad interpretation, reflected in the Russian Federation State Acts, identified have been conceptual entity parameters of the up-to-date broad interpretation of BS, which have formed a part of the developed by the authors system for surveillance (prophylaxis, localization, indication, identification, and diagnostics) and control (prophylaxis, localization, and response/elimination) over the emergency situations of biological (sanitary-epidemiological) character. The System functionality is activated through supplying the content with information data which are concerned with monitoring and control of specific internal and external threats in the sphere of BS provision fixed in the Supplement 2 of the International Health Regulations (IHR, 2005), and with the previously characterized nomenclature of hazardous biological factors. The system is designed as a network-based research-and-practice tool for evaluation of the situation in the sphere of BS provision, as well as assessment of efficacy of management decision making as regards BS control and proper State policy implementation. Most of the system elements either directly or indirectly relate to the scope of activities conducted by Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, being substantial argument for allocating coordination functions in the sphere of BS provision to this government agency and consistent with its function as the State Coordinator on IHR (2005). The data collected serve as materials to Draft Federal Law "Concerning biological safety provision of the population". PMID:25971137

  9. [Topical issues of biological safety under current conditions. Part 3. Scientific provision for the national regulation of the biological safety framework in its broad interpretation].

    PubMed

    Onishchenko, G G; Smolensky, V Yu; Ezhlova, E B; Demina, Yu V; Toporkov, V P; Toporkov, A V; Lyapin, M N; Kutyrev, V V

    2014-01-01

    Consequent of investigation concerned with biological safety (BS) framework development in its broad interpretation, reflected in the Russian Federation State Acts, identified have been conceptual entity parameters of the up-to-date broad interpretation of BS, which have formed a part of the developed by the authors system for surveillance (prophylaxis, localization, indication, identification, and diagnostics) and control (prophylaxis, localization, and response/elimination) over the emergency situations of biological (sanitary-epidemiological) character. The System functionality is activated through supplying the content with information data which are concerned with monitoring and control of specific internal and external threats in the sphere of BS provision fixed in the Supplement 2 of the International Health Regulations (IHR, 2005), and with the previously characterized nomenclature of hazardous biological factors. The system is designed as a network-based research-and-practice tool for evaluation of the situation in the sphere of BS provision, as well as assessment of efficacy of management decision making as regards BS control and proper State policy implementation. Most of the system elements either directly or indirectly relate to the scope of activities conducted by Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, being substantial argument for allocating coordination functions in the sphere of BS provision to this government agency and consistent with its function as the State Coordinator on IHR (2005). The data collected serve as materials to Draft Federal Law "Concerning biological safety provision of the population".

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

    NASA Astrophysics Data System (ADS)

    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

    SciTech Connect

    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. Thematic mapper flight model preshipment review data package. Volume 4: Appendix. Part B: Scan mirror assembly data

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Data from the thematic mapper scan mirror assembly (SMA) acceptance test are presented. Documentation includes: (1) a list of the acceptance test discrepancies; (2) flight 1 SMA test data book; (3) flight 1 SMA environmental report; (4) the configuration verification index; (5) the flight 1 SMA test failure reports; (6) the flight 1 data tapes log; and (7) the requests for deviation/waivers.

  13. Space biology class as part of science education programs for high schools in Japan.

    PubMed

    Kamada, Motoshi; Takaoki, Muneo

    2004-11-01

    Declining incentives and scholastic abilities in science class has been concerned in Japan. The Ministry of Education, Culture, Sports, Science and Technology encourages schools to cooperate with research institutions to raise student's interest in natural sciences. The Science Partnership Program (SPP) and the Super Science High-School (SSH) are among such efforts. Our short SPP course consists of an introductory lecture on space biology in general and a brief laboratory practice on plant gravitropism. Space biology class is popular to students, despite of the absence of flight experiments. We suppose that students are delighted when they find that their own knowledge is not a mere theory, but has very practical applications. Space biology is suitable in science class, since it synthesizes mathematics, physics, chemistry and many other subjects that students might think uninteresting.

  14. Biology-Chemistry-Physics, Teachers' Guide, a Three-Year Sequence, Parts I and II.

    ERIC Educational Resources Information Center

    Scott, Arthur; And Others

    This is one of two teacher's guides for a three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee. This committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical Education Materials Study,…

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

    ERIC Educational Resources Information Center

    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. Energy from biological processes. Volume III. Appendixes, Part B: Agriculture, unconventional crops, and select biomass wastes

    SciTech Connect

    Not Available

    1980-09-01

    This volume contains the following working papers written for OTA to assist in preparation of the report, Energy from Biological Processes: The Potential of Producing Energy From Agriculture; Cropland Availability for Biomass Production; Energy From Agriculture: Unconventional Crops; Energy From Aquaculture Biomass Systems: Fresh and Brackish Water Aquatic Plants; Energy From Agriculture: Animal Wastes; and Energy From Agriculture: Agricultural Processing Wastes.

  17. Rapid Assembly of DNA via Ligase Cycling Reaction (LCR).

    PubMed

    Chandran, Sunil

    2017-01-01

    The assembly of multiple DNA parts into a larger DNA construct is a requirement in most synthetic biology laboratories. Here we describe a method for the efficient, high-throughput, assembly of DNA utilizing the ligase chain reaction (LCR). The LCR method utilizes non-overlapping DNA parts that are ligated together with the guidance of bridging oligos. Using this method, we have successfully assembled up to 20 DNA parts in a single reaction or DNA constructs up to 26 kb in size. PMID:27671935

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

    PubMed

    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.

  19. Imaging of Tumor Angiogenesis for Radiologists--Part 1: Biological and Technical Basis.

    PubMed

    García-Figueiras, Roberto; Padhani, Anwar R; Beer, Ambros J; Baleato-González, Sandra; Vilanova, Joan C; Luna, Antonio; Oleaga, Laura; Gómez-Caamaño, Antonio; Koh, Dow-Mu

    2015-01-01

    Angiogenesis is a key cancer hallmark involved in tumor growth and metastasis development. Tumor angiogenesis is the process whereby new blood vessels are formed to supply nutrients and oxygen to support the growth of tumors. This article reviews the biological basis behind imaging features and the different imaging modalities used to assess the status of tumor neovasculature in vivo at different scales: structural, functional, and molecular.

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

    SciTech Connect

    Not Available

    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.

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

    SciTech Connect

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

    PubMed Central

    Lapraz, Jean-Claude

    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-approach to life and based on new mathematical paradigms of pattern recognition. PMID:24381827

  3. Endobiogeny: a global approach to systems biology (part 1 of 2).

    PubMed

    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-approach to life and based on new mathematical paradigms of pattern recognition. PMID:24381827

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

    PubMed Central

    Lapraz, Jean-Claude; Pauly, Patrice

    2013-01-01

    Endobiogeny and the biology of functions are based on four scientific concepts that are known and generally accepted: (1) human physiology is complex and multifactorial and exhibits the properties of a system; (2) the endocrine system manages metabolism, which is the basis of the continuity of life; (3) the metabolic activity managed by the endocrine system results in the output of biomarkers that reflect the functional achievement of specific aspects of metabolism; and (4) when biomarkers are related to each other in ratios, it contextualizes one type of function relative to another to which is it linked anatomically, sequentially, chronologically, biochemically, etc. PMID:24416662

  5. New glycosylated conjugate copolymer N-acetyl-β-D-glucosaminyl-pluronic: Synthesis, self-assembly and biological assays.

    PubMed

    Frizon, Tiago Elias Allievi; Micheletto, Yasmine Miguel Serafini; Westrup, José Luiz; Wakabayashi, Priscila Sayoko Silva; Serafim, Francieli Rocha; Damiani, Adriani Paganini; Longaretti, Luiza Martins; de Andrade, Vanessa Moraes; Giacomelli, Fernando Carlos; Fort, Sébastien; Dal Bó, Alexandre Gonçalves

    2015-09-01

    This work describes the synthesis of a new glycosylated conjugate copolymer, GlcNAc-PEO75-PPO30-PEO75-GlcNAc (GlcNAc-PluronicF68-GlcNAc), using click chemistry from Pluronic(®) F68 and propargyl-2-N-acetamido-2-deoxy-β-D-glucopyranoside. Micelles were prepared by the self-assembly of GlcNAc-PluronicF68-GlcNAc in phosphate-buffered solution. The critical micelle concentration was determined by fluorescence spectroscopy, and the value was found to be equal to 5.8mgmL(-1). The Gibbs free energy (ΔG) of micellization is negative, indicating that the organization of amphiphiles is governed by the hydrophobic effects in an entropy-driven process. The scattering characterization of GlcNAc-PluronicF68-GlcNAc micelles showed a hydrodynamic radius of 8.7nm and negative zeta potential (-21.0±0.9mV). The TEM image evidences the spherical shape of the objects self-assemble into highly regular micelles having a mean diameter of 10nm. The SAXS profile confirmed the spherical shape of the assemblies comprising a swollen PPO core (Rcore=2.25nm) stabilized by PEO chains following Gaussian statistics. The results of the comet assay showed that the GlcNAc-PluronicF68-GlcNAc micelles were not genotoxic, and the cell viability test was higher than 97% for all concentrations, demonstrating that GlcNAc-PluronicF68-GlcNAc is not toxic. PMID:26123853

  6. Biological autoxidation. II. Cholesterol esters as inert barrier antioxidants. Self-assembly of porous membrane sacs. An hypothesis.

    PubMed

    Kon, S H

    1978-01-01

    The antioxidation defenses recognized thus far appear too weak. Needed are inert barriers to encapsulate foci of activated oxygen (FAOs) and contain their spreading. These capsules must: 1. self-assemble nonenzymatically and spontaneously in face of adversity; 2. resist oxidation and dissolution in water; and 3. be moderately fluid and elastic enough to withstand flexing by tissues. Evidence shows activated oxygen: a. is produced by common cholesterolester (CE)-raising agents; b. boosts accumulation of CEs; and c. splits low-density lipoproteins (LDL), thus releasing CE-rich coalescence-prone lipid micelles. I am proposing that CEs, combined with polar lipids, are uniquely suited to form inert-lipid antioxidation barriers (ILABs). Porous ILAB capsules self-assemble from lipid micelles released by oxidatively degraded LDL. The capsules are thermodynamically unstable but elastic, durable and capable of self-repair through oxidation of ambient LDL. All capsules tend to contract into spheres. Enclosed needle-like "foreign bodies", such as asbestos, puncture the contracting capsules. Hence the odd bulbous architecture of asbestos bodies. ILABs protect from--and their failure initiates and promotes--carcinogenesis and atherosclerosis. ILABs may be mediators of membrane biogenesis. The loss of arterial flexibility in atherosclerosis protects ILAB capsules from breakage. PMID:748727

  7. Assembly of Multigene Constructs Using Golden Gate Cloning.

    PubMed

    Marillonnet, Sylvestre; Werner, Stefan

    2015-01-01

    Efficient DNA assembly methods are required for synthetic biology. Standardization of DNA parts is an essential element that not only facilitates reuse of the same parts for various constructs but also allows standardization of the assembly strategy. We provide here a protocol for assembly of multigene constructs from standard biological parts using the modular cloning system MoClo. Making constructs using this system requires to first define the structure of the final construct and to identify all basic parts and vectors required for the construction strategy. The cloning strategy is in large part determined by the structure of the final construct, which is then made using a series of one-pot Golden Gate cloning reactions. PMID:26082229

  8. Spatiotemporal variation of metabolism in a plant circadian rhythm: the biological clock as an assembly of coupled individual oscillators.

    PubMed

    Rascher, U; Hütt, M T; Siebke, K; Osmond, B; Beck, F; Lüttge, U

    2001-09-25

    The complex dynamic properties of biological timing in organisms remain a central enigma in biology despite the increasingly precise genetic characterization of oscillating units and their components. Although attempts to obtain the time constants from oscillations of gene activity and biochemical units have led to substantial progress, we are still far from a full molecular understanding of endogenous rhythmicity and the physiological manifestations of biological clocks. Applications of nonlinear dynamics have revolutionized thinking in physics and in biomedical and life sciences research, and spatiotemporal considerations are now advancing our understanding of development and rhythmicity. Here we show that the well known circadian rhythm of a metabolic cycle in a higher plant, namely the crassulacean acid metabolism mode of photosynthesis, is expressed as dynamic patterns of independently initiated variations in photosynthetic efficiency (phi(PSII)) over a single leaf. Noninvasive highly sensitive chlorophyll fluorescence imaging reveals randomly initiated patches of varying phi(PSII) that are propagated within minutes to hours in wave fronts, forming dynamically expanding and contracting clusters and clearly dephased regions of phi(PSII). Thus, this biological clock is a spatiotemporal product of many weakly coupled individual oscillators, defined by the metabolic constraints of crassulacean acid metabolism. The oscillators operate independently in space and time as a consequence of the dynamics of metabolic pools and limitations of CO(2) diffusion between tightly packed cells.

  9. Study of cardiovascular disease biomarkers among tobacco consumers, part 2: biomarkers of biological effect

    PubMed Central

    Nordskog, Brian K.; Brown, Buddy G.; Marano, Kristin M.; Campell, Leanne R.; Jones, Bobbette A.; Borgerding, Michael F.

    2015-01-01

    Abstract An age-stratified, cross-sectional study was conducted in the US among healthy adult male cigarette smokers, moist snuff consumers, and non-tobacco consumers to evaluate cardiovascular biomarkers of biological effect (BoBE). Physiological assessments included flow-mediated dilation, ankle-brachial index, carotid intima-media thickness and expired carbon monoxide. Approximately one-half of the measured serum BoBE showed statistically significant differences; IL-12(p70), sICAM-1 and IL-8 were the BoBE that best differentiated among the three groups. A significant difference in ABI was observed between the cigarette smokers and non-tobacco consumer groups. Significant group and age effect differences in select biomarkers were identified. PMID:25787701

  10. A steady-state model for aerobic biological treatment: Part 1

    SciTech Connect

    McHarg, W.H. )

    1993-12-01

    In the aerobic biological treatment of wastewater, microorganisms use oxygen to decompose organic contaminants. Carbon dioxide, water and biosolids -- or sludge -- are the primary products. After a predetermined time in the reactor or aeration basin, the sludge is either removed from the process or sent to a clarifier, where it settles. Some of this sludge is recycled back to the aeration basin to initiate further oxidation, and some is removed from the process. In many aerobic processes, the average retention time of the sludge in the aeration basin -- called the sludge age -- is the main design parameter. However, other parameters, such as the rate of oxygen transfer rates and the capacity of the clarifier can affect the quality of the effluent. A simple mathematical model can be used to calculate these parameters.

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

    PubMed

    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.

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

    PubMed Central

    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

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

    PubMed

    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. PMID:26609063

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

    SciTech Connect

    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.

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

    PubMed

    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. 

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

    PubMed

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

    2014-01-01

    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.  PMID:25081274

  17. Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes.

    PubMed

    Wu, Zhiqiang; Tembrock, Luke R; Ge, Song

    2015-01-01

    DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, GU592209 was more similar to the reference genome (O. sativa: AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of GU592209 and KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Development and evaluation of a pliable biological valved conduit. Part II: Functional and hemodynamic evaluation.

    PubMed

    Sung, H W; Witzel, T H; Hata, C; Tu, R; Shen, S H; Lin, D; Noishiki, Y; Tomizawa, Y; Quijano, R C

    1993-04-01

    Many congenital cardiac malformations may require a valved conduit for the reconstruction of the right ventricular outflow tract. In spite of many endeavors made in the last 25 years, the clinical results of right ventricular outflow tract reconstruction with currently available valved conduits are still not satisfactory. Specific problems encountered clinically include suboptimal hemodynamic performance, conduit kinking or compression, and fibrous peeling from the luminal surface. To address these deficiencies, we undertook the development of a biological valved conduit: a bovine external jugular vein graft with a retained native valve cross-linked with a diglycidyl ether (DE). This study, using a canine model, was to evaluate the functional and hemodynamic performance of this newly developed valved conduit. Three 14 mm conduits, implanted as bypass grafts, right ventricle to pulmonary artery, were evaluated. The evaluation was conducted with a noninvasive color Doppler flow mapping system at pre-implantation, immediately post implantation, one- and three-months post implantation, and prior to retrieval (five-months post implantation). The two-dimensional tomographic inspection of the leaflet motion at various periods post implantation showed that the valvular leaflets in the DE treated conduit was quite pliable. No cardiac failure or valvular dysfunction was observed in any of the studied cases. The color Doppler flow mapping study demonstrated that the valve in the DE treated conduit was competent, with no conduit kinking or compression observed in any of the three cases. The spectral Doppler velocity study evidenced that the transvalvular pressure gradients of the DE treated conduit were minimal as compared to those of the currently available conduits. In conclusion, from the functional and hemodynamic performance points of view, this newly developed valved conduit is superior to those currently available. PMID:8325697

  1. Two New Flavonoids and Biological Activity of Astragalus abyssinicus (Hochst.) Steud. ex A. Rich. Aerial Parts.

    PubMed

    El Dib, R A; Soliman, H S M; Hussein, M H; Attia, H G

    2015-05-01

    2 new flavonoid glycosides, kaempferol 3-O-(4",6"-di-O-α-L-rhamnopyranosyl)-β-D-glucopyranoside (1) and quercetin 3-O-(4",6"-di-O-α-L-rhamnopyranosyl)-β-D-glucopyranoside (2), were isolated from the n-butanol soluble fraction of the methanol extract (BF) of Astragalus abyssinicus aerial parts, together with 3 known compounds, rutin (3), kaempferol 3-O-β-D-rutinoside (4) and 5,7,4'-trihydroxy-3'-methoxyisoflavone (5). The structures of the isolated compounds were characterized on the basis of UV, NMR and negative ESI-MS analyses. The BF fraction showed in vitro weak antibacterial activity against Staphylococcus aureus, while 2 and 3 exhibited in vitro antioxidant activity higher than ascorbic acid using DPPH free radical scavenging activity method.

  2. Test design description for the Fusion Materials Open Test Assembly (Fusion MOTA-2A): Volume 1A, Part 1

    SciTech Connect

    Bauer, R.E.

    1988-11-01

    This document encompasses the test requirements, hardware design, fabrication, and safety analysis for the Fusion Materials Open Test Assembly experiment for irradiation in FFTF Cycle 11 (Fusion MOTA-2A). Fusion MOTA is equally shared by the US Fusion Material (DOE), Japanese Fusion Materials (MONBUSHO), and BEATRIX-II (IEA) programs. In the interest of providing optimum use of the irradiation space in the Fusion MOTA-2A and LMR MOTA-1G, eight of the Fusion MOTA canisters will be placed in MOTA-1G and an equal number of LMR canisters placed in Fusion MOTA-2A (Powell/Doran 1988). This eliminates the need to process Fusion MOTA-2A through the IEM cell prior to insertion for FFTF Cycle 11A. The LMR MOTA design and safety analysis (Greenslade 1984) is the basis for much of this design and safety analysis report. This design description and safety analysis for the Fusion MOTA-2A is presented per the outline given in Chapter IV of the FTR User`s Guide (Taylor 1978). 35 refs., 17 figs., 9 tabs.

  3. Synthesis, characterization, molecular docking and biological studies of self assembled transition metal dithiocarbamates of substituted pyrrole-2-carboxaldehyde.

    PubMed

    Nami, Shahab A A; Ullah, Irfan; Alam, Mahboob; Lee, Dong-Ung; Sarikavakli, Nursabah

    2016-07-01

    A series of self assembled 3d transition metal dithiocarbamate, M(pdtc) [where M=Mn(II), Fe(II), Co(II), Ni(II) and Cu(II)] have been synthesized and spectroscopically characterized. The bidentate dithiocarbamate ligand Na2pdtc (Disodium-1,4-phenyldiaminobis (pyrrole-1-sulfino)dithioate) was prepared by insertion reaction of carbondisulfide with Schiff base, N,N'-bis-(1H-pyrrol-2-ylmethylene)-benzene-1,4-diamine (L1) in basic medium. The simple substitution reaction between the metal halide and Na2pdtc yielded the title complexes in moderate yields. However, the in situ procedure gives high yield with the formation of single product as evident by TLC. Elemental analysis, IR, (1)H and (13)C NMR spectra, UV-vis., magnetic susceptibility and conductance measurements were done to characterize the complexes, M(pdtc). All the evidences suggest that the complexes have tetrahedral geometry excepting Cu(II) which is found to be square planar. A symmetrical bidentate coordination of the dithiocarbamato moiety has been observed in all the complexes. The conductivity data show that the complexes are non-electrolyte in nature. The anti-oxidant activity of the ligand, Na2pdtc and its transition metal complexes, M(pdtc) have been carried out using DPPH and Cu(pdtc) was found to be most effective. The anti-microbial activity of the Na2pdtc and M(pdtc) complexes have been carried out and on this basis the molecular docking study of the most effective complex, Cu(pdtc) has also been reported. PMID:27197060

  4. The proliferation marker Chromatin Assembly Factor-1 is of clinical value in predicting the biological behaviour of salivary gland tumours.

    PubMed

    Staibano, Stefania; Mascolo, Massimo; Rocco, Alba; Lo Muzio, Lorenzo; Ilardi, Gennaro; Siano, Maria; Pannone, Giuseppe; Vecchione, Maria Luisa; Nugnes, Loredana; Califano, Luigi; Zamparese, Rosanna; Bufo, Pantaleo; De Rosa, Gaetano

    2011-01-01

    Salivary gland tumours (SGT) constitute a diagnostically challenging group of neoplasms with frequently unpredictable clinical outcome. The proliferation rate facilitates the identification of aggressive SGT. The Chromatin Assembly Factor-1 (CAF-1) is a major epigenetic regulator of nuclear chromatin organization during DNA replication. It plays a critical function in human tumourigenesis and has been proposed as a new proliferation and prognostic marker for some malignancies. This study focused on the role of CAF-1/p60 protein as a marker of clinical value for SGT. The expression of CAF-1/p60 was evaluated by immunohistochemistry on a retrospective series of 362 surgically excised benign and malignant SGT with different histogenesis and, when available, on fine-needle pre-surgical cytological biopsies. The resulting data were compared with traditional prognostic parameters, including the expression of the routine proliferation marker ki67/MIB1. CAF-1/p60 was detectable in all SGT, with highest degree of expression in metastasizing malignant tumours. Moreover, the cases of benign tumours which progressed to carcinoma during the follow-up, showed significantly higher CAF-1/p60 expression than non-progressing benign SGT, both on histological sections and cytological smears of the primary tumour. Cox's multiple regression analysis selected CAF-1/p60 expression as the best independent predictor of cancer development for benign SGT (p<0.0001), and the best independent predictor of metastasis onset for malignant tumours (p<0.0004). Overexpression of CAF-1/p60, on histological and/or cytological samples, characterizes malignant SGT with aggressive behaviour, irrespective of their specific histotype, and allows the early diagnosis of progression toward malignancy of morphologically benign tumours.

  5. Developments in the Tools and Methodologies of Synthetic Biology

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    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 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 considered likely to

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

    PubMed

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

    2012-01-01

    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 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 considered likely to

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

    PubMed

    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

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

    PubMed Central

    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

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

    PubMed Central

    Johnson, April; Akhundova, Gulshan; Aliyeva, Saida; Strelow, Lisa

    2015-01-01

    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 (EDPs), 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. PMID:26501051

  12. Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

    PubMed

    Stark, Holger; Chari, Ashwin

    2016-02-01

    Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination. PMID:26671943

  13. Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

    PubMed

    Stark, Holger; Chari, Ashwin

    2016-02-01

    Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination.

  14. Molecular dynamics simulations and neutron reflectivity as an effective approach to characterize biological membranes and related macromolecular assemblies.

    PubMed

    Darré, L; Iglesias-Fernandez, J; Kohlmeyer, A; Wacklin, H; Domene, C

    2015-10-13

    In combination with other spectroscopy, microscopy, and scattering techniques, neutron reflectivity is a powerful tool to characterize biological systems. Specular reflection of neutrons provides structural information at the nanometer and subnanometer length scales, probing the composition and organization of layered materials. Currently, analysis of neutron reflectivity data involves several simplifying assumptions about the structure of the sample under study, affecting the extraction and interpretation of information from the experimental data. Computer simulations can be used as a source of structural and dynamic data with atomic resolution. We present a novel tool to compare the structural properties determined by neutron reflectivity experiments with those obtained from molecular simulations. This tool allows benchmarking the ability of molecular dynamics simulations to reproduce experimental data, but it also promotes unbiased interpretation of experimentally determined quantities. Two application examples are presented to illustrate the capabilities of the new tool. The first example is the generation of reflectivity profiles for a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer from molecular dynamics simulations using data from both atomistic and coarse-grained models, and comparison with experimentally measured data. The second example is the calculation of lipid volume changes with temperature and composition from all atoms simulations of single and mixed 1,2-di-palmitoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC) bilayers. PMID:26574275

  15. Interlocked molecules: Aqueous assembly

    NASA Astrophysics Data System (ADS)

    Bai, Linyi; Zhao, Yanli

    2015-12-01

    The quantitative self-assembly of mechanically interlocked molecules in water, instead of organic solvents, opens up the possibility of such systems being used in a biological context where their functions can be interfaced with biomolecular systems.

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

    PubMed

    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.

  17. Nitric Oxide and Redox Regulation in the Liver: Part I General Considerations and Redox biology in Hepatitis

    PubMed Central

    Diesen, Diana L.; Kuo, Paul C.

    2010-01-01

    Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are created in normal hepatocytes and are critical for normal physiological 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, non-alcoholic). In part II of this review, we will review oxidative stress in common pathophysiological 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. PMID:20444470

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

    PubMed

    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.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    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

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

    NASA Astrophysics Data System (ADS)

    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

  2. [Design and construction of artificial biological systems for complex natural products biosynthesis].

    PubMed

    Wang, Jianfeng; Meng, Hailin; Xiong, Zhiqiang; Wang, Yong

    2013-08-01

    Natural products (NPs) are important drug pools for human disease prevention and treatment. The great advances in synthetic biology have greatly revolutionized the strategies of NPs development and production. This review entitled with design and construction of artificial biological systems for complex NPs biosynthesis, mainly introduced the progresses in artificial design of synthetic biological parts, naturally mining novel synthetic parts of NPs, the assembly & adaption of the artificial biological modules & systems.

  3. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... surface aeration, submerged aeration rates, biomass concentration, concentrations of organic compounds... the biomass concentration are obtained for the open biological treatment unit. After the site specific... concentrations; and (3) The biomass concentration in the open biological treatment unit. C. One...

  4. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... surface aeration, submerged aeration rates, biomass concentration, concentrations of organic compounds... the biomass concentration are obtained for the open biological treatment unit. After the site specific... concentrations; and (3) The biomass concentration in the open biological treatment unit. C. One...

  5. Automated assembly in space

    NASA Technical Reports Server (NTRS)

    Srivastava, Sandanand; Dwivedi, Suren N.; Soon, Toh Teck; Bandi, Reddy; Banerjee, Soumen; Hughes, Cecilia

    1989-01-01

    The installation of robots and their use of assembly in space will create an exciting and promising future for the U.S. Space Program. The concept of assembly in space is very complicated and error prone and it is not possible unless the various parts and modules are suitably designed for automation. Certain guidelines are developed for part designing and for an easy precision assembly. Major design problems associated with automated assembly are considered and solutions to resolve these problems are evaluated in the guidelines format. Methods for gripping and methods for part feeding are developed with regard to the absence of gravity in space. The guidelines for part orientation, adjustments, compliances and various assembly construction are discussed. Design modifications of various fasteners and fastening methods are also investigated.

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

    PubMed

    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

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

    PubMed

    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.

  8. Impact of Deforestation on Clouds and Rainfall On the Northern Part of the Proposed Mesoamerican Biological Corridor

    NASA Astrophysics Data System (ADS)

    Ray, D. K.; Nair, U. S.; Welch, R. M.; Lawton, R. O.

    2004-12-01

    Central America exhibits the typical pattern of complex deforestation now seen throughout the tropics. The region is a mixture of lowlands, mostly converted to agriculture, and mountainous regions, where pristine forests still persist. To protect the biodiversity of this region from further loss, a network of biological corridors and protected areas has been proposed by the governments of Central American countries and international organizations. The present study examines the impact of deforestation in the northern part of Central America on the proposed corridor network, the Mesoamerican Biological Corridor. We use high-resolution numerical model simulations using the Colorado State University Regional Atmospheric Modeling System (CSU RAMS) to study the impact of three types of conditions: 1) pristine, 2) current and 3) extensive deforestation. In addition, GOES-8 satellite imagery is used for comparing with the numerical simulations of cloud formation. Since vegetation in the proposed protected areas would is under maximum stress in the dry season, this study is focused in the dry season month of March. During the dry season, the soil dries progressively from the soil surface down to increasing depths. Contrary to expectations, in-situ measurements of soil moisture in Costa Rica show similar values both in forests and pastures in the dry season. Measured soil moisture values in March are around 10% of the field capacity in the upper few centimeters, increasing to values of around 30% at depths of 1 m. Yet, observations show that the vegetation in pasture regions is stressed at this time while vegetation in the forested regions is not affected, implying that the forest vegetation is accessing deep soil water. Similar behavior is expected in other regions of Central America. This observation has significant implications to the design of the numerical modeling experiments. Currently the vegetation parameterization used in the RAMS does not specify rooting depth

  9. Community assembly of biological soil crusts of different successional stages in a temperate sand ecosystem, as assessed by direct determination and enrichment techniques.

    PubMed

    Langhans, Tanja Margrit; Storm, Christian; Schwabe, Angelika

    2009-08-01

    In temperate regions, biological soil crusts (BSCs: complex communities of cyanobacteria, eukaryotic algae, bryophytes, and lichens) are not well investigated regarding community structure and diversity. Furthermore, studies on succession are rare. For that reason, the community assembly of crusts representing two successional stages (initial, 5 years old; and stable, >20 years old) were analyzed in an inland sand ecosystem in Germany in a plot-based approach (2 x 18 plots, each 20 x 20 cm). Two different methods were used to record the cyanobacteria and eukaryotic algae in these communities comprehensively: determination directly out of the soil and enrichment culture techniques. Additionally, lichens, bryophytes, and phanerogams were determined. We examine four hypotheses: (1) A combination of direct determination and enrichment culture technique is necessary to detect cyanobacteria and eukaryotic algae comprehensively. In total, 45 species of cyanobacteria and eukaryotic algae were detected in the study area with both techniques, including 26 eukaryotic algae and 19 cyanobacteria species. With both determination techniques, 22 identical taxa were detected (11 eukaryotic algae and 11 cyanobacteria). Thirteen taxa were only found by direct determination, and ten taxa were only found in enrichment cultures. Hence, the hypothesis is supported. Additionally, five lichen species (three genera), five bryophyte species (five genera), and 24 vascular plant species occurred. (2) There is a clear difference between the floristic structure of initial and stable crusts. The different successional stages are clearly separated by detrended correspondence analysis, showing a distinct structure of the community assembly in each stage. In the initial crusts, Klebsormidium flaccidum, Klebsormidium cf. klebsii, and Stichococcus bacillaris were important indicator species, whereas the stable crusts are especially characterized by Tortella inclinata. (3) The biodiversity of BSC taxa

  10. Community assembly of biological soil crusts of different successional stages in a temperate sand ecosystem, as assessed by direct determination and enrichment techniques.

    PubMed

    Langhans, Tanja Margrit; Storm, Christian; Schwabe, Angelika

    2009-08-01

    In temperate regions, biological soil crusts (BSCs: complex communities of cyanobacteria, eukaryotic algae, bryophytes, and lichens) are not well investigated regarding community structure and diversity. Furthermore, studies on succession are rare. For that reason, the community assembly of crusts representing two successional stages (initial, 5 years old; and stable, >20 years old) were analyzed in an inland sand ecosystem in Germany in a plot-based approach (2 x 18 plots, each 20 x 20 cm). Two different methods were used to record the cyanobacteria and eukaryotic algae in these communities comprehensively: determination directly out of the soil and enrichment culture techniques. Additionally, lichens, bryophytes, and phanerogams were determined. We examine four hypotheses: (1) A combination of direct determination and enrichment culture technique is necessary to detect cyanobacteria and eukaryotic algae comprehensively. In total, 45 species of cyanobacteria and eukaryotic algae were detected in the study area with both techniques, including 26 eukaryotic algae and 19 cyanobacteria species. With both determination techniques, 22 identical taxa were detected (11 eukaryotic algae and 11 cyanobacteria). Thirteen taxa were only found by direct determination, and ten taxa were only found in enrichment cultures. Hence, the hypothesis is supported. Additionally, five lichen species (three genera), five bryophyte species (five genera), and 24 vascular plant species occurred. (2) There is a clear difference between the floristic structure of initial and stable crusts. The different successional stages are clearly separated by detrended correspondence analysis, showing a distinct structure of the community assembly in each stage. In the initial crusts, Klebsormidium flaccidum, Klebsormidium cf. klebsii, and Stichococcus bacillaris were important indicator species, whereas the stable crusts are especially characterized by Tortella inclinata. (3) The biodiversity of BSC taxa

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Double fiber probe with a single fiber Bragg grating based on the capillary-driven self-assembly fabrication method for dimensional measurement of micro parts.

    PubMed

    Cui, Jiwen; Feng, Kunpeng; Hu, Yang; Li, Junying; Dang, Hong; Tan, Jiubin

    2015-12-28

    Focusing on the ultra-precision dimensional measurement of parts with micro-scale dimensions and high aspect ratios, a two-dimensional double fiber probe with a single fiber Bragg grating (DS-FBG probe) is investigated in detail in this paper. The theoretical analysis of the sensing principle is verified by spectrum simulations of the DS-FBG probe with a modified transfer matrix method using the strain distribution within the DS-FBG probe. The fabrication process and physical principle of the capillary-driven self-assembly of double fibers in the UV adhesive with a low viscosity are demonstrated. Experimental results indicate that resolutions of 30 nm in radial direction and 15 nm in axial direction can be achieved, and the short-term displacement drifts within 90 seconds are 28.0 nm in radial direction and 7.9 nm in axial direction, and the long-term displacement drifts within 1 hour are 61.3 nm in radial direction and 17.3 nm in axial direction. The repeatability of the probing system can reach 60 nm and the measurement result of a standard nozzle is 300.49 μm with a standard deviation of 20 nm. PMID:26831960

  13. Biologic Activity of Autologous, Granulocyte-Macrophage Colony Stimulating Factor Secreting Alveolar Soft Parts Sarcoma and Clear Cell Sarcoma Vaccines

    PubMed Central

    Goldberg, John; Fisher, David E.; Demetri, George D.; Neuberg, Donna; Allsop, Stephen A.; Fonseca, Catia; Nakazaki, Yukoh; Nemer, David; Raut, Chandrajit P.; George, Suzanne; Morgan, Jeffrey A.; Wagner, Andrew J.; Freeman, Gordon J.; Ritz, Jerome; Lezcano, Cecilia; Mihm, Martin; Canning, Christine; Hodi, F. Stephen; Dranoff, Glenn

    2015-01-01

    Purpose Alveolar soft parts sarcoma (ASPS) and clear cell sarcoma (CCS) are rare mesenchymal malignancies driven by chromosomal translocations that activate members of the microphthalmia transcription factor (MITF) family. However, in contrast to malignant melanoma, little is known about their immunogenicity. To learn more about the host response to ASPS and CCS, we conducted a phase I clinical trial of vaccination with irradiated, autologous sarcoma cells engineered by adenoviral mediated gene transfer to secrete granulocyte-macrophage colony stimulating factor (GM-CSF). Experimental Design Metastatic tumors from ASPS and CCS patients were resected, processed to single cell suspensions, transduced with a replication defective adenoviral vector encoding GM-CSF, and irradiated. Immunizations were administered subcutaneously and intradermally weekly times three and then every other week. Results Vaccines were successfully manufactured for 11 of the 12 enrolled patients. Eleven subjects received from 3 to 13 immunizations. Toxicities were restricted to grade 1–2 skin reactions at inoculation sites. Vaccination elicited local dendritic cell infiltrates and stimulated T cell mediated delayed type-hypersensitivity reactions to irradiated, autologous tumor cells. Antibody responses to tissue-type plasminogen activator (tTPA) and angiopoietins-1/2 were detected. Tumor biopsies showed programmed death-1 (PD-1) positive CD8+ T cells in association with PD ligand-1 (PD-L1) expressing sarcoma cells. No tumor regressions were observed. Conclusions Vaccination with irradiated, GM-CSF secreting autologous sarcoma cell vaccines is feasible, safe, and biologically active. Concurrent targeting of angiogenic cytokines and antagonism of the PD-1 negative regulatory pathway might intensify immune-mediated tumor destruction. PMID:25805798

  14. Radiation damage and repair in cells and cell components. Part 2. Physical radiations and biological significance. Final report

    SciTech Connect

    Fluke, D.J.

    1984-08-01

    The report comprises a teaching text, encompassing all physical radiations likely to be of biological interest, and the relevant biological effects and their significance. Topics include human radiobiology, delayed effects, radiation absorption in organisms, aqueous radiation chemistry, cell radiobiology, mutagenesis, and photobiology. (ACR)

  15. JAK/STAT signalling--an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology.

    PubMed

    Blätke, Mary Ann; Dittrich, Anna; Rohr, Christian; Heiner, Monika; Schaper, Fred; Marwan, Wolfgang

    2013-06-01

    Mathematical models of molecular networks regulating biological processes in cells or organisms are most frequently designed as sets of ordinary differential equations. Various modularisation methods have been applied to reduce the complexity of models, to analyse their structural properties, to separate biological processes, or to reuse model parts. Taking the JAK/STAT signalling pathway with the extensive combinatorial cross-talk of its components as a case study, we make a natural approach to modularisation by creating one module for each biomolecule. Each module consists of a Petri net and associated metadata and is organised in a database publically accessible through a web interface (). The Petri net describes the reaction mechanism of a given biomolecule and its functional interactions with other components including relevant conformational states. The database is designed to support the curation, documentation, version control, and update of individual modules, and to assist the user in automatically composing complex models from modules. Biomolecule centred modules, associated metadata, and database support together allow the automatic creation of models by considering differential gene expression in given cell types or under certain physiological conditions or states of disease. Modularity also facilitates exploring the consequences of alternative molecular mechanisms by comparative simulation of automatically created models even for users without mathematical skills. Models may be selectively executed as an ODE system, stochastic, or qualitative models or hybrid and exported in the SBML format. The fully automated generation of models of redesigned networks by metadata-guided modification of modules representing biomolecules with mutated function or specificity is proposed. PMID:23443149

  16. What Part of NO Don't You Understand? Some Answers to the Cardinal Questions in Nitric Oxide Biology*

    PubMed Central

    Hill, Bradford G.; Dranka, Brian P.; Bailey, Shannon M.; Lancaster, Jack R.; Darley-Usmar, Victor M.

    2010-01-01

    Nitric oxide (NO) regulates biological processes through signaling mechanisms that exploit its unique biochemical properties as a free radical. For the last several decades, the key aspects of the chemical properties of NO relevant to biological systems have been defined, but it has been a challenge to assign these to specific cellular processes. Nevertheless, it is now clear that the high affinity of NO for transition metal centers, particularly iron, and the rapid reaction of NO with oxygen-derived free radicals can explain many of its biological and pathological properties. Emerging studies also highlight a growing importance of the secondary metabolites of NO-dependent reactions in the post-translational modification of key metabolic and signaling proteins. In this minireview, we emphasize the current understanding of the biochemistry of NO and place it in a biological context. PMID:20410298

  17. Acute and Impaired Wound Healing: Pathophysiology and Current Methods for Drug Delivery, Part 1: Normal and Chronic Wounds: Biology, Causes, and Approaches to Care

    PubMed Central

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

    2012-01-01

    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. PMID:22713781

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

    PubMed

    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.

  19. Interfacial and mechanical properties of self-assembling systems

    NASA Astrophysics Data System (ADS)

    Carvajal, Daniel

    Self-assembly is a fascinating phenomena where interactions between small subunits allow them to aggregate and form complex structures that can span many length scales. These self-assembled structures are especially important in biology where they are necessary for life as we know it. This dissertation is a study of three very different self-assembling systems, all of which have important connections to biology and biological systems. Drop shape analysis was used to study the interfacial assembly of amphiphilic block copolymers at the oil/water interface. When biologically functionalyzed copolymers are used, this system can serve as a model for receptor-ligand interactions that are used by cells to perform many activities, such as interact with their surroundings. The physical properties of a self-assembling membrane system were quantified using membrane inflation and swelling experiments. These types of membranes may have important applications in medicine such as drug eluting (growth factor eluting) scaffolds to aid in wound healing. The factors affecting the properties of bis(leucine) oxalamide gels were also explored. We believe that this particular system will serve as an appropriate model for biological gels that are made up of fiber-like and/or rod-like structures. During the course of the research presented in this dissertation, many new techniques were developed specifically to allow/aid the study of these distinct self-assembling systems. For example, numerical methods were used to predict drop stability for drop shape analysis experiments and the methods used to create reproducibly create self-assembling membranes were developed specifically for this purpose. The development of these new techniques is an integral part of the thesis and should aid future students who work on these projects. A number ongoing projects and interesting research directions for each one of the projects is also presented.

  20. Comparative Phytochemical Analysis of Essential Oils from Different Biological Parts of Artemisia herba alba and Their Cytotoxic Effect on Cancer Cells

    PubMed Central

    Tilaoui, Mounir; Ait Mouse, Hassan; Jaafari, Abdeslam; Zyad, Abdelmajid

    2015-01-01

    Purpose Carrying out the chemical composition and antiproliferative effects against cancer cells from different biological parts of Artemisia herba alba. Methods Essential oils were studied by gas chromatography coupled to mass spectrometry (GC–MS) and their antitumoral activity was tested against P815 mastocytoma and BSR kidney carcinoma cell lines; also, in order to evaluate the effect on normal human cells, oils were tested against peripheral blood mononuclear cells PBMCs. Results Essential oils from leaves and aerial parts (mixture of capitulum and leaves) were mainly composed by oxygenated sesquiterpenes 39.89% and 46.15% respectively; capitulum oil contained essentially monoterpenes (22.86%) and monocyclic monoterpenes (21.48%); esters constituted the major fraction (62.8%) of stem oil. Essential oils of different biological parts studied demonstrated a differential antiproliferative activity against P815 and BSR cancer cells; P815 cells are the most sensitive to the cytotoxic effect. Leaves and capitulum essential oils are more active than aerial parts. Interestingly, no cytotoxic effect of these essential oils was observed on peripheral blood mononuclear cells. Conclusion Our results showed that the chemical composition variability of essential oils depends on the nature of botanical parts of Artemisia herba alba. Furthermore, we have demonstrated that the differential cytotoxic effect depends not only on the essential oils concentration, but also on the target cells and the botanical parts of essential oils used. PMID:26196123

  1. Structural biological composites: An overview

    NASA Astrophysics Data System (ADS)

    Meyers, Marc A.; Lin, Albert Y. M.; Seki, Yasuaki; Chen, Po-Yu; Kad, Bimal K.; Bodde, Sara

    2006-07-01

    Biological materials are complex composites that are hierarchically structured and multifunctional. Their mechanical properties are often outstanding, considering the weak constituents from which they are assembled. They are for the most part composed of brittle (often, mineral) and ductile (organic) components. These complex structures, which have risen from millions of years of evolution, are inspiring materials scientists in the design of novel materials. This paper discusses the overall design principles in biological structural composites and illustrates them for five examples; sea spicules, the abalone shell, the conch shell, the toucan and hornbill beaks, and the sheep crab exoskeleton.

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

    PubMed Central

    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

  3. Molecular Self-Assembly and Nanochemistry: A Chemical Strategy for the Synthesis of Nanostructures

    NASA Astrophysics Data System (ADS)

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

    1991-11-01

    Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent 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 noncovalent 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 nonbiological structures with dimensions of 1 to 10^2 nanometers (with molecular weights of 10^4 to 1010 daltons). 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.

  4. Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures.

    PubMed

    Whitesides, G M; Mathias, J P; Seto, C T

    1991-11-29

    Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent 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 noncovalent 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 nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). 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.

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

    PubMed

    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. PMID:19145154

  6. Switching from usual brand cigarettes to a tobacco-heating cigarette or snus: Part 3. Biomarkers of biological effect.

    PubMed

    Ogden, Michael W; Marano, Kristin M; Jones, Bobbette A; Morgan, Walter T; Stiles, Mitchell F

    2015-01-01

    A randomized, multi-center study of adult cigarette smokers switched to tobacco-heating cigarettes, snus or ultra-low machine yield tobacco-burning cigarettes (50/group) for 24 weeks was conducted. Evaluation of biomarkers of biological effect (e.g. inflammation, lipids, hypercoaguable state) indicated that the majority of consistent and statistically significant improvements over time within each group were observed in markers of inflammation. Consistent and statistically significant differences in pairwise comparisons between product groups were not observed. These findings are relevant to the understanding of biomarkers of biological effect related to cigarette smoking as well as the risk continuum across various tobacco products (ClinicalTrials.gov Identifier: NCT02061917). PMID:26525962

  7. Switching from usual brand cigarettes to a tobacco-heating cigarette or snus: Part 3. Biomarkers of biological effect

    PubMed Central

    Ogden, Michael W.; Marano, Kristin M.; Jones, Bobbette A.; Morgan, Walter T.; Stiles, Mitchell F.

    2015-01-01

    Abstract A randomized, multi-center study of adult cigarette smokers switched to tobacco-heating cigarettes, snus or ultra-low machine yield tobacco-burning cigarettes (50/group) for 24 weeks was conducted. Evaluation of biomarkers of biological effect (e.g. inflammation, lipids, hypercoaguable state) indicated that the majority of consistent and statistically significant improvements over time within each group were observed in markers of inflammation. Consistent and statistically significant differences in pairwise comparisons between product groups were not observed. These findings are relevant to the understanding of biomarkers of biological effect related to cigarette smoking as well as the risk continuum across various tobacco products (ClinicalTrials.gov Identifier: NCT02061917). PMID:26525962

  8. Biologic Treatments for Sports Injuries II Think Tank—Current Concepts, Future Research, and Barriers to Advancement, Part 2

    PubMed Central

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

    2016-01-01

    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. PMID:27099865

  9. Site Alteration Effects from Rocket Exhaust Impingement During a Simulated Viking Mars Landing. Part 2: Chemical and Biological Site Alteration

    NASA Technical Reports Server (NTRS)

    Husted, R. R.; Smith, I. D.; Fennessey, P. V.

    1977-01-01

    Chemical and biological alteration of a Mars landing site was investigated experimentally and analytically. The experimental testing was conducted using a specially designed multiple nozzle configuration consisting of 18 small bell nozzles. The chemical test results indicate that an engine using standard hydrazine fuel will contaminate the landing site with ammonia (50-500ppm), nitrogen (5-50ppm), aniline (0.01-0.5ppm), hydrogen cyanide (0.01-0.5ppm), and water. A purified fuel, with impurities (mostly aniline) reduced by a factor of 50-100, limits the amount of hydrogen cyanide and aniline to below detectable limits for the Viking science investigations and leaves the amounts of ammonia, nitrogen, and water in the soil unchanged. The large amounts of ammonia trapped in the soil will make interpretation of the organic analysis investigation results more difficult. The biological tests indicate that the combined effects of plume gases, surface heating, surface erosion, and gas composition resulting from the retrorockets will not interfere with the Viking biology investigation.

  10. Shoreline ecology program for Prince William Sound, Alaska, following the Exxon Valdez oil spill. Part 3: Biology

    SciTech Connect

    Gilfillan, E.S.; Page, D.S.; Harner, E.J.; Boehm, P.D.

    1995-12-31

    This study describes the biological results of a comprehensive shoreline ecology program designed to assess ecological recovery in Prince William Sound following the Exxon Valdez oil spill on march 24, 1989. The program is an application of the ``Sediment Quality Triad`` approach, combining chemical, toxicological, and biological measurements. The study was designed so that results could be extrapolated to the entire spill zone in Prince William Sound. The spill affected four major shoreline habitat types in Prince William Sound: pebble/gravel, boulder/cobble, sheltered bedrock, and exposed bedrock. The study design had two components: (1) one-time stratified random sampling at 64 sites representing four habitats and four oiling levels (including unoiled reference sites) and (2) periodic sampling at 12 nonrandomly chosen sites that included some of the most heavily oiled locations in the sound. Biological communities on rock surfaces and in intertidal and shallow subtidal sediments were analyzed for differences resulting from to oiling in each of 16 habitat/tide zone combinations. Statistical methods included univariate analyses of individual species abundances and community parameter variables (total abundance, species richness, and Shannon diversity), and multivariate correspondence analysis of community structure. 58 refs., 13 figs., 9 tabs.

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

    PubMed Central

    Bhikoo, Riyaz; Srinivasa, Sanket; Yu, Tzu-Chieh; Moss, David; Hill, Andrew G

    2011-01-01

    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. PMID:24212815

  12. Biologic Treatments for Sports Injuries II Think Tank—Current Concepts, Future Research, and Barriers to Advancement, Part 3

    PubMed Central

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

    2016-01-01

    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. PMID:27123466

  13. Self-assembled Ni/TiO{sub 2} nanocomposite anodes synthesized via electroless plating and atomic layer deposition on biological scaffolds

    SciTech Connect

    Gerasopoulos, K; Chen, X L; Culver, J N; Wang, Chunsheng; Ghodssi, Reza

    2010-01-01

    Ni(core)/TiO{sub 2}(shell) nanocomposite anodes were fabricated on three-dimensional, self-assembled nanotemplates of Tobacco mosaic virus using atomic layer deposition, exhibiting high capacities and rate capability and extremely low average capacity fading ([similar]0.024% per cycle) for [similar]1000 cycles.

  14. Mesoscale Polymer Assemblies

    NASA Astrophysics Data System (ADS)

    Choudhary, Satyan; Pham, Jonathan; Crosby, Alfred

    2015-03-01

    Materials encompassing structural hierarchy and multi-functionality allow for remarkable physical properties across different length scales. Mesoscale Polymer (MSP) assemblies provide a critical link, from nanometer to centimeter scales, in the definition of such hierarchical structures. Recent focus has been on exploiting these MSP assemblies for optical, electronic, photonics and biological applications. We demonstrate a novel fabrication method for MSP assemblies. Current fabrication methods restrict the length scale and volume of such assemblies. A new method developed uses a simple piezo-actuated motion for de-pinning of a polymer solution trapped by capillary forces between a flexible blade and a rigid substrate. The advantages of new method include ability to make MSP of monodisperse length and to fabricate sufficient volumes of MSP to study their physical properties and functionality in liquid dispersions. We demonstrate the application of MSP as filler for soft materials, providing rheological studies of the MSP with surrounding matrices.

  15. Observations on the biology of Afrotropical Hesperiidae (Lepidoptera). Part 9. Hesperiinae incertae sedis: Zingiberales feeders, genera of unknown biology and an overview of the Hesperiinae incertae sedis.

    PubMed

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

    2016-01-01

    The Afrotropical genera that have been recorded to feed on Zingiberales are documented. Partial life histories are presented for Erionota torus Evans (a South-East Asian species established in Mauritius), Semalea arela (Mabille), S. pulvina (Plötz), Xanthodisca vibius (Hewitson), X. rega (Mabille), Hypoleucis ophiusa (Hewitson), Caenides dacena (Hewitson), Osmodes adon (Mabille), Gretna cylinda (Hewitson) and Moltena fiara (Butler). Additional notes from the literature are provided on the genera Leona and Rhabdomantis. Notes on natural enemies of E. torus and M. fiara are included. We find that the Zingiberaceae and Costaceae feeding genera, Semalea, Xanthodiscus, Hypoleucis and Caenides (part) are united by a C-shaped raised rim to the prothoracic spiracle of the pupa. The pupa of Osmodes adon indicates this genus may have no close affinities to other Afrotropical genera for which the life history is known. The pupa of G. cylinda is unlike any other that we have documented and may reflect that this is the only species which we have found to be formed on the open leaf under surface rather than in a shelter. The early stages of M. fiara indicate affinities with Zophopetes and related genera. The paper concludes with a brief comparative discussion of the early stages of the Afrotropical Hesperiinae incertae sedis as a whole. There appear to be useful characters to group species by the ova and pupae but less so by the caterpillars. Based on pupae alone, the Hesperiinae incertae sedis might be divided into nine groups. PMID:27395548

  16. 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.

    PubMed

    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.

  17. 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.

    PubMed

    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.

  18. 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.

    PubMed

    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. PMID:25822804

  19. Novel biologic agents for non-Hodgkin lymphoma and chronic lymphocytic leukemia-part 2: adoptive cellular immunotherapy, small-molecule inhibitors, and immunomodulation.

    PubMed

    Siddiqi, Tanya; Rosen, Steven T

    2015-04-01

    Globally, the incidence of non-Hodgkin lymphoma is increasing. Aggressive non-Hodgkin lymphomas like diffuse large B-cell lymphoma are treated with curative intent in the frontline setting, but indolent diseases like chronic lymphocytic leukemia/small lymphocytic lymphoma are not considered to be curable in general. Additionally, relapsed/refractory non-Hodgkin lymphomas have a poor overall outcome, with treatment response durations often decreasing with each relapse. Novel therapies are sought to improve outcomes in this patient population. In a two-part review, we describe the promising new biologic therapies that have emerged over the last 5 years, some approved by the US Food and Drug Administration and others undergoing active investigation. In Part 1, we discussed monoclonal antibodies. Here, in Part 2, we discuss adoptive cellular immunotherapies, small-molecule inhibitors, and immunomodulatory agents. We also mention other novel therapies on the horizon.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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

    NASA Astrophysics Data System (ADS)

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

    SciTech Connect

    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.

  4. Nonclassical antifolates, part 3: synthesis, biological evaluation and molecular modeling study of some new 2-heteroarylthio-quinazolin-4-ones.

    PubMed

    Al-Omary, Fatmah A M; Hassan, Ghada S; El-Messery, Shahenda M; Nagi, Mahmoud N; Habib, El-Sayed E; El-Subbagh, Hussein I

    2013-05-01

    A new series of 2-heteroarylthio-6-substituted-quinazolin-4-one analogs was designed, synthesized, and evaluated for their in vitro DHFR inhibition, antimicrobial, and antitumor activities. Compounds 21, 25, and 39 proved to be active DHFR inhibitors with IC50 range of 0.3-0.8 μM. Compounds 25, 28, 33, 35 and 36 showed broad spectrum antimicrobial activity comparable to the known antibiotic gentamicin. Compound 29 showed broad spectrum antitumor activity toward several tumor cell lines with GI values range of 25.8-41.2%. Molecular modeling studies concluded that recognition with key amino acid Arg38 and Lys31 are essential for binding and biological activities. Flexible alignment; electrostatic and hydrophobic mappings revealed that the obtained model could be useful for the development of new DHFR inhibitors.

  5. Persistence of biological traces at inside parts of a firearm from a case of multiple familial homicide.

    PubMed

    Courts, Cornelius; Gahr, Britta; Madea, Burkhard; Schyma, Christian

    2014-07-01

    Backspatter from wounds caused by contact shots against a biological target had before been shown to be propelled into firearms' barrels where they can persist and be retrieved from as relevant forensic evidence. Herein, that insight was applied to the investigation of a case of multiple familial homicide with a firearm. Samples of backspatter were collected from the firearm using DNA-free swabs. DNA was extracted from the swabs, and 16 STR systems were PCR-amplified to generate DNA profiles of all victims shot by the firearm. The quality of the resulting DNA profiles was sufficient to exclude the perpetrator as donor and to differentiate the three closely related victims thereby proving that all three victims had been shot by the same firearm from very close or contact distance. A key insight gained from this case was that not only a firearms' barrel inside but other inner surfaces may be charged with profilable DNA.

  6. Development and evaluation of a pliable biological valved conduit. Part I: Preparation, biochemical properties, and histological findings.

    PubMed

    Noishiki, Y; Hata, C; Tu, R; Shen, S H; Lin, D; Sung, H W; Witzel, T; Wang, E; Thyagarajan, K; Tomizawa, Y

    1993-04-01

    Different types of external valved conduits have been used for the repair of complex congenital cardiac anomalies that may have otherwise been inoperable. However, an ideal conduit has yet to be found due to complications such as stenosis, thrombosis, calcification of the valve and graft wall, and "peeling" of the neointima. To address those problems, a new extracardiac valved conduit made of bovine jugular vein was developed and evaluated in a preliminary animal study. Harvested bovine vein containing a naturally existing valve was initially incorporated with protamine on the inner surface and then was cross-linked in diglycidyl ether (DE). Fixation with DE allowed the vein and its leaflets to retain a tissue-like elasticity. To provide antithrombogenicity to the graft, heparin was introduced into the lumen to bind ionically to the pre-entrapped protamine. The biological valved conduit of approximately 14 mm diameter was implanted from the right ventricle to pulmonary artery as bypass graft in three dogs. After implantation, the native main pulmonary artery was ligated between the anastomotic sites of the bypass conduit. No anticoagulant or antiplatelet drugs were administered after surgery. One DE-fixed valved conduit was retrieved at 3 months, and the others were removed at 5 months. Only small thrombus areas were found on the white luminal surfaces. The valves and the conduits maintained softness and pliability, similar to before implantation. Additionally, the collagen content, shrink temperature, and tanning index of this newly developed biological valved conduit before and after fixation were measured in the study.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8325696

  7. Joint assembly

    NASA Technical Reports Server (NTRS)

    Wilson, Andrew (Inventor); Punnoose, Andrew (Inventor); Strausser, Katherine (Inventor); Parikh, Neil (Inventor)

    2010-01-01

    A joint assembly is provided which includes a drive assembly and a swivel mechanism. The drive assembly features a motor operatively associated with a plurality of drive shafts for driving auxiliary elements, and a plurality of swivel shafts for pivoting the drive assembly. The swivel mechanism engages the swivel shafts and has a fixable element that may be attached to a foundation. The swivel mechanism is adapted to cooperate with the swivel shafts to pivot the drive assembly with at least two degrees of freedom relative to the foundation. The joint assembly allows for all components to remain encased in a tight, compact, and sealed package, making it ideal for space, exploratory, and commercial applications.

  8. Self-Assembly: How Nature Builds

    ERIC Educational Resources Information Center

    Jones, M. Gail; Falvo, Michael R.; Broadwell, Bethany; Dotger, Sharon

    2006-01-01

    Self-assembly or spontaneous assembly is a process in which materials build themselves without assistance. This process plays a central role in the construction of biological structures and materials such as cells, viruses, and bone, and also in abiotic processes like phase transitions and crystal formation. The principles of self-assembly help…

  9. Enhanced biological phosphorus removal from wastewater by biomass with different phosphorus contents, Part III: Anaerobic sources of reducing equivalents.

    PubMed

    Schuler, Andrew J; Jenkins, David

    2003-01-01

    Laboratory-scale sequencing batch reactors exhibiting enhanced biological phosphorus removal (EBPR) operated at different influent phosphorus/chemical oxygen demand (COD) ratios were analyzed to evaluate possible anaerobic sources of reducing equivalents. Assuming anaerobic glycogen degradation was the sole anaerobic reducing equivalent source, an anaerobic phase carbon balance showed that glycogen-accumulating metabolism (GAM)-dominated systems were nearly carbon-balanced, but that polyphosphate-accumulating metabolism (PAM)-dominated systems had end-anaerobic phase carbon deficits. An anaerobic-phase reducing equivalent balance showed a reducing equivalent excess for the GAM-dominated systems and a deficit for the PAM-dominated systems, suggesting that glycogen degradation was not the sole reducing equivalent source for PAM. Reducing equivalent balances showed that metabolic models including complete anaerobic tricarboxylic acid (TCA) cycle activity, partial TCA cycle activity, and the glyoxylate bypass could provide the reducing equivalents required in PAM. Metabolic precursors produced in glycolysis, the TCA cycle, or modified versions of the TCA cycle could allow anaerobic growth and account for the PAM carbon deficits. The importance of considering both PAM and GAM activity in evaluating EBPR metabolic models was illustrated.

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

    PubMed

    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.

  11. Chemical and biological studies of a new cigarette that primarily heats tobacco. Part 1. Chemical composition of mainstream smoke.

    PubMed

    Borgerding, M F; Bodnar, J A; Chung, H L; Mangan, P P; Morrison, C C; Risner, C H; Rogers, J C; Simmons, D F; Uhrig, M S; Wendelboe, F N; Wingate, D E; Winkler, L S

    1998-07-01

    A new-technology cigarette has been developed. While the new cigarette burns some tobacco, it does not use tobacco as the fuel to sustain combustion and provide heat to the cigarette. Rather, the new cigarette primarily heats tobacco thereby reducing products of smoke formation mechanisms such as tobacco combustion, tobacco pyrolysis and pyrosynthesis. The mainstream smoke composition from a cigarette based on the new design (TOB-HT) has been characterized in comparative chemical testing with two reference cigarettes using the FTC puffing regimen. Thermal properties, UV absorption characteristics, elemental composition and materials balance studies all suggest a simplified smoke aerosol. Twenty-five smoke constituents ("target compounds") identified by the scientific community as compounds that may contribute to the diseases statistically associated with smoking have also been measured. Mainstream smoke concentrations of most target compounds are significantly lower with the TOB-HT cigarette when compared with reference cigarettes in the ultra-light "tar" and light "tar" categories. Taken together, chemical analysis results suggest simplified TOB-HT smoke chemistry with marked reductions in specific chemicals reported to be biologically active.

  12. Chemical and biological studies of a new cigarette that primarily heats tobacco. Part 1. Chemical composition of mainstream smoke.

    PubMed

    Borgerding, M F; Bodnar, J A; Chung, H L; Mangan, P P; Morrison, C C; Risner, C H; Rogers, J C; Simmons, D F; Uhrig, M S; Wendelboe, F N; Wingate, D E; Winkler, L S

    1998-03-01

    A new-technology cigarette has been developed. While the new cigarette burns some tobacco, it does not use tobacco as the fuel to sustain combustion and provide heat to the cigarette. Rather, the new cigarette primarily heats tobacco thereby reducing products of smoke formation mechanisms such as tobacco combustion, tobacco pyrolysis and pyrosynthesis. The mainstream smoke composition from a cigarette based on the new design (TOB-HT) has been characterized in comparative chemical testing with two reference cigarettes using the FTC puffing regimen. Thermal properties, UV absorption characteristics, elemental composition and materials balance studies all suggest a simplified smoke aerosol. Twenty-five smoke constituents ("target compounds") identified by the scientific community as compounds that may contribute to the diseases statistically associated with smoking have also been measured. Mainstream smoke concentrations of most target compounds are significantly lower with the TOB-HT cigarette when compared with reference cigarettes in the ultra-light "tar" and light "tar" categories. Taken together, chemical analysis results suggest simplified TOB-HT smoke chemistry with marked reductions in specific chemicals reported to be biologically active.

  13. Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination

    PubMed Central

    Zhang, Lin; Zhao, Guoping; Ding, Xiaoming

    2011-01-01

    We describe a site-specific recombination-based tandem assembly (SSRTA) method for reconstruction of biological parts in synthetic biology. The system was catalyzed by Streptomyces phage φBT1 integrase, which belongs to the large serine recombinase subfamily. This one-step approach was efficient and accurate, and able to join multiple DNA molecules in vitro in a defined order. Thus, it could have applications in constructing metabolic pathways and genetic networks. PMID:22355658

  14. Geometric reasoning about assembly tools

    SciTech Connect

    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.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed Central

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

    2013-01-01

    Nanoparticles (NPs) are being extensively studied as carriers for drug delivery, but they often have limited penetration inside tumor. We envision that by targeting an endocytic receptor on cell surface, the uptake of NPs can be significantly enhanced through receptor mediated endocytosis. In addition, if the receptor is recycled to cell surface, the NP cargo can be transported out of the cells, which are 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 (SNP) containing a highly fluorescent core to target CD44, a receptor expressed on 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, thermal gravimetric 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-SNP 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-SNP was mainly through CD44 mediated endocytosis. HA-SNPs with DOX immobilized were endocytosed efficiently by the SKOV-3 cells as well. The enhanced tumor penetration and drug delivery properties of HA-SNP will be evaluated in 3D tumor models in the subsequent paper. PMID:23529646

  18. External Tank Assembly

    NASA Technical Reports Server (NTRS)

    1977-01-01

    This photograph shows the liquid hydrogen tank and liquid oxygen tank for the Space Shuttle external tank (ET) being assembled in the weld assembly area of the Michoud Assembly Facility (MAF). The ET provides liquid hydrogen and liquid oxygen to the Shuttle's three main engines during the first eight 8.5 minutes of flight. At 154-feet long and more than 27-feet in diameter, the ET is the largest component of the Space Shuttle, the structural backbone of the entire Shuttle system, and the only part of the vehicle that is not reusable. The ET is manufactured at the Michoud Assembly Facility near New Orleans, Louisiana, by the Martin Marietta Corporation under management of the Marshall Space Flight Center.

  19. 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.

    PubMed

    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

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

    PubMed

    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. PMID:27026396

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

    PubMed

    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.

  2. 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

    PubMed Central

    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

  3. 5-N-Substituted-2-(substituted benzenesulphonyl) glutamines as antitumor agents. Part II: synthesis, biological activity and QSAR study.

    PubMed

    Samanta, Soma; Srikanth, K; Banerjee, Suchandra; Debnath, Bikash; Gayen, Shovanlal; Jha, Tarun

    2004-03-15

    Cancer is a major killer disease throughout human history. Thus, cancer becomes a major point of interest in life science. It was proved that cancer is a nitrogen trap and tumor cells are avid glutamine consumers. The non-essential amino acid glutamine, which is a glutamic acid derivative, supplies its amide nitrogen to tumor cells in the biosynthesis of purine and pyrimidine bases of nucleic acids as well as takes part in protein synthesis. Based on these and in continuation of our composite programme of development of new potential anticancer agents through rational drug design, 17 new 5-N-Substituted-2-(substituted benzenesulphonyl) glutamines were selected for synthesis. These compounds as well as 36 earlier synthesized glutamine analogues were screened for antitumor activity using percentage inhibition of tumor cell count as the activity parameter. QSAR study was performed with 53 compounds in order to design leads with increased effectiveness for antitumor activity using both physicochemical and topological parameters. QSAR study showed that steric effect on the aromatic ring is conducive to the activity. n-butyl substitution on aliphatic side chain and atom no 12 is important for antitumor activity of glutamine analogues.

  4. Liaison based assembly design

    SciTech Connect

    Ames, A.; Kholwadwala, D.; Wilson, R.H.

    1996-12-01

    Liaison Based Assembly Design extends the current information infrastructure to support design in terms of kinematic relationships between parts, or liaisons. These liaisons capture information regarding contact, degrees-of-freedom constraints and containment relationships between parts in an assembly. The project involved defining a useful collection of liaison representations, investigating their properties, and providing for maximum use of the data in downstream applications. We tested our ideas by implementing a prototype system involving extensions to Pro/Engineer and the Archimedes assembly planner. With an expanded product model, the design system is more able to capture design intent. When a product update is attempted, increased knowledge availability improves our ability to understand the effect of design changes. Manufacturing and analysis disciplines benefit from having liaison information available, so less time is wasted arguing over incomplete design specifications and our enterprise can be more completely integrated.

  5. Physical attributes and assembly of PEG-linked immuno-labeled gold nanoparticles for OCM image contrast in tissue engineering and developmental biology

    NASA Astrophysics Data System (ADS)

    Weisberg, Alanna L.; Bean, Nathaniel J. H.; DuBose, Theodore B.; Orwin, Elizabeth J.; Haskell, Richard C.

    2014-03-01

    Excessive nonspecific binding often occurs when labeling cells with immuno-labeled gold nanoparticles (IgG-AuNPs). We have investigated the physical properties of IgG-AuNPs assembled with three different protocols in an attempt to understand and eliminate this non-specific binding. One of these protocols involves conjugating the secondary antibody AP124F via van der Waals (vdW) and/or electrostatic forces to the AuNPs, and the other two employ a PEG-linker, OPSS-PEG-NHS (OPN). In all three protocols we follow with PEG-SH to provide protection against aggregation in saline solution. OPN and PEG-SH chains of varying molecular weights were examined in different combinations to determine the optimally protective layer. The hydrodynamic radius and surface plasmon resonance (SPR) were monitored at each stage of assembly using a dynamic light scattering (DLS) instrument and spectrophotometer, respectively. SPR measurements indicate a different physical structure near the gold surface when the PEG-linker is bound to gold first and then bound to the antibody second (AP124F-[OPN-Au]) rather than vice versa ([AP124F-OPN]- Au). These observed structural differences may lead to differences in the amount of non-specific binding observed when immuno-labeling cells. SPR measurements also yielded a half-life of 27 minutes for the binding of the PEG-linker to the surface of the AuNPs and a half-life of 133 minutes for the hydrolysis of the NHS functional groups on the OPN molecule. These different reaction rates led us to add AP124F 40 minutes after the linker began binding to the AuNPs, so that the antibody can bind covalently to the correct end of the OPN linker.

  6. On Constraints in Assembly Planning

    SciTech Connect

    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.

  7. Modeling Protein Self Assembly

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton Buck; Hull, Elizabeth

    2004-01-01

    Understanding the structure and function of proteins is an important part of the standards-based science curriculum. Proteins serve vital roles within the cell and malfunctions in protein self assembly are implicated in degenerative diseases. Experience indicates that this topic is a difficult one for many students. We have found that the concept…

  8. Dynamic Nanoparticles Assemblies

    PubMed Central

    WANG, LIBING; XU, LIGUANG; KUANG, HUA; XU, CHUANLAI; KOTOV, NICHOLAS A.

    2012-01-01

    in the field may include different size dimensionalities: discrete assemblies (artificial molecules), one-dimensional (spaced chains) and 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. Preparation 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 and/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. Applications 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 the review is devoted to the fundamental questions facing dynamic assemblies of NPs in the future. PMID:22449243

  9. DNA Assembly in 3D Printed Fluidics.

    PubMed

    Patrick, William G; Nielsen, Alec A K; Keating, Steven J; Levy, Taylor J; Wang, Che-Wei; Rivera, Jaime J; Mondragón-Palomino, Octavio; Carr, Peter A; Voigt, Christopher A; Oxman, Neri; Kong, David S

    2015-01-01

    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. PMID:26716448

  10. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules.

    PubMed

    Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I; Juárez, Paloma; Fernández-del-Carmen, Asun; Granell, Antonio; Orzaez, Diego

    2011-01-01

    Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop ("braid") topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described. PMID:21750718

  11. Crew Assembly

    NASA Video Gallery

    Train to improve your dexterity and hand-eye coordination by assembling a puzzle.The Train Like an Astronaut project uses the excitement of exploration to challenge students to set goals, practice ...

  12. Fabrication of novel biomaterials through molecular self-assembly.

    PubMed

    Zhang, Shuguang

    2003-10-01

    Two complementary strategies can be used in the fabrication of molecular biomaterials. In the 'top-down' approach, biomaterials are generated by stripping down a complex entity into its component parts (for example, paring a virus particle down to its capsid to form a viral cage). This contrasts with the 'bottom-up' approach, in which materials are assembled molecule by molecule (and in some cases even atom by atom) to produce novel supramolecular architectures. The latter approach is likely to become an integral part of nanomaterials manufacture and requires a deep understanding of individual molecular building blocks and their structures, assembly properties and dynamic behaviors. Two key elements in molecular fabrication are chemical complementarity and structural compatibility, both of which confer the weak and noncovalent interactions that bind building blocks together during self-assembly. Using natural processes as a guide, substantial advances have been achieved at the interface of nanomaterials and biology, including the fabrication of nanofiber materials for three-dimensional cell culture and tissue engineering, the assembly of peptide or protein nanotubes and helical ribbons, the creation of living microlenses, the synthesis of metal nanowires on DNA templates, the fabrication of peptide, protein and lipid scaffolds, the assembly of electronic materials by bacterial phage selection, and the use of radiofrequency to regulate molecular behaviors.

  13. Seal assembly

    SciTech Connect

    Johnson, Roger Neal; Longfritz, William David

    2001-01-01

    A seal assembly that seals a gap formed by a groove comprises a seal body, a biasing element, and a connection that connects the seal body to the biasing element to form the seal assembly. The seal assembly further comprises a concave-shaped center section and convex-shaped contact portions at each end of the seal body. The biasing element is formed from an elastic material and comprises a convex-shaped center section and concave-shaped biasing zones that are opposed to the convex-shaped contact portions. The biasing element is adapted to be compressed to change a width of the seal assembly from a first width to a second width that is smaller than the first width. In the compressed state, the seal assembly can be disposed in the groove. After release of the compressing force, the seal assembly expands. The contact portions will move toward a surface of the groove and the biasing zones will move into contact with another surface of the groove. The biasing zones will bias the contact portions of the seal body against the surface of the groove.

  14. Very large assemblies: Optimizing for automatic generation of assembly sequences

    SciTech Connect

    CALTON,TERRI L.

    2000-02-01

    Sandia's Archimedes 3.0{copyright} Automated Assembly Analysis System has been applied successfully to several large industrial and weapon assemblies. These have included Sandia assemblies such as portions of the B61 bomb, and assemblies from external customers such as Cummins Engine Inc., Raytheon (formerly Hughes) Missile Systems and Sikorsky Aircraft. While Archimedes 3.0{copyright} represents the state-of-the-art in automated assembly planning software, applications of the software made prior to the technological advancements presented here showed several limitations of the system, and identified the need for extensive modifications to support practical analysis of assemblies with several hundred to a few thousand parts. It was believed that there was substantial potential for enhancing Archimedes 3.0{copyright} to routinely handle much larger models and/or to handle more modestly sized assemblies more efficiently. Such a mature assembly analysis capability was needed to support routine application to industrial assemblies that overstressed the system, such as full nuclear weapon assemblies or full-scale aerospace or military vehicles.

  15. Biotechnology of flavonoids and other phenylpropanoid-derived natural products. Part I: Chemical diversity, impacts on plant biology and human health.

    PubMed

    Ververidis, Filippos; Trantas, Emmanouil; Douglas, Carl; Vollmer, Guenter; Kretzschmar, Georg; Panopoulos, Nickolas

    2007-10-01

    Plant natural products derived from phenylalanine and the phenylpropanoid pathway are impressive in their chemical diversity and are the result of plant evolution, which has selected for the acquisition of large repertoires of pigments, structural and defensive compounds, all derived from a phenylpropanoid backbone via the plant-specific phenylpropanoid pathway. These compounds are important in plant growth, development and responses to environmental stresses and thus can have large impacts on agricultural productivity. While plant-based medicines containing phenylpropanoid-derived active components have long been used by humans, the benefits of specific flavonoids and other phenylpropanoid-derived compounds to human health and their potential for long-term health benefits have been only recognized more recently. In this part of the review, we discuss the diversity and biosynthetic origins of phenylpropanoids and particularly of the flavonoid and stilbenoid natural products. We then review data pertaining to the modes of action and biological properties of these compounds, referring on their effects on human health and physiology and their roles as plant defense and antimicrobial compounds. This review continues in Part II discussing the use of biotechnological tools targeting the rational reconstruction of multienzyme pathways in order to modify the production of such compounds in plants and model microbial systems for the benefit of agriculture and forestry.

  16. The Emergence of Modularity in Biological Systems

    PubMed Central

    Lorenz, Dirk M.; Jeng, Alice; Deem, Michael W.

    2015-01-01

    In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks. There once were two watchmakers, named Hora and Tempus, who manufactured very fine watches. Both of them were highly regarded, and the phones in their workshops rang frequently — new customers were constantly calling them. However, Hora prospered, while Tempus became poorer and poorer and finally lost his shop. What was the reason? The watches the men made consisted of about 1,000 parts each. Tempus had so constructed his that if he had one partly assembled and had to put it down — to answer the phone say— it immediately fell to pieces and had to be reassembled from the elements. The better the customers liked his watches, the more they phoned him, the more difficult it became for him to find enough uninterrupted time to finish a watch. The watches that Hora made were no less complex than those of Tempus. But he had designed them so that he could put together subassemblies of about ten elements each. Ten of these subassemblies, again, could be put together into a larger subassembly; and a system of ten of the latter sub-assemblies

  17. Hinge assembly

    DOEpatents

    Vandergriff, D.H.

    1999-08-31

    A hinge assembly is disclosed having a first leaf, a second leaf and linking member. The first leaf has a contact surface. The second leaf has a first contact surface and a second contact surface. The linking member pivotally connects to the first leaf and to the second leaf. The hinge assembly is capable of moving from a closed position to an open position. In the closed position, the contact surface of the first leaf merges with the first contact surface of the second leaf. In the open position, the contact surface of the first leaf merges with the second contact surface of the second leaf. The hinge assembly can include a seal on the contact surface of the first leaf. 8 figs.

  18. Hinge assembly

    DOEpatents

    Vandergriff, David Houston

    1999-01-01

    A hinge assembly having a first leaf, a second leaf and linking member. The first leaf has a contact surface. The second leaf has a first contact surface and a second contact surface. The linking member pivotally connects to the first leaf and to the second leaf. The hinge assembly is capable of moving from a closed position to an open position. In the closed position, the contact surface of the first leaf merges with the first contact surface of the second leaf. In the open position, the contact surface of the first leaf merges with the second contact surface of the second leaf. The hinge assembly can include a seal on the contact surface of the first leaf.

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Latch assembly

    DOEpatents

    Frederickson, James R.; Harper, William H.; Perez, Raymond

    1986-01-01

    A latch assembly for releasably securing an article in the form of a canister within a container housing. The assembly includes a cam pivotally mounted on the housing wall and biased into the housing interior. The cam is urged into a disabled position by the canister as it enters the housing and a latch release plate maintains the cam disabled when the canister is properly seated in the housing. Upon displacement of the release plate, the cam snaps into latching engagement against the canister for securing the same within the housing.

  1. Latch assembly

    DOEpatents

    Frederickson, J.R.; Harper, W.H.; Perez, R.

    1984-08-17

    A latch assembly for releasably securing an article in the form of a canister within a container housing. The assembly includes a cam pivotally mounted on the housing wall and biased into the housing interior. The cam is urged into a disabled position by the canister as it enters the housing and a latch release plate maintains the cam disabled when the canister is properly seated in the housing. Upon displacement of the release plate, the cam snaps into latching engagement against the canister for securing the same within the housing. 2 figs.

  2. Valve assembly

    SciTech Connect

    Marshala, D.L.

    1986-12-16

    This patent describes a subsurface pump actuated by a reciprocatable sucker rod for producing well liquids from a subsurface reservoir involving a piston adapted to reciprocate within a cylinder immersed in the reservoir, the piston being provided with a traveling valve. The improvement described here comprises valve means connected to the sucker tod for lifting a body of fluid during upstrokes of the sucker rod, the valve means comprising: a barrel assembly having an internal bore and comprising: a lower barrel member; and an upper barrel assembly connected to the lower barrel and having a beveled seating surface with at least one fluid port therethrough.

  3. Assembly Test Article (ATA)

    NASA Technical Reports Server (NTRS)

    Ricks, Glen A.

    1988-01-01

    The assembly test article (ATA) consisted of two live loaded redesigned solid rocket motor (RSRM) segments which were assembled and disassembled to simulate the actual flight segment stacking process. The test assembly joint was flight RSRM design, which included the J-joint insulation design and metal capture feature. The ATA test was performed mid-November through 24 December 1987, at Kennedy Space Center (KSC), Florida. The purpose of the test was: certification that vertical RSRM segment mating and separation could be accomplished without any damage; verification and modification of the procedures in the segment stacking/destacking documents; and certification of various GSE to be used for flight assembly and inspection. The RSRM vertical segment assembly/disassembly is possible without any damage to the insulation, metal parts, or seals. The insulation J-joint contact area was very close to the predicted values. Numerous deviations and changes to the planning documents were made to ensure the flight segments are effectively and correctly stacked. Various GSE were also certified for use on flight segments, and are discussed in detail.

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

    PubMed

    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.

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

    PubMed

    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. PMID:27341289

  6. Furnace assembly

    DOEpatents

    Panayotou, N.F.; Green, D.R.; Price, L.S.

    A method of and apparatus for heating test specimens to desired elevated temperatures for irradiation by a high energy neutron source. A furnace assembly is provided for heating two separate groups of specimens to substantially different, elevated, isothermal temperatures in a high vacuum environment while positioning the two specimen groups symmetrically at equivalent neutron irradiating positions.

  7. Furnace assembly

    DOEpatents

    Panayotou, Nicholas F.; Green, Donald R.; Price, Larry S.

    1985-01-01

    A method of and apparatus for heating test specimens to desired elevated temperatures for irradiation by a high energy neutron source. A furnace assembly is provided for heating two separate groups of specimens to substantially different, elevated, isothermal temperatures in a high vacuum environment while positioning the two specimen groups symmetrically at equivalent neutron irradiating positions.

  8. The Archimedes 2 mechanical assembly planning system

    SciTech Connect

    Kaufman, S.G.; Wilson, R.H.; Jones, R.E.; Calton, T.L.; Ames, A.L.

    1996-03-01

    We describe the implementation and performance of Archimedes 2, an integrated mechanical assembly planning system. Archimedes 2 includes two planners, two assembly sequence animation facilities, and an associated robotic workcell. Both planners use full 3 dimensional data. A rudimentary translator from high level assembly plans to control code for the robotic workcell has also been implemented. We can translate data from a commercial CAD system into input data for the system, which has allowed us to plan assembly sequences for many industrial assemblies. Archimedes 2 has been used to plan sequences for assemblies consisting of 5 to 109 parts. We have also successfully taken a CAD model of an assembly, produced an optimized assembly sequence for it, and translated the plan into robot code, which successfully assembles the device specified in the model.

  9. Systems Biology

    SciTech Connect

    Wiley, H S.

    2006-06-01

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

  10. BIOLOGICAL WARFARE

    PubMed Central

    Beeston, John

    1953-01-01

    The use of biological agents as controlled weapons of war is practical although uncertain. Three types of agents are feasible, including pathogenic organisms and biological pests, toxins, and synthetic hormones regulating plant growth. These agents may be chosen for selective effects varying from prolonged incipient illness to death of plants, man and domestic animals. For specific preventive and control measures required to combat these situations, there must be careful and detailed planning. The nucleus of such a program is available within the existing framework of public health activities. Additional research and expansion of established activities in time of attack are necessary parts of biological warfare defense. PMID:13059641

  11. Planning Assembly Of Large Truss Structures In Outer Space

    NASA Technical Reports Server (NTRS)

    De Mello, Luiz S. Homem; Desai, Rajiv S.

    1992-01-01

    Report dicusses developmental algorithm used in systematic planning of sequences of operations in which large truss structures assembled in outer space. Assembly sequence represented by directed graph called "assembly graph", in which each arc represents joining of two parts or subassemblies. Algorithm generates assembly graph, working backward from state of complete assembly to initial state, in which all parts disassembled. Working backward more efficient than working forward because it avoids intermediate dead ends.

  12. Sensor assembly

    DOEpatents

    Bennett, Thomas E.; Nelson, Drew V.

    2004-04-13

    A ribbon-like sensor assembly is described wherein a length of an optical fiber embedded within a similar lengths of a prepreg tow. The fiber is ""sandwiched"" by two layers of the prepreg tow which are merged to form a single consolidated ribbon. The consolidated ribbon achieving a generally uniform distribution of composite filaments near the embedded fiber such that excess resin does not ""pool"" around the periphery of the embedded fiber.

  13. Seeing Circuits Assemble

    PubMed Central

    Lichtman, Jeff W.; Smith, Stephen J.

    2009-01-01

    Developmental neurobiology has been greatly invigorated by a recent string of breakthroughs in molecular biology and optical physics that permit direct in vivo observation of neural circuit assembly. The imaging done thus far suggests that as brains are built, a significant amount of unbuilding is also occurring. We offer the view that this tumult is the result of the intersecting behaviors of the many single-celled creatures (i.e., neurons, glia, and progenitors) that inhabit brains. New tools will certainly be needed if we wish to monitor the myriad cooperative and competitive interactions at play in the cellular society that builds brains. PMID:18995818

  14. A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology

    PubMed Central

    Chen, Bor-Sen; Lin, Ying-Po

    2013-01-01

    Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties that are observed in biological systems at many different levels. The underlying principles for robust stabilization and environmental disturbance attenuation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be large enough to confer: intrinsic robustness for tolerating intrinsic parameter fluctuations; genetic robustness for buffering genetic variations; and environmental robustness for resisting environmental disturbances. Network robustness is needed so phenotype stability of biological network can be maintained, guaranteeing phenotype robustness. Synthetic biology is foreseen to have important applications in biotechnology and medicine; it is expected to contribute significantly to a better understanding of functioning of complex biological systems. This paper presents a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation for synthetic gene networks in synthetic biology. Further, from the unifying mathematical framework, we found that the phenotype robustness criterion for synthetic gene networks is the following: if intrinsic robustness + genetic robustness + environmental robustness ≦ network robustness, then the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in synthetic biology can also be investigated through corresponding phenotype robustness criteria from the systematic point of view. Finally, a robust synthetic design that involves network evolution algorithms with desired behavior under intrinsic parameter fluctuations, genetic variations, and environmental

  15. A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-off on Phenotype Robustness in Biological Networks Part I: Gene Regulatory Networks in Systems and Evolutionary Biology

    PubMed Central

    Chen, Bor-Sen; Lin, Ying-Po

    2013-01-01

    Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties observed in biological systems at different levels. The underlying principles for robust stabilization and environmental disturbance attenuation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be enough to confer intrinsic robustness in order to tolerate intrinsic parameter fluctuations, genetic robustness for buffering genetic variations, and environmental robustness for resisting environmental disturbances. With this, the phenotypic stability of biological network can be maintained, thus guaranteeing phenotype robustness. This paper presents a survey on biological systems and then develops a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation in systems and evolutionary biology. Further, from the unifying mathematical framework, it was discovered that the phenotype robustness criterion for biological networks at different levels relies upon intrinsic robustness + genetic robustness + environmental robustness ≦ network robustness. When this is true, the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in systems and evolutionary biology can also be investigated through their corresponding phenotype robustness criterion from the systematic point of view. PMID:23515240

  16. AutoAssemblyD: a graphical user interface system for several genome assemblers

    PubMed Central

    Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

    2013-01-01

    Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. Availability AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher. PMID:24143057

  17. Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler

    PubMed Central

    Bankar, Kiran Gopinath; Todur, Vivek Nagaraj; Shukla, Rohit Nandan; Vasudevan, Madavan

    2015-01-01

    Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays. PMID:26484285

  18. Biology Notes.

    ERIC Educational Resources Information Center

    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)

  19. Pushrod assembly

    DOEpatents

    Potter, J.D.

    1984-03-30

    A pushrod assembly including a carriage mounted on a shaft for movement therealong and carrying a pushrod engageable with a load to be moved is described. A magnet is mounted on a supporting bracket for movement along such shaft. Means are provided for adjustably spacing magnet away from the carriage to obtain a selected magnetic attractive or coupling force therebetween. Movement of the supporting bracket and the magnet carried thereby pulls the carriage along with it until the selected magnetic force is exceeded by a resistance load acting on the carriage.

  20. Pushrod assembly

    DOEpatents

    Potter, Jerry D.

    1987-01-01

    A pushrod assembly including a carriage mounted on a shaft for movement therealong and carrying a pushrod engageable with a load to be moved. A magnet is mounted on a supporting bracket for movement along such shaft. Means are provided for adjustably spacing said magnet away from said carriage to obtain a selected magnetic attractive or coupling force therebetween. Movement of the supporting bracket and the magnet carried thereby pulls the carriage along with it until the selected magnetic force is exceeded by a resistance load acting on the carriage.

  1. Shingle assembly

    DOEpatents

    Dinwoodie, Thomas L.

    2007-02-20

    A barrier, such as a PV module, is secured to a base by a support to create a shingle assembly with a venting region defined between the barrier and base for temperature regulation. The first edge of one base may be interengageable with the second edge of an adjacent base to be capable of resisting first and second disengaging forces oriented perpendicular to the edges and along planes oriented parallel to and perpendicular to the base. A deflector may be used to help reduce wind uplift forces.

  2. Dump assembly

    DOEpatents

    Goldmann, L.H.

    1984-12-06

    This is a claim for 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. 4 figs.

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

    PubMed

    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]. PMID:27671933

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

    PubMed

    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].

  5. Metagenomic Assembly: Overview, Challenges and Applications

    PubMed Central

    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.

  6. Metagenomic Assembly: Overview, Challenges and Applications

    PubMed Central

    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

  7. Chemical synthetic biology: a mini-review

    PubMed Central

    Chiarabelli, Cristiano; Stano, Pasquale; Luisi, Pier Luigi

    2013-01-01

    Chemical synthetic biology (CSB) is a branch of synthetic biology (SB) oriented toward 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” 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. PMID:24065964

  8. Bottom-up design of biomimetic assemblies.

    PubMed

    Tu, Raymond S; Tirrell, Matthew

    2004-09-22

    Nature has evolved the ability to assemble a variety of molecules into functional architectures that can specifically bind cellular ligands. Mimicking this strategy requires the design of a set of multifaceted molecules, where elements that direct assembly were conjugated to biologically specific components. The development of functional molecular building-blocks that assemble to form compartments for therapeutics addresses the desire to have controllable morphologies that interact with biological interfaces at nanometer length scales. The practical application of such 'bottom-up' assemblies requires the ability to predict the type of aggregated structure and to synthesize molecules in a highly controlled fashion. This bottom-up approach results in a molecular platform that mimics biological systems with potential for encapsulating and delivering drug molecules.

  9. Assembly auxiliary system for narrow cabins of spacecraft

    NASA Astrophysics Data System (ADS)

    Liu, Yi; Li, Shiqi; Wang, Junfeng

    2015-09-01

    Due to the narrow space and complex structure of spacecraft cabin, the existing asssembly systems can not well suit for the assembly process of cabin products. This paper aims to introduce an assembly auxiliary system for cabin products. A hierarchical-classification method is proposed to re-adjust the initial assembly relationship of cabin into a new hierarchical structure for efficient assembly planning. An improved ant colony algorithm based on three assembly principles is established for searching a optimizational assembly sequence of cabin parts. A mixed reality assembly environment is constructed with enhanced information to promote interaction efficiency of assembly training and guidance. Based on the machine vision technology, the inspection of left redundant objects and measurement of parts distance in inner cabin are efficiently performed. The proposed system has been applied to the assembly work of a spacecraft cabin with 107 parts, which includes cabin assembly planning, assembly training and assembly quality inspection. The application result indicates that the proposed system can be an effective assistant tool to cabin assembly works and provide an intuitive and real assembly experience for workers. This paper presents an assembly auxiliary system for spacecraft cabin products, which can provide technical support to the spacecraft cabin assembly industry.

  10. Thermocouple assembly

    DOEpatents

    Thermos, Anthony Constantine; Rahal, Fadi Elias

    2002-01-01

    A thermocouple assembly includes a thermocouple; a plurality of lead wires extending from the thermocouple; an insulating jacket extending along and enclosing the plurality of leads; and at least one internally sealed area within the insulating jacket to prevent fluid leakage along and within the insulating jacket. The invention also provides a method of preventing leakage of a fluid along and through an insulating jacket of a thermocouple including the steps of a) attaching a plurality of lead wires to a thermocouple; b) adding a heat sensitive pseudo-wire to extend along the plurality of lead wires; c) enclosing the lead wires and pseudo-wire inside an insulating jacket; d) locally heating axially spaced portions of the insulating jacket to a temperature which melts the pseudo-wire and fuses it with an interior surface of the jacket.

  11. Swivel assembly

    DOEpatents

    Hall, David R.; Pixton, David S.; Briscoe, Michael; Bradford, Kline; Rawle, Michael; Bartholomew, David B.; McPherson, James

    2007-03-20

    A swivel assembly for a downhole tool string comprises a first and second coaxial housing cooperatively arranged. The first housing comprises a first transmission element in communication with surface equipment. The second housing comprises a second transmission element in communication with the first transmission element. The second housing further comprises a third transmission element adapted for communication with a network integrated into the downhole tool string. The second housing may be rotational and adapted to transmit a signal between the downhole network and the first housing. Electronic circuitry is in communication with at least one of the transmission elements. The electronic circuitry may be externally mounted to the first or second housing. Further, the electronic circuitry may be internally mounted in the second housing. The electronic circuitry may be disposed in a recess in either first or second housing of the swivel.

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

    PubMed

    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.

  13. Chemical reactions directed Peptide self-assembly.

    PubMed

    Rasale, Dnyaneshwar B; Das, Apurba K

    2015-01-01

    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.

  14. Chemical Reactions Directed Peptide Self-Assembly

    PubMed Central

    Rasale, Dnyaneshwar B.; Das, Apurba K.

    2015-01-01

    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. PMID:25984603

  15. Zebrafish vimentin: molecular characterization, assembly properties and developmental expression.

    PubMed

    Cerdà, J; Conrad, M; Markl, J; Brand, M; Herrmann, H

    1998-11-01

    To provide a basis for the investigation of the intermediate filament (IF) protein vimentin in one of the most promising experimental vertebrate systems, the zebrafish (Danio rerio), we have isolated a cDNA clone of high sequence identity to and with the characteristic features of human vimentin. Using this clone we produced recombinant zebrafish vimentin and studied its assembly behaviour. Unlike other vimentins, zebrafish vimentin formed unusually thick filaments when assembled at temperatures below 21 degrees C. At 37 degrees C few filaments were observed, which often also terminated in aggregated masses, indicating that its assembly was severely disturbed at this temperature. Between 21 and 34 degrees C apparently normal IFs were generated. By viscometry, the temperature optimum of assembly was determined to be around 28 degrees C. At this temperature, zebrafish vimentin partially rescued, in mixing experiments, the temperature-dependent assembly defect of trout vimentin. Therefore it is apparently able to "instruct" the misorganized trout vimentin such that it can enter normal IFs. This feature, that assembly is best at the normal body temperature of various species, puts more weight on the assumption that vimentin is vital for some aspects of generating functional adult tissues. Remarkably, like in most other vertebrates, zebrafish vimentin appears to be an abundant factor in the lens and the retina as well as transiently, during development, in various parts of the central and peripheral nervous system. Therefore, promising cell biological investigations may now be performed with cells involved in the generation of the vertebrate eye and brain, and, in particular, the retina. Moreover, the power of genetics of the zebrafish system may be employed to investigate functional properties of vimentin in vivo. PMID:9860133

  16. Adaptive Accommodation Control Method for Complex Assembly

    NASA Astrophysics Data System (ADS)

    Kang, Sungchul; Kim, Munsang; Park, Shinsuk

    Robotic systems have been used to automate assembly tasks in manufacturing and in teleoperation. Conventional robotic systems, however, have been ineffective in controlling contact force in multiple contact states of complex assemblythat involves interactions between complex-shaped parts. Unlike robots, humans excel at complex assembly tasks by utilizing their intrinsic impedance, forces and torque sensation, and tactile contact clues. By examining the human behavior in assembling complex parts, this study proposes a novel geometry-independent control method for robotic assembly using adaptive accommodation (or damping) algorithm. Two important conditions for complex assembly, target approachability and bounded contact force, can be met by the proposed control scheme. It generates target approachable motion that leads the object to move closer to a desired target position, while contact force is kept under a predetermined value. Experimental results from complex assembly tests have confirmed the feasibility and applicability of the proposed method.

  17. Constraint-based interactive assembly planning

    SciTech Connect

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

    1997-03-01

    The constraints on assembly plans vary depending on the product, assembly facility, assembly volume, and many other factors. This paper describes the principles and implementation of a framework that supports a wide variety of user-specified constraints for interactive assembly planning. Constraints from many sources can be expressed on a sequencing level, specifying orders and conditions on part mating operations in a number of ways. All constraints are implemented as filters 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. Replanning is fast enough to enable a natural 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 several complex assemblies. 12 refs., 2 figs., 3 tabs.

  18. Biological effects and physics of solar and galactic cosmic radiation, Part B; Proceedings of a NATO Advanced Study Institute on Biological Effects and Physics of Solar and Galactic Cosmic Radiation, Algarve, Portugal, Oct. 13-23, 1991

    NASA Technical Reports Server (NTRS)

    Swenberg, Charles E. (Editor); Horneck, Gerda (Editor); Stassinopoulos, E. G. (Editor)

    1993-01-01

    Since there is an increasing interest in establishing lunar bases and exploring Mars by manned missions, it is important to develop appropriate risk estimates and radiation protection guidelines. The biological effects and physics of solar and galactic cosmic radiation are examined with respect to the following: the radiation environment of interplanetary space, the biological responses to radiation in space, and the risk estimates for deep space missions. There is a need for a long-term program where ground-based studies can be augmented by flight experiments and an international standardization with respect to data collection, protocol comparison, and formulation of guidelines for future missions.

  19. Gateway Vectors for Efficient Artificial Gene Assembly In Vitro and Expression in Yeast Saccharomyces cerevisiae

    PubMed Central

    Giuraniuc, Claudiu V.; MacPherson, Murray; Saka, Yasushi

    2013-01-01

    Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created a series of Gateway shuttle vectors and an integration vector, which facilitate the assembly of artificial genes and their expression in the budding yeast Saccharomyces cerevisiae. Our method enables the rapid construction of an artificial gene from a promoter and an open reading frame (ORF) cassette by one-step recombination reaction in vitro. Furthermore, the plasmid thus created can readily be introduced into yeast cells to test the assembled gene’s functionality. As flexible regulatory components of a synthetic genetic network, we also created new versions of the tetracycline-regulated transactivators tTA and rtTA by fusing them to the auxin-inducible degron (AID). Using our gene assembly approach, we made yeast expression vectors of these engineered transactivators, AIDtTA and AIDrtTA and then tested their functions in yeast. We showed that these factors can be regulated by doxycycline and degraded rapidly after addition of auxin to the medium. Taken together, the method for combinatorial gene assembly described here is versatile and would be a valuable tool for yeast synthetic biology. PMID:23675537

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

    PubMed Central

    Wajid, Bilal; Sohail, Muhammad U.; Ekti, Ali R.; Serpedin, Erchin

    2016-01-01

    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. PMID:27247941

  1. Workload analyse of assembling process

    NASA Astrophysics Data System (ADS)

    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.

  2. j5 DNA assembly design automation software.

    PubMed

    Hillson, Nathan J; Rosengarten, Rafael D; Keasling, Jay D

    2012-01-20

    Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. Here, we report the development and deployment of a web-based software tool, j5, which automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. coli. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.

  3. Systems biology and physical biology of clathrin-mediated endocytosis.

    PubMed

    Ramanan, Vyas; Agrawal, Neeraj J; Liu, Jin; Engles, Sean; Toy, Randall; Radhakrishnan, Ravi

    2011-08-01

    In this review, we describe the application of experimental data and modeling of intracellular endocytic trafficking mechanisms with a focus on the process of clathrin-mediated endocytosis. A detailed parts-list for the protein-protein interactions in clathrin-mediated endocytosis has been available for some time. However, recent experimental, theoretical, and computational tools have proved to be critical in establishing a sequence of events, cooperative dynamics, and energetics of the intracellular process. On the experimental front, total internal reflection fluorescence microscopy, photo-activated localization microscopy, and spinning-disk confocal microscopy have focused on assembly and patterning of endocytic proteins at the membrane, while on the theory front, minimal theoretical models for clathrin nucleation, biophysical models for membrane curvature and bending elasticity, as well as methods from computational structural and systems biology, have proved insightful in describing membrane topologies, curvature mechanisms, and energetics.

  4. Crusts: biological

    USGS Publications Warehouse

    Belnap, Jayne; Elias, Scott A.

    2013-01-01

    Biological soil crusts, a community of cyanobacteria, lichens, mosses, and fungi, are an essential part of dryland ecosystems. They are critical in the stabilization of soils, protecting them from wind and water erosion. Similarly, these soil surface communities also stabilized soils on early Earth, allowing vascular plants to establish. They contribute nitrogen and carbon to otherwise relatively infertile dryland soils, and have a strong influence on hydrologic cycles. Their presence can also influence vascular plant establishment and nutrition.

  5. 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.

    PubMed

    D'Ascoli, R; Rao, M A; Adamo, P; Renella, G; Landi, L; Rutigliano, F A; Terribile, F; Gianfreda, L

    2006-11-01

    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.

  6. 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.

    PubMed

    D'Ascoli, R; Rao, M A; Adamo, P; Renella, G; Landi, L; Rutigliano, F A; Terribile, F; Gianfreda, L

    2006-11-01

    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. PMID:16406624

  7. Dynamics of assembly production flow

    NASA Astrophysics Data System (ADS)

    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.

  8. Backward assembly planning with DFA analysis

    NASA Technical Reports Server (NTRS)

    Lee, Sukhan (Inventor)

    1992-01-01

    An assembly planning system that operates based on a recursive decomposition of assembly into subassemblies is presented. The planning system analyzes assembly cost in terms of stability, directionality, and manipulability to guide the generation of preferred assembly plans. The planning in this system incorporates the special processes, such as cleaning, testing, labeling, etc., that must occur during the assembly. Additionally, the planning handles nonreversible, as well as reversible, assembly tasks through backward assembly planning. In order to decrease the planning efficiency, the system avoids the analysis of decompositions that do not correspond to feasible assembly tasks. This is achieved by grouping and merging those parts that can not be decomposable at the current stage of backward assembly planning due to the requirement of special processes and the constraint of interconnection feasibility. The invention includes methods of evaluating assembly cost in terms of the number of fixtures (or holding devices) and reorientations required for assembly, through the analysis of stability, directionality, and manipulability. All these factors are used in defining cost and heuristic functions for an AO* search for an optimal plan.

  9. Backward assembly planning with DFA analysis

    NASA Technical Reports Server (NTRS)

    Lee, Sukhan (Inventor)

    1995-01-01

    An assembly planning system that operates based on a recursive decomposition of assembly into subassemblies, and analyzes assembly cost in terms of stability, directionality, and manipulability to guide the generation of preferred assembly plans is presented. The planning in this system incorporates the special processes, such as cleaning, testing, labeling, etc. that must occur during the assembly, and handles nonreversible as well as reversible assembly tasks through backward assembly planning. In order to increase the planning efficiency, the system avoids the analysis of decompositions that do not correspond to feasible assembly tasks. This is achieved by grouping and merging those parts that can not be decomposable at the current stage of backward assembly planning due to the requirement of special processes and the constraint of interconnection feasibility. The invention includes methods of evaluating assembly cost in terms of the number of fixtures (or holding devices) and reorientations required for assembly, through the analysis of stability, directionality, and manipulability. All these factors are used in defining cost and heuristic functions for an AO* search for an optimal plan.

  10. Backward assembly planning with DFA analysis

    NASA Astrophysics Data System (ADS)

    Lee, Sukhan

    1995-08-01

    An assembly planning system that operates based on a recursive decomposition of assembly into subassemblies, and analyzes assembly cost in terms of stability, directionality, and manipulability to guide the generation of preferred assembly plans is presented. The planning in this system incorporates the special processes, such as cleaning, testing, labeling, etc. that must occur during the assembly, and handles nonreversible as well as reversible assembly tasks through backward assembly planning. In order to increase the planning efficiency, the system avoids the analysis of decompositions that do not correspond to feasible assembly tasks. This is achieved by grouping and merging those parts that can not be decomposable at the current stage of backward assembly planning due to the requirement of special processes and the constraint of interconnection feasibility. The invention includes methods of evaluating assembly cost in terms of the number of fixtures (or holding devices) and reorientations required for assembly, through the analysis of stability, directionality, and manipulability. All these factors are used in defining cost and heuristic functions for an AO* search for an optimal plan.

  11. Telemetry Simulation Assembly Implementation in the DSN

    NASA Technical Reports Server (NTRS)

    Alberda, M. E.

    1984-01-01

    The telemetry simulation was implemented as part of the MARK IV network implementation project. The telemetry simulation assembly (TSA) is replacing the Simulation Conversion Assembly (SCA) throughout the DSN. The development of the TSA is discussed, and the design is described to the block diagram level.

  12. M13 Bacteriophage-Based Self-Assembly Structures and Their Functional Capabilities

    PubMed Central

    Moon, Jong-Sik; Kim, Won-Geun; Kim, Chuntae; Park, Geun-Tae; Heo, Jeong; Yoo, So Y; Oh, Jin-Woo

    2015-01-01

    Controlling the assembly of basic structural building blocks in a systematic and orderly fashion is an emerging issue in various areas of science and engineering such as physics, chemistry, material science, biological engineering, and electrical engineering. The self-assembly technique, among many other kinds of ordering techniques, has several unique advantages and the M13 bacteriophage can be utilized as part of this technique. The M13 bacteriophage (Phage) can easily be modified genetically and chemically to demonstrate specific functions. This allows for its use as a template to determine the homogeneous distribution and percolated network structures of inorganic nanostructures under ambient conditions. Inexpensive and environmentally friendly synthesis can be achieved by using the M13 bacteriophage as a novel functional building block. Here, we discuss recent advances in the application of M13 bacteriophage self-assembly structures and the future of this technology. PMID:26146494

  13. Nanoparticle induced self-assembly.

    PubMed

    Helgesen, G; Svåsand, E; Skjeltorp, A T

    2008-05-21

    Self-assembly has for the large part focused on the assembly of molecules without guidance or management from an outside source. However, self-assembly is in principle by no means limited to molecules or the nanoscale. A particularly interesting method to the self-assembly of micro- to millimetre sized components is the use of the 'magnetic hole' effect. In this method, nonmagnetic particles can be manipulated by external magnetic fields by immersing them in a dispersion of colloidal, magnetic nanoparticles, denoted ferrofluids. Nonmagnetic particles in magnetized ferrofluids are in many ways ideal model systems to test various forms of particle self-assembly and dynamics. When microspheres are confined to a monolayer between two parallel plates and subjected to static or oscillating magnetic fields they show a variety of dynamical behaviours and assemblages, depending on the frequency and direction of the external fields. A single pair of magnetic holes oscillating in a ferrofluid layer may be used to measure the viscosity of tiny volumes of the fluid. We have also observed ordering of dilute dispersions of macromolecules and nanoparticles in magnetized ferrofluids. The self-assembly at this length scale results from structural correlations between these nanostructures and ferrofluid particles rather than from the macroscopic magnetostatic effect for the magnetic holes.

  14. Self-Assembly of Peptides to Nanostructures

    PubMed Central

    Mandal, Dindyal; Shirazi, Amir Nasrolahi; Parang, Keykavous

    2014-01-01

    The formation of well-ordered nanostructures through self-assembly of diverse organic and inorganic building blocks has drawn much attention owing to their potential applications in biology and chemistry. Among all organic building blocks, peptides are one of the most promising platforms due to their biocompatibility, chemical diversity, and resemblance with proteins. Inspired from the protein assembly in biological systems, various self-assembled peptide structures have been constructed using several amino acids and sequences. This review focuses on this emerging area, the recent advances in peptide self-assembly, and formation of different nanostructures, such as tubular, fibers, vesicles, spherical, and rod coil structures. While different peptide nanostructures are discovered, potential applications will be explored in drug delivery, tissue engineering, wound healing, and surfactants. PMID:24756480

  15. Nanoscale assemblies and their biomedical applications.

    PubMed

    Doll, Tais A P F; Raman, Senthilkumar; Dey, Raja; Burkhard, Peter

    2013-03-01

    Nanoscale assemblies are a unique class of materials, which can be synthesized from inorganic, polymeric or biological building blocks. The multitude of applications of this class of materials ranges from solar and electrical to uses in food, cosmetics and medicine. In this review, we initially highlight characteristic features of polymeric nanoscale assemblies as well as those built from biological units (lipids, nucleic acids and proteins). We give special consideration to protein nanoassemblies found in nature such as ferritin protein cages, bacterial microcompartments and vaults found in eukaryotic cells and designed protein nanoassemblies, such as peptide nanofibres and peptide nanotubes. Next, we focus on biomedical applications of these nanoscale assemblies, such as cell targeting, drug delivery, bioimaging and vaccine development. In the vaccine development section, we report in more detail the use of virus-like particles and self-assembling polypeptide nanoparticles as new vaccine delivery platforms.

  16. Nanoscale assemblies and their biomedical applications

    PubMed Central

    Doll, Tais A. P. F.; Raman, Senthilkumar; Dey, Raja; Burkhard, Peter

    2013-01-01

    Nanoscale assemblies are a unique class of materials, which can be synthesized from inorganic, polymeric or biological building blocks. The multitude of applications of this class of materials ranges from solar and electrical to uses in food, cosmetics and medicine. In this review, we initially highlight characteristic features of polymeric nanoscale assemblies as well as those built from biological units (lipids, nucleic acids and proteins). We give special consideration to protein nanoassemblies found in nature such as ferritin protein cages, bacterial microcompartments and vaults found in eukaryotic cells and designed protein nanoassemblies, such as peptide nanofibres and peptide nanotubes. Next, we focus on biomedical applications of these nanoscale assemblies, such as cell targeting, drug delivery, bioimaging and vaccine development. In the vaccine development section, we report in more detail the use of virus-like particles and self-assembling polypeptide nanoparticles as new vaccine delivery platforms. PMID:23303217

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

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

    Shen, Hsin-Hui; Leyton, Denisse L.; Shiota, Takuya; 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

    2014-10-01

    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 and assembly module (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 1 Å, 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.

  19. A small linear peptide encompassing the NGF N-terminus partly mimics the biological activities of the entire neurotrophin in PC12 cells.

    PubMed

    Travaglia, Alessio; Pietropaolo, Adriana; Di Martino, Rossana; Nicoletti, Vincenzo G; La Mendola, Diego; Calissano, Pietro; Rizzarelli, Enrico

    2015-08-19

    Ever since the discovery of its neurite growth promoting activity in sympathetic and sensory ganglia, nerve growth factor (NGF) became the prototype of the large family of neurotrophins. The use of primary cultures and clonal cell lines has revealed several distinct actions of NGF and other neurotrophins. Among several models of NGF activity, the clonal cell line PC12 is the most widely employed. Thus, in the presence of NGF, through the activation of the transmembrane protein TrkA, these cells undergo a progressive mitotic arrest and start to grow electrically excitable neuritis. A vast number of studies opened intriguing aspects of NGF mechanisms of action, its biological properties, and potential use as therapeutic agents. In this context, identifying and utilizing small portions of NGF is of great interest and involves several human diseases including Alzheimer's disease. Here we report the specific action of the peptide encompassing the 1-14 sequence of the human NGF (NGF(1-14)), identified on the basis of scattered indications present in literature. The biological activity of NGF(1-14) was tested on PC12 cells, and its binding with TrkA was predicted by means of a computational approach. NGF(1-14) does not elicit the neurite outgrowth promoting activity, typical of the whole protein, and it only has a moderate action on PC12 proliferation. However, this peptide exerts, in a dose and time dependent fashion, an effective and specific NGF-like action on some highly conserved and biologically crucial intermediates of its intracellular targets such as Akt and CREB. These findings indicate that not all TrkA pathways must be at all times operative, and open the possibility of testing each of them in relation with specific NGF needs, biological actions, and potential therapeutic use.

  20. Silk: molecular organization and control of assembly.

    PubMed

    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.

  1. DNA Assembly in 3D Printed Fluidics

    PubMed Central

    Patrick, William G.; Nielsen, Alec A. K.; Keating, Steven J.; Levy, Taylor J.; Wang, Che-Wei; Rivera, Jaime J.; Mondragón-Palomino, Octavio; Carr, Peter A.; Voigt, Christopher A.; Oxman, Neri; Kong, David S.

    2015-01-01

    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. PMID:26716448

  2. Latching relay switch assembly

    DOEpatents

    Duimstra, Frederick A.

    1991-01-01

    A latching relay switch assembly which includes a coil section and a switch or contact section. The coil section includes at least one permanent magnet and at least one electromagnet. The respective sections are, generally, arranged in separate locations or cavities in the assembly. The switch is latched by a permanent magnet assembly and selectively switched by an overriding electromagnetic assembly.

  3. Hapsembler: An Assembler for Highly Polymorphic Genomes

    NASA Astrophysics Data System (ADS)

    Donmez, Nilgun; Brudno, Michael

    As whole genome sequencing has become a routine biological experiment, algorithms for assembly of whole genome shotgun data has become a topic of extensive research, with a plethora of off-the-shelf methods that can reconstruct the genomes of many organisms. Simultaneously, several recently sequenced genomes exhibit very high polymorphism rates. For these organisms genome assembly remains a challenge as most assemblers are unable to handle highly divergent haplotypes in a single individual. In this paper we describe Hapsembler, an assembler for highly polymorphic genomes, which makes use of paired reads. Our experiments show that Hapsembler produces accurate and contiguous assemblies of highly polymorphic genomes, while performing on par with the leading tools on haploid genomes. Hapsembler is available for download at http://compbio.cs.toronto.edu/hapsembler.

  4. Co-translational assembly of protein complexes.

    PubMed

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

    2015-12-01

    The interaction of biological macromolecules is a fundamental attribute of cellular life. Proteins, in particular, often form stable complexes with one another. Although the importance of protein complexes is widely recognized, we still have only a very limited understanding of the mechanisms underlying their assembly within cells. In this article, we review the available evidence for one such mechanism, namely the coupling of protein complex assembly to translation at the polysome. We discuss research showing that co-translational assembly can occur in both prokaryotic and eukaryotic organisms and can have important implications for the correct functioning of the complexes that result. Co-translational assembly can occur for both homomeric and heteromeric protein complexes and for both proteins that are translated directly into the cytoplasm and those that are translated into or across membranes. Finally, we discuss the properties of proteins that are most likely to be associated with co-translational assembly.

  5. Archimedes : An experiment in automating mechanical assembly

    SciTech Connect

    Strip, D. ); Maciejewski, A.A. . Dept. of Electrical Engineering)

    1990-01-01

    Archimedes is a prototype mechanical assembly system which generates and executes robot assembly programs from a CAD model input. The system addresses the unrealized potential for flexibility in robotic mechanical assembly applications by automating the programming task. Input is a solid model of the finished assembly. Using this model. Archimedes deduces geometric assembly constraints and then produces an assembly plan that satisfies the geometric constraints, as well as other constraints such as stability and accessibility. A retargetable plan compiler converts the generic plan into robot and cell specific code, including recognition routines for a vision system. In the prototype system the code is executed in a workcell containing an Adept Two robot, a vision system, and other parts handling equipment. 8 refs., 2 figs.

  6. Nano-enabled synthetic biology

    PubMed Central

    Doktycz, Mitchel J; Simpson, Michael L

    2007-01-01

    Biological systems display a functional diversity, density and efficiency that make them a paradigm for synthetic systems. In natural systems, the cell is the elemental unit and efforts to emulate cells, their components, and organization have relied primarily on the use of bioorganic materials. Impressive advances have been made towards assembling simple genetic systems within cellular scale containers. These biological system assembly efforts are particularly instructive, as we gain command over the directed synthesis and assembly of synthetic nanoscale structures. Advances in nanoscale fabrication, assembly, and characterization are providing the tools and materials for characterizing and emulating the smallest scale features of biology. Further, they are revealing unique physical properties that emerge at the nanoscale. Realizing these properties in useful ways will require attention to the assembly of these nanoscale components. Attention to systems biology principles can lead to the practical development of nanoscale technologies with possible realization of synthetic systems with cell-like complexity. In turn, useful tools for interpreting biological complexity and for interfacing to biological processes will result. PMID:17625513

  7. Filament assemblies in foreign nucleic acid sensors.

    PubMed

    Sohn, Jungsan; Hur, Sun

    2016-04-01

    Helical filamentous assembly is ubiquitous in biology, but was only recently realized to be broadly employed in the innate immune system of vertebrates. Accumulating evidence suggests that the filamentous assemblies and helical oligomerization play important roles in detection of foreign nucleic acids and activation of the signaling pathways to produce antiviral and inflammatory mediators. In this review, we focus on the helical assemblies observed in the signaling pathways of RIG-I-like receptors (RLRs) and AIM2-like receptors (ALRs). We describe ligand-dependent oligomerization of receptor, receptor-dependent oligomerization of signaling adaptor molecules, and their functional implications and regulations.

  8. Inlet nozzle assembly

    DOEpatents

    Christiansen, David W.; Karnesky, Richard A.; Precechtel, Donald R.; Smith, Bob G.; Knight, Ronald C.

    1987-01-01

    An inlet nozzle assembly for directing coolant into the duct tube of a fuel assembly attached thereto. The nozzle assembly includes a shell for housing separable components including an orifice plate assembly, a neutron shield block, a neutron shield plug, and a diffuser block. The orifice plate assembly includes a plurality of stacked plates of differently configurated and sized openings for directing coolant therethrough in a predesigned flow pattern.

  9. Inlet nozzle assembly

    DOEpatents

    Christiansen, D.W.; Karnesky, R.A.; Knight, R.C.; Precechtel, D.R.; Smith, B.G.

    1985-09-09

    An inlet nozzle assembly for directing coolant into the duct tube of a fuel assembly attached thereto. The nozzle assembly includes a shell for housing separable components including an orifice plate assembly, a neutron shield block, a neutron shield plug, and a diffuser block. The orifice plate assembly includes a plurality of stacked plates of differently configurated and sized openings for directing coolant therethrough in a predesigned flow pattern.

  10. Structural assembly in space

    NASA Technical Reports Server (NTRS)

    Stokes, J. W.; Pruett, E. C.

    1980-01-01

    A cost algorithm for predicting assembly costs for large space structures is given. Assembly scenarios are summarized which describe the erection, deployment, and fabrication tasks for five large space structures. The major activities that impact total costs for structure assembly from launch through deployment and assembly to scientific instrument installation and checkout are described. Individual cost elements such as assembly fixtures, handrails, or remote minipulators are also presented.

  11. Protein self-assembly via supramolecular strategies.

    PubMed

    Bai, Yushi; Luo, Quan; Liu, Junqiu

    2016-05-21

    Proteins, as the elemental basis of living organisms, mostly execute their biological tasks in the form of supramolecular self-assemblies with subtle architectures, dynamic interactions and versatile functionalities. Inspired by the structural harmony and functional beauty of natural protein self-assemblies to fabricate sophisticated yet highly ordered protein superstructures represents an adventure in the pursuit of nature's supreme wisdom. In this review, we focus on building protein self-assembly systems based on supramolecular strategies and classify recent progress by the types of utilized supramolecular driving forces. Especially, the design strategy, structure control and the thermodynamic/kinetic regulation of the self-assemblies, which will in turn provide insights into the natural biological self-assembly mechanism, are highlighted. In addition, recently, this research field is starting to extend its interest beyond constructing complex morphologies towards the potential applications of the self-assembly systems; several attempts to design functional protein complexes are also discussed. As such, we hope that this review will provide a panoramic sketch of the field and draw a roadmap towards the ultimate construction of advanced protein self-assemblies that even can serve as analogues of their natural counterparts.

  12. Tilt assembly for tracking solar collector assembly

    DOEpatents

    Almy, Charles; Peurach, John; Sandler, Reuben

    2012-01-24

    A tilt assembly is used with a solar collector assembly of the type comprising a frame, supporting a solar collector, for movement about a tilt axis by pivoting a drive element between first and second orientations. The tilt assembly comprises a drive element coupler connected to the drive element and a driver, the driver comprising a drive frame, a drive arm and a drive arm driver. The drive arm is mounted to the drive frame for pivotal movement about a drive arm axis. Movement on the drive arm mimics movement of the drive element. Drive element couplers can extend in opposite directions from the outer portion of the drive arm, whereby the assembly can be used between adjacent solar collector assemblies in a row of solar collector assemblies.

  13. Building biological foundries for next-generation synthetic biology.

    PubMed

    Chao, Ran; Yuan, YongBo; Zhao, HuiMin

    2015-07-01

    Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries. PMID:25985756

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

    PubMed

    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

  15. Cognitively automated assembly processes: a simulation based evaluation of performance.

    PubMed

    Mayer, Marcel Ph; Odenthal, Barbara; Faber, Marco; Schlick, Christopher M

    2012-01-01

    The numerical control of an experimental assembly cell with two robots--termed a cognitive control unit (CCU)--is able to simulate human information processing at a rule-based level of cognitive control. To enable the CCU to work on a large range of assembly tasks expected of a human operator, the cognitive architecture SOAR is used. The CCU can plan assembly processes autonomously and react to ad-hoc changes in assembly sequences effectively. Extensive simulation studies have shown that cognitive automation based on SOAR is especially suitable for random parts supply, which reduces planning effort in logistics. Conversely, a disproportional increase in processing time was observed for deterministic parts supply, especially for assemblies containing large numbers of identical parts. In this contribution, the effect of phase-shifts in deterministic part supply is investigated for assemblies containing maximal different parts. It can be shown that the concept of cognitive automation is as well suitable for these planning problems.

  16. Multifunctional assembly of micrometer-sized colloids for cell sorting.

    PubMed

    Nie, Chenyao; Wang, Bing; Zhang, Jiangyan; Cheng, Yongqiang; Lv, Fengting; Liu, Libing; Wang, Shu

    2015-06-01

    Compared to the extensively studied nanometer-sized colloids, less attention has been paid to the assembly of micrometer-sized colloids with multifunctional characteristics. To address this need, a bottom-up approach is developed for constructing self-assemblies of micrometer-sized magnetic colloids possessing multifunctionality, including magnetic, optical, and biological activities. Biotinylated oligo (p-phenylene vinylene) (OPV) derivatives are designed to mediate the self-assembly of streptavidin-modified magnetic beads. The optical element OPV derivatives provide a fluorescence imaging ability for tracing the assembly process. Target cells can be recognized and assembled by the colloidal assembly with bioactive element antibodies. The colloidal assembly reveals better cell isolation performance by its amplified magnetic response in comparison to monodisperse colloids. The self-assembly of micrometer-sized magnetic colloids through a combination of different functional ingredients to realize multifunction is conceptually simple and easy to achieve.

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

    SciTech Connect

    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

  18. Bricks and blueprints: methods and standards for DNA assembly.

    PubMed

    Casini, Arturo; Storch, Marko; Baldwin, Geoffrey S; Ellis, Tom

    2015-09-01

    DNA assembly is a key part of constructing gene expression systems and even whole chromosomes. In the past decade, a plethora of powerful new DNA assembly methods - including Gibson Assembly, Golden Gate and ligase cycling reaction (LCR) - have been developed. In this Innovation article, we discuss these methods as well as standards such as the modular cloning (MoClo) system, GoldenBraid, modular overlap-directed assembly with linkers (MODAL) and PaperClip, which have been developed to facilitate a streamlined assembly workflow, to aid the exchange of material between research groups and to create modular reusable DNA parts.

  19. Pattern formation in centrosome assembly.

    PubMed

    Mahen, Robert; Venkitaraman, Ashok R

    2012-02-01

    A striking but poorly explained feature of cell division is the ability to assemble and maintain organelles not bounded by membranes, from freely diffusing components in the cytosol. This process is driven by information transfer across biological scales such that interactions at the molecular scale allow pattern formation at the scale of the organelle. One important example of such an organelle is the centrosome, which is the main microtubule organising centre in the cell. Centrosomes consist of two centrioles surrounded by a cloud of proteins termed the pericentriolar material (PCM). Profound structural and proteomic transitions occur in the centrosome during specific cell cycle stages, underlying events such as centrosome maturation during mitosis, in which the PCM increases in size and microtubule nucleating capacity. Here we use recent insights into the spatio-temporal behaviour of key regulators of centrosomal maturation, including Polo-like kinase 1, CDK5RAP2 and Aurora-A, to propose a model for the assembly and maintenance of the PCM through the mobility and local interactions of its constituent proteins. We argue that PCM structure emerges as a pattern from decentralised self-organisation through a reaction-diffusion mechanism, with or without an underlying template, rather than being assembled from a central structural template alone. Self-organisation of this kind may have broad implications for the maintenance of mitotic structures, which, like the centrosome, exist stably as supramolecular assemblies on the micron scale, based on molecular interactions at the nanometer scale. PMID:22245706

  20. Autonomous electrochromic assembly

    SciTech Connect

    Berland, Brian Spencer; Lanning, Bruce Roy; Stowell, Jr., Michael Wayne

    2015-03-10

    This disclosure describes system and methods for creating an autonomous electrochromic assembly, and systems and methods for use of the autonomous electrochromic assembly in combination with a window. Embodiments described herein include an electrochromic assembly that has an electrochromic device, an energy storage device, an energy collection device, and an electrochromic controller device. These devices may be combined into a unitary electrochromic insert assembly. The electrochromic assembly may have the capability of generating power sufficient to operate and control an electrochromic device. This control may occur through the application of a voltage to an electrochromic device to change its opacity state. The electrochromic assembly may be used in combination with a window.

  1. Firearm trigger assembly

    SciTech Connect

    Crandall, David L.; Watson, Richard W.

    2010-02-16

    A firearm trigger assembly for use with a firearm includes a trigger mounted to a forestock of the firearm so that the trigger is movable between a rest position and a triggering position by a forwardly placed support hand of a user. An elongated trigger member operatively associated with the trigger operates a sear assembly of the firearm when the trigger is moved to the triggering position. An action release assembly operatively associated with the firearm trigger assembly and a movable assembly of the firearm prevents the trigger from being moved to the triggering position when the movable assembly is not in the locked position.

  2. Biological Threats

    MedlinePlus

    ... Thunderstorms & Lightning Tornadoes Tsunamis Volcanoes Wildfires Main Content Biological Threats Biological agents are organisms or toxins that ... Centers for Disease Control and Prevention . Before a Biological Threat Unlike an explosion, a biological attack may ...

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

    PubMed

    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.

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

    PubMed

    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.

  5. Assessment of some innate immune responses in dab (Limanda limanda L.) from the North Sea as part of an integrated biological effects monitoring

    NASA Astrophysics Data System (ADS)

    Skouras, Andreas; Lang, Thomas; Vobach, Michael; Danischewski, Dirk; Wosniok, Werner; Scharsack, Jörn Peter; Steinhagen, Dieter

    2003-10-01

    The marine flatfish dab (Limanda limanda), which lives in direct contact with contaminated sediments, is frequently used as a sentinel species in international monitoring programmes on the biological effects of contaminants. In this study, immune responses were recorded as indicators of sublethal chronic effects of contaminants, in addition to measurement of the induction of mono-oxygenase ethoxyresorufin O-deethylase (EROD) in liver cells, the inhibition of acetylcholin esterase (AChE) in muscle and a quantification of grossly visible diseases and parasites. In total, 336 dab were analysed from five sampling areas in the North Sea, including the German Bight, the Dogger Bank, the Firth of Forth, and two locations close to oil and gas platforms (Ekofisk and Danfield). When considering plasma lysozyme levels, pinocytosis and respiratory burst activity of head kidney leucocytes, a clear gradient could be observed with decreased levels in individuals collected from the Firth of Forth and locations near the oil or gas platforms compared with dab from the Dogger Bank or the German Bight. Individuals with induced EROD activity displayed reduced lysozyme and respiratory burst activities. Lysozyme levels were also reduced in dab with lymphocystis or with nematodes. The data obtained indicate that the assessment of innate immune parameters in a monitoring programme provides supplementary information about immunomodulatory effects associated with the exposure of fish to contaminants. In particular, concentrations of plasma lysozyme, which can be analysed in an easy and inexpensive assay, are considered to be an appropriate parameter for use in a battery of other bioindicators.

  6. 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.

    PubMed

    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. PMID:26211503

  7. 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.

    PubMed

    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.

  8. Reversibly assembled cellular composite materials.

    PubMed

    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. Marine biology

    SciTech Connect

    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.

  10. Coarse-grained Simulations of Viral Assembly

    NASA Astrophysics Data System (ADS)

    Elrad, Oren M.

    2011-12-01

    The formation of viral capsids is a marvel of natural engineering and design. A large number (from 60 to thousands) of protein subunits assemble into complete, reproducible structures under a variety of conditions while avoiding kinetic and thermodynamic traps. Small single-stranded RNA viruses not only assemble their coat proteins in this fashion but also package their genome during the self-assembly process. Recent experiments have shown that the coat proteins are competent to assemble not merely around their own genomes but heterologous RNA, synthetic polyanions and even functionalized gold nanoparticles. Remarkably these viruses can even assemble around cargo not commensurate with their native state by adopting different morphologies. Understanding the properties that confer such exquisite precision and flexibility to the assembly process could aid biomedical research in the search for novel antiviral remedies, drug-delivery vehicles and contrast agents used in bioimaging. At the same time, viral assembly provides an excellent model system for the development of a statistical mechanical understanding of biological self-assembly, in the hopes of that we will identify some universal principles that underly such processes. This work consists of computational studies using coarse-grained representations of viral coat proteins and their cargoes. We find the relative strength of protein-cargo and protein-protein interactions has a profound effect on the assembly pathway, in some cases leading to assembly mechanisms that are markedly different from those found in previous work on the assembly of empty capsids. In the case of polymeric cargo, we find the first evidence for a previously theorized mechanism in which the polymer actively participates in recruiting free subunits to the assembly process through cooperative polymer-protein motions. We find that successful assembly is non-monotonic in protein-cargo affinity, such affinity can be detrimental to assembly if it

  11. Membrane module assembly

    DOEpatents

    Kaschemekat, Jurgen

    1994-01-01

    A membrane module assembly adapted to provide a flow path for the incoming feed stream that forces it into prolonged heat-exchanging contact with a heating or cooling mechanism. Membrane separation processes employing the module assembly are also disclosed. The assembly is particularly useful for gas separation or pervaporation.

  12. Cage redesign explains assembly

    PubMed Central

    Theil, Elizabeth C; Turano, Paola

    2013-01-01

    Control of protein self-assembly and disassembly, which is central to metabolism and engineering applications, remains challenging. Here, a perspicacious redesign of interfaces in the multisubunit ferritin protein cage provides single, modifiable subunits that assemble with Cu2+ templating and give insights into the cage assembly code. PMID:23416399

  13. Membrane module assembly

    DOEpatents

    Kaschemekat, J.

    1994-03-15

    A membrane module assembly is described which is adapted to provide a flow path for the incoming feed stream that forces it into prolonged heat-exchanging contact with a heating or cooling mechanism. Membrane separation processes employing the module assembly are also disclosed. The assembly is particularly useful for gas separation or pervaporation. 2 figures.

  14. Self-assembled chitin nanofibers and applications.

    PubMed

    Rolandi, Marco; Rolandi, Ranieri

    2014-05-01

    Self-assembled natural biomaterials offer a variety of ready-made nanostructures available for basic science research and technological applications. Most natural structural materials are made of self-assembled nanofibers with diameters in the nanometer range. Among these materials, chitin is the second most abundant polysaccharide after cellulose and is part of the exoskeleton or arthropods and mollusk shells. Chitin has several desirable properties as a biomaterial including mechanical strength, chemical and thermal stability, and biocompatibility. However, chitin insolubility in most organic solvents has somewhat limited its use. In this research highlight, we describe recent developments in producing biogenic chitin nanofibers using self-assembly from a solution of squid pen β-chitin in hexafluoroisopropanol. With this solution based assembly, we have demonstrated chitin-silk composite self-assembly, chitin nanofiber fabrication across length-scales, and manufacturing of chitin nanofiber substrates for tissue engineering. PMID:24556234

  15. Forwardly movable assembly for a firearm

    SciTech Connect

    Crandall, David L.; Watson, Richard W.

    2007-06-05

    A forwardly movable assembly for a firearm, the forwardly movable assembly adapted to be disposed in operative relationship relative to the other operative parts of a firearm, the firearm having in operative relationship each with one or more of the others: a barrel, a receiver, and at least one firing mechanism; the forwardly movable assembly comprising: the barrel and the receiver operatively connected with each other; a movable hand support structure to which at least one of the barrel and the receiver is connected, the barrel being movable therewith, the movable hand support structure being adapted to be gripped by an operator of the firearm; the forwardly movable assembly being adapted to be moved forward by an operator upon gripping the movable hand support structure and manually maneuvering the hand support structure forwardly; and, as the forwardly movable assembly is moved forwardly, the firing mechanism is completely disengaged therefrom and held substantially stationary relative thereto.

  16. Complexation of oppositely charged polyelectrolytes in gene delivery and biology

    NASA Astrophysics Data System (ADS)

    Shklovskii, Boris

    2009-03-01

    Charge inversion of a DNA double helix by a positively charged flexible polymer (polyelectrolyte) is widely used to facilitate DNA contact with negative cell membranes for gene delivery. Motivated by this application in the first part of the talk I study the phase diagram a solution of long polyanions (PA) with a shorter polycations (PC) as a function the ratio of total charges of PC and PA in the solution, x, and the concentration of monovalent salt. Each PA attracts many PCs to form a complex. When x= 1, the complexes are neutral and condense in a macroscopic drop. When x is far away from 1, complexes are strongly charged and stable. PA are overcharged by PC at x > 1 and undercharged by PC at x < 1. As x approaches 1, PCs attached to PA disproportionate between complexes. Some complexes become neutral and condensed in a macroscopic drop while others become even stronger charged and stay free. The second part of the talk deals with biological example of PA -PC complexes namely self-assembly of vegetable viruses from long ss-RNA molecule paying role of scaffold and identical capsid proteins with long positive tails. I show that optimization Coulomb energy of the virus leads to the charge of RNA twice larger than the total charge of the capsid, in agreement with the experimental data. Then I discuss kinetics of the Coulomb complexation driven virus self-assembly. Capsid proteins stick to unassembled chain of ss RNA (which we call ``antenna'') and slide on it towards the assembly site. I show that at excess of capsid proteins such one-dimensional diffusion accelerates self-assembly more than ten times. On the other hand at excess of ss-RNA, antenna slows self-assembly down. Several experiments are proposed to verify the role of ss-RNA antenna in self-assembly.

  17. Self-assembling magnetic "snakes"

    SciTech Connect

    2010-01-01

    Nickel particles float peacefully in a liquid medium until a giant snake seems to swim by and snatch several particles up, adding to its own mass. The self-assembled "snakes" act like biological systems, but they are not alive and are driven by a magnetic field. The research may someday offer some insight into the organization of life itself. Read more at Wired: http://www.wired.com/wiredscience/2009/03/snakes/ Research and video by Alex Snezhko and Igor Aronson, Argonne National Laboratory.

  18. Sensor mount assemblies and sensor assemblies

    DOEpatents

    Miller, David H.

    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.

  19. An end-to-end workflow for engineering of biological networks from high-level specifications.

    PubMed

    Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; Yaman, Fusun

    2012-08-17

    We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells. PMID:23651286

  20. An end-to-end workflow for engineering of biological networks from high-level specifications.

    PubMed

    Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; Yaman, Fusun

    2012-08-17

    We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.

  1. Accounting for the impact of short-term variations in the levels of trihalomethane in drinking water on exposure assessment for epidemiological purposes. Part II: biological aspects.

    PubMed

    Catto, Cyril; Charest-Tardif, Ginette; Rodriguez, Manuel; Tardif, Robert

    2013-01-01

    The variability of trihalomethane (THM) levels in drinking water raises the question of whether or not short-term variations (within-day) should be accounted for when assessing exposure to contaminants suspected of being carcinogenic and reprotoxic agents. The purpose of this study was to determine the magnitude of the impact on predicted biological levels of THMs (internal doses) exerted by within-day variations of THMs in drinking water. A database extracted from a campaign in the Québec City distribution system served to produce 81, 79 and 64 concentration profiles for the three most abundant THMs, namely chloroform (TCM), dichlorobromomethane (DCBM) and chlorodibromomethane (CDBM), respectively. Using a physiologically based toxicokinetic modeling approach, we simulated exposures (1.5 l water per day and a 10-min shower) based on each of these profiles and predicted, for 2000 individuals (Monte-Carlo simulations), maximum blood concentrations (Cmax), areas under the time versus blood concentrations curve (24 h-AUCcv) and total absorbed doses (ADs). Three different hypotheses were tested: [A] assuming a constant THM concentration in water (e.g., mean value of a day); [B] accounting for within-day variations in THM levels; and [C] a worst-case scenario assuming within-day variations and showering while THM levels were maximal. For each exposure profile, exposure indicator and individual, we calculated the ratios of values obtained according to each hypothesis (e.g., CmaxB/CmaxA and CmaxC/CmaxA) and the values corresponding to the 5th and 95th percentiles of these ratios. The closer these percentiles are to the value of 1, the smaller the error associated with assuming constant THM concentrations rather than their actual variability. Results showed that the minimal gap between these percentiles was TCM-AD(B)/TCM-AD(A) (5th=0.91; 95th=1.09), whereas the maximal gap was CDBM-Cmax(C)/CDBM-Cmax(A) (5th=0.50; 95th=3.40). Overall, TCM and ADs were the less affected

  2. Systems biology and the origins of life? Part I. Are biochemical networks possible ancestors of living systems? Reproduction, identity and sensitivity to signals of biochemical networks.

    PubMed

    Ricard, Jacques

    2010-01-01

    The set of these two theoretical papers offers an alternative to the hypothesis of a primordial RNA-world. The basic idea of these papers is to consider that the first prebiotic systems could have been networks of catalysed reactions encapsulated by a membrane. In order to test this hypothesis it was attempted to list the main obligatory features of living systems and see whether encapsulated biochemical networks could possibly display these features. The traits of living systems are the following: the ability they have to reproduce; the fact they possess an identity; the fact that biological events should be considered in the context of a history; the fact that living systems are able to evolve by selection of alterations of their structure and self-organization. The aim of these two papers is precisely to show that encapsulated biochemical networks can possess these properties and can be considered good candidates for the first prebiotic systems. In the present paper it is shown that if the proteinoids are not very specific catalysts and if some of the reactions of the network are autocatalytic whereas others are not, the resulting system does not reach a steady-state and tends to duplicate. In the same line, these biochemical networks possess an identity, viz. an information, defined from the probability of occurrence of these nodes. Moreover interaction of two ligands can increase, or decrease, this information. In the first case, the system is defined as emergent, in the second case it is considered integrated. Another property of living systems is that their behaviour is defined in the context of a time-arrow. For instance, they are able to sense whether the intensity of a signal is reached after an increase, or a decrease. This property can be mimicked by a simple physico-chemical system made up of the diffusion of a ligand followed by its chemical transformation catalysed by a proteinoid displaying inhibition by excess substrate. Under these conditions the

  3. Assembly planning at the micro scale

    SciTech Connect

    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.

  4. Hemoprotein-based supramolecular assembling systems.

    PubMed

    Oohora, Koji; Hayashi, Takashi

    2014-04-01

    Hemoproteins are metalloproteins which include iron porphyrin as a cofactor. These proteins have received much attention as promising building blocks for development of new types of biomaterials. This review summarizes recent efforts in the rational design of supramolecular hemoprotein assemblies using myoglobin, horseradish peroxidase, cytochrome b562 and cytochrome c as a monomer unit. The processes of coordination bond-mediated assembly or domain swapping-mediated assembly provide defined oligomers, while hemoprotein reconstitution with synthetic heme derivatives provides submicrometer-sized structures such as fibrils, vesicles/micelles, or networks. Interestingly, several of these assembled structures maintain the intrinsic functions of monomer units. The chemical and/or biological strategies described in this review will lead to the creation of unique hemoprotein-based functional biomaterials. PMID:24658057

  5. Parallel Assembly of LIGA Components

    SciTech Connect

    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.

  6. Shaping the science-industry-policy interface in synthetic biology.

    PubMed

    Gaisser, Sibylle; Reiss, Thomas

    2009-12-01

    Current advances in the emerging field of synthetic biology and the improvements in key technologies promise great impacts, not only on future scientific development, but also on the economy. In this paper we will adopt the triple helix concept for analyzing the early stages of a new field of science and innovation, namely synthetic biology. Synthetic biology is based on the creation and assembly of parts in order to create new and more complex structures and functions. These features of synthetic biology raise questions related to standardization and intellectual property, but also to security and public perception issues that go beyond the classical biotechnology discussions. These issues concern all involved actors in the synthetic biology field and affect the interrelationship between science, industry and policy. Based on the results of the recently finished EU FP-6 funded project TESSY ( http://www.tessy-europe.de ), the article analyzes these issues. Additionally, it illustrates the setting of clear framework conditions for synthetic biology research and development and the identification and definition of common goals for the future development of the field which will be needed for efficient science-industry-policy interaction. It was shown that it will be crucial to develop approaches that consider the needs of science and industry, on the one hand, and comply with the expectations of society, on the other hand. As synthetic biology is a global activity, the involvement of national decision-makers in international initiatives will further stimulate the development of the field. PMID:19816806

  7. Interconnect assembly for an electronic assembly and assembly method therefor

    DOEpatents

    Gerbsch, Erich William

    2003-06-10

    An interconnect assembly and method for a semiconductor device, in which the interconnect assembly can be used in lieu of wirebond connections to form an electronic assembly. The interconnect assembly includes first and second interconnect members. The first interconnect member has a first surface with a first contact and a second surface with a second contact electrically connected to the first contact, while the second interconnect member has a flexible finger contacting the second contact of the first interconnect member. The first interconnect member is adapted to be aligned and registered with a semiconductor device having a contact on a first surface thereof, so that the first contact of the first interconnect member electrically contacts the contact of the semiconductor device. Consequently, the assembly method does not require any wirebonds, but instead merely entails aligning and registering the first interconnect member with the semiconductor device so that the contacts of the first interconnect member and the semiconductor device make electrically contact, and then contacting the second contact of the first interconnect member with the flexible finger of the second interconnect member.

  8. Emerging Technologies for Assembly of Microscale Hydrogels

    PubMed Central

    Kavaz, Doga; Demirel, Melik C.; Demirci, Utkan

    2013-01-01

    Assembly of cell encapsulating building blocks (i.e., microscale hydrogels) has significant applications in areas including regenerative medicine, tissue engineering, and cell-based in vitro assays for pharmaceutical research and drug discovery. Inspired by the repeating functional units observed in native tissues and biological systems (e.g., the lobule in liver, the nephron in kidney), assembly technologies aim to generate complex tissue structures by organizing microscale building blocks. Novel assembly technologies enable fabrication of engineered tissue constructs with controlled properties including tunable microarchitectural and predefined compositional features. Recent advances in micro- and nano-scale technologies have enabled engineering of microgel based three dimensional (3D) constructs. There is a need for high-throughput and scalable methods to assemble microscale units with a complex 3D micro-architecture. Emerging assembly methods include novel technologies based on microfluidics, acoustic and magnetic fields, nanotextured surfaces, and surface tension. In this review, we survey emerging microscale hydrogel assembly methods offering rapid, scalable microgel assembly in 3D, and provide future perspectives and discuss potential applications. PMID:23184717

  9. The Thermodynamics of Virus Capsid Assembly

    PubMed Central

    Katen, Sarah; Zlotnick, Adam

    2009-01-01

    Virus capsid assembly is a critical step in the viral life cycle. The underlying basis of capsid stability is key to understanding this process. Capsid subunits interact with weak individual contact energies to form a globally stable icosahedral lattice; this structure is ideal for encapsidating the viral genome and host partners and protecting its contents upon secretion, yet the unique properties of its assembly and intersubunit contacts allows for the capsid to dissociate upon entering a new host cell. The stability of the capsid can be analyzed by treating capsid assembly as an equilibrium polymerization reaction, modified from the traditional polymer model to account for the fact that a separate nucleus is formed for each individual capsid. From the concentrations of reactants and products in an equilibrated assembly reaction, it is possible to extract the thermodynamic parameters of assembly for a wide array of icosahedral viruses using well-characterized biochemical and biophysical methods. In this chapter we describe the basic analysis and provide examples of thermodynamic assembly data for several different icosahedral viruses. These data provide new insights into the assembly mechanisms of spherical virus capsids, as well as the biology of the viral life cycle. PMID:19289214

  10. Long-read sequence assembly of the gorilla genome.

    PubMed

    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

    2016-04-01

    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.

  11. Long-read sequence assembly of the gorilla genome

    PubMed Central

    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

  12. Long-read sequence assembly of the gorilla genome.

    PubMed

    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

    2016-04-01

    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

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Reverse engineering of complex biological body parts by squared distance enabled non-uniform rational B-spline technique and layered manufacturing.

    PubMed

    Pandithevan, Ponnusamy

    2015-02-01

    In tissue engineering, the successful modeling of scaffold for the replacement of damaged body parts depends mainly on external geometry and internal architecture in order to avoid the adverse effects such as pain and lack of ability to transfer the load to the surrounding bone. Due to flexibility in controlling the parameters, layered manufacturing processes are widely used for the fabrication of bone tissue engineering scaffold with the given computer-aided design model. This article presents a squared distance minimization approach for weight optimization of non-uniform rational B-spline curve and surface to modify the geometry that exactly fits into the defect region automatically and thus to fabricate the scaffold specific to subject and site. The study showed that though the errors associated in the B-spline curve and surface were minimized by squared distance method than point distance method and tangent distance method, the errors could be minimized further in the rational B-spline curve and surface as the optimal weight could change the shape that desired for the defect site. In order to measure the efficacy of the present approach, the results were compared with point distance method and tangent distance method in optimizing the non-rational and rational B-spline curve and surface fitting for the defect site. The optimized geometry then allowed to construct the scaffold in fused deposition modeling system as an example. The result revealed that the squared distance-based weight optimization of the rational curve and surface in making the defect specific geometry best fits into the defect region than the other methods used.

  15. Telerobotic truss assembly

    NASA Technical Reports Server (NTRS)

    Sheridan, Philip L.

    1987-01-01

    The ACCESS truss was telerobotically assembled in order to gain experience with robotic assembly of hardware designed for astronaut extravehicular (EVA) assembly. Tight alignment constraints of the ACCESS hardware made telerobotic assembly difficult. A wider alignment envelope and a compliant end effector would have reduced the problem. The manipulator had no linear motion capability, but many of the assembly operations required straight line motion. The manipulator was attached to a motion table in order to provide the X, Y, and Z translations needed. A programmable robot with linear translation capability would have eliminated the need for the motion table and streamlined the assembly. Poor depth perception was a major problem. Shaded paint schemes and alignment lines were helpful in reducing this problem. The four cameras used worked well for only some operations. It was not possible to identify camera locations that worked well for all assembly steps. More cameras or movable cameras would have simplified some operations. The audio feedback system was useful.

  16. Precedence relationship representations of mechanical assembly sequences

    NASA Technical Reports Server (NTRS)

    Homendemello, L. S.; Sanderson, A. C.

    1989-01-01

    Two types of precedence relationship representations for mechanical assembly sequences are presented: precedence relationships between the establishment of one connection between two parts and the establishment of another connection, and precedence relationships between the establishment of one connection and states of the assembly process. Precedence relationship representations have the advantage of being very compact. The problem with these representations was how to guarantee their correctness and completeness. Two theorems are presented each of which leads to the generation of one type of precedence relationship representation guaranteeing its correctness and completeness for a class of assemblies.

  17. Modular robotic assembly of small devices.

    PubMed

    Frauenfelder, M

    2000-01-01

    The use of robots for the automatic assembly of devices of up to 100 x 100 x 100 mm is relatively uncommon today. Insufficient return on investment and the long lead times that are required have been limiting factors. Innovations in vision technology have led to the development of robotic assembly systems that employ flexible part-feeding. The benefits of these systems are described, which suggest that better ratios of price to productivity and deployment times are now achievable.

  18. Materials Assembly and Formation Using Engineered Polypeptides

    NASA Astrophysics Data System (ADS)

    Sarikaya, Mehmet; Tamerler, Candan; Schwartz, Daniel T.; Baneyx, Francois

    2004-08-01

    Molecular biomimetics can be defined as mimicking function, synthesis, or structure of materials and systems at the molecular scale using biological pathways. Here, inorganic-binding polypeptides are used as molecular building blocks to control assembly and formation of functional inorganic and hybrid materials and systems for nano- and nanobiotechnology applications. These polypeptides are selected via phage or cell surface display technologies and modified by molecular biology to tailor their binding and multifunctionality properties. The potential of this approach in creating new materials systems with useful physical and biological properties is enormous. This mostly stems from molecular recognition and self-assembly characteristics of the polypeptides plus the added advantage of genetic manipulation of their composition and structure. In this review, we highlight the basic premises of molecular biomimetics, describe the approaches in selecting and engineering inorganic-binding polypeptides, and present examples of their utility as molecular linkers in current and future applications.

  19. Virus Assemblies as Templates for Nanocircuits

    SciTech Connect

    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.

  20. Synthetic biology: insights into biological computation.

    PubMed

    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

  1. Synthetic biology: insights into biological computation.

    PubMed

    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

  2. Self-assembled tunable photonic hyper-crystals

    NASA Astrophysics Data System (ADS)

    Smolyaninov, Igor; Smolyaninova, Vera; Yost, Bradley; Lahneman, David; Gresock, Thomas; Narimanov, Evgenii

    2015-03-01

    We demonstrate a novel artificial optical material, the photonic hyper-crystal, which combines the most interesting features of hyperbolic metamaterials and photonic crystals. Similar to hyperbolic metamaterials, photonic hyper-crystals exhibit broadband divergence in their photonic density of states due to the lack of usual diffraction limit on the photon wave vector. On the other hand, similar to photonic crystals, hyperbolic dispersion law of extraordinary photons is modulated by forbidden gaps near the boundaries of photonic Brillouin zones. Three dimensional self-assembly of photonic hyper-crystals has been achieved by application of external magnetic field to a cobalt nanoparticle-based ferrofluid. Unique spectral properties of photonic hyper-crystals lead to extreme sensitivity of the material to monolayer coatings of cobalt nanoparticles, which should find numerous applications in biological and chemical sensing. This work was supported in part by NSF Grant DMR-1104676, NSF Center for Photonic and Multiscale Nanomaterials, ARO MURI and Gordon and Berry Moore Foundation.

  3. The logic of automated glycan assembly.

    PubMed

    Seeberger, Peter H

    2015-05-19

    Carbohydrates are the most abundant biopolymers on earth and part of every living creature. Glycans are essential as materials for nutrition and for information transfer in biological processes. To date, in few cases a detailed correlation between glycan structure and glycan function has been established. A molecular understanding of glycan function will require pure glycans for biological, immunological, and structural studies. Given the immense structural complexity of glycans found in living organisms and the lack of amplification methods or expression systems, chemical synthesis is the only means to access usable quantities of pure glycan molecules. While the solid-phase synthesis of DNA and peptides has become routine for decades, access to glycans has been technically difficult, time-consuming and confined to a few expert laboratories. In this Account, the development of a comprehensive approach to the automated synthesis of all classes of mammalian glycans, including glycosaminoglycans and glycosylphosphatidyl inositol (GPI) anchors, as well as bacterial and plant carbohydrates is described. A conceptual advance concerning the logic of glycan assembly was required in order to enable automated execution of the synthetic process. Based on the central glycosidic bond forming reaction, a general concept for the protecting groups and leaving groups has been developed. Building blocks that can be procured on large scale, are stable for prolonged periods of time, but upon activation result in high yields and selectivities were identified. A coupling-capping and deprotection cycle was invented that can be executed by an automated synthesis instrument. Straightforward postsynthetic protocols for cleavage from the solid support as well as purification of conjugation-ready oligosaccharides have been established. Introduction of methods to install selectively a wide variety of glycosidic linkages has enabled the rapid assembly of linear and branched oligo- and

  4. 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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    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

  6. Algorithms for automated DNA assembly

    PubMed Central

    Densmore, Douglas; Hsiau, Timothy H.-C.; Kittleson, Joshua T.; DeLoache, Will; Batten, Christopher; Anderson, J. Christopher

    2010-01-01

    Generating a defined set of genetic constructs within a large combinatorial space provides a powerful method for engineering novel biological functions. However, the process of assembling more than a few specific DNA sequences can be costly, time consuming and error prone. Even if a correct theoretical construction scheme is developed manually, it is likely to be suboptimal by any number of cost metrics. Modular, robust and formal approaches are needed for exploring these vast design spaces. By automating the design of DNA fabrication schemes using computational algorithms, we can eliminate human error while reducing redundant operations, thus minimizing the time and cost required for conducting biological engineering experiments. Here, we provide algorithms that optimize the simultaneous assembly of a collection of related DNA sequences. We compare our algorithms to an exhaustive search on a small synthetic dataset and our results show that our algorithms can quickly find an optimal solution. Comparison with random search approaches on two real-world datasets show that our algorithms can also quickly find lower-cost solutions for large datasets. PMID:20335162

  7. Laser light stripe measurements assure correct piston assembly

    NASA Astrophysics Data System (ADS)

    Stein, Norbert; Frohn, Heiko

    1993-12-01

    Two VIKON-3D optical inspection systems assure the correct assembly of piston rings and guard rings in a new Volkswagen piston/rod assembly line. Both systems use laser light stripe measurements to locate and identify the relevant parts with high accuracy. The piston ring assembly is checked dynamically in video real time using laser light stripe and parallel projection techniques. In addition structured light is used to verify the correct piston/rod assembly. Both inspection systems are fully integrated into the manufacturing line. All types of pistons assembled can be checked without any mechanical changes to the measurement setup.

  8. Molecular biomimetics: nanotechnology through biology

    NASA Astrophysics Data System (ADS)

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

    2003-09-01

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

  9. Molecular biomimetics: nanotechnology through biology.

    PubMed

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

    2003-09-01

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

  10. Designer self-assembling peptide materials.

    PubMed

    Zhao, Xiaojun; Zhang, Shuguang

    2007-01-01

    Understanding of macromolecular materials at the molecular level is becoming increasingly important for a new generation of nanomaterials for nanobiotechnology and other disciplines, namely, the design, synthesis, and fabrication of nanodevices at the molecular scale from bottom up. Basic engineering principles for microfabrication can be learned through fully grasping the molecular self-assembly and programmed assembly phenomena. Self- and programmed-assembly phenomena are ubiquitous in nature. Two key elements in molecular macrobiological material productions are chemical complementarity and structural compatibility, both of which require weak and non-covalent interactions that bring building blocks together during self-assembly. Significant advances have been made during the 1990s at the interface of materials chemistry and biology. They include the design of helical ribbons, peptide nanofiber scaffolds for three-dimensional cell cultures and tissue engineering, peptide surfactants for solubilizing and stabilizing diverse types of membrane proteins and their complexes, and molecular ink peptides for arbitrary printing and coating surfaces as well as coiled-coil helical peptides for multi-length scale fractal structures. These designer self-assembling peptides have far reaching implications in a broad spectrum of applications in biology, medicine, nanobiotechnology, and nanobiomedical technology, some of which are beyond our current imaginations. [image: see text

  11. Wind turbine rotor assembly

    SciTech Connect

    Kaiser, H. W.

    1984-11-20

    A vertical axis wind turbine having a horizontal arm member which supports an upright blade assembly. Bearing structure coupling the blade assembly to the turbine arm permits blade movement about its longitudinal axis as well as flexing motion of the blade assembly about axes perpendicular to the longitudinal axis. A latching mechanism automatically locks the blade assembly to its supporting arm during normal turbine operation and automatically unlocks same when the turbine is at rest. For overspeed prevention, a centrifugally actuated arm functions to unlatch the blade assembly permitting same to slipstream or feather into the wind. Manually actuated means are also provided for unlatching the moving blade assembly. The turbine arm additionally carries a switching mechanism in circuit with a turbine generator with said mechanism functioning to open and hence protect the generator circuit in the event of an overspeed condition of the turbine.

  12. A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly.

    PubMed

    Lee, Michael E; DeLoache, William C; Cervantes, Bernardo; Dueber, John E

    2015-09-18

    Saccharomyces cerevisiae is an increasingly attractive host for synthetic biology because of its long history in industrial fermentations. However, until recently, most synthetic biology systems have focused on bacteria. While there is a wealth of resources and literature about the biology of yeast, it can be daunting to navigate and extract the tools needed for engineering applications. Here we present a versatile engineering platform for yeast, which contains both a rapid, modular assembly method and a basic set of characterized parts. This platform provides a framework in which to create new designs, as well as data on promoters, terminators, degradation tags, and copy number to inform those designs. Additionally, we describe genome-editing tools for making modifications directly to the yeast chromosomes, which we find preferable to plasmids due to reduced variability in expression. With this toolkit, we strive to simplify the process of engineering yeast by standardizing the physical manipulations and suggesting best practices that together will enable more straightforward translation of materials and data from one group to another. Additionally, by relieving researchers of the burden of technical details, they can focus on higher-level aspects of experimental design.

  13. Splice assembly tool and method of splicing

    DOEpatents

    Silva, Frank A.

    1980-01-01

    A splice assembly tool for assembling component parts of an electrical conductor while producing a splice connection between electrical cables therewith, comprises a first structural member adaptable for supporting force applying means thereon, said force applying means enabling a rotary force applied manually thereto to be converted to a longitudinal force for subsequent application against a first component part of said electrical connection, a second structural member adaptable for engaging a second component part in a manner to assist said first structural member in assembling the component parts relative to one another and transmission means for conveying said longitudinal force between said first and said second structural members, said first and said second structural members being coupled to one another by said transmission means, wherein at least one of said component parts comprises a tubular elastomeric sleeve and said force applying means provides a relatively high mechanical advantage when said rotary force is applied thereto so as to facilitate assembly of said at least one tubular elastomeric sleeve about said other component part in an interference fit manner.

  14. Controlling molecular assemblies

    NASA Astrophysics Data System (ADS)

    Dameron, Arrelaine A.

    Using molecules designed to have only specific differences in their functionality, we have explored the influence of molecular conformation on the structural, electronic, and physical properties of self-assembled monolayers using both scanning probe and ensemble techniques. In the former case, we used two structurally similar molecules that differ in the degrees of freedom afforded to each. We found that this influenced the degree of order and conductance of self-assembled monolayers of each molecule, but had little influence of conductance switching of individual molecules inserted in alkanethiolate self-assembled monolayers. We further demonstrated how molecular structure influences phase separation, displace-ability, and molecular mobility of self-assembled monolayers by assembling 1-adamantanethiol on Au{111}. Molecular-resolution imaging of the self-assembled monolayers with the scanning tunneling microscopy confirmed a highly ordered hexagonally close-packed molecular lattice. We found that the 1-adamantanethiolate self-assembled monolayers were susceptible to replacement by the presence of another thiolated species, both from solution and vapor phases. Additionally, we determined that the displacement process is a nucleation and growth mechanism and the structure of the resulting self-assembled monolayers is dependent on the strength of the intermolecular interactions of the displacing molecules. It was hypothesized that 1-adamantanethiolate displacement was driven by a combination of energies gained from the exchange of one self-assembled monolayer for a denser self-assembled monolayer and from the increased stability due to intermolecular interaction forces. Exploiting the susceptibility of the 1-adamantanethiolate self-assembled monolayers to displacement, we have designed a novel patterning strategy, termed 'microdisplacement printing', by combining these sacrificial self-assembled monolayers with microcontact printing. During microdisplacement printing

  15. Composite turbine bucket assembly

    DOEpatents

    Liotta, Gary Charles; Garcia-Crespo, Andres

    2014-05-20

    A composite turbine blade assembly includes a ceramic blade including an airfoil portion, a shank portion and an attachment portion; and a transition assembly adapted to attach the ceramic blade to a turbine disk or rotor, the transition assembly including first and second transition components clamped together, trapping said ceramic airfoil therebetween. Interior surfaces of the first and second transition portions are formed to mate with the shank portion and the attachment portion of the ceramic blade, and exterior surfaces of said first and second transition components are formed to include an attachment feature enabling the transition assembly to be attached to the turbine rotor or disk.

  16. Algorithm to assemble pathways from processes

    SciTech Connect

    Mittenthal, J.E.

    1996-12-31

    To understand or to modify a biological pathway, the first step is to determine the patterns of coupling among its processes that are compatible with its input-output relation. Algorithms for this purpose have been devised for metabolic pathways, in which the reactions typically leave the enzymes unmodified. As shown here, one of these algorithms can also assemble molecular networks in which reactions modify proteins, if the proteins are included among the inputs to the reactions. Thus one procedure suffices to assemble pathways for metabolism, cytoplasmic signal transduction, and gene regulation. 9 refs., 3 figs.

  17. Biological Technicians

    MedlinePlus

    ... Biological technicians typically need a bachelor’s degree in biology or a closely related field. It is important ... Biological technicians typically need a bachelor’s degree in biology or a closely related field. It is important ...

  18. Cell-free protein synthesis and assembly on a biochip

    NASA Astrophysics Data System (ADS)

    Heyman, Yael; Buxboim, Amnon; Wolf, Sharon G.; Daube, Shirley S.; Bar-Ziv, Roy H.

    2012-06-01

    Biologically active complexes such as ribosomes and bacteriophages are formed through the self-assembly of proteins and nucleic acids. Recapitulating these biological self-assembly processes in a cell-free environment offers a way to develop synthetic biodevices. To visualize and understand the assembly process, a platform is required that enables simultaneous synthesis, assembly and imaging at the nanoscale. Here, we show that a silicon dioxide grid, used to support samples in transmission electron microscopy, can be modified into a biochip to combine in situ protein synthesis, assembly and imaging. Light is used to pattern the biochip surface with genes that encode specific proteins, and antibody traps that bind and assemble the nascent proteins. Using transmission electron microscopy imaging we show that protein nanotubes synthesized on the biochip surface in the presence of antibody traps efficiently assembled on these traps, but pre-assembled nanotubes were not effectively captured. Moreover, synthesis of green fluorescent protein from its immobilized gene generated a gradient of captured proteins decreasing in concentration away from the gene source. This biochip could be used to create spatial patterns of proteins assembled on surfaces.

  19. Mitochondrial ribosome assembly in health and disease

    PubMed Central

    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. PMID:26030272

  20. Mitochondrial ribosome assembly in health and disease.

    PubMed

    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.

  1. Plant synthetic biology.

    PubMed

    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.

  2. Assembly design system based on engineering connection

    NASA Astrophysics Data System (ADS)

    Yin, Wensheng

    2016-05-01

    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.

  3. Plant and Animal Gravitational Biology. Part 2

    NASA Technical Reports Server (NTRS)

    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.

  4. Design-driven, multi-use research agendas to enable applied synthetic biology for global health.

    PubMed

    Carothers, James M

    2013-09-01

    Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commercially-important applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems.

  5. Expanding coordination chemistry from protein to protein assembly.

    PubMed

    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.

  6. Demisable Reaction-Wheel Assembly

    NASA Technical Reports Server (NTRS)

    Roder, Russell; Ahronovich, Eliezer; Davis, Milton C., III

    2008-01-01

    A document discusses the concept of a demisable motor-drive-and-flywheel assembly [reaction-wheel assembly (RWA)] used in controlling the attitude of a spacecraft. Demisable as used here does not have its traditional legal meaning; instead, it signifies susceptible to melting, vaporizing, and/or otherwise disintegrating during re-entry of the spacecraft into the atmosphere of the Earth so as not to pose a hazard to anyone or anything on the ground. Prior RWAs include parts made of metals (e.g., iron, steel, and titanium) that melt at high temperatures and include structures of generally closed character that shield some parts (e.g., magnets) against re-entry heating. In a demisable RWA, the flywheel would be made of aluminum, which melts at a lower temperature. The flywheel web would not be a solid disk but would have a more open, nearly-spoke-like structure so that it would disintegrate more rapidly; hence, the flywheel rim would separate more rapidly so that parts shielded by the rim would be exposed sooner to re-entry heating. In addition, clearances between the flywheel and other components would be made greater, imparting a more open character and thus increasing the exposure of those components.

  7. Perspective: Geometrically frustrated assemblies

    NASA Astrophysics Data System (ADS)

    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.

  8. Laser bottom hole assembly

    DOEpatents

    Underwood, Lance D; Norton, Ryan J; McKay, Ryan P; Mesnard, David R; Fraze, Jason D; Zediker, Mark S; Faircloth, Brian O

    2014-01-14

    There is provided for laser bottom hole assembly for providing a high power laser beam having greater than 5 kW of power for a laser mechanical drilling process to advance a borehole. This assembly utilizes a reverse Moineau motor type power section and provides a self-regulating system that addresses fluid flows relating to motive force, cooling and removal of cuttings.

  9. High speed door assembly

    DOEpatents

    Shapiro, Carolyn

    1993-01-01

    A high speed door assembly, comprising an actuator cylinder and piston rods, a pressure supply cylinder and fittings, an electrically detonated explosive bolt, a honeycomb structured door, a honeycomb structured decelerator, and a structural steel frame encasing the assembly to close over a 3 foot diameter opening within 50 milliseconds of actuation, to contain hazardous materials and vapors within a test fixture.

  10. High speed door assembly

    DOEpatents

    Shapiro, C.

    1993-04-27

    A high speed door assembly is described, comprising an actuator cylinder and piston rods, a pressure supply cylinder and fittings, an electrically detonated explosive bolt, a honeycomb structured door, a honeycomb structured decelerator, and a structural steel frame encasing the assembly to close over a 3 foot diameter opening within 50 milliseconds of actuation, to contain hazardous materials and vapors within a test fixture.

  11. Permanent magnet assembly

    DOEpatents

    Chell, Jeremy; Zimm, Carl B.

    2006-12-12

    A permanent magnet assembly is disclosed that is adapted to provide a magnetic field across an arc-shaped gap. Such a permanent magnet assembly can be used, for example, to provide a time-varying magnetic field to an annular region for use in a magnetic refrigerator.

  12. Liquid rocket valve assemblies

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The design and operating characteristics of valve assemblies used in liquid propellant rocket engines are discussed. The subjects considered are as follows: (1) valve selection parameters, (2) major design aspects, (3) design integration of valve subassemblies, and (4) assembly of components and functional tests. Information is provided on engine, stage, and spacecraft checkout procedures.

  13. Turbine disc sealing assembly

    DOEpatents

    Diakunchak, Ihor S.

    2013-03-05

    A disc seal assembly for use in a turbine engine. The disc seal assembly includes a plurality of outwardly extending sealing flange members that define a plurality of fluid pockets. The sealing flange members define a labyrinth flow path therebetween to limit leakage between a hot gas path and a disc cavity in the turbine engine.

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

    PubMed

    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.

  15. Assembly partitioning with a constant number of translations

    SciTech Connect

    Halperin, D.; Wilson, R.H.

    1994-08-24

    The authors consider the following problem that arises in assembly planning: given an assembly, identify a subassembly that can be removed as a rigid object without disturbing the rest of the assembly. This is the assembly partitioning problem. Specifically, they consider planar assemblies of simple polygons and subassembly removal paths consisting of a single finite translation followed by a translation to infinity. They show that such a subassembly and removal path can be determined in O(n{sup 1.46}N{sup 6}) time, where n is the number of polygons in the assembly and N is the total number of edges and vertices of all the parts together. They then extend this formulation to removal paths consisting of a small number of finite translations, followed by a translation to infinity. In this case the algorithm runs in time polynomial in the number of parts, but exponential in the number of translations a path may contain.

  16. Assembly: a resource for assembled genomes at NCBI

    PubMed Central

    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

    2016-01-01

    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. PMID:26578580

  17. Mechanisms of Virus Assembly

    PubMed Central

    Perlmutter, Jason D.; Hagan, Michael F.

    2015-01-01

    Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assembles within their host cells and in vitro. We describe the thermodynamics and kinetics for assembly of protein subunits into icosahedral capsid shells, and how these are modified in cases where the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques that have been used to characterize capsid assembly, and we highlight aspects of virus assembly which are likely to receive significant attention in the near future. PMID:25532951

  18. Superconductive radiofrequency window assembly

    DOEpatents

    Phillips, H.L.; Elliott, T.S.

    1998-05-19

    The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The SRF window assembly has a superconducting metal-ceramic design. The SRF window assembly comprises a superconducting frame, a ceramic plate having a superconducting metallized area, and a superconducting eyelet for sealing plate into frame. The plate is brazed to eyelet which is then electron beam welded to frame. A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the SRF window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator. 11 figs.

  19. Superconducting radiofrequency window assembly

    DOEpatents

    Phillips, H.L.; Elliott, T.S.

    1997-03-11

    The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The srf window assembly has a superconducting metal-ceramic design. The srf window assembly comprises a superconducting frame, a ceramic plate having a superconducting metallized area, and a superconducting eyelet for sealing plate into frame. The plate is brazed to eyelet which is then electron beam welded to frame. A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the srf window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator. 11 figs.

  20. Modeling Viral Capsid Assembly

    PubMed Central

    2014-01-01

    I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened. PMID:25663722

  1. Constrained space camera assembly

    DOEpatents

    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.

  2. Air bearing vacuum seal assembly

    DOEpatents

    Booth, Rex

    1978-01-01

    An air bearing vacuum seal assembly capable of rotating at the speed of several thousand revolutions per minute using an air cushion to prevent the rotating and stationary parts from touching, and a two stage differential pumping arrangement to maintain the pressure gradient between the air cushion and the vacuum so that the leak rate into the vacuum is, for example, less than 1 .times. 10.sup.-4 Pa m.sup.3 /s. The air bearing vacuum seal has particular application for mounting rotating targets to an evacuated accelerator beam tube for bombardment of the targets with high-power charged particle beams in vacuum.

  3. Self-assembling and self-limiting monolayer deposition

    NASA Astrophysics Data System (ADS)

    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.

  4. EDITORIAL: MEMS in biology and medicine MEMS in biology and medicine

    NASA Astrophysics Data System (ADS)

    Pruitt, Beth L.; Herr, Amy E.

    2011-05-01

    Stimulating—the first word that springs to mind regarding the emerging and expanding role of MEMS in biological inquiry. When invited to guest-edit this special issue on 'MEMS in biology and medicine' for JMM, we jumped at the opportunity. Partly owing to the breadth of the stimulating research in this nascent area and partly owing to the stimulating of biological function made possible with MEMS accessible length and time scales, we were eager to assemble manuscripts detailing some of the most cutting edge biological research being conducted around the globe. In addition to cutting edge engineering, this special issue features challenging biological questions addressed with innovative MEMS technologies. Topics span from Yetisen and colleagues' inquiry into quantifying pollen tube behaviour in response to pistil tissues [1] to Morimoto and colleagues' engineering efforts to produce monodisperse droplets capable of encapsulating single cells (without surface modification) [2]. Questions are bold, including a means to achieve therapeutically-relevant scaling for enrichment of leukocytes from blood (Inglis et al [3]), assessing the dependence of Escherichia coli biofilm formation on bacterial signalling (Meyer et al [4]), and elucidation of adhesion dynamics of circulating tumour cells (Cheung et al [5]) among others. Technologies are diverse, including microfabricated magnetic actuators (Lee et al [6]), stimuli-responsive polymer nanocomposites (Hess et al [7]), and SU-8 electrothermal microgrippers (Chu et al [8]) to name but a few. Contributing authors do indeed span a large swathe of the globe, with contributions from Australia, Italy, China, Canada, Denmark, Japan, the USA and numerous other locations. Collaboration finds a home here—with researchers from macromolecular science and electrical engineering collaborating with the Veterans Affairs Medical Center or neurosurgery researchers working with biological and electrical engineers. The questions posed by

  5. Protein-DNA chimeras for nano assembly.

    PubMed

    Pippig, Diana A; Baumann, Fabian; Strackharn, Mathias; Aschenbrenner, Daniela; Gaub, Hermann E

    2014-07-22

    In synthetic biology, "understanding by building" requires exquisite control of the molecular constituents and their spatial organization. Site-specific coupling of DNA to proteins allows arrangement of different protein functionalities with emergent properties by self-assembly on origami-like DNA scaffolds or by direct assembly via Single-Molecule Cut & Paste (SMC&P). Here, we employed the ybbR-tag/Sfp system to covalently attach Coenzyme A-modified DNA to GFP and, as a proof of principle, arranged the chimera in different patterns by SMC&P. Fluorescence recordings of individual molecules proved that the proteins remained folded and fully functional throughout the assembly process. The high coupling efficiency and specificity as well as the negligible size (11 amino acids) of the ybbR-tag represent a mild, yet versatile, general and robust way of adding a freely programmable and highly selective attachment site to virtually any protein of interest.

  6. A continuum model for hierarchical fibril assembly

    NASA Astrophysics Data System (ADS)

    van Lith, B. S.; Muntean, A.; Storm, C.

    2014-06-01

    Most of the biological polymers that make up our cells and tissues are hierarchically structured. For biopolymers ranging from collagen, to actin, to fibrin and amyloid fibrils this hierarchy provides vitally important versatility. The structural hierarchy must be encoded in the self-assembly process, from the earliest stages onward, in order to produce the appropriate substructures. In this letter, we explore the kinetics of multistage self-assembly processes in a model system which allows comparison to bulk probes such as light scattering. We apply our model to recent turbidimetry data on the self-assembly of collagen fibrils. Our analysis suggests a connection between diffusion-limited aggregation kinetics and fibril growth, supported by slow, power-law growth at very long time scales.

  7. Dissipative self-assembly of vesicular nanoreactors.

    PubMed

    Maiti, Subhabrata; Fortunati, Ilaria; Ferrante, Camilla; Scrimin, Paolo; Prins, Leonard J

    2016-07-01

    Dissipative self-assembly is exploited by nature to control important biological functions, such as cell division, motility and signal transduction. The ability to construct synthetic supramolecular assemblies that require the continuous consumption of energy to remain in the functional state is an essential premise for the design of synthetic systems with lifelike properties. Here, we show a new strategy for the dissipative self-assembly of functional supramolecular structures with high structural complexity. It relies on the transient stabilization of vesicles through noncovalent interactions between the surfactants and adenosine triphosphate (ATP), which acts as the chemical fuel. It is shown that the lifetime of the vesicles can be regulated by controlling the hydrolysis rate of ATP. The vesicles sustain a chemical reaction but only as long as chemical fuel is present to keep the system in the out-of-equilibrium state. The lifetime of the vesicles determines the amount of reaction product produced by the system.

  8. Flexible, symmetry-directed approach to assembling protein cages.

    PubMed

    Sciore, Aaron; Su, Min; Koldewey, Philipp; Eschweiler, Joseph D; Diffley, Kelsey A; Linhares, Brian M; Ruotolo, Brandon T; Bardwell, James C A; Skiniotis, Georgios; Marsh, E Neil G

    2016-08-01

    The assembly of individual protein subunits into large-scale symmetrical structures is widespread in nature and confers new biological properties. Engineered protein assemblies have potential applications in nanotechnology and medicine; however, a major challenge in engineering assemblies de novo has been to design interactions between the protein subunits so that they specifically assemble into the desired structure. Here we demonstrate a simple, generalizable approach to assemble proteins into cage-like structures that uses short de novo designed coiled-coil domains to mediate assembly. We assembled eight copies of a C3-symmetric trimeric esterase into a well-defined octahedral protein cage by appending a C4-symmetric coiled-coil domain to the protein through a short, flexible linker sequence, with the approximate length of the linker sequence determined by computational modeling. The structure of the cage was verified using a combination of analytical ultracentrifugation, native electrospray mass spectrometry, and negative stain and cryoelectron microscopy. For the protein cage to assemble correctly, it was necessary to optimize the length of the linker sequence. This observation suggests that flexibility between the two protein domains is important to allow the protein subunits sufficient freedom to assemble into the geometry specified by the combination of C4 and C3 symmetry elements. Because this approach is inherently modular and places minimal requirements on the structural features of the protein building blocks, it could be extended to assemble a wide variety of proteins into structures with different symmetries. PMID:27432965

  9. Assembly of objects with not fully predefined shapes

    NASA Technical Reports Server (NTRS)

    Arlotti, M. A.; Dimartino, V.

    1989-01-01

    An assembly problem in a non-deterministic environment, i.e., where parts to be assembled have unknown shape, size and location, is described. The only knowledge used by the robot to perform the assembly operation is given by a connectivity rule and geometrical constraints concerning parts. Once a set of geometrical features of parts has been extracted by a vision system, applying such a rule allows the dtermination of the composition sequence. A suitable sensory apparatus allows the control the whole operation.

  10. Fibrillin: from microfibril assembly to biomechanical function.

    PubMed

    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.

  11. Brain oncology. Biology, diagnosis and therapy

    SciTech Connect

    Chatel, M.; Darcel, F.; Pecker, J.

    1987-01-01

    The book's contents are as follows: Part I: Oncogenesis. Part II: Neuropathology. Part III: Tumoral Immunobiology and Oncobiology. Part IV: Biological and Diagnostic Imaging. Part V: Clinico-Pathological Studies. Part VI: Neurosurgical Procedures and Radiotherapy Trends. Part VII: Chemotherapy and Immunotherapy.

  12. Biological Filters.

    ERIC Educational Resources Information Center

    Klemetson, S. L.

    1978-01-01

    Presents the 1978 literature review of wastewater treatment. The review is concerned with biological filters, and it covers: (1) trickling filters; (2) rotating biological contractors; and (3) miscellaneous reactors. A list of 14 references is also presented. (HM)

  13. Biological Agents

    MedlinePlus

    ... to Z Index Contact Us FAQs What's New Biological Agents This page requires that javascript be enabled ... and Health Topics A-Z Index What's New Biological agents include bacteria, viruses, fungi, other microorganisms and ...

  14. Visualizing viral assemblies in a nanoscale biosphere.

    PubMed

    Gilmore, Brian L; Showalter, Shannon P; Dukes, Madeline J; Tanner, Justin R; Demmert, Andrew C; McDonald, Sarah M; Kelly, Deborah F

    2013-01-21

    We present a novel microfluidic platform to examine biological assemblies at high-resolution. We have engineered a functionalized chamber that serves as a "nanoscale biosphere" to capture and maintain rotavirus double-layered particles (DLPs) in a liquid environment. The chamber can be inserted into the column of a transmission electron microscope while being completely isolated from the vacuum system. This configuration allowed us to determine the structure of biological complexes at nanometer-resolution within a self-contained vessel. Images of DLPs were used to calculate the first 3D view of macromolecules in solution. We refer to this new fluidic visualization technology as in situ molecular microscopy.

  15. Vancomycin assembly: nature's way.

    PubMed

    Hubbard, Brian K; Walsh, Christopher T

    2003-02-17

    Antibiotics are precious resources in the fight to combat bacterial infections caused by pathogenic organisms. Vancomycin is one of the antibiotics of last resort in the treatment of life-threatening infections by gram-positive bacteria. The rules by which nature assembles the glycopeptide (vancomycin) and lipoglycopeptide (teicoplanin) antibiotics are becoming elucidated and verified: first amino acids are synthesized, then joined together and cross-linked. This knowledge opens up approaches for reprogramming strategies at the level of altered monomers, swapped assembly lines, and different post-assembly tailoring enzymes.

  16. Protective helmet assembly

    NASA Technical Reports Server (NTRS)

    Dawn, Frederic S. (Inventor); Weiss, Fred R. (Inventor); Eck, John D. (Inventor)

    1992-01-01

    The invention is a protective helmet assembly with improved safety and impact resistance, high resistance to ignition and combustion, and reduced offgassing. The assembly comprises a hard rigid ballistic outer shell with one or more impact absorbing pads fitted to the interior surface. The pads are made of open cell flexible polyimide foam material, each of which is attached to the inner surface of the ballistic outer shell by cooperative VELCRO fastener strips of hook-and-loop material affixed respectively to the rigid outer shell and the impact absorbing pads. The helmet assembly with shell and pads is sized to fit relatively close over a wearer's head.

  17. TPX assembly plan

    SciTech Connect

    Knutson, D.

    1993-11-01

    The TPX machine will be assembled in the TFTR Test Cell at the Plasma Physics Laboratory, utilizing the existing TFTR machine foundation. Preparation of the area for assembly will begin after completion of the decontamination and decommissioning phase on TFTR and certification that the radiation levels remaining, if any, are consistent with the types of operations planned. Assembly operations begin with the arrival of the first components, and conclude, approximately 24 months later, with the successful completion of the integrated systems tests and the achievement of a first plasma.

  18. DC source assemblies

    DOEpatents

    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.

  19. Biological aerosol background characterization

    NASA Astrophysics Data System (ADS)

    Blatny, Janet; Fountain, Augustus W., III

    2011-05-01

    To provide useful information during military operations, or as part of other security situations, a biological aerosol detector has to respond within seconds or minutes to an attack by virulent biological agents, and with low false alarms. Within this time frame, measuring virulence of a known microorganism is extremely difficult, especially if the microorganism is of unknown antigenic or nucleic acid properties. Measuring "live" characteristics of an organism directly is not generally an option, yet only viable organisms are potentially infectious. Fluorescence based instruments have been designed to optically determine if aerosol particles have viability characteristics. Still, such commercially available biological aerosol detection equipment needs to be improved for their use in military and civil applications. Air has an endogenous population of microorganisms that may interfere with alarm software technologies. To design robust algorithms, a comprehensive knowledge of the airborne biological background content is essential. For this reason, there is a need to study ambient live bacterial populations in as many locations as possible. Doing so will permit collection of data to define diverse biological characteristics that in turn can be used to fine tune alarm algorithms. To avoid false alarms, improving software technologies for biological detectors is a crucial feature requiring considerations of various parameters that can be applied to suppress alarm triggers. This NATO Task Group will aim for developing reference methods for monitoring biological aerosol characteristics to improve alarm algorithms for biological detection. Additionally, they will focus on developing reference standard methodology for monitoring biological aerosol characteristics to reduce false alarm rates.

  20. 49 CFR 572.193 - Neck assembly.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... environment as specified in 49 CFR 572.200(j); (2) Attach the neck-headform assembly, as shown in Figure V2-A or V2-B in appendix A to this subpart, to the 49 CFR Part 572 pendulum test fixture (Figure 22, 49 CFR 572.33) in either the left or right lateral impact orientations, respectively, so that...

  1. 49 CFR 572.193 - Neck assembly.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... environment as specified in 49 CFR 572.200(j); (2) Attach the neck-headform assembly, as shown in Figure V2-A or V2-B in appendix A to this subpart, to the 49 CFR Part 572 pendulum test fixture (Figure 22, 49 CFR 572.33) in either the left or right lateral impact orientations, respectively, so that...

  2. 49 CFR 572.193 - Neck assembly.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... environment as specified in 49 CFR 572.200(j); (2) Attach the neck-headform assembly, as shown in Figure V2-A or V2-B in appendix A to this subpart, to the 49 CFR Part 572 pendulum test fixture (Figure 22, 49 CFR 572.33) in either the left or right lateral impact orientations, respectively, so that...

  3. 49 CFR 572.193 - Neck assembly.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... environment as specified in 49 CFR 572.200(j); (2) Attach the neck-headform assembly, as shown in Figure V2-A or V2-B in appendix A to this subpart, to the 49 CFR Part 572 pendulum test fixture (Figure 22, 49 CFR 572.33) in either the left or right lateral impact orientations, respectively, so that...

  4. 49 CFR 572.193 - Neck assembly.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... environment as specified in 49 CFR 572.200(j); (2) Attach the neck-headform assembly, as shown in Figure V2-A or V2-B in appendix A to this subpart, to the 49 CFR Part 572 pendulum test fixture (Figure 22, 49 CFR 572.33) in either the left or right lateral impact orientations, respectively, so that...

  5. Measurement Protocols for Optimized Fuel Assembly Tags

    SciTech Connect

    Gerlach, David C.; Mitchell, Mark R.; Reid, Bruce D.; Gesh, Christopher J.; Hurley, David E.

    2008-11-01

    This report describes the measurement protocols for optimized tags that can be applied to standard fuel assemblies used in light water reactors. This report describes work performed by the authors at Pacific Northwest National Laboratory for NA-22 as part of research to identify specific signatures that can be developed to support counter-proliferation technologies.

  6. 49 CFR 572.113 - Neck assembly.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal...

  7. 49 CFR 572.113 - Neck assembly.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal...

  8. 49 CFR 572.113 - Neck assembly.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal...

  9. 49 CFR 572.113 - Neck assembly.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal...

  10. Improved method of solar-cell assembly

    NASA Technical Reports Server (NTRS)

    Broder, J. D.; Forestieri, A. F.; Mandelkorn, J.

    1979-01-01

    Method bonds solar-cell modules between rigid or flexible base and plastic protective cover. Method relies on using one of several commercially-available, transparent, silicone adhesives as bonding agent. Should it ever be necessary to repair or replace some part of assembly, it may be possible to remove cover without destroying package since adhesive remains flexible.

  11. Internal Aspects of the Skill Transfer of Manual Assembly Work

    ERIC Educational Resources Information Center

    Doyo, Daisuke

    2009-01-01

    In manual assembly work, parts are often assembled by applying force with a simple tool or by hand. A worker thus needs control the force he or she applies in working, as an appropriate level of force is requisite for minimizing work failures and improving efficiency. The object of this study is to clarify the relationship between the level of…

  12. Biology of Nanobots

    NASA Astrophysics Data System (ADS)

    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.

  13. Attomolar DNA detection with chiral nanorod assemblies

    NASA Astrophysics Data System (ADS)

    Ma, Wei; Kuang, Hua; Xu, Liguang; Ding, Li; Xu, Chuanlai; Wang, Libing; Kotov, Nicholas A.

    2013-10-01

    Nanoscale plasmonic assemblies display exceptionally strong chiral optical activity. So far, their structural design was primarily driven by challenges related to metamaterials whose practical applications are remote. Here we demonstrate that gold nanorods assembled by the polymerase chain reaction into DNA-bridged chiral systems have promising analytical applications. The chiroplasmonic activity of side-by-side assembled patterns is attributed to a 7-9 degree twist between the nanorod axes. This results in a strong polarization rotation that matches theoretical expectations. The amplitude of the bisignate ‘wave’ in the circular dichroism spectra of side-by-side assemblies demonstrates excellent linearity with the amount of target DNA. The limit of detection for DNA using side-by-side assemblies is as low as 3.7 aM. This chiroplasmonic method may be particularly useful for biological analytes larger than 2-5 nm which are difficult to detect by methods based on plasmon coupling and ‘hot spots’. Circular polarization increases for inter-nanorod gaps between 2 and 20 nm when plasmonic coupling rapidly decreases. Reaching the attomolar limit of detection for simple and reliable bioanalysis of oligonucleotides may have a crucial role in DNA biomarker detection for early diagnostics of different diseases, forensics and environmental monitoring.

  14. Self-assembly of smallest magnetic particles

    PubMed Central

    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

    2015-01-01

    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. PMID:26554000

  15. Self-assembly of smallest magnetic particles.

    PubMed

    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.

  16. Metrology Techniques for the Assembly of NCSX

    SciTech Connect

    C. Priniski, T. Dodson, M. Duco, S. Raftopoulos, R. Ellis, and A. Brooks

    2009-09-24

    In support of the National Compact Stellerator Experiment (NCSX), stellerator assembly activities continued this past year at the Princeton Plasma Physics Laboratory (PPPL) in partnership with the Oak Ridge National Laboratory (ORNL). The construction program saw the completion of the first two Half Field-Period Assemblies (HPA), each consisting of three modular coils. The full machine includes six such sub-assemblies. A single HPA consists of three of the NCSX modular coils wound and assembled at PPPL. These geometrically-complex threedimensional coils were wound using computer-aided metrology and CAD models to tolerances within +/- 0.5mm. The assembly of these coils required similar accuracy on a larger scale with the added complexity of more individual parts and fewer degrees of freedom for correction. Several new potential positioning issues developed for which measurement and control techniques were developed. To accomplish this, CAD coordinate-based computer metrology equipment and software similar to the solutions employed for winding the modular coils was used. Given the size of the assemblies, the primary tools were both interferometeraided and Absolute Distance Measurement (ADM)-only based laser trackers. In addition, portable Coordinate Measurement Machine (CMM) arms and some novel indirect measurement techniques were employed. This paper will detail both the use of CAD coordinate-based metrology technology and the techniques developed and employed for dimensional control of NSCX subassemblies. The results achieved and possible improvements to techniques will be discussed.

  17. Rnnotator Assembly Pipeline

    SciTech Connect

    Martin, Jeff

    2010-06-03

    Jeff Martin of the DOE Joint Genome Institute discusses a de novo transcriptome assembly pipeline from short RNA-Seq reads on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  18. Integrated thruster assembly program

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The program is reported which has provided technology for a long life, high performing, integrated ACPS thruster assembly suitable for use in 100 typical flights of a space shuttle vehicle over a ten year period. The four integrated thruster assemblies (ITA) fabricated consisted of: propellant injector; a capacitive discharge, air gap torch type igniter assembly; fast response igniter and main propellant valves; and a combined regen-dump film cooled chamber. These flightweight 6672 N (1500 lb) thruster assemblies employed GH2/GO2 as propellants at a chamber pressure of 207 N/sq cm (300 psia). Test data were obtained on thrusted performance, thermal and hydraulic characteristics, dynamic response in pulsing, and cycle life. One thruster was fired in excess of 42,000 times.

  19. Microtubule Self- Assembly

    NASA Astrophysics Data System (ADS)

    Jho, Yongseok; Choi, M. C.; Farago, O.; Kim, Mahnwon; Pincus, P. A.

    2008-03-01

    Microtubules are important structural elements for neurons. Microtubles are cylindrical pipes that are self-assembled from tubulin dimers, These structures are intimately related to the neuron transport system. Abnormal microtubule disintegration contributes to neuro-disease. For several decades, experimentalists investigated the structure of the microtubules using TEM and Cryo-EM. However, the detailed structure at a molecular level remain incompletely understood. . In this presentation, we report numerically studies of the self-assembly process using a toy model for tubulin dimers. We investigate the nature of the interactions which are essential to stabilize such the cylindrical assembly of protofilaments. We use Monte Carlo simulations to suggest the pathways for assembly and disassembly of the microtubules.

  20. Steam separator latch assembly

    DOEpatents

    Challberg, R.C.; Kobsa, I.R.

    1994-02-01

    A latch assembly removably joins a steam separator assembly to a support flange disposed at a top end of a tubular shroud in a nuclear reactor pressure vessel. The assembly includes an annular head having a central portion for supporting the steam separator assembly thereon, and an annular head flange extending around a perimeter thereof for supporting the head to the support flange. A plurality of latches are circumferentially spaced apart around the head flange with each latch having a top end, a latch hook at a bottom end thereof, and a pivot support disposed at an intermediate portion therebetween and pivotally joined to the head flange. The latches are pivoted about the pivot supports for selectively engaging and disengaging the latch hooks with the support flange for fixedly joining the head to the shroud or for allowing removal thereof. 12 figures.