Science.gov

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

    PubMed

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

    2016-03-15

    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. 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 joel.bader@jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  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 (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

  6. 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.

  7. Standard biological parts knowledgebase.

    PubMed

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

    2011-02-24

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

  8. Small Parts Assembler Work Sample.

    ERIC Educational Resources Information Center

    Shawsheen Valley Regional Vocational-Technical High School, Billerica, MA.

    This manual contains a work sample intended to assess a handicapped student's interest in and potential to enter a training program in small parts assembly or in a similar job. Section 1 describes the assessment, correlates the work performed and worker traits required for completing the work sample, and lists related occupations and DOT codes.…

  9. Prions: Protein assemblies that convey biological information

    PubMed Central

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

    2016-01-01

    Prions derived from the prion protein (PrP) were first characterized as infectious agents that transmit pathology between individuals. However, the majority of cases of neurodegeneration caused by PrP prions occur sporadically. Proteins that self-assemble as cross-beta sheet amyloids are a defining pathological feature of infectious prion disorders and all major age-associated neurodegenerative diseases. In fact, multiple non-infectious proteins exhibit properties of template-driven self-assembly that are strikingly similar to PrP. Evidence suggests that like PrP, many proteins form aggregates that propagate between cells and convert cognate monomer into ordered assemblies. We now recognize that numerous proteins assemble into macromolecular complexes as part of normal physiology, some of which are self-amplifying. This review highlights similarities among infectious and non-infectious neurodegenerative diseases associated with prions, emphasizing the normal and pathogenic roles of higher-order protein assemblies. We propose that studies of the structural and cellular biology of pathological vs. physiological aggregates will be mutually informative. PMID:26844828

  10. 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.

  11. Part as an Object of Assembly

    NASA Astrophysics Data System (ADS)

    Václav, Štefan; Jurko, Jozef; Lecký, Šimon

    2016-09-01

    We deal with static prearranged couples in practice quite often. Constructers are using them a lot to improve rigidity of product. Some examples are mentioned in this article. The paper also discusses the models of kinematic couples in plane and models of kinematic couples in space. Spatial movable and non-movable couples are commented on as well. The article particularly focuses on application of statics in the assembly in spatial couples (movable, non-movable) for intentional allowance fix which leads to a non-problem assembly. With fix like this, it is possible to manufacture selected parts in series while assuring non-problem assembly.

  12. 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.

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

    PubMed

    Patron, Nicola J

    2014-06-01

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

  14. 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

  15. Engineering colloidal assembly via biological adhesion

    NASA Astrophysics Data System (ADS)

    Hiddessen, Amy Lynn

    Due to highly specialized recognition properties, biological receptor-ligand interactions offer valuable tools for engineering the assembly of novel colloidal materials. A unique sub-class of these macromolecules, called selectins, was exploited to develop binary suspensions where particles are programmed to associate reversibly or irreversibly via specific biomolecular cross-linking. Flow cytometry and videomicroscopy were used to examine factors controlling suspension assembly and structure, including biomolecular affinity and density, and individual and total particle volume fractions. By functionalizing small (RA = 0.47 mum) and larger (RB = 2.75 mum) particles with high surface densities of complementary E-selectin/sialyl Lewis X (sLeX) carbohydrate chemistry, a series of structures, from colloidal micelles (large particle coated with smaller particles) and clusters, to rings and elongated chains, was synthesized by decreasing the number ratio, NA/NB, of small (A) to large (B) particles (2 ≤ NA/NB ≤ 200) at low total volume fraction (10-4 ≤ φT ≤ 10-3 ). Using significantly lower surface densities, the low affinity binding between E-selectin and sLeX was exploited to create particles that interact reversibly, and average particle interaction lifetimes were tuned from minutes down to single selectin-carbohydrate bond lifetimes (≈1 s) by reducing sLeX density, a significant step toward assembling ordered microstructures. Particle binding lifetimes were analyzed with a receptor-ligand binding model, yielding estimates for molecular parameters, including on rate, 10-2 s-1 < kon < 10-1 s-1, and unstressed off rate, 0.25 s-1 ≤ kor ≤ 1.0 s-1, that characterize the docking dynamics of particles. Finally, at significantly higher volume fraction (φ T ≥ 10-1) and low number ratio, the rheology of space-filling networks crosslinked by high affinity streptavidin-biotin chemistry was probed to acquire knowledge on bulk properties of biocolloidal suspensions

  16. Supramolecular Assemblies Responsive to Biomolecules toward Biological Applications.

    PubMed

    Shigemitsu, Hajime; Hamachi, Itaru

    2015-10-01

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

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

    SciTech Connect

    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.

  18. 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

  19. 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.

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

    PubMed

    Kentsis, Alex; Borden, Katherine L B

    2004-04-01

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

  1. Biologically-Based Self-Assembling Hydrogels

    DTIC Science & Technology

    2002-04-01

    Based Self-Assembling Hydrogels Brandon L. Seal and Alyssa Panitch Department of Bioengineering, Arizona State University Tempe, AZ 85287-9709, U.S.A...the ligand from the a- chain of human fibrinogen as well as substrates for factor Xlla (Fa XllIa) (Table f) were synthesized using solid- state Fmoc...chemistry in the Arizona State University Protein Chemistry Laboratory. All peptides were purified with a C4 reverse phase preparatory column on an

  2. Biological Assembly of Hybrid Inorganic Nanomaterials (Preprint)

    DTIC Science & Technology

    2007-03-01

    particles [10,11]. In the former, a magnetic particle with three different 60-mer DNA targets to the BRCAI breast- cancer gene was assembled using a sandwich...particle conjugated with anti -rat IgG antibodies and then rat polyclonal antibodies specific to glutathione [15]. The Fe304-metal structures were...specific types of cancers and only become activated when that cancer is present. Peptides designed with multi-functionality have expanded nanoparticle

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

    SciTech Connect

    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.

  4. Detecting necessary and sufficient parts for assembling a functional weapon

    NASA Astrophysics Data System (ADS)

    Hempelmann, Christian F.; Solomon, Divya; Arslan, Abdullah N.; Attardo, Salvatore; Blount, Grady P.; Adkins, Tracy; Sirakov, Nikolay M.

    2017-05-01

    Continuing our previous research to visually extract and visually and conceptually match weapons, this study develops a method to determine whether a set of weapon parts visually extracted from images taken from different scenes can be assembled as a firing weapon. This new approach identifies potential weapons in the ontology via tracing detected necessary and sufficient parts through their meronymic relation to the whole weapon. A fast algorithm for identifying potential weapons that can be assembled from a given set of detected parts is presented.

  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. 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.

  7. 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.

  8. Phase diagram for assembly of biologically-active peptide amphiphiles.

    PubMed

    Tsonchev, Stefan; Niece, Krista L; Schatz, George C; Ratner, Mark A; Stupp, Samuel I

    2008-01-17

    We construct a phase diagram for self-assembling biologically active peptide amphiphiles. The structure and stability of the assemblies are studied as a function of pH and salinity of the solution. The general features of the phase diagram are predicted based on theoretical modeling of the self-assembly process, as well as experimental data, and further experiments are performed to verify and ascertain the boundary locations of the diagram. Depending on solution conditions, the amphiphiles can form cylindrical or spherical micelles, intermediate structures between these, or may not assemble at all. We also demonstrate that changing conditions may result in phase transitions among these structures. This type of phase diagram could be useful in the design of certain supramolecular nanostructures by providing information on the necessary conditions to form them.

  9. Readout electrode assembly for measuring biological impedance

    NASA Technical Reports Server (NTRS)

    Montgomery, L. D.; Moody, D. L., Jr. (Inventor)

    1976-01-01

    The invention comprises of a pair of readout ring electrodes which are used in conjunction with apparatus for measuring the electrical impedance between different points in the body of a living animal to determine the amount of blood flow therebetween. The readout electrodes have independently adjustable diameters to permit attachment around different parts of the body between which it is desired to measure electric impedance. The axial spacing between the electrodes is adjusted by a pair of rods which have a first pair of ends fixedly attached to one electrode and a second pair of ends slidably attached to the other electrode. Indicia are provided on the outer surface of the ring electrodes and on the surface of the rods to permit measurement of the circumference and spacing between the ring electrodes.

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

    PubMed Central

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

    2014-01-01

    Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications. PMID:24153110

  11. 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.

  12. 76 FR 9984 - Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-23

    ..., Continuous Flow Passenger Oxygen Mask Assembly, Part Numbers 174006-(), 174080-(), 174085-(), 174095... manufacturer and part number of the oxygen mask assemblies installed, an inspection to determine the manufacturing date and modification status if certain oxygen mask assemblies are installed, and...

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

    PubMed

    Barr-Gillespie, Peter-G

    2015-08-01

    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.

  14. 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.

  15. 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…

  16. 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…

  17. Towards biologically active self-assemblies: model nucleotide chimeras.

    PubMed

    Vebert-Nardin, Corinne

    2011-01-01

    With this article, we wish to give an overview of our main research activities assessing the potential of a suitable polymer modification of DNA fragments to self-assemble biologically active nanostructures. Specifically, the grafting of a hydrophobic polymer segment on DNA fragments results in amphiphilic nucleotide-based macromolecules, which, owing to both chemical and physical incompatibility, organize in self-assembled structures either on surfaces or in aqueous solution. Through the combination of the existing know-how in polymer chemistry with modern analytical techniques, we are currently focusing on establishing the mechanism of self-assembly of the polymer-modified nucleotide sequences in solution and on surfaces prior to the assessment of their hybridization capacity once involved in the ensemble. With the evaluation of the potential of the functional nanostructures to undergo biological-like adhesion through hybridization one can eventually foresee that the optimal functionality of these bio-inspired systems could be fine-tuned for biological applications such as drug delivery, gene therapy, tissue engineering and the design of either biomedical devices or biosensors.

  18. 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... oxygen mask assemblies installed, an inspection to determine the manufacturing date and modification status if certain oxygen mask assemblies are installed, and corrective action for certain oxygen mask...

  19. Sensitive ammonia gas sensors fabricated using biologically assembled copper sulfide

    NASA Astrophysics Data System (ADS)

    Shahriar Zaman, Mohammed; Moon, Chung Hee; Haberer, Elaine D.

    2014-11-01

    Copper sulfide-based ammonia (NH3) gas sensors were assembled using a genetically modified viral template. Glutamic acid residues on the filament-shaped bioscaffold surface facilitated the synthesis of nanocrystalline Cu1.8S. Each device comprised a network of biological materials decorated with a nonstoichiometric semiconductor. These chemiresistive devices had high sensitivity to NH3 concentrations from 10 to 80 ppm under room-temperature operation. Response times greater than 15 min were observed. These results demonstrate the potential of biotemplated materials for sensitive gas detection at room temperature.

  20. A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

    SciTech Connect

    Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim; Ayad, Leïla; Louie, Katherine B.; Bowen, Benjamin P.; Northen, Trent R.; Loqué, Dominique

    2016-10-26

    The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies for stacking genes and traits to address many impending environmental and agricultural challenges.

  1. A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

    PubMed Central

    Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim; Ayad, Leïla; Louie, Katherine B.; Bowen, Benjamin P.; Northen, Trent R.; Loqué, Dominique

    2016-01-01

    The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. However, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. Here, we describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies for stacking genes and traits to address many impending environmental and agricultural challenges. PMID:27782150

  2. A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

    DOE PAGES

    Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim; ...

    2016-10-26

    The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies formore » stacking genes and traits to address many impending environmental and agricultural challenges.« less

  3. Micro-grippers for assembly of LIGA parts

    SciTech Connect

    Feddema, J.; Polosky, M.; Christenson, T.; Spletzer, B.; Simon, R.

    1997-12-31

    This paper describes ongoing testing of two microgrippers for assembly of LIGA (Lithographie Galvanoformung Abformung) parts. The goal is to place 100 micron outside diameter (OD) LIGA gears with a 50 micron inner diameter hole onto pins ranging from 35 to 49 microns. The first micro gripper is a vacuum gripper made of a 100 micron OD stainless steel tube. The second micro gripper is a set of tweezers fabricated using the LIGA process. Nickel, Permalloy, and copper materials are tested. The tweezers are actuated by a collet mechanism which is closed by a DC linear motor.

  4. 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

  5. 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

  6. 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

  7. 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. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  8. Our Hidden Past: Biology, Part 1

    SciTech Connect

    Smith, Ray; Congdon, Charles; Bervin, Barry; Gaulden, Mary Esther; Russell, Liane

    2017-01-01

    After World War II, vacant buildings at Y-12 and a growing new Biology Division for which there was not adequate space at Oak Ridge National Laboratory combined to provide a home for genetic research at Y-12. In January 1949, the Biology Division moved into Building 9210.

  9. 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

  10. Our Hidden Past: Biology, Part 2

    SciTech Connect

    Smith, Ray; Russell, Liane; Mazur, Peter

    2017-01-01

    In their new home at "The Mouse House" at Y-12, researchers from ORNL's Biology Division conducted studies that led to standards such as dose rate effects that form the basis for current international standards for radiation exposure in humans.

  11. 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.

  12. 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.

  13. Development of Methodologies for Structure Determination of Biological Macromolecular Assemblies Using Synchrotron Radiation and Its Applications

    NASA Astrophysics Data System (ADS)

    Nakagawa, Atsushi

    Synchrotron radiation contributed to the recent progress in protein crystallography. High brilliance and small divergence synchrotron radiation X-ray beam is indispensable to collect diffraction data from crystals of biological macromolecular assemblies. Recent advance on methodologies and technologies on protein crystallography including synchrotron radiation allows us to solve huge biological macromolecular assemblies, such as large virus particles.

  14. Fourier-Transform Raman Spectroscopy Of Biological Assemblies

    NASA Astrophysics Data System (ADS)

    Levin, Ira W.; Lewis, E. Neil

    1989-12-01

    Although the successful coupling of Raman scattered near-infrared radiation to a Michelson interferometer has recently created an outburst of intense interest in Fourier-transform (FT) Raman spectrometry," extended applications of the technique to macromolecular assemblies of biochemical and biophysical relevance have not progressed as rapidly as studies directed primarily at more conventional chemical characterizations. Since biological materials sampled with visible laser excitation sources typically emit a dominant fluorescence signal originating either from the intrinsic fluorescence of the molecular scatterer or from unrelenting contaminants, the use of near-infrared Nd:YAG laser excitation offers a convenient approach for avoiding this frequently overwhelming effect. In addition, the FT-Raman instrumentation provides a means of eliminating the deleterious resonance and decomposition effects often observed with the more accessible green and blue laser emissions. However, in choosing the incident near-infrared wavelength at, for example, 1064nm, the Raman scattered intensity decreases by factors of eighteen to forty from the Raman emissions induced by the shorter, visible excitations. Depending upon the experiment, this disadvantage is offset by the throughput and multiplex advantages afforded by the interferometric design. Thus, for most chemical systems, near-infrared FT-Raman spectroscopy, clearly provides a means for obtaining vibrational Raman spectra from samples intractable to the use of visible laser sources. In particular, for neat liquids, dilute solutions or polycrystalline materials, the ability to achieve high quality, reproducible spectra is, with moderate experience and perhaps relatively high laser powers, as straightforward as the conventional methods used to obtain Raman spectra with visible excitation and dispersive monochromators. In using near-infrared FT techniques to determine the Raman spectra of biological samples, one encounters new

  15. 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.

  16. 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. © 2016 The Author(s).

  17. Design for Manufacturing and Assembly in Apparel. Part 1. Handbook

    DTIC Science & Technology

    1994-02-01

    ASSEMBLY IN APPAREL Preface iii PREFACE DESIGN FOR MANUFACTURING AND ASSEM- The step-by-step pictorially documented proce- BLY ( DFMA ) is defined as a...available production facilities has been illustrated by this handbook. Designing with manufacturing and assembly in mind ( DFMA ) requires a systems ap

  18. 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.

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

    PubMed

    Juhas, Mario; Ajioka, James W

    2017-05-01

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

  20. Modeling assemblies of biological cells exposed to electric fields.

    PubMed

    Fear, E C; Stuchly, M A

    1998-10-01

    Gap junctions are channels through the cell membrane that electrically connect the interiors of neighboring cells. Most cells are connected by gap junctions, and gaps play an important role in local intercellular communication by allowing for the exchange of certain substances between cells. Gap communication has been observed to change when cells are exposed to electromagnetic (EM) fields. In this work, we examine the behavior of cells connected by gap junctions when exposed to electric fields, in order to better understand the influence of the presence of gap junctions on cell behavior. This may provide insights into the interactions between biological cells and weak, low-frequency EM fields. Specifically, we model gaps in greater detail than is usually the case, and use the finite element method (FEM) to solve the resulting geometrically complex cell models. The responses of gap-connected cell configurations to both dc and time harmonic fields are investigated and compared with those of similarly shaped (equivalent) cells. To further assess the influence of the gap junctions, properties such as gap size, shape, and conductivity are varied. Our findings indicate that simple models, such as equivalent cells, are sufficient for describing the behavior of small gap-connected cell configurations exposed to dc electric fields. With larger configurations, some adjustments to the simple models are necessary to account for the presence of the gaps. The gap junctions complicate the frequency behavior of gap-connected cell assemblies. An equivalent cell exhibits low-pass behavior. Gaps effectively add a bandstop filter in series with the low-pass behavior, thus lowering the relaxation frequency. The characteristics of this bandstop filter change with changes to gap properties. Comparison of the FEM results to those obtained with simple models indicates that more complex models are required to represent gap-connected cells.

  1. 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.

  2. Two sides of the coin. Part 1. Lipid and surfactant self-assembly revisited.

    PubMed

    Ninham, Barry W; Larsson, Kåre; Lo Nostro, Pierandrea

    2017-04-01

    Hofmeister, specific ion effects, hydration and van der Waals forces at and between interfaces are factors that determine curvature and microstructure in self assembled aggregates of surfactants and lipids; and in microemulsions. Lipid and surfactant head group interactions and between aggregates vary enormously and are highly specific. They act on the hydrophilic side of a bilayer, micelle or other self assembled aggregate. It is only over the last three decades that the origin of Hofmeister effects has become generally understood. Knowledge of their systematics now provides much flexibility in designing nanostructured fluids. The other side of the coin involves equally specific forces. These (opposing) forces work on the hydrophobic side of amphiphilic interfaces. They are due to the interaction of hydrocarbons and other "oils" with hydrophobic tails of surfactants and lipids. The specificity of oleophilic solutes in microemulsions and lipid membranes provides a counterpoint to Hofmeister effects and hydration. Together with global packing constraints these effects determine microstructure. Another factor that has hardly been recognised is the role of dissolved gas. This introduces further, qualitative changes in forces that prescribe microstructure. The systematics of these effects and their interplay are elucidated. Awareness of these competing factors facilitates formulation of self assembled nanostructured fluids. New and predictable geometries that emerge naturally provide insights into a variety of biological phenomena like anaesthetic and pheromone action and transmission of the nervous impulse (see Part 2).

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

    PubMed

    Gibson, Daniel G

    2014-05-01

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

  4. 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.

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

    PubMed

    Thiruvengadathan, Rajagopalan; Korampally, Venumadhav; Ghosh, Arkasubhra; Chanda, Nripen; Gangopadhyay, Keshab; Gangopadhyay, Shubhra

    2013-06-01

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

  6. A unified convention for biological assemblies with helical symmetry.

    PubMed

    Tsai, Chung Jung; Nussinov, Ruth

    2011-08-01

    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(1), n(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.

  7. A unified convention for biological assemblies with helical symmetry

    PubMed Central

    Tsai, Chung-Jung; Nussinov, Ruth

    2011-01-01

    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 1, n 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. PMID:21795813

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

    PubMed

    Sreejith, R; Gulati, Sahil; Gupta, Sanjay

    2013-06-01

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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Qiao, Cong

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

  11. 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.

  12. 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

  13. Quantitative computational models of molecular self-assembly in systems biology

    NASA Astrophysics Data System (ADS)

    Thomas, Marcus; Schwartz, Russell

    2017-06-01

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  14. 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 ...

  15. 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 ...

  16. 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 ...

  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, 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 ...

  19. 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.

  20. Graph mining for next generation sequencing: leveraging the assembly graph for biological insights.

    PubMed

    Warnke-Sommer, Julia; Ali, Hesham

    2016-05-06

    The assembly of Next Generation Sequencing (NGS) reads remains a challenging task. This is especially true for the assembly of metagenomics data that originate from environmental samples potentially containing hundreds to thousands of unique species. The principle objective of current assembly tools is to assemble NGS reads into contiguous stretches of sequence called contigs while maximizing for both accuracy and contig length. The end goal of this process is to produce longer contigs with the major focus being on assembly only. Sequence read assembly is an aggregative process, during which read overlap relationship information is lost as reads are merged into longer sequences or contigs. The assembly graph is information rich and capable of capturing the genomic architecture of an input read data set. We have developed a novel hybrid graph in which nodes represent sequence regions at different levels of granularity. This model, utilized in the assembly and analysis pipeline Focus, presents a concise yet feature rich view of a given input data set, allowing for the extraction of biologically relevant graph structures for graph mining purposes. Focus was used to create hybrid graphs to model metagenomics data sets obtained from the gut microbiomes of five individuals with Crohn's disease and eight healthy individuals. Repetitive and mobile genetic elements are found to be associated with hybrid graph structure. Using graph mining techniques, a comparative study of the Crohn's disease and healthy data sets was conducted with focus on antibiotics resistance genes associated with transposase genes. Results demonstrated significant differences in the phylogenetic distribution of categories of antibiotics resistance genes in the healthy and diseased patients. Focus was also evaluated as a pure assembly tool and produced excellent results when compared against the Meta-velvet, Omega, and UD-IDBA assemblers. Mining the hybrid graph can reveal biological phenomena captured

  1. 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

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

    PubMed

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

    2013-02-01

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

  3. 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

  4. Chemically directed assembly of nanoparticles for material and biological applications

    NASA Astrophysics Data System (ADS)

    Park, Myoung-Hwan

    The unique electronic, magnetic, and optical properties of nanoparticles (NPs) make them useful building blocks for nanodevices and biofabrication. Site-selective immobilization/deposition of NPs on surfaces at desired positions is an important fabrication step in realizing the potential of nanomaterials in these applications. In this thesis, my research has focused on developing new strategies for mono- and multilayered-NP deposition on surfaces, increasing the stability of NP-assembles upon various surfaces for practical use of NP-based devices. Chemically directed dithiocarbamate binding of amine groups to NPs in the presence of CS2 was used for enhancing the robustness of NP assembles. Such patterning methodologies have allowed me to use site-directed NP immobilization in applications as diverse as microcontact printing, nanomolding in capillaries, nanoimprint lithography, and photolithography. Also, I have developed a simple and reliable one-step technique to form robust dendrimer-NP nanocomposites using dithiocarbamate-based chemistry. These composites are able to encapsulate and release various therapeutics, providing controllable sustained release and to separate small molecules and biomacromolecules.

  5. 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.

  6. Biologically inspired strategy for programmed assembly of viral building blocks with controlled dimensions.

    PubMed

    Rego, Jennifer M; Lee, Jae-Hun; Lee, David H; Yi, Hyunmin

    2013-02-01

    Facile fabrication of building blocks with precisely controlled dimensions is imperative in the development of functional devices and materials. We demonstrate the assembly of nanoscale viral building blocks of controlled lengths using a biologically motivated strategy. To achieve this we exploit the simple self-assembly mechanism of Tobacco mosaic virus (TMV), whose length is solely governed by the length of its genomic mRNA. We synthesize viral mRNA of desired lengths using simple molecular biology techniques, and in vitro assemble the mRNA with viral coat proteins to yield viral building blocks of controlled lengths. The results indicate that the assembly of the viral building blocks is consistent and reproducible, and can be readily extended to assemble building blocks with genetically modified coat proteins (TMV1cys). Additionally, we confirm the potential utility of the TMV1cys viral building blocks with controlled dimensions via covalent and quantitative conjugation of fluorescent markers. We envision that our biologically inspired assembly strategy to design and construct viral building blocks of controlled dimensions could be employed to fabricate well-controlled nanoarchitectures and hybrid nanomaterials for a wide variety of applications including nanoelectronics and nanocatalysis.

  7. 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.

  8. 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

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

    PubMed

    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.

  10. 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

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

    PubMed

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

    2015-07-27

    It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. SPring-8 BL44XU, beamline designed for structure analysis of large biological macromolecular assemblies

    SciTech Connect

    Higashiura, Akifumi Yamashita, Eiki; Yoshimura, Masato; Hasegawa, Kazuya; Furukawa, Yukito; Kumasaka, Takashi; Tsukihara, Tomitake; Nakagawa, Atsushi

    2016-07-27

    Beamline BL44XU at SPring-8 is operated by the Institute for Protein Research of Osaka University. The beamline is designed for X-ray crystallography of large biological macromolecular assemblies. Here we show its detailed performances, results, and the ongoing upgrade plans.

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

    PubMed

    Church, Deanna M; Goodstadt, Leo; 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

    2009-05-05

    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.

  14. 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

  15. GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology1[C][W][OA

    PubMed Central

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

    2013-01-01

    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 ever-growing 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

  16. 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;…

  17. 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;…

  18. Application of machine vision based measurement in precise assembly of miniature parts

    NASA Astrophysics Data System (ADS)

    Zhu, Cui; Wang, Xiaodong; Zhang, Xiwen; Wang, Lin; Luo, Yi

    2010-08-01

    In manufacturing of precise miniature devices, automatic assembly is the trend to replace manual work for better quality and higher yield. Precise measurement is a critical issue during assembly process because the parts are often complicated and quite different in size, shapes, surface condition, etc. The position and orientation error must be determined precisely before assembly. In the developed automatic assembly system, microscopic machine vision and precise linear stages were integrated in the measurement system for higher detection resolution and larger measurement range in working space. As to the extract of contour of parts with different surface condition, dynamic illumination control and different combination of feature detection algorithms were applied. The errors brought by non-perpendicularity among precision linear stages were compensated and the movement errors were reduced with effective measurement strategy. The measuring accuracy was validated with a special fabricated precise template. Assembly tests were done with the developed system and results indicate that the required position and orientation accuracy can be met successfully and consequently the assembly task can be fulfilled.

  19. 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

  20. The year's new drugs & biologics 2016: Part I.

    PubMed

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

    2017-01-01

    Nearly 90 new drugs and biologics, including important new line extensions, were approved or launched for the first time globally in 2016, a comparatively lower number with respect to previous years. Forty-four new drugs and biologics reached their first markets worldwide in 2016, nearly 10% fewer than the previous year. Seven of the new launches were first-in-class agents, meaning the first drug with a novel mechanism of action to be approved and launched anywhere in the world. In addition, 23 novel line extensions (i.e., new formulations, new combinations and new indications) were introduced last year. The remaining 21 products discussed in this article were approved for the first time during the year just passed, but had not yet been launched as of December 15, 2016. Information on these new arrivals is covered in depth in part I of our annual review of the pharma and biotech industry. Copyright 2017 Clarivate Analytics.

  1. 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

    2012-08-06

    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.

  2. Biological passivation of porous silicon by a self-assembled nanometric biofilm of proteins

    NASA Astrophysics Data System (ADS)

    de Stefano, Luca; Rea, Ilaria; de Tommasi, Eduardo; Giardina, Paola; Armenante, Annunziata; Longobardi, Sara; Giocondo, Michele; Rendina, Ivo

    2009-10-01

    Self-assembled monolayers are surfaces consisting of a single layer of molecules on a substrate: widespread examples of chemical and biological nature are alkylsiloxane, fatty acids, and alkanethiolate which can be deposited by different techniques on a large variety of substrates ranging from metals to oxides. We have found that a self-assembled biofilm of proteins can passivate porous silicon (PSi) based optical structures without affecting the transducing properties. Moreover, the protein coated PSi layer can also be used as a functionalized surface for proteomic applications.

  3. 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

  4. 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,...

  5. 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,...

  6. 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,...

  7. 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,...

  8. 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,...

  9. Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

    PubMed

    Cooling, M T; Rouilly, V; Misirli, G; Lawson, J; Yu, T; Hallinan, J; Wipat, A

    2010-04-01

    Fabrication of synthetic biological systems is greatly enhanced by incorporating engineering design principles and techniques such as computer-aided design. To this end, the ongoing standardization of biological parts presents an opportunity to develop libraries of standard virtual parts in the form of mathematical models that can be combined to inform system design. We present an online Repository, populated with a collection of standardized models that can readily be recombined to model different biological systems using the inherent modularity support of the CellML 1.1 model exchange format. The applicability of this approach is demonstrated by modeling gold-medal winning iGEM machines. The Repository is available online as part of http://models.cellml.org. We hope to stimulate the worldwide community to reuse and extend the models therein, and contribute to the Repository of Standard Virtual Parts thus founded. Systems Model architecture information for the Systems Model described here, along with an additional example and a tutorial, is also available as Supplementary information. The example Systems Model from this manuscript can be found at http://models.cellml.org/workspace/bugbuster. The Template models used in the example can be found at http://models.cellml.org/workspace/SVP_Templates200906.

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

    PubMed

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

    2015-02-01

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

  11. 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    SciTech Connect

    Benedek, George; Casparay, Alfred H.

    2016-08-19

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

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  15. An assembly method for micro parts jointing with given space angle based on projection matching

    NASA Astrophysics Data System (ADS)

    Bi, Lie; Wu, Wenrong; Zhang, Juan; Yang, Honggang

    2017-02-01

    It is difficult to assemble micro parts jointing with given space angle as the parts assembled are not on the same flat and the visual depth of microscopic vision is small, which can cause the images gathered by the microscopic vision unintelligible and feature extraction difficult. For the problem, this paper presents an assembly method of micro parts based on projection matching. It can assemble micro parts jointing with given space angle accurately. Firstly, an ideal assembly model is established as the size of the micro parts through the drawing software. Secondly, a graphics algorithm based on the primitive information from CAD is designed. Thirdly, according to the pixel value calibration and the graphics algorithm, the projection pictures are shown on the control interface. Lastly, the control method of micro parts is proposed to assemble them with given space angle. And we accomplished an assembly experiment of micro-tube and micro-column in this way, whose assembly deviation is 0.12∘. Experiment results indicate that the angle between two micro parts assembled can be controlled within the given deviation.

  16. 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

  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, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt. 1633, Fig. 6 Figure 6 to Part 1633—Burner Assembly Showing...

  18. 16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt. 1633, Fig. 6 Figure 6 to Part 1633—Burner Assembly Showing...

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

    PubMed

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

    2014-01-01

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

  20. 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

  1. Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery.

    PubMed

    Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

    2017-08-25

    This work reports the second part of a review intending to give the state of the art of major metabolic phenotyping strategies. It particularly deals with inherent advantages and limits regarding data analysis issues and biological information retrieval tools along with translational challenges. This Part starts with introducing the main data preprocessing strategies of the different metabolomics data. Then, it describes the main data analysis techniques including univariate and multivariate aspects. It also addresses the challenges related to metabolite annotation and characterization. Finally, functional analysis including pathway and network strategies are discussed. The last section of this review is devoted to practical considerations and current challenges and pathways to bring metabolomics into clinical environments.

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

    PubMed Central

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

    2009-01-01

    One of the long-term goals of synthetic biology is to reliably engineer biological systems that perform human-defined functions. Currently, researchers face several scientific and technical challenges in designing and building biological systems, one of which is associated with our limited ability to access, transmit, and control molecular information through the design of functional biomolecules exhibiting novel properties. The fields of RNA biology and nucleic acid engineering, along with the tremendous interdisciplinary growth of synthetic biology, are fueling advances in the emerging field of RNA programming in living systems. Researchers are designing functional RNA molecules that exhibit increasingly complex functions and integrating these molecules into cellular circuits to program higher-level biological functions. The continued integration and growth of RNA design and synthetic biology presents exciting potential to transform how we interact with and program biology. PMID:19318211

  3. Electrostatically self-assembled biodegradable microparticles from pseudoproteins and polysaccharide: fabrication, characterization, and biological properties.

    PubMed

    Potuck, Alicia N; Weed, Beth L; Leifer, Cynthia A; Chu, C C

    2015-02-09

    Electrostatically self-assembling hybrid microparticles derived from novel cationic unsaturated arginine-based poly(ester amide) polymers (UArg-PEA) and anionic hyaluronic acid (HA) were fabricated into sub-micron-sized particles in aqueous medium with subsequent UV crosslinking treatment to stabilize the structure. These hybrid microparticles were characterized for size, charge, viscosity, chemical structure, morphology, and biological properties. Depending on the feed ratio of cationic UArg-PEA to anionic HA, the crosslinked microparticles formed spherical structures of 0.772-22.08 μm in diameter, whereas the uncrosslinked microparticles formed a core with an outer petal-like structure of 2.49-15 μm in diameter. It was discovered that the morphological structure of the self-assembled microparticles had a profound influence on their biological properties. At a 1:1 feed ratio of UArg-PEA to HA, the uncrosslinked microparticles showed no cytotoxicity toward NIH 3T3 fibroblasts at concentrations up to 20 μg/mL, and the crosslinked particles exhibited no cytotoxicity at concentrations up to 10 μg/mL. The UArg-PEA/HA hybrid microparticles exhibited a significantly lower macrophage-induced proinflammatory response (via TNF-α) than that from a pure hyaluronic acid control while retaining the beneficial anti-inflammatory IL-10 production by HA. The UArg-PEA/HA microparticles also stimulated size-dependent induction of arginase activity. Therefore, self-assembling these two types of biomaterials in a favorable nontoxic aqueous environment, having complementary biological properties like those of the currently reported UArg-PEA/HA hybrid microparticles, may provide a new class of biomaterials to improve the overall tissue microenvironment for promoting wound healing.

  4. Parts plus pipes: synthetic biology approaches to metabolic engineering

    PubMed Central

    Boyle, Patrick M.; Silver, Pamela A.

    2011-01-01

    Synthetic biologists combine modular biological “parts” to create higher-order devices. Metabolic engineers construct biological “pipes” by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design. PMID:22037345

  5. Self-assembly of three-dimensional DNA nanostructures and potential biological applications.

    PubMed

    Lo, Pik Kwan; Metera, Kimberly L; Sleiman, Hanadi F

    2010-10-01

    A current challenge in nanoscience is to achieve controlled organization in three-dimensions, to provide tools for biophysics, molecular sensors, enzymatic cascades, drug delivery, tissue engineering, and device fabrication. DNA displays some of the most predictable and programmable interactions of any molecule, natural or synthetic. As a result, 3D-DNA nanostructures have emerged as promising tools for biology and materials science. In this review, strategies for 3D-DNA assembly are discussed. DNA cages, nanotubes, dendritic networks, and crystals are formed, with deliberate variation of their size, shape, persistence length, and porosities. They can exhibit dynamic character, allowing their selective switching with external stimuli. They can encapsulate and position materials into arbitrarily designed patterns, and show promise for numerous biological and materials applications.

  6. Biological Photothermal Nanodots Based on Self-Assembly of Peptide-Porphyrin Conjugates for Antitumor Therapy.

    PubMed

    Zou, Qianli; Abbas, Manzar; Zhao, Luyang; Li, Shukun; Shen, Guizhi; Yan, Xuehai

    2017-02-08

    Photothermal agents can harvest light energy and convert it into heat, offering a targeted and remote-controlled way to destroy carcinomatous cells and tissues. Inspired by the biological organization of polypeptides and porphyrins in living systems, here we have developed a supramolecular strategy to fabricate photothermal nanodots through peptide-modulated self-assembly of photoactive porphyrins. The self-assembling nature of porphyrins induces the formation of J-aggregates as substructures of the nanodots, and thus enables the fabrication of nanodots with totally inhibited fluorescence emission and singlet oxygen production, leading to a high light-to-heat conversion efficiency of the nanodots. The peptide moieties not only provide aqueous stability for the nanodots through hydrophilic interactions, but also provide a spatial barrier between porphyrin groups to inhibit the further growth of nanodots through the strong π-stacking interactions. Thermographic imaging reveals that the conversion of light to heat based on the nanodots is efficient in vitro and in vivo, enabling the nanodots to be applied for photothermal acoustic imaging and antitumor therapy. Antitumor therapy results show that these nanodots are highly biocompatible photothermal agents for tumor ablation, demonstrating the feasibility of using bioinspired nanostructures of self-assembling biomaterials for biomedical photoactive applications.

  7. When self-assembly meets biology: luminescent platinum complexes for imaging applications.

    PubMed

    Mauro, Matteo; Aliprandi, Alessandro; Septiadi, Dedy; Kehr, Nermin Seda; De Cola, Luisa

    2014-06-21

    Luminescent platinum complexes have attractive chemical and photophysical properties such as high stability, emission in the visible region, high emission quantum yields and long excited state lifetimes. However the absorption spectrum of the compounds in the UV region, preventing their excitation in the harmless visible/red region, as well as the strong quenching of the luminescent triplet state, caused by dioxygen in water and biological fluids, reduces their possible applications for imaging. Therefore a possible solution to these drawbacks is to take advantage of the high tendency of such square planar compounds to self-assemble in supramolecular structures. The assemblies can be considered new chemical species with enhanced and tunable properties. Furthermore the assembly and disassembly process can be explored as a tool to obtain dynamic labels that can be applied in biomedicine. The change in color, the turn on and off of luminescence but also of the reactivity, the protection from quenching and environmental degradation are some of the attractive properties connected to the aggregation of the complexes.

  8. 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

  9. 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)

  10. Politics & Prejudice: Dissection in Biology Education. Part II.

    ERIC Educational Resources Information Center

    Gilmore, David R.

    1991-01-01

    The issues, roles, dynamics, rationales and events embroiled in the dissection controversy are discussed. Insights into where the politics of biology education without speciesism or dissection are likely to take science education in the future are provided. (KR)

  11. 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)

  12. 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)

  13. 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.

  14. 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

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

    PubMed

    Goel, Anita; Vogel, Viola

    2008-08-01

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

  16. A Cell Biological Perspective on Past, Present and Future Investigations of the Spindle Assembly Checkpoint

    PubMed Central

    Joglekar, Ajit P.

    2016-01-01

    The spindle assembly checkpoint (SAC) is a quality control mechanism that ensures accurate chromosome segregation during cell division. It consists of a mechanochemical signal transduction mechanism that senses the attachment of chromosomes to the spindle, and a signaling cascade that inhibits cell division if one or more chromosomes are not attached. Extensive investigations of both these component systems of the SAC have synthesized a comprehensive understanding of the underlying molecular mechanisms. This review recounts the milestone results that elucidated the SAC, compiles a simple model of the complex molecular machinery underlying the SAC, and highlights poorly understood facets of the biochemical design and cell biological operation of the SAC that will drive research forward in the near future. PMID:27869759

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

    NASA Astrophysics Data System (ADS)

    Asfaw, Mesfin

    2011-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Goel, Anita; Vogel, Viola

    2008-08-01

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

  19. Protein folding and misfolding: a paradigm of self-assembly and regulation in complex biological systems.

    PubMed

    Vendruscolo, Michele; Zurdo, Jesús; MacPhee, Cait E; Dobson, Christopher M

    2003-06-15

    Understanding biological complexity is one of the grand scientific challenges for the future. A living organism is a highly evolved system made up of a large number of interwoven molecular networks. These networks primarily involve proteins, the macromolecules that enable and control virtually every chemical process that takes place in the cell. Proteins are also key elements in the essential characteristic of living systems, their ability to function and replicate themselves through controlled molecular interactions. Recent progress in understanding the most fundamental aspect of polypeptide self-organization, the process by which proteins fold to attain their active conformations, provides a global platform to gain knowledge about the function of biological systems and the regulatory mechanisms that underpin their ability to adapt to changing conditions. In order to exploit such progress effectively, we are developing a variety of approaches, including procedures that use experimental data to restrain the properties of complex systems in computer simulations, to describe their behaviour under a wide variety of conditions. We believe that such approaches can lead to significant advances in understanding biological complexity, in general, and protein folding and misfolding in particular. These advances would contribute to: a more effective exploitation of the information from genome sequences; more rational therapeutic approaches to diseases, particularly those associated with ageing; the responsible control of our own evolution; and the development of new technologies based on mimicking the principles of biological self-assembly, for instance in nanotechnology. More fundamentally, we believe that this research will result in a more coherent understanding of the origin, evolution and functional properties of living systems.

  20. 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)

  1. 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)

  2. 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…

  3. 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…

  4. 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.

  5. Biological and polymeric self-assembled hybrid systems: structure and properties of thylakoid/polyelectrolyte complexes.

    PubMed

    Dementiev, A A; Baikov, A A; Ptushenko, V V; Khomutov, G B; Tikhonov, A N

    2005-06-15

    A novel hybrid system composed of biological components and synthetic polymer, thylakoid/polycation complex, has been formed and studied. Effects of complex formation on the structure, electrostatics and functioning of thylakoid membranes have been examined. Thylakoids from bean leaves were used to form complexes with polycation polyallylamine hydrochloride (PAAH) in two systems: (i) thylakoid/polycation complexes formed in an aqueous bulk phase, and (ii) immobilized thylakoid/polycation planar complexes. Immobilized on a solid substrate surface, thylakoid/polycation complexes were prepared using layer-by-layer stepwise alternate adsorption technique, i.e., via the sequential alternate adsorption of thylakoids and polycation molecules. The morphology of built up structures was investigated by scanning electron microscopy. Light-induced electron transport in chloroplasts was studied by the electron paramagnetic resonance (EPR) method. Spin probe technique was employed to study the structural and electrostatic characteristics of thylakoid membranes. We have found that efficiency of light-induced electron transport in thylakoid membranes and membrane structure were not changed noticeably by PAAH binding to thylakoids in a wide range of PAAH concentrations. The data obtained indicate the physiologically-soft character of polycation interactions with thylakoid membranes and demonstrate effectiveness of interfacial self-assembly approach to fabrication of complex planar functional nanostructures from biological components and synthetic polymers.

  6. 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.

  7. Attraction by repulsion: compounds with like charges undergo self-assembly in water that improves in high salt and persists in real biological fluids.

    PubMed

    Garnett, Graham A E; Daze, Kevin D; Peña Diaz, Jorge A; Fagen, Noah; Shaurya, Alok; Ma, Manuel C F; Collins, Mary S; Johnson, Darren W; Zakharov, Lev N; Hof, Fraser

    2016-02-14

    We report a family of highly anionic calixarenes that form discrete homo-dimeric assemblies in pure water, that get stronger in high salt solutions, and that remain assembled in complex, denaturing solutions like real urine. The results reveal the potential of like-charged subunits for self-assembly in high-salt solutions and biological fluids.

  8. 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

  9. 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

  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. 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.

  12. Orienting rigid and flexible biological assemblies in ferrofluids for small-angle neutron scattering studies

    PubMed Central

    Sosnick, T.; Charles, S.; Stubbs, G.; Yau, P.; Bradbury, E. M.; Timmins, P.; Trewhella, J.

    1991-01-01

    Small-angle scattering from macromolecules in solution is widely used to study their structures, but the information content is limited because the molecules are generally randomly oriented and hence the data are spherically averaged. The use of oriented rodlike structures for scattering, as in fiber diffraction, greatly increases the amount of structural detail that can be obtained. A new technique using a ferromagnetic fluid has been developed to align elongated structures independent of their intrinsic magnetic properties. This technique is ideal for small-angle neutron scattering because the scattering from the ferrofluid particles can be reduced significantly by matching the neutron scattering length density of the particles to a D2O solvent (“contrast matching”). The net result is scattering primarily from the ordered biological assembly in a solution environment that can be adjusted to physiological pH and ionic strength. Scattering results from ordered tobacco mosaic virus, tobacco rattle virus, and chromain fibers are presented. ImagesFIGURE 4FIGURE 4 PMID:19431809

  13. Biologically active quinoline and quinazoline alkaloids part I.

    PubMed

    Shang, Xiao-Fei; Morris-Natschke, Susan L; Liu, Ying-Qian; Guo, Xiao; Xu, Xiao-Shan; Goto, Masuo; Li, Jun-Cai; Yang, Guan-Zhou; Lee, Kuo-Hsiung

    2017-09-13

    Quinoline and quinazoline alkaloids, two important classes of N-based heterocyclic compounds, have attracted tremendous attention from researchers worldwide since the 19th century. Over the past 200 years, many compounds from these two classes were isolated from natural sources, and most of them and their modified analogs possess significant bioactivities. Quinine and camptothecin are two of the most famous and important quinoline alkaloids, and their discoveries opened new areas in antimalarial and anticancer drug development, respectively. In this review, we survey the literature on bioactive alkaloids from these two classes and highlight research achievements prior to the year 2008 (Part I). Over 200 molecules with a broad range of bioactivities, including antitumor, antimalarial, antibacterial and antifungal, antiparasitic and insecticidal, antiviral, antiplatelet, anti-inflammatory, herbicidal, antioxidant and other activities, were reviewed. This survey should provide new clues or possibilities for the discovery of new and better drugs from the original naturally occurring quinoline and quinazoline alkaloids. © 2017 Wiley Periodicals, Inc.

  14. Assembly of smart adaptronic piezo-metal composites by use of prefabricated batches of piezoceramic micro parts

    NASA Astrophysics Data System (ADS)

    Neugebauer, Reimund; Koriath, Hans-Joachim; Müller, Michael

    2013-04-01

    Current technologies for smart sheet metal part production base upon adhesive bonding of piezo-patches to the surface. A novel concept and process chain is the assembly of piezoceramic micro parts into local microstructures of metal sheets and subsequent joining by forming. This results in a full functional integration of the piezoceramic in the metal for sensor and actuator purposes. Mechanical coupling is non-positive without elastic interlayers and the electrical coupling is characterized by the metal being the ground electrode of the sensor. The paper describes the design, methods and tolerance management to overcome the challenges for reliable parallel microassembly and joining of prefabricated batches of 10 piezoceramic fibers with dimensions of 0.267 × 0.250 × 10 mm3 and nominal assembly clearances of +/-0.018 mm. The prefabrication of the batches is achieved by stacking and dicing of piezoceramic plates. Both the principles of precision machining and elastic averaging are applied for reliable production and joining of the batches. In experiments, equally spaced piezoceramic fibers within the batches were achieved. Prototypes were assembled and joined by forming achieving functional piezo-metal composites. With the given tolerances of the parts and the microstructure a statistical tolerance analysis has been performed in order to determine the maximum allowable position uncertainty of the microassembly system. An assembly yield of > 95% is expected for future scaled up high volume assembly of piezo-metal composites.

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. Interactions regulating the head-to-tail directed assembly of biological Janus rods

    DOE PAGES

    Greene, A. C.; Bachand, M.; Gomez, A.; ...

    2017-03-31

    We can generalize the directed, head-to-tail self-assembly of microtubule filaments in the context of Janus colloidal rods. Specifically, their assembly at the tens of micron-length scale involves a careful balance between long-range electrostatic repulsion and short-range attractive forces. We show that the addition of counterion salts increases the rate of directed assembly by screening the electrostatic forces and enhancing the effectiveness of short-range interactions at the microtubule ends.

  2. Creating parts that allow for rational design: synthetic biology and the problem of context-sensitivity.

    PubMed

    Güttinger, Stephan

    2013-06-01

    The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins' account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. 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.

  4. 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.

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

    PubMed

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

    2017-02-03

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

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

    PubMed Central

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

    2017-01-01

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

  7. 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.

  8. Basic Biology of Oxidative Stress and the Cardiovascular System: Part 1 of a 3-Part Series.

    PubMed

    Sack, Michael N; Fyhrquist, Frej Y; Saijonmaa, Outi J; Fuster, Valentin; Kovacic, Jason C

    2017-07-11

    The generation of reactive oxygen species (ROS) is a fundamental aspect of normal human biology. However, when ROS generation exceeds endogenous antioxidant capacity, oxidative stress arises. If unchecked, ROS production and oxidative stress mediate tissue and cell damage that can spiral in a cycle of inflammation and more oxidative stress. This article is part 1 of a 3-part series covering the role of oxidative stress in cardiovascular disease. The broad theme of this first paper is the mechanisms and biology of oxidative stress. Specifically, the authors review the basic biology of oxidative stress, relevant aspects of mitochondrial function, and stress-related cell death pathways (apoptosis and necrosis) as they relate to the heart and cardiovascular system. They then explore telomere biology and cell senescence. As important regulators and sensors of oxidative stress, telomeres are segments of repetitive nucleotide sequence at each end of a chromosome that protect the chromosome ends from deterioration. Copyright © 2017 American College of Cardiology Foundation. All rights reserved.

  9. 16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to, Portable Frame Allowing...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt.1633, Fig. 6 Figure 6 to Part 1633—Burner Assembly Showing...

  10. 16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to Portable Frame Allowing...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... FLAMMABILITY (OPEN FLAME) OF MATTRESS SETS Pt.1633, Fig. 6 Figure 6 to Part 1633—Burner Assembly Showing...

  11. Kinetically Assembled Nanoparticles of Bioactive Macromolecules Exhibit Enhanced Stability and Cell-Targeted Biological Efficacy

    PubMed Central

    York, Adam W.; Zablocki, Kyle R.; Lewis, Daniel R.; Gu, Li; Uhrich, Kathryn E.; Prud’homme, Robert K.

    2012-01-01

    Kinetically assembled nanoparticles are fabricated from an advanced class of bioactive macromolecules that have potential utility in counteracting atherosclerotic plaque development via receptor-level blockage of inflammatory cells. In contrast to micellar analogs that exhibit poor potency and structural integrity under physiologic conditions, these kinetic nanoparticle assemblies maintain structural stability and demonstrate superior bioactivity in mediating oxidized low-density lipoprotein (oxLDL) uptake in inflammatory cells. PMID:22223224

  12. 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

  13. Nuclear, biological and chemical warfare. Part I: Medical aspects of nuclear warfare.

    PubMed

    Kasthuri, A S; Pradhan, A B; Dham, S K; Bhalla, I P; Paul, J S

    1990-04-01

    Casualties in earlier wars were due much more to diseases than to weapons. Mention has been made in history of the use of biological agents in warfare, to deny the enemy food and water and to cause disease. In the first world war chemical agents were used to cause mass casualties. Nuclear weapons were introduced in the second world war. Several countries are now involved in developing nuclear, biological and chemical weapon systems, for the mass annihilation of human beings, animals and plants, and to destroy the economy of their enemies. Recently, natural calamities and accidents in nuclear, chemical and biological laboratories and industries have caused mass instantaneous deaths in civilian population. The effects of future wars will not be restricted to uniformed persons. It is time that physicians become aware of the destructive potential of these weapons. Awareness, immediate protective measures and first aid will save a large number of persons. This series of articles will outline the medical aspects of nuclear, biological and chemical weapon systems in three parts. Part I will deal with the biological effects of a nuclear explosion. The short and long term effects due to blast, heat and associated radiation are highlighted. In Part II, the role of biological agents which cause commoner or new disease patterns is mentioned. Some of the accidents from biological warfare laboratories are a testimony to its potential deleterious effects. Part III deals with medical aspects of chemical warfare agents, which in view of their mass effects can overwhelm the existing medical resources, both civilian and military.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. 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.

  15. Nucleic acid-programmed assemblies: translating instruction into function in chemical biology.

    PubMed

    Winssinger, Nicolas

    2013-01-01

    The predictability of nucleic acid hybridization offers an attractive platform to program the assembly of tagged ligands or reactants. Hybridization can be used to display multiple ligands in order to gain affinity and/or selectivity through the cooperative interaction of each ligand. Additionally, hybridization of tagged reagents increases their effective concentration and accelerates reactions. In both cases, an oligonucleotide directs an assembly to yield a functional output in the form of enhanced binding, inhibition, or reaction; for example, a reaction can be used to unmask a fluorophore or a bioactive molecule. This review provides an account of our research in this area as well as future directions.

  16. Ultralow voltage operation of biologically assembled all carbon nanotube nanomesh transistors with ion-gel gate dielectrics.

    PubMed

    Byeon, Hye-Hyeon; Kim, Kein; Kim, Woong; Yi, Hyunjung

    2017-07-20

    The demonstration of field-effect transistors (FETs) based entirely on single-walled carbon nanotubes (SWNTs) would enable the fabrication of high-on-current, flexible, transparent and stretchable devices owing to the excellent electrical, optical, and mechanical properties of SWNTs. Fabricating all-SWNT-based FETs via simple solution process, at room temperature and without using lithography and vacuum process could further broaden the applicability of all-SWNT-FETs. In this work, we report on biologically assembled all SWNT-based transistors and demonstrate that ion-gel-gated network structures of unsorted SWNTs assembled using a biological template material enabled operation of SWNT-based transistors at a very low voltage. The compatibility of the biologically assembled SWNT networks with ion gel dielectrics and the large capacitance of both the three-dimensional channel networks and the ion gel allowed an ultralow operation voltage. The all-SWNT-based FETs showed an I on /I off value of >10(2), an on-current density per channel width of 2.16 × 10(-4) A/mm at VDS = 0.4 V, and a field-effect hole mobility of 1.12 cm(2)/V · s in addition to the low operation voltage of <-0.5 V. We envision that our work suggests a solution-based simple and low-cost approach to realizing all-carbon-based FETs for low voltage operation and flexible applications.

  17. 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

  18. Biology--Chemistry--Physics, Students' Guide, A Three-Year Sequence, Parts I and II.

    ERIC Educational Resources Information Center

    Scott, Arthur; And Others

    Parts I and II of the students' guide to the three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee are contained in this guide. A committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical…

  19. 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…

  20. 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…

  1. 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.

  2. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Organization, integration, and assembly of genetic and epigenetic regulatory machinery in nuclear microenvironments: implications for biological control in cancer.

    PubMed

    Stein, Gary S; Zaidi, Sayyed K; Stein, Janet L; Lian, Jane B; van Wijnen, Andre J; Montecino, Martin; Young, Daniel W; Javed, Amjad; Pratap, Jitesh; Choi, Je-Yong; Ali, Syed A; Pande, Sandhya; Hassan, Mohammad Q

    2009-02-01

    There is growing awareness that the fidelity of gene expression necessitates coordination of transcription factor metabolism and organization of genes and regulatory proteins within the three-dimensional context of nuclear architecture. The regulatory machinery that governs genetic and epigenetic control of gene expression is compartmentalized in nuclear microenvironments. Temporal and spatial parameters of regulatory complex organization and assembly are functionally linked to biological control and are compromised with the onset and progression of tumorigenesis. High throughput imaging of cells, tissues, and tumors, including live cell analysis, is expanding research's capabilities toward translating components of nuclear organization into novel strategies for cancer diagnosis and therapy.

  4. Design of Nanostructured Biological Materials Through Self-Assembly of Peptides and Proteins

    DTIC Science & Technology

    2002-01-01

    impact in the coming decades. Engineering principles for micro - and nano -fabrication can be learned by understanding molecular self-assembly...range of applications in nano -biotechnology. Addresses Center for Biomedical Engineering, 56-341 Massachusetts Institute of Technology, 77...acids form stacked nanotubes that can insert into membranes and change their properties. These nano porous structures have potential anti-bacterial

  5. 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.

  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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    Wood, Craig P.; Trolinger, James D.

    1991-01-01

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

  8. Design for Manufacturing and Assembly in Apparel. Part 2. Printing, Publishing, and Distribution

    DTIC Science & Technology

    1994-02-01

    PRIVTIUG* PWLIUKlE, ANDDISIUIWT!l I I Design for Manufacturing and Assembly ( DFMA ) as a concept is defined as the methodology used by product designers which...will be made, has received a fair measure of success in the hard goods industries. DFMA , however, has not received any great measure of attention or...requesting parties. It was the objective of Phase II to complete the process of dissemination of DFMA concepts to the apparel industry by distributing

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

    PubMed Central

    Böke, Frederik; Schickle, Karolina; Fischer, Horst

    2014-01-01

    High-strength ceramics as materials for medical implants have a long, research-intensive history. Yet, especially on applications where the ceramic components are in direct contact with the surrounding tissue, an unresolved issue is its inherent property of biological inertness. To combat this, several strategies have been investigated over the last couple of years. One promising approach investigates the technique of Self-Assembled Monolayers (SAM) and subsequent chemical functionalization to create a biologically active tissue-facing surface layer. Implementation of this would have a beneficial impact on several fields in modern implant medicine such as hip and knee arthroplasty, dental applications and related fields. This review aims to give a summarizing overview of the latest advances in this recently emerging field, along with thorough introductions of the underlying mechanism of SAMs and surface cell attachment mechanics on the cell side. PMID:28788687

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

    PubMed

    Levy, Roie; Borenstein, Elhanan

    2014-01-01

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

  11. Analyzing native membrane protein assembly in nanodiscs by combined non-covalent mass spectrometry and synthetic biology

    PubMed Central

    Henrich, Erik; Peetz, Oliver; Hein, Christopher; Laguerre, Aisha; Hoffmann, Beate; Hoffmann, Jan; Dötsch, Volker; Bernhard, Frank; Morgner, Nina

    2017-01-01

    Membrane proteins frequently assemble into higher order homo- or hetero-oligomers within their natural lipid environment. This complex formation can modulate their folding, activity as well as substrate selectivity. Non-disruptive methods avoiding critical steps, such as membrane disintegration, transfer into artificial environments or chemical modifications are therefore essential to analyze molecular mechanisms of native membrane protein assemblies. The combination of cell-free synthetic biology, nanodisc-technology and non-covalent mass spectrometry provides excellent synergies for the analysis of membrane protein oligomerization within defined membranes. We exemplify our strategy by oligomeric state characterization of various membrane proteins including ion channels, transporters and membrane-integrated enzymes assembling up to hexameric complexes. We further indicate a lipid-dependent dimer formation of MraY translocase correlating with the enzymatic activity. The detergent-free synthesis of membrane protein/nanodisc samples and the analysis by LILBID mass spectrometry provide a versatile platform for the analysis of membrane proteins in a native environment. DOI: http://dx.doi.org/10.7554/eLife.20954.001 PMID:28067619

  12. Analyzing native membrane protein assembly in nanodiscs by combined non-covalent mass spectrometry and synthetic biology.

    PubMed

    Henrich, Erik; Peetz, Oliver; Hein, Christopher; Laguerre, Aisha; Hoffmann, Beate; Hoffmann, Jan; Dötsch, Volker; Bernhard, Frank; Morgner, Nina

    2017-01-09

    Membrane proteins frequently assemble into higher order homo- or hetero-oligomers within their natural lipid environment. This complex formation can modulate their folding, activity as well as substrate selectivity. Non-disruptive methods avoiding critical steps, such as membrane disintegration, transfer into artificial environments or chemical modifications are therefore essential to analyze molecular mechanisms of native membrane protein assemblies. The combination of cell-free synthetic biology, nanodisc-technology and non-covalent mass spectrometry provides excellent synergies for the analysis of membrane protein oligomerization within defined membranes. We exemplify our strategy by oligomeric state characterization of various membrane proteins including ion channels, transporters and membrane-integrated enzymes assembling up to hexameric complexes. We further indicate a lipid-dependent dimer formation of MraY translocase correlating with the enzymatic activity. The detergent-free synthesis of membrane protein/nanodisc samples and the analysis by LILBID mass spectrometry provide a versatile platform for the analysis of membrane proteins in a native environment.

  13. 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.

  14. BioPartsDB: a synthetic biology workflow web-application for education and research.

    PubMed

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

    2016-11-15

    Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones.

  15. Structure of biological graded refractive index materials, and possible routes to self-assembly

    NASA Astrophysics Data System (ADS)

    Cai, Jing; Heiney, Paul; Sweeney, Alison

    2014-03-01

    For a camera-like eye, a spherical lens with a radially graded refractive index is required for high-quality image formation. Squids have evolved this lens design, and the index gradient results from variation in the density of protein in the lens from the center (70% packing fraction) to the periphery (2% packing fraction). However, density fluctuations must also remain low in all regions to maintain lens transparency. Squids have achieved this by an evolutionary radiation of the isoforms of one protein, S-crystallin; different protein isoforms are synthesized in different radial positions of the lens. We studied whether these proteins self-assemble into the observed gradient index material. X-ray scattering was performed on both intact lenses and solubilized lens protein. Our results show that protein packing is organized, and that the organization changes with radial position. We identify possible self-assembled routes to the observed structures via the predicted interactions between the proteins. Our study may provide insights into engineering new self-assembling graded refractive index materials.

  16. 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.

  17. 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.

  18. BioPartsDB: a synthetic biology workflow web-application for education and research

    PubMed Central

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

    2016-01-01

    Summary: Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones. Availability and Implementation: BioPartsDB is released under the MIT license and available for download at https://github.com/baderzone/biopartsdb. Additional documentation and video tutorials are available at https://github.com/baderzone/biopartsdb/wiki. An Amazon Web Services image is available from the AWS Market Place (ami-a01d07c8). Contact: joel.bader@jhu.edu PMID:27412090

  19. 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.

  20. A US perspective on fast reactor fuel fabrication technology and experience part I: metal fuels and assembly design

    NASA Astrophysics Data System (ADS)

    Burkes, Douglas E.; Fielding, Randall S.; Porter, Douglas L.; Crawford, Douglas C.; Meyer, Mitchell K.

    2009-06-01

    This paper is part I of a review focusing on the United States experience with metallic fast reactor fuel fabrication and assembly design for the Experimental Breeder Reactor-II (EBR-II) and the Fast Flux Test Facility (FFTF). Experience with metal fuel fabrication in the United States is extensive, including over 60 years of research conducted by the government, national laboratories, industry, and academia. This experience has culminated in a considerable amount of research that resulted in significant improvements to the technologies employed to fabricate metallic fast reactor fuel. This part of the review documents the current state of fuel fabrication technologies for metallic fuels, some of the challenges faced by previous researchers, and how these were overcome. Knowledge gained from reviewing previous investigations will aid both researchers and policy makers in forming future decisions relating to nuclear fuel fabrication technologies.

  1. Test design description, Volume 1B, Part 2; FSP-1R FFTF test assembly (HF191A): Revision

    SciTech Connect

    McWethy, L.M.

    1989-07-01

    The principal objective of the FSP-1 test series is to provide the required fuel behavior data needed for fuel modeling and data on the performance of Reference Flight System prototypic cladding and liners at goal burnup. The test series includes two reconstitutions, designated FSP-1R and FSP-1RR, respectively. The irradiation times specified are: 150 equivalent full power days (EFPDs) for the initial FSP-1, 300 EFPDs for FSP-1R, and 400 EFPDs for FSP-1RR. A TDD-IB, part 1 document was issued to specify the design and fabrication requirements for fuel pins in the FSP-1R test. This TDD-IB, Part 2 document will specify the requirements for encapsulation of the FSP-1R fuel pins and fabrication of the FSP-1R test assembly. 6 figs., 5 tabs.

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

    PubMed

    Schubert, Walter

    2014-01-01

    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.

  3. 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

    ... Mixed Open Biological Treatment Systems at Kraft Pulp Mills Under Unsafe Sampling Conditions E Appendix E to Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS..., App. E Appendix E to Part 63—Monitoring Procedure for Nonthoroughly Mixed Open Biological...

  4. Synthesis and biological evaluation of polymethoxylated 4-heteroarylcoumarins as tubulin assembly inhibitor.

    PubMed

    Ganina, Olga G; Daras, Etienne; Bourgarel-Rey, Véronique; Peyrot, Vincent; Andresyuk, Alexey N; Finet, Jean-Pierre; Fedorov, Alexey Yu; Beletskaya, Irina P; Combes, Sébastien

    2008-10-01

    A series of syn-restricted polymethoxylated 4-heteroarylcoumarins--the isostuctural analogs of combretastatin A-4--was synthesized by Suzuki-Miyaura cross-coupling reaction and evaluated for antiproliferative activity. The 4-(1-methyl-1H-indol-5-yl)chromen-2-ones exhibit a potent cytotoxicity against HBL100 epithelial cell line with an IC(50) value amounting to 0.098 and 0.078 microM, respectively. The two compounds, having an indolyl moiety, potent inhibit in vitro microtubule assembly with a substoichiometric mode of action. A structure-activity relationship was discussed and the indolyl moiety was proved to be a good surrogate for the 3-hydroxy-4-methoxyphenyl ring of CA-4.

  5. The biology of desmin filaments: how do mutations affect their structure, assembly, and organisation?

    PubMed

    Bär, Harald; Strelkov, Sergei V; Sjöberg, Gunnar; Aebi, Ueli; Herrmann, Harald

    2004-11-01

    Desmin, the major intermediate filament (IF) protein of muscle, is evolutionarily highly conserved from shark to man. Recently, an increasing number of mutations of the desmin gene has been described to be associated with human diseases such as certain skeletal and cardiac myopathies. These diseases are histologically characterised by intracellular aggregates containing desmin and various associated proteins. Although there is progress regarding our knowledge on the cellular function of desmin within the cytoskeleton, the impact of each distinct mutation is currently not understood at all. In order to get insight into how such mutations affect filament assembly and their integration into the cytoskeleton we need to establish IF structure at atomic detail. Recent progress in determining the dimer structure of the desmin-related IF-protein vimentin allows us to assess how such mutations may affect desmin filament architecture.

  6. Assembled core-shell nanostructures of gold nanoparticles with biocompatible polymers toward biology.

    PubMed

    Li, Dongxiang; Li, Qianru; Hao, Xiongwen; Zhang, Yaojun; Zhang, Zhupeng; Li, Chunfang

    2014-03-01

    The present review focuses on core-shell nanostructures of spherical gold nanoparticles (Au NPs) and biocompatible polymers mainly from the view points of preparation approaches, nanocomposite properties and potential applications for biology. The preparation approaches are assorted into direct-reduction, covalent "graft-to", "graft-from" approach, surface bonding and physical adsorption. Various biocompatible polymers are involved such as the thermosensitive polymers, pH-responsive polymers, antibiofouling polymers, conductive polymers and several natural polymers. The encapsulating and loading properties, cellular uptake and drug release control, as well as biorecognition, targeting and sensing potential are discussed in connection with biological systems. These polymeric gold nanocomposites will have a great potential in biotechnology and life science but also face enormous challenge in future applications.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Kraemer, S. M.

    2005-12-01

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

  9. Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome.

    PubMed

    Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

    2017-08-24

    Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed.

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

    PubMed

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

    2014-06-18

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

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

    PubMed

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

    2014-12-01

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

  12. 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.

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

    PubMed

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

    2016-03-01

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

  14. 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.

  15. 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

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

    PubMed

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

    2008-01-01

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

  17. 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

  18. [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

  19. 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.

  20. 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.

  1. Biological markers for anxiety disorders, OCD and PTSD - a consensus statement. Part I: Neuroimaging and genetics.

    PubMed

    Bandelow, Borwin; Baldwin, David; Abelli, Marianna; Altamura, Carlo; Dell'Osso, Bernardo; Domschke, Katharina; Fineberg, Naomi A; Grünblatt, Edna; Jarema, Marek; Maron, Eduard; Nutt, David; Pini, Stefano; Vaghi, Matilde M; Wichniak, Adam; Zai, Gwyneth; Riederer, Peter

    2016-08-01

    Biomarkers are defined as anatomical, biochemical or physiological traits that are specific to certain disorders or syndromes. The objective of this paper is to summarise the current knowledge of biomarkers for anxiety disorders, obsessive-compulsive disorder (OCD) and post-traumatic stress disorder (PTSD). Findings in biomarker research were reviewed by a task force of international experts in the field, consisting of members of the World Federation of Societies for Biological Psychiatry Task Force on Biological Markers and of the European College of Neuropsychopharmacology Anxiety Disorders Research Network. The present article (Part I) summarises findings on potential biomarkers in neuroimaging studies, including structural brain morphology, functional magnetic resonance imaging and techniques for measuring metabolic changes, including positron emission tomography and others. Furthermore, this review reports on the clinical and molecular genetic findings of family, twin, linkage, association and genome-wide association studies. Part II of the review focuses on neurochemistry, neurophysiology and neurocognition. Although at present, none of the putative biomarkers is sufficient and specific as a diagnostic tool, an abundance of high-quality research has accumulated that will improve our understanding of the neurobiological causes of anxiety disorders, OCD and PTSD.

  2. T cell synapse assembly: proteins, motors and the underlying cell biology.

    PubMed

    Tooley, Aaron J; Jacobelli, Jordan; Moldovan, Maria-Cristina; Douglas, Adam; Krummel, Matthew F

    2005-02-01

    A tantalizing feature of the 'immunological synapse' is the segregation of transmembrane proteins into activating clusters and their underlying signalosomes. The mechanisms by which transmembrane proteins are initially recruited to and then stably segregated at the synapse remains an outstanding question in the field; and one likely to reveal key modes of signaling regulation. Ongoing real-time imaging approaches and a refocusing of efforts upon understanding the basic cell biology of T cells have all contributed to a developing model of T cell behavior; elementary TCR-derived signaling quickly feeds back into the basic cellular programs controlling cell shape, adhesiveness, motility, as well as some poorly understood aspects of membrane fluidity and segregation. It is increasingly clear that the mechanisms for control at this level are shared between T cells and other cell types and may not be revealed in differential genomic screening. To this end, imaging-based genetic screens are now coming online to aid in identifying the ubiquitous proteins that function at polarized signaling surfaces.

  3. Analysis of Production Lead Time for Missile Repair Parts: Contracts Dealing with Cable Assemblies and Wiring Harnesses

    DTIC Science & Technology

    1975-04-01

    contracts dealing with cable assemblies and wiring harnesses . Techniques of regression analysis and graphical analysis were employed on the data observations from thirty cable assembly and wiring harness contracts.

  4. Copy number variability in Parkinson's disease: assembling the puzzle through a systems biology approach.

    PubMed

    La Cognata, Valentina; Morello, Giovanna; D'Agata, Velia; Cavallaro, Sebastiano

    2017-01-01

    Parkinson's disease (PD), the second most common progressive neurodegenerative disorder of aging, was long believed to be a non-genetic sporadic origin syndrome. The proof that several genetic loci are responsible for rare Mendelian forms has represented a revolutionary breakthrough, enabling to reveal molecular mechanisms underlying this debilitating still incurable condition. While single nucleotide polymorphisms (SNPs) and small indels constitute the most commonly investigated DNA variations accounting for only a limited number of PD cases, larger genomic molecular rearrangements have emerged as significant PD-causing mutations, including submicroscopic Copy Number Variations (CNVs). CNVs constitute a prevalent source of genomic variations and substantially participate in each individual's genomic makeup and phenotypic outcome. However, the majority of genetic studies have focused their attention on single candidate-gene mutations or on common variants reaching a significant statistical level of acceptance. This gene-centric approach is insufficient to uncover the genetic background of polygenic multifactorial disorders like PD, and potentially masks rare individual CNVs that all together might contribute to disease development or progression. In this review, we will discuss literature and bioinformatic data describing the involvement of CNVs on PD pathobiology. We will analyze the most frequent copy number changes in familiar PD genes and provide a "systems biology" overview of rare individual rearrangements that could functionally act on commonly deregulated molecular pathways. Assessing the global genome-wide burden of CNVs in PD patients may reveal new disease-related molecular mechanisms, and open the window to a new possible genetic scenario in the unsolved PD puzzle.

  5. 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 of...

  6. 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 of...

  7. 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 of...

  8. 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 of...

  9. 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...; 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 of...

  10. 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.

  11. 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.

  12. 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.

  13. Investigating adsorption of synthetic nanoparticles and biological species using surface-grafted molecular and macromolecular gradient assemblies

    NASA Astrophysics Data System (ADS)

    Bhat, Rajendra R.

    We utilize novel surface-grafted molecular and macromolecular gradient assemblies to investigate: (1) dispersion of nanoparticles in organic matrices tethered to a substrate, and (2) adsorption of proteins and adhesion of cells to synthetic polymeric surfaces. First, we demonstrate control over the two-dimensional assemblies of nanoparticles bound to a flat substrate by utilizing a concentration gradient template formed via vapor transport of organosilane molecules. Number density of particles is shown to be directly proportional to the surface concentration of organosilane species comprising the monolayer. Subsequently, we create three-dimensional assemblies of nanoparticles by dispersing particles in surface-anchored polymers. For comprehensive exploration of this new class of nanocomposite materials, we employ novel architectures of surface-grafted polymers that offer either (1) unidirectional variation of polymer molecular weight (linear gradient) or (2) bidirectional, simultaneous variation of molecular weight and grafting density (orthogonal gradient). The number of particles in the polymer brush/particle hybrid increases with increasing polymer molecular weight due to an increase in the number of particle attachment sites. While particles larger than thickness of the brush predominantly reside near the brush-air interface, smaller nanoparticles penetrate deeper into the brush, thus forming a three-dimensional structure. Upon increasing grafting density of the chains, larger particles show a continuous increase in particle loading. In contrast, smaller particles exhibit a maximum in particle concentration at some intermediate value of grafting density. We rationalize the latter behavior in terms of competition between enthalpic gain upon particle attachment to the polymer chains and entropic penalty induced by the insertion of particles in the dense brush. Finally, we harness gradients of protein repelling polymer to tailor the amount of adsorbed fibronectin

  14. Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices

    PubMed Central

    Pasotti, Lorenzo; Politi, Nicolò; Zucca, Susanna; Cusella De Angelis, Maria Gabriella; Magni, Paolo

    2012-01-01

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

  15. [Are there pseudophototropic reactions in biology? Part 4: On the reversibility of biologic/synthetic polymere systems (author's transl)].

    PubMed

    Patschorke, J

    1979-01-01

    In further research on pseudophototropic behaviour in cellular membranes of halobacteria the reversibility of vinylmethylethermaleic anhydride-copolymeres with biological liquids is tested and the basic principles of different colour generating reactions are studied.

  16. 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.

  17. Biological effects of ultrasound: development of safety guidelines. Part II: general review.

    PubMed

    Nyborg, W L

    2001-03-01

    In the 1920s, the availability of piezoelectric materials and electronic devices made it possible to produce ultrasound (US) in water at high amplitudes, so that it could be detected after propagation through large distances. Laboratory experiments with this new mechanical form of radiation showed that it was capable of producing an astonishing variety of physical, chemical and biologic effects. In this review, the early findings on bioeffects are discussed, especially those from experiments done in the first few decades, as well as the concepts employed in explaining them. Some recent findings are discussed also, noting how the old and the new are related. In the first few decades, bioeffects research was motivated partly by curiosity, and partly by the wish to increase the effectiveness and ensure the safety of therapeutic US. Beginning in the 1970s, the motivation has come also from the need for safety guidelines relevant to diagnostic US. Instrumentation was developed for measuring acoustic pressure in the fields of pulsed and focused US employed, and standards were established for specifying the fields of commercial equipment. Critical levels of US quantities were determined from laboratory experiments, together with biophysical analysis, for bioeffects produced by thermal and nonthermal mechanisms. These are the basis for safety advice and guidelines recommended or being considered by national, international, professional and governmental organizations.

  18. 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.

  19. Self-assembled structures and pKa value of oleic acid in systems of biological relevance.

    PubMed

    Salentinig, Stefan; Sagalowicz, Laurent; Glatter, Otto

    2010-07-20

    In the human digestion process, triglycerides are hydrolyzed by lipases to monoglycerides and the corresponding fatty acids. Here we report the self-assembly of structures in biologically relevant, emulsified oleic acid-monoolein mixtures at various pH values and oleic acid concentrations. Small-angle X-ray scattering, cryogenic transmission electron microscopy, and dynamic light scattering were used to investigate the structures formed, and to follow their transitions while these factors were varied. The addition of oleic acid to monoolein-based cubosomes was found to increase the critical packing parameter in the system. Structural transitions from bicontinuous cubosomes through hexosomes and micellar cubosomes (Fd3m symmetry) to emulsified microemulsions occur with increasing oleic acid concentration. At sufficiently high oleic acid concentration, the internal particle structure was also found to strongly depend on the pH of the aqueous phase: transformations from emulsified microemulsion through micellar cubosomes, hexosomes, and bicontinuous cubosomes to vesicles can be observed as a function of increasing pH. The reversible transition from liquid crystals to vesicles occurs at intestinal pH values (between pH 7 and 8). The hydrodynamic radius of the particles decreases from around 120 nm for internally structured particles to around 60 nm for vesicles. All transitions with pH are reversible. Finally, the apparent pK(a) for oleic acid in monoolein could be determined from the change of structure with pH. This value is within the physiological pH range of the intestine and depends somewhat on composition.

  20. 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.

  1. Enzyme-free and label-free ultrasensitive electrochemical detection of human immunodeficiency virus DNA in biological samples based on long-range self-assembled DNA nanostructures.

    PubMed

    Chen, Xian; Hong, Cheng-Yi; Lin, Ya-Hui; Chen, Jing-Hua; Chen, Guo-Nan; Yang, Huang-Hao

    2012-10-02

    Biosensors based on nanomaterials have been used for detection of various biological molecules with high sensitivity and selectivity. Herein, we developed a simple and ultrasensitive electrochemical DNA biosensor using long-range self-assembled DNA nanostructures as carriers for signal amplification, which can achieve an impressive detection limit of 5 aM human immunodeficiency virus (HIV) DNA even in complex biological samples. In this study, we designed two auxiliary probes. A cascade of hybridization events between the two auxiliary probes can lead to long-range self-assembly and form micrometer-long one-dimensional DNA nanostructures. In the presence of target DNA, each copy of the target can act as a trigger to connect a DNA nanostructure to a capture probe on the electrode surface. Then, a great amount of redox indicator [Ru(NH(3))(6)](3+) can be electrostatically bound to the DNA nanostructures and eventually result in significantly amplified electrochemical signals.

  2. Integration of biological parts toward the synthesis of a minimal cell.

    PubMed

    Caschera, Filippo; Noireaux, Vincent

    2014-10-01

    Various approaches are taken to construct synthetic cells in the laboratory, a challenging goal that became experimentally imaginable over the past two decades. The construction of protocells, which explores scenarios of the origin of life, has been the original motivations for such projects. With the advent of the synthetic biology era, bottom-up engineering approaches to synthetic cells are now conceivable. The modular design emerges as the most robust framework to construct a minimal cell from natural molecular components. Although significant advances have been made for each piece making this complex puzzle, the integration of the three fundamental parts, information-metabolism-self-organization, into cell-sized liposomes capable of sustained reproduction has failed so far. Our inability to connect these three elements is also a major limitation in this research area. New methods, such as machine learning coupled to high-throughput techniques, should be exploited to accelerate the cell-free synthesis of complex biochemical systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Modelling of a biologically inspired robotic fish driven by compliant parts.

    PubMed

    El Daou, Hadi; Salumäe, Taavi; Chambers, Lily D; Megill, William M; Kruusmaa, Maarja

    2014-03-01

    Inspired by biological swimmers such as fish, a robot composed of a rigid head, a compliant body and a rigid caudal fin was built. It has the geometrical properties of a subcarangiform swimmer of the same size. The head houses a servo-motor which actuates the compliant body and the caudal fin. It achieves this by applying a concentrated moment on a point near the compliant body base. In this paper, the dynamics of the compliant body driving the robotic fish is modelled and experimentally validated. Lighthill's elongated body theory is used to define the hydrodynamic forces on the compliant part and Rayleigh proportional damping is used to model damping. Based on the assumed modes method, an energetic approach is used to write the equations of motion of the compliant body and to compute the relationship between the applied moment and the resulting lateral deflections. Experiments on the compliant body were carried out to validate the model predictions. The results showed that a good match was achieved between the measured and predicted deformations. A discussion of the swimming motions between the real fish and the robot is presented.

  4. 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.

  5. Systematic review of biological effects of exposure to static electric fields. Part II: Invertebrates and plants.

    PubMed

    Schmiedchen, Kristina; Petri, Anne-Kathrin; Driessen, Sarah; Bailey, William H

    2017-09-27

    The construction of high-voltage direct current (HVDC) lines for the long-distance transport of energy is becoming increasingly popular. This has raised public concern about potential environmental impacts of the static electric fields (EF) produced under and near HVDC power lines. As the second part of a comprehensive literature analysis, the aim of this systematic review was to assess the effects of static EF exposure on biological functions in invertebrates and plants and to provide the basis for an environmental impact assessment of such exposures. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) was used to guide the methodological conduct and reporting. Thirty-three studies - 14 invertebrate and 19 plant studies - met the eligibility criteria and were included in this review. The reported behavioral responses of insects and planarians upon exposure strongly suggest that invertebrates are able to perceive the presence of a static EF. Many other studies reported effects on physiological functions that were expressed as, for example, altered metabolic activity or delayed reproductive and developmental stages in invertebrates. In plants, leaf damage, alterations in germination rates, growth and yield, or variations in the concentration of essential elements, for example, have been reported. However, these physiological responses and changes in plant morphology appear to be secondary to surface stimulation by the static EF or caused by concomitant parameters of the electrostatic environment. Furthermore, all of the included studies suffered from methodological flaws, which lowered credibility in the results. At field levels encountered from natural sources or HVDC lines (< 35kV/m), the available data provide reliable evidence that static EF can trigger behavioral responses in invertebrates, but they do not provide evidence for adverse effects of static EF on other biological functions in invertebrates and plants. At far higher field

  6. Molecular biology for the critical care physician part I: terminology and technology.

    PubMed

    Santis, G; Evans, T W

    1999-04-01

    The past few years have seen a profound revolution in biological sciences. The enormous advances in molecular biology are providing novel insights into the etiology and treatment of human disease. These insights will undoubtedly have implications for intensive care research and practice. In this first of two articles, the basic principles and techniques of molecular biology are discussed to provide the intensive care physician with background information on the subject.

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

    DOE PAGES

    Zeqiraj, Elton; Tian, Lei; Piggott, Christopher  A.; ...

    2015-09-03

    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. Here, 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 (supermore » dimers) was required for DUB activity and interaction with targeting proteins SHMT2 and RAP80. Lastly, these data provide an 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.« less

  8. 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

  9. 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.

  10. 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.

  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. Large-scale study of the interactions between proteins involved in type IV pilus biology in Neisseria meningitidis: characterization of a subcomplex involved in pilus assembly.

    PubMed

    Georgiadou, Michaella; Castagnini, Marta; Karimova, Gouzel; Ladant, Daniel; Pelicic, Vladimir

    2012-06-01

    The functionally versatile type IV pili (Tfp) are one of the most widespread virulence factors in bacteria. However, despite generating much research interest for decades, the molecular mechanisms underpinning the various aspects of Tfp biology remain poorly understood, mainly because of the complexity of the system. In the human pathogen Neisseria meningitidis for example, 23 proteins are dedicated to Tfp biology, 15 of which are essential for pilus biogenesis. One of the important gaps in our knowledge concerns the topology of this multiprotein machinery. Here we have used a bacterial two-hybrid system to identify and quantify the interactions between 11 Pil proteins from N. meningitidis. We identified 20 different binary interactions, many of which are novel. This represents the most complex interaction network between Pil proteins reported to date and indicates, among other things, that PilE, PilM, PilN and PilO, which are involved in pilus assembly, indeed interact. We focused our efforts on this subset of proteins and used a battery of assays to determine the membrane topology of PilN and PilO, map the interaction domains between PilE, PilM, PilN and PilO, and show that a widely conserved N-terminal motif in PilN is essential for both PilM-PilN interactions and pilus assembly. Finally, we show that PilP (another protein involved in pilus assembly) forms a complex with PilM, PilN and PilO. Taken together, these findings have numerous implications for understanding Tfp biology and provide a useful blueprint for future studies.

  13. Guidelines for biological treatment of substance use and related disorders, part 1: Alcoholism, first revision.

    PubMed

    Soyka, Michael; Kranzler, Henry R; Hesselbrock, Victor; Kasper, Siegfried; Mutschler, Jochen; Möller, Hans-Jürgen

    2017-03-01

    These practice guidelines for the biological treatment of alcohol use disorders are an update of the first edition, published in 2008, which was developed by an international Task Force of the World Federation of Societies of Biological Psychiatry (WFSBP). For this 2016 revision, we performed a systematic review (MEDLINE/PUBMED database, Cochrane Library) of all available publications pertaining to the biological treatment of alcoholism and extracted data from national guidelines. The Task Force evaluated the identified literature with respect to the strength of evidence for the efficacy of each medication and subsequently categorised it into six levels of evidence (A-F) and five levels of recommendation (1-5). Thus, the current guidelines provide a clinically and scientifically relevant, evidence-based update of our earlier recommendations. These guidelines are intended for use by clinicians and practitioners who evaluate and treat people with alcohol use disorders and are primarily concerned with the biological treatment of adults with such disorders.

  14. Biological uniqueness and the definition of normality. Part 1--The concept of 'intrinsic' homeostasis.

    PubMed

    Schulz, P

    1994-01-01

    The patterns of biochemical and physiological variables values are subject-specific and quite stable over time. Thus, within the limits imposed by physiological requirements, the composition of the 'milieu intérieur' varies between individuals. It follows that having all values of blood constituents within the norm (defined statistically from populations of healthy subjects) might not be sufficient to identify biological normality, and a revised definition of biological normality should take into account inter-individual differences. Our concept of 'intrinsic' homeostasis means that the differences between subjects' concentrations of blood constituents express subject-specific constraints in the organization of their physiology, and that these differences might play a greater role than usually recognized. We list the consequences for medical research of the existence of biological uniqueness and propose to give more importance to the study of biological 'fingerprints' and 'intrinsic' homeostasis in physiology and clinical medicine.

  15. [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".

  16. Nitrogenase assembly

    PubMed Central

    Hu, Yilin; Ribbe, Markus W.

    2013-01-01

    Nitrogenase contains two unique metalloclusters: the P-cluster and the M-cluster. The assembly processes of P- and M-clusters are arguably the most complicated processes in bioinorganic chemistry. There is considerable interest in decoding the biosynthetic mechanisms of the P- and M-clusters, because these clusters are not only biologically important, but also chemically unprecedented. Understanding the assembly mechanisms of these unique metalloclusters is crucial for understanding the structure-function relationship of nitrogenase. Here, we review the recent advances in this research area, with an emphasis on our work that provide important insights into the biosynthetic pathways of these high-nuclearity metal centers. PMID:23232096

  17. 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.

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

    PubMed

    Wu, Minming; Guo, Kai; Dong, Hongwei; Zeng, Rong; Tu, Mei; Zhao, Jianhao

    2014-12-01

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

  19. 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,…

  20. 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…

  1. 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.

  2. 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…

  3. Morphomics: An integral part of systems biology of the human placenta.

    PubMed

    Mayhew, T M

    2015-04-01

    The placenta is a transient organ the functioning of which has health consequences far beyond the embryo/fetus. Understanding the biology of any system (organ, organism, single cell, etc) requires a comprehensive and inclusive approach which embraces all the biomedical disciplines and 'omic' technologies and then integrates information obtained from all of them. Among the latest 'omics' is morphomics. The terms morphome and morphomics have been applied incoherently in biology and biomedicine but, recently, they have been given clear and widescale definitions. Morphomics is placed in the context of other 'omics' and its pertinent technologies and tools for sampling and quantitation are reviewed. Emphasis is accorded to the importance of random sampling principles in systems biology and the value of combining 3D quantification with alternative imaging techniques to advance knowledge and understanding of the human placental morphome. By analogy to other 'omes', the morphome is the totality of morphological features within a system and morphomics is the systematic study of those structures. Information about structure is required at multiple levels of resolution in order to understand better the processes by which a given system alters with time, experimental treatment or environmental insult. Therefore, morphomics research includes all imaging techniques at all levels of achievable resolution from gross anatomy and medical imaging, via optical and electron microscopy, to molecular characterisation. Quantification is an important element of all 'omics' studies and, because biological systems exist and operate in 3-dimensional (3D) space, precise descriptions of form, content and spatial relationships require the quantification of structure in 3D. These considerations are relevant to future study contributions to the Human Placenta Project. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. 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.

  5. Structure of a proteasome Pba1-Pba2 complex: implications for proteasome assembly, activation, and biological function.

    PubMed

    Stadtmueller, Beth M; Kish-Trier, Erik; Ferrell, Katherine; Petersen, Charisse N; Robinson, Howard; Myszka, David G; Eckert, Debra M; Formosa, Tim; Hill, Christopher P

    2012-10-26

    The 20S proteasome is an essential, 28-subunit protease that sequesters proteolytic sites within a central chamber, thereby repressing substrate degradation until proteasome activators open the entrance/exit gate. Two established activators, Blm10 and PAN/19S, induce gate opening by binding to the pockets between proteasome α-subunits using C-terminal HbYX (hydrophobic-tyrosine-any residue) motifs. Equivalent HbYX motifs have been identified in Pba1 and Pba2, which function in proteasome assembly. Here, we demonstrate that Pba1-Pba2 proteins form a stable heterodimer that utilizes its HbYX motifs to bind mature 20S proteasomes in vitro and that the Pba1-Pba2 HbYX motifs are important for a physiological function of proteasomes, the maintenance of mitochondrial function. Other factors that contribute to proteasome assembly or function also act in the maintenance of mitochondrial function and display complex genetic interactions with one another, possibly revealing an unexpected pathway of mitochondrial regulation involving the Pba1-Pba2 proteasome interaction. Our determination of a proteasome Pba1-Pba2 crystal structure reveals a Pba1 HbYX interaction that is superimposable with those of known activators, a Pba2 HbYX interaction that is different from those reported previously, and a gate structure that is disrupted but not sufficiently open to allow entry of even small peptides. These findings extend understanding of proteasome interactions with HbYX motifs and suggest multiple roles for Pba1-Pba2 interactions throughout proteasome assembly and function.

  6. 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.

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

    PubMed

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

    2016-04-11

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

  8. The role of interleukin-1 in wound biology. Part II: In vivo and human translational studies.

    PubMed

    Hu, Yajing; Liang, Deyong; Li, Xiangqi; Liu, Hong-Hsing; Zhang, Xun; Zheng, Ming; Dill, David; Shi, Xiaoyou; Qiao, Yanli; Yeomans, David; Carvalho, Brendan; Angst, Martin S; Clark, J David; Peltz, Gary

    2010-12-01

    In the accompanying paper, we demonstrate that genetic variation within Nalp1 could contribute to interstrain differences in wound chemokine production through altering the amount of interleukin (IL)-1 produced. We further investigate the role of IL-1 in incisional wound biology and its effect on wound chemokine production in vivo and whether this mechanism could be active in human subjects. A well-characterized murine model of incisional wounding was used to assess the in vivo role of IL-1 in wound biology. The amount of 7 different cytokines/chemokines produced within an experimentally induced skin incision on a mouse paw and the nociceptive response was analyzed in mice treated with an IL-1 inhibitor. We also investigated whether human IL-1β or IL-1α stimulated the production of chemokines by primary human keratinocytes in vitro, and whether there was a correlation between IL-1β and chemokine levels in 2 experimental human wound paradigms. Administration of an IL-1 receptor antagonist to mice decreased the nociceptive response to an incisional wound, and reduced the production of multiple inflammatory mediators, including keratinocyte-derived chemokine (KC) and macrophage inhibitory protein (MIP)-1α, within the wounds. IL-1α and IL-1β stimulated IL-8 and GRO-α (human homologues of murine keratinocyte-derived chemokine) production by primary human keratinocytes in vitro. IL-1β levels were highly correlated with IL-8 in human surgical wounds, and at cutaneous sites of human ultraviolet B-induced sunburn injury. IL-1 plays a major role in regulating inflammatory mediator production in wounds through a novel mechanism; by stimulating the production of multiple cytokines and chemokines, it impacts clinically important aspects of wound biology. These data suggest that administration of an IL-1 receptor antagonist within the perioperative period could decrease postsurgical wound pain.

  9. MITOCHONDRIAL DISEASES PART I: MOUSE MODELS OF OXPHOS DEFICIENCIES CAUSED BY DEFECTS ON RESPIRATORY COMPLEX SUBUNITS OR ASSEMBLY FACTORS

    PubMed Central

    Torraco, Alessandra; Peralta, Susana; Iommarini, Luisa; Diaz, Francisca

    2015-01-01

    Mitochondrial disorders are the most common inborn errors of metabolism affecting the oxidative phosphorylation system (OXPHOS). Because the poor knowledge of the pathogenic mechanisms, a cure for these disorders is still unavailable and all the treatments currently in use are supportive more than curative. Therefore, in the past decade a great variety of mouse models have been developed to assess the in vivo function of several mitochondrial proteins involved in human diseases. Due to the genetic and physiological similarity to humans, mice represent reliable models to study the pathogenic mechanisms of mitochondrial disorders and are precious to test new therapeutic approaches. Here we summarize the features of several mouse models of mitochondrial diseases directly related to defects in subunits of the OXPHOS complexes or in assembly factors. We discuss how these models recapitulate many human conditions and how they have contributed to the understanding of mitochondrial function in health and disease. PMID:25660179

  10. 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

  11. 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

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

    PubMed

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

    2017-02-01

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

  13. Tectonic assembly of Gondwana

    NASA Astrophysics Data System (ADS)

    Rogers, John J. W.; Unrug, Raphael; Sultan, Mohamed

    1995-01-01

    The Paleozoic assembly of Pangea, with Gondwana as its southern half, completed the last full cycle of growth and dispersal of supercontinents during earth history. This assembly apparently resulted from reorganization of a preceding supercontinent (Rodinia) that existed at ˜1000 Ma. In addition to Laurentia and fragments that formed nuclei for Europe and Asia, the rifting of Rodinia produced: (1) East Gondwana, consisting largely of Western Australia, India, East Antarctica, and possibly part of southern Africa; and (2) various smaller fragments that converged to form West Gondwana, consisting of most of Africa and South America. East Gondwana appears to have been a stable block at a time no younger than ˜1000 Ma and possibly older. West Gondwana accreted largely in the latest Proterozoic and early Paleozoic by closure of the Pharusian Ocean in the north, the Adamaster Ocean in the south, and the ANEKT/Mozambique Ocean between West and East Gondwana. The assembly process was diachronous along numerous mobile belts, accompanied by syn- and post-collisional shearing and magmatism, and led to development of successor basins and rifts. Uncertainties in the timing and mechanism of assembly of Gondwana greatly limit our understanding of the supercontinent cycle. Thus, we propose investigations of Gondwana to determine more precisely the nature and age of apparent cratonic blocks, the locations and ages of orogenic belts, the configuration of former ocean basins, the significance of transcontinental shears, the extent of reactivation of older terranes, and the relationship of Gondwana to North America. Detailed knowledge of the assembly of Gondwana should also provide information on its relationship to other major processes such as mantle evolution and atmospheric, oceanic, and biologic changes.

  14. Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field.

    PubMed

    Heinz, Hendrik; Lin, Tzu-Jen; Mishra, Ratan Kishore; Emami, Fateme S

    2013-02-12

    The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and

  15. 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

  16. Impact of Two Ant Species on Egg Parasitoids Released as Part of a Biological Control Program

    PubMed Central

    Kergunteuil, Alan; Basso, César; Pintureau, Bernard

    2013-01-01

    Biological control using Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae), an egg parasitoid wasp, was tested in Uruguay to reduce populations of lepidopteran pests on soybeans. It was observed that the commercial parasitoid dispensers, which were made of cardboard, were vulnerable to small predators that succeeded in entering and emptying the containers of all the eggs parasitized by T. pretiosum. Observations in a soybean crop showed that the only small, common predators present were two ant species. The species responsible for the above mentioned predation was determined from the results of a laboratory experiment in which the behavior of the two common ants was tested. A modification of the dispensers to prevent introduction of this ant has been proposed and successfully tested in the laboratory and in the field. PMID:24738954

  17. 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

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

    PubMed

    Greenbury, S F; Ahnert, S E

    2015-12-06

    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.

  19. Quality of Bottled Water Brands in Egypt Part II: Biological Water Examination.

    PubMed

    Abd El-Salam, Magda M; Al-Ghitany, Engy M; Kassem, Mohamed M

    2008-01-01

    People can survive several days without food, but just a few days without water. People buy bottled water for a variety of reasons, including convenience, fashion, and taste or because they think it is safer than tap water. The taste of the water has to do with the way it is treated and the quality of its source, including its natural mineral content. However, taste does not always indicate safeness. Refrigeration has a significant effect on the bacteriological quality of the purchased bottle. To asses the quality of bottled water in Egypt, samples of 14 Egyptian brands of uncarbonated natural bottled water were evaluated within 6 months. Biological examinations of a total of 84 samples were carried out using standard methods comparing them with the Egyptian standards No. 1589/2005. Also bacteriological examinations of 56 samples were carried out after "1-3" months and "3-6" months storage time at room temperature to detect the effect of storage on their quality. More than half (54.8%) of biological parameters were violated the Egyptian standards. A percentage of 28.6% of all bottled water samples were contaminated with coliform, but surprisingly fecal coliforms and E.coli were not detected. Moreover, Staphylococcus aureus and Pseudomonas aeruginosa were isolated from 5.95% and 3.6%, respectively of all samples. Giardia lamblia cysts has been found in 2.4% of samples, while absence of Cryptosporidium oocysts in all samples was reported. More than half (52%) of the unrefrigerated samples were unacceptable compared to only 19.4% of the refrigerated bottles. These results suggest the need for continuous monitoring for evidence of contamination at source or during the bottling process.

  20. 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.

  1. 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.

  2. 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. 

  3. New pyridazine-fluorine derivatives: synthesis, chemistry and biological activity. Part II.

    PubMed

    Tucaliuc, Roxana-Angela; Cotea, Valeriu V; Niculaua, Marius; Tuchilus, Cristina; Mantu, Dorina; Mangalagiu, Ionel I

    2013-09-01

    A comprehensive study concerning synthesis, structure and biological activity of new pyridazine-fluorine (PYF) derivatives is presented. The first synthesis of PYF derivatives in phase-transfer catalysis (PTC) under microwave (MW) and conventional thermal heating (TH) is reported. Under MW irradiation the consumed energy decreases considerably, the amount of used solvent in liquid phase is at least five-fold less comparative with conventional TH, while PTC did not use solvents. Consequently these reactions could be considered environmentally friendly. Also, the reaction time decrease substantially and, in some cases, the yields are higher. A feasible explanation for MW efficiency is presented. Regiochemistry and chorochemistry involved in these reactions are also discussed; the reactions are regioselective and chorospecific or choroselective, respectively. Ten new pyridazine-fluorine cycloadducts are obtained. The in vitro antibacterial and antifungal activities of the PYF compounds were tested. Introduction of a trifluoromethyl moiety on the pyridazine skeleton is leading to an increasing of the antimicrobial activity. Structure-activity correlationships have been done.

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

    SciTech Connect

    Northcutt, W.G. Jr.

    1993-12-27

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

  5. Biological markers for anxiety disorders, OCD and PTSD: A consensus statement. Part II: Neurochemistry, neurophysiology and neurocognition

    PubMed Central

    Bandelow, Borwin; Baldwin, David; Abelli, Marianna; Bolea-Alamanac, Blanca; Bourin, Michel; Chamberlain, Samuel R.; Cinosi, Eduardo; Davies, Simon; Domschke, Katharina; Fineberg, Naomi; Grünblatt, Edna; Jarema, Marek; Kim, Yong-Ku; Maron, Eduard; Masdrakis, Vasileios; Mikova, Olya; Nutt, David; Pallanti, Stefano; Pini, Stefano; Ströhle, Andreas; Thibaut, Florence; Vaghix, Matilde M.; Won, Eunsoo; Wedekind, Dirk; Wichniak, Adam; Woolley, Jade; Zwanzger, Peter; Riederer, Peter

    2017-01-01

    Objective Biomarkers are defined as anatomical, biochemical or physiological traits that are specific to certain disorders or syndromes. The objective of this paper is to summarise the current knowledge of biomarkers for anxiety disorders, obsessive-compulsive disorder (OCD) and posttraumatic stress disorder (PTSD). Methods Findings in biomarker research were reviewed by a task force of international experts in the field, consisting of members of the World Federation of Societies for Biological Psychiatry Task Force on Biological Markers and of the European College of Neuropsychopharmacology Anxiety Disorders Research Network. Results The present article (Part II) summarises findings on potential biomarkers in neurochemistry (neurotransmitters such as serotonin, norepinephrine, dopamine or GABA, neuropeptides such as cholecystokinin, neurokinins, atrial natriuretic peptide, or oxytocin, the HPA axis, neurotrophic factors such as NGF and BDNF, immunology and CO2 hypersensitivity), neurophysiology (EEG, heart rate variability) and neurocognition. The accompanying paper (Part I) focuses on neuroimaging and genetics. Conclusions Although at present, none of the putative biomarkers is sufficient and specific as a diagnostic tool, an abundance of high quality research has accumulated that should improve our understanding of the neurobiological causes of anxiety disorders, OCD and PTSD. PMID:27419272

  6. Specialty Tier-Level Cost Sharing and Biologic Agent Use in the Medicare Part D Initial Coverage Period Among Beneficiaries With Rheumatoid Arthritis.

    PubMed

    Doshi, Jalpa A; Hu, Tianyan; Li, Pengxiang; Pettit, Amy R; Yu, Xinyan; Blum, Marissa

    2016-11-01

    To examine associations between specialty tier-level cost sharing and use of biologic agents for rheumatoid arthritis (RA) during Medicare Part D's initial coverage period (ICP). This was a retrospective study using 2007-2010 5% sample Medicare files to examine RA patients with use of a Part D RA biologic agent in the prior year. Patients without low-income subsidies (non-LIS group), who faced specialty tier-level cost sharing, were compared to a control group of low-income subsidy patients (LIS group), who faced nominal out-of-pocket costs in the ICP. Outcomes included use of a Part D or Part B RA biologic agent during the ICP and presence of a ≥30-day continuous gap in treatment among Part D biologic agent users in the ICP. Risk-adjusted outcomes were estimated using logistic regressions, controlling for patient demographic, clinical, and Part D plan characteristics. On average, a 30-day Part D biologic agent supply cost the non-LIS group $484 out of pocket (29.9% cost sharing) versus $5 (0.3% cost sharing) for the LIS group. The non-LIS group was less likely to fill Part D biologic agents (61.2% versus 72.7%, odds ratio [OR] 0.58 [95% confidence interval (95% CI) 0.46-0.72]; P < 0.001), more than twice as likely to receive Part B biologic agents (9.9% versus 4.4%, OR 2.41 [95% CI 1.61-3.60]; P < 0.001), and less likely to use any biologic agent (70.1% versus 76.9%, OR 0.69 [95% CI 0.55-0.88]; P = 0.002). The non-LIS subgroup filling Part D biologic agents had approximately twice the odds of a gap in both Part D biologic agent and any biologic agent availability. Specialty tier-level cost sharing was associated with interruptions in RA biologic agent treatment among Medicare patients. © 2016, American College of Rheumatology.

  7. 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

  8. 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

  9. Peptide-directed self-assembly of functionalized polymeric nanoparticles part I: design and self-assembly of peptide-copolymer conjugates into nanoparticle fibers and 3D scaffolds.

    PubMed

    Ding, Xiaochu; Janjanam, Jagadeesh; Tiwari, Ashutosh; Thompson, Martin; Heiden, Patricia A

    2014-06-01

    A robust self-assembly of nanoparticles into fibers and 3D scaffolds is designed and fabricated by functionalizing a RAFT-polymerized amphiphilic triblock copolymer with designer ionic complementary peptides so that the assembled core-shell polymeric nanoparticles are directed by peptide assembly into continuous "nanoparticle fibers," ultimately leading to 3D fiber scaffolds. The assembled nanostructure is confirmed by FESEM and optical microscopy. The assembly is not hindered when a protein (insulin) is incorporated within the nanoparticles as an active ingredient. MTS cytotoxicity tests on SW-620 cell lines show that the peptides, copolymers, and peptide-copolymer conjugates are biocompatible. The methodology of self-assembled nanoparticle fibers and 3D scaffolds is intended to combine the advantages of a flexible hydrogel scaffold with the versatility of controlled release nanoparticles to offer unprecedented ability to incorporate desired drug(s) within a self-assembled scaffold system with individual control over the release of each drug.

  10. Chemical compositions and biological activities of Scutellaria pinnatifida A. Hamilt aerial parts

    PubMed Central

    Delazar, Abbas; Nazemiyeh, Hossein; Afshar, Fariba Heshmati; Barghi, Niloofar; Esnaashari, Solmaz; Asgharian, Parina

    2017-01-01

    Phytochemical analysis of the methanolic and dichloromethane extracts of the aerial parts of Scutellaria pinnatifida led to the isolation of a phenylpropanoid, 1-o-feruloyl-β-D-glucose (1), two known flavonoids including luteolin-7-o-glucoside (2) and apigenin-7-o-glucoside (3), three known phenylethanoid glycosides composed of phlomisethanoside (4), syringalide A (5), and verbascoside (6), and oleic acid (7). Isolation and structural elucidation of compounds were accomplished by HPLC and spectroscopic methods (UV, 1H-NMR, 13C-NMR). The extracts were also evaluated for their radical scavenging activity and insecticidal property by 2,2-diphenyl-1-picryl-hydrazyl (DPPH) assay and contact toxicity method, respectively. Among the extracts, the methanol extract showed the most potent free radical scavenging activity with a RC50 value of 0.044 ± 0.350 mg/mL which could be attributed to the presence of the isolated phenolic compounds. In the case of insecticidal activity, the n-hexane extract displayed the most potent activity and caused 10%, 15%, and 40% mortality to Oryzaephilus mercator at the concentration of 5, 10, and 15 mg/mL after 4 h of exposure. PMID:28626476

  11. A List of Currently Credible Biology Concepts Judged by a National Panel To Be Important for Inclusion in K-12 Curricula, Parts 1, 2, and 3.

    ERIC Educational Resources Information Center

    Thompson, Benjamin Edwin

    This three-part document identified 114 currently credible biology concepts judged important for inclusion in the K-12 curriculum. The literature related to the production of lists of scientific concepts was reviewed, emphasizing the techniques available for such studies. The technique for this study was to ask individual biological scientists at…

  12. 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

  13. The Introduction of Social Biology into the Curriculum: Part II of the Influence of the British Social Hygiene Council on the Development of Social Biology.

    ERIC Educational Resources Information Center

    Scoggins, Ann

    1977-01-01

    Describes the secondary and college level courses in social biology taught in the early 1960s that first linked the human situation to basic biological principles and concepts. Provides a general description of the present status of social biology in England. (CS)

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

    PubMed Central

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

    2013-01-01

    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

  15. 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

  16. 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

  17. 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.

  18. Biological activity of waste dump substrates in the eastern part of the Kansk-Achinsk coal field

    NASA Astrophysics Data System (ADS)

    Trefilova, O. V.; Oskorbin, P. A.

    2014-02-01

    The results of a field experiment for studying the seasonal dynamics of the CO2 (Rall) emitted from the overburden and enclosing rocks of a coal mine are presented as an integral index of their biological activity. The mean rate of the CO2 emission from the control substrate was 1.2 g C/m2 per 24 h. The intensity of Rall for the variant with the application of mineral and complex fertilizers, along with a microbiological preparation, was higher by 28 and 34%, respectively. In the same variants, the Rall values little changed during the whole growing period. The measurements of the potential respiration of the rock mixture in the laboratory showed that a significant part of the CO2 flux was formed at the expense of carbon dioxide of abiotic origin. The values of the CO2 emission are concluded to be overestimated as compared to those for the real level of the biological activity of the substrates studied.

  19. 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

  20. Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks.

    PubMed

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a whole entity in cancer functional studies. With the advances of genome sequencing and computational analysis, we are able to quantify and computationally dissect clones from tumors, and then conduct clone-based analysis. Emerging technologies such as single-cell genome sequencing and RNA-Seq could profile tumor clones. Thus, we should reconsider how to conduct cancer systems biology studies in the genome sequencing era. We will outline new directions for conducting cancer systems biology by considering that genome sequencing technology can be used for dissecting, quantifying and genetically characterizing clones from tumors. Topics discussed in Part 1 of this review include computationally quantifying of tumor subpopulations; clone-based network modeling, cancer hallmark-based networks and their high-order rewiring principles and the principles of cell survival networks of fast-growing clones. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

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

    PubMed

    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.

  2. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.

    PubMed

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients.

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

    PubMed

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

    2016-12-01

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

  4. 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

  5. Aryldiones incorporating a [1,4,5]oxadiazepane ring. Part 2: chemistry and biology of the cereal herbicide pinoxaden.

    PubMed

    Muehlebach, Michel; Cederbaum, Fredrik; Cornes, Derek; Friedmann, Adrian A; Glock, Jutta; Hall, Gavin; Indolese, Adriano F; Kloer, Daniel P; Le Goupil, Gael; Maetzke, Thomas; Meier, Hans; Schneider, Rudolf; Stoller, André; Szczepanski, Henry; Wendeborn, Sebastian; Widmer, Hansjuerg

    2011-12-01

    Pinoxaden is a new cereal herbicide that provides outstanding levels of post-emergence activity against a broad spectrum of grass weed species for worldwide selective use in both wheat and barley. Factors influencing activity and tolerance to pinoxaden were in part linked to distinct structural parts of the active ingredient. Three complementary contributions that decisively impact upon the herbicidal potency against grasses were identified: a preferred 2,6-diethyl-4-methyl aromatic substitution pattern, a dione area suitable for proherbicide formation and beneficial adjuvant effects. The uptake and translocation pattern of pinoxaden when coapplied with its tailored adjuvant were analysed by autoradiography, indicating extensive and rapid penetration, followed by effective distribution throughout the plant. Crop injury reduction on incorporation of the [1,4,5]oxadiazepane ring into the aryldione template was reinforced with safener technology. Comparative studies on the behaviour of pinoxaden applied either alone or in combination with the safener cloquintocet-mexyl demonstrated that addition of the safener resulted in significant enhancement of metabolic degradation in wheat and barley, providing excellent crop tolerance and a substantial selectivity margin without adverse effects on weed control. The biological potential of pinoxaden and its active principle pinoxaden dione in terms of grass weed control and tolerance in cereals was fully exploited by inclusion of the safener cloquintocet-mexyl in the formulation in combination with a specific and tailor-made tank-mix adjuvant based on methylated rape seed oil. Copyright © 2011 Society of Chemical Industry.

  6. 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.

  7. The dynamics of nacre self-assembly

    PubMed Central

    Cartwright, Julyan H.E; Checa, Antonio G

    2006-01-01

    We show how nacre and pearl construction in bivalve and gastropod molluscs can be understood in terms of successive processes of controlled self-assembly from the molecular- to the macro-scale. This dynamics involves the physics of the formation of both solid and liquid crystals and of membranes and fluids to produce a nanostructured hierarchically constructed biological composite of polysaccharides, proteins and mineral, whose mechanical properties far surpass those of its component parts. PMID:17251136

  8. 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

  9. 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

  10. Enhancement of antigen-specific CD4(+) and CD8(+) T cell responses using a self-assembled biologic nanolipoprotein particle vaccine.

    PubMed

    Weilhammer, Dina; Dunkle, Alexis D; Blanchette, Craig D; Fischer, Nicholas O; Corzett, Michele; Lehmann, Doerte; Boone, Tyler; Hoeprich, Paul; Driks, Adam; Rasley, Amy

    2017-03-13

    To address the need for vaccine platforms that induce robust cell-mediated immunity, we investigated the potential of utilizing self-assembling biologic nanolipoprotein particles (NLPs) as an antigen and adjuvant delivery system to induce antigen-specific murine T cell responses. We utilized OT-I and OT-II TCR-transgenic mice to investigate the effects of NLP-mediated delivery of the model antigen ovalbumin (OVA) on T cell activation. Delivery of OVA with the TLR4 agonist monophosphoryl lipid A (MPLA) in the context of NLPs significantly enhanced the activation of both CD4(+) and CD8(+) T cells in vitro compared to co-administration of free OVA and MPLA. Upon intranasal immunization of mice harboring TCR-transgenic cells, NLPs enhanced the adjuvant effects of MPLA and the in vivo delivery of OVA, leading to significantly increased expansion of CD4(+) and CD8(+) T cells in lung-draining lymph nodes. Therefore, NLPs are a promising vaccine platform for inducing T cell responses following intranasal administration.

  11. 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

  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.

  13. 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.

  14. 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

  15. Biologically Assembled Quantum Electronic Arrays

    DTIC Science & Technology

    2013-06-07

    isomorphic to certain alkali - metal intercalation compounds of fullerene C6o (e.g., ~C6o). On the basis of the space-filling principle, we further...Burch, R. R.; Dong, Y.; Fincher, C.; Goldfinger, M.; Rouviere, P. E. Synth. Metals . "Electrical properties of polyunsaturated natural products: field...somewhat disordered. The most reliable way to visualize a metallic particles in the crystalline context is through ’ anomalous ’ scattering. This phenomenon

  16. Directed evolution: new parts and optimized function.

    PubMed

    Dougherty, Michael J; Arnold, Frances H

    2009-08-01

    Constructing novel biological systems that function in a robust and predictable manner requires better methods for discovering new functional molecules and for optimizing their assembly in novel biological contexts. By enabling functional diversification and optimization in the absence of detailed mechanistic understanding, directed evolution is a powerful complement to 'rational' engineering approaches. Aided by clever selection schemes, directed evolution has generated new parts for genetic circuits, cell-cell communication systems, and non-natural metabolic pathways in bacteria.

  17. 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

  18. Adeno-associated Virus (AAV) Assembly-Activating Protein Is Not an Essential Requirement for Capsid Assembly of AAV Serotypes 4, 5, and 11.

    PubMed

    Earley, Lauriel F; Powers, John M; Adachi, Kei; Baumgart, Joshua T; Meyer, Nancy L; Xie, Qing; Chapman, Michael S; Nakai, Hiroyuki

    2017-02-01

    Adeno-associated virus (AAV) vectors have made great progress in their use for gene therapy; however, fundamental aspects of AAV's capsid assembly remain poorly characterized. In this regard, the discovery of assembly-activating protein (AAP) sheds new light on this crucial part of AAV biology and vector production. Previous studies have shown that AAP is essential for assembly; however, how its mechanistic roles in assembly might differ among AAV serotypes remains uncharacterized. Here, we show that biological properties of AAPs and capsid assembly processes are surprisingly distinct among AAV serotypes 1 to 12. In the study, we investigated subcellular localizations and assembly-promoting functions of AAP1 to -12 (i.e., AAPs derived from AAV1 to -12, respectively) and examined the AAP dependence of capsid assembly processes of these 12 serotypes using combinatorial approaches that involved immunofluorescence and transmission electron microscopy, barcode-Seq (i. e., a high-throughput quantitative method using DNA barcodes and a next-generation sequencing technology), and quantitative dot blot assays. This study revealed that AAP1 to -12 are all localized in the nucleus with serotype-specific differential patterns of nucleolar association; AAPs and assembled capsids do not necessarily colocalize; AAPs are promiscuous in promoting capsid assembly of other serotypes, with the exception of AAP4, -5, -11, and -12; assembled AAV5, -8, and -9 capsids are excluded from the nucleolus, in contrast to the nucleolar enrichment of assembled AAV2 capsids; and, surprisingly, AAV4, -5, and -11 capsids are not dependent on AAP for assembly. These observations highlight the serotype-dependent heterogeneity of the capsid assembly process and challenge current notions about the role of AAP and the nucleolus in capsid assembly.

  19. A shuttle and space station manipulator system for assembly, docking, maintenance, cargo handling and spacecraft retrieval (preliminary design). Volume 3: Concept analysis. Part 1: Technical

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Information backing up the key features of the manipulator system concept and detailed technical information on the subsystems are presented. Space station assembly and shuttle cargo handling tasks are emphasized in the concept analysis because they involve shuttle berthing, transferring the manipulator boom between shuttle and station, station assembly, and cargo handling. Emphasis is also placed on maximizing commonality in the system areas of manipulator booms, general purpose end effectors, control and display, data processing, telemetry, dedicated computers, and control station design.

  20. 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.

  1. 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.

  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. 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

  6. 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.

  7. 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

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

    PubMed

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

    2015-01-01

    Carrying out the chemical composition and antiproliferative effects against cancer cells from different biological parts of Artemisia herba alba. 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. 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. 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.

  9. 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

  10. Part A. Neutron activation analysis of selenium and vanadium in biological matrices. Part B. Isomeric transition activation in aqueous solutions of alkyl bromides

    SciTech Connect

    Ebrahim, A.

    1988-01-01

    Several procedures were evaluated for determination of selenium in biological fluids and vanadium in biological tissues by neutron activation analysis (NAA) employing {sup 77m}Se and {sup 52}V isotopes, respectively. Procedures for determination of total selenium, trimethylselenonium (TMSe) ion and selenite (SeO{sub 3}{sup 2{minus}}) ion in urine and serum and for total selenoamino acids in urine were developed by utilizing anion exchange chromatography and molecular NAA. A pre-column derivatization of selenoamino acids with o-phthalaldehyde was necessary for their determination. Also an analytical approach was developed for determination of trace vanadium in liver samples from normal and diabetic rats as well as human and cow. Reactions of bromine-80 activated by radiative neutron capture and bromine-82 activated by isomeric transition were investigated in aqueous solutions of bromomethane and 1-bromobutane. Bromine-80 organic yields decreased with decreasing solute concentrations. The tendency for aggregation of the solute molecules diminished as the solute concentration approached zero where the probable state of the solute approached a monomolecular dispersion. Unlike reactions of {sup 80}Br born by {sup 79}Br(n,{gamma}){sup 80}Br reaction, the total organic product yields resulting from the {sup 82m}Br(I.T.){sup 82}Br process showed no solute concentration dependence.

  11. 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.

  12. [Application of genome engineering in medical synthetic biology].

    PubMed

    Wang, Fangyuan; Zhao, Dehua; Qi, Lei Stanley

    2017-03-25

    Synthetic biology aims to establish a complete set of engineering principles, theories, and methods, via the rational design and assembly of basic biological parts, for the goal of effective implementation of complex biological systems with programmable functions. In recent years, with emerging novel classes of programmable genetic parts, in particular, the establishment and optimization of CRISPR and CRISPRi technology platforms, synthetic biology is entering a new era. This review summarizes recent advances on CRISPR genome editing and gene regulation technologies, their applications in constructing programmable biological parts, and their roles in building sophisticated gene circuits. We also provide a future vision on how synthetic biology can transform medicine (named medical synthetic biology, MSB) and therapeutics.

  13. Assembly and infection process of bacteriophage T4

    NASA Astrophysics Data System (ADS)

    Arisaka, Fumio

    2005-12-01

    Bacterophage T4 consists of three parts, namely, a head, a tail, and six tail fibers, each of which is assembled along an independent pathway and then joined. In contrast to simple plant viruses such as tobacco mosaic virus, disassembly and reassembly of the virion is not possible. This is due mainly to the fact that the assembly involves not only irreversible steps such as cleavage of covalent bonds of some constituent proteins, but also that it requires a scaffold and involves the inner membrane of the host cell. Another unique feature of the assembly as a biological nanomachine is the involvement of specific protein devices such as a "ruler molecule," which determines the length of the tail, an ATP-driven DNA packaging protein complex, and phage-encoded molecular chaperones. Recent structural biological studies of the phage started to unveil the molecular mechanics of structural transformation of the tail upon infection.

  14. DeviceEditor visual biological CAD canvas

    PubMed Central

    2012-01-01

    Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

  15. Recursive DNA Assembly Using Protected Oligonucleotide Duplex Assisted Cloning (PODAC).

    PubMed

    Van Hove, Bob; Guidi, Chiara; De Wannemaeker, Lien; Maertens, Jo; De Mey, Marjan

    2017-06-16

    A problem rarely tackled by current DNA assembly methods is the issue of cloning additional parts into an already assembled construct. Costly PCR workflows are often hindered by repeated sequences, and restriction based strategies impose design constraints for each enzyme used. Here we present Protected Oligonucleotide Duplex Assisted Cloning (PODAC), a novel technique that makes use of an oligonucleotide duplex for iterative Golden Gate cloning using only one restriction enzyme. Methylated bases confer protection from digestion during the assembly reaction and are removed during replication in vivo, unveiling a new cloning site in the process. We used this method to efficiently and accurately assemble a biosynthetic pathway and demonstrated its robustness toward sequence repeats by constructing artificial CRISPR arrays. As PODAC is readily amenable to standardization, it would make a useful addition to the synthetic biology toolkit.

  16. 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.

  17. Biomimetic polymers responsive to a biological signaling molecule: nitric oxide triggered reversible self-assembly of single macromolecular chains into nanoparticles.

    PubMed

    Hu, Jinming; Whittaker, Michael R; Duong, Hien; Li, Yang; Boyer, Cyrille; Davis, Thomas P

    2014-07-21

    Novel nitric oxide (NO) responsive monomers (NAPMA and APUEMA) containing o-phenylenediamine functional groups have been polymerized to form NO-responsive macromolecular chains as truly biomimetic polymers. Upon exposure to NO--a ubiquitous cellular signaling molecule--the NAPMA- and APUEMA-labeled thermoresponsive copolymers exhibited substantial changes in solubility, clearly characterized by tuneable LCST behavior, thereby inducing self-assembly into nanoparticulate structures. Moreover, the NO-triggered self-assembly process in combination with environmentally sensitive fluorescence dyes could be employed to detect and image endogenous NO.

  18. Bacteriophage assembly.

    PubMed

    Aksyuk, Anastasia A; Rossmann, Michael G

    2011-03-01

    Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.

  19. [Are there pseudophototropic reactions in biology? Part 3: The pseudophototropic behaviour of the cell membrane of halobacteria (author's transl)].

    PubMed

    Patschorke, J

    1979-01-01

    The behaviour of coloured membrane portions of "halobacteria" is studied with respect to spectral response and reversibility. The results are in good correlation with colour generating effects of pseudophototropic reactions. The disclosed and dicussed systems are in the range from purely synthetic to purely biological.

  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. 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.

  2. Self-assembled Ni/TiO2 nanocomposite anodes synthesized via electroless plating and atomic layer deposition on biological scaffolds.

    PubMed

    Gerasopoulos, Konstantinos; Chen, Xilin; Culver, James; Wang, Chunsheng; Ghodssi, Reza

    2010-10-21

    Ni(core)/TiO(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 (∼0.024% per cycle) for ∼1000 cycles.

  3. 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

  4. 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).

  5. 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

  6. Representations of mechanical assembly sequences

    NASA Technical Reports Server (NTRS)

    Homem De Mello, Luiz S.; Sanderson, Arthur C.

    1991-01-01

    Five types of representations for assembly sequences are reviewed: the directed graph of feasible assembly sequences, the AND/OR graph of feasible assembly sequences, the set of establishment conditions, and two types of sets of precedence relationships. (precedence relationships between the establishment of one connection between parts and the establishment of another connection, and precedence relationships between the establishment of one connection and states of the assembly process). The mappings of one representation into the others are established. The correctness and completeness of these representations are established. The results presented are needed in the proof of correctness and completeness of algorithms for the generation of mechanical assembly sequences.

  7. Observations on the Biology of Afrotropical Hesperiidae (Lepidoptera) with particular reference to Kenya. Part 11. Heteropterinae.

    PubMed

    Cock, Matthew J W; Congdon, T Colin E

    2017-01-30

    Partial life histories from Kenya or Tanzania are presented for Metisella midas midas (Butler), M. medea medea Evans, M. orientalis orientalis Aurivillius, M. quadrisignatus nanda Evans, M. congdoni De Jong & Kielland and M. willemi Wallengren. The ovum of Metisella formosus linda Evans is also illustrated from Zambia. All feed on species of grasses (Poaceae). The convergence of the biology of the grass-feeding skippers, particularly Heteropterinae and Hesperiinae, Baorini is discussed.

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

    PubMed

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

    1978-01-01

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

  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. 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

  12. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:24078086

  14. Synthetic biology

    PubMed Central

    Bower, Adam G; McClintock, Maria K

    2010-01-01

    The field of synthetic biology has made rapid progress in a number of areas including method development, novel applications and community building. In seeking to make biology “engineerable,” synthetic biology is increasing the accessibility of biological research to researchers of all experience levels and backgrounds. One of the underlying strengths of synthetic biology is that it may establish the framework for a rigorous bottom-up approach to studying biology starting at the DNA level. Building upon the existing framework established largely by the Registry of Standard Biological Parts, careful consideration of future goals may lead to integrated multi- scale approaches to biology. Here we describe some of the current challenges that need to be addressed or considered in detail to continue the development of synthetic biology. Specifically, discussion on the areas of elucidating biological principles, computational methods and experimental construction methodologies are presented. PMID:21326830

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

    NASA Astrophysics Data System (ADS)

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

    2006-10-01

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

  16. 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

    2016-01-15

    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.

  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 1: update 2012 on the acute treatment of schizophrenia and the management of treatment resistance.

    PubMed

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

    2012-07-01

    These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry Guidelines for Biological Treatment of Schizophrenia published in 2005. For this 2012 revision, all available publications pertaining to the biological treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations that are clinically and scientifically meaningful and these guidelines 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; Bandelow et al. 2008b, World J Biol Psychiatry 9:242). This first part of the updated guidelines covers the general descriptions of antipsychotics and their side effects, the biological treatment of acute schizophrenia and the management of treatment-resistant schizophrenia.

  19. 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.

  20. 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.

  1. Pod Assembly.

    DTIC Science & Technology

    An improved pod assembly for positively securing the equipment contained therein to the wingtip of an aircraft and having a readily removable...podshell for in situ service and repair. The pod assembly includes a strongback assembly of an acurate saddle and support beam secured to the outboard ends...of the aircraft wing beams, to which a satellite communications antenna array is mounted. A fiberglass reinforced laminated thin wall plastic pod

  2. Clean then Assemble Versus Assemble then Clean: Several Comparisons

    NASA Technical Reports Server (NTRS)

    Welker, Roger W.

    2004-01-01

    Cleanliness of manufactured parts and assemblies is a significant issue in many industries including disk drives, semiconductors, aerospace, and medical devices. Clean manufacturing requires cleanroom floor space and cleaning technology that are both expensive to own and expensive to operate. Strategies to reduce these costs are an important consideration. One strategy shown to be effective at reducing costs is to assemble parts into subassemblies and then clean the subassembly, rather than clean the individual parts first and then assemble them. One advantage is that assembly outside of the cleanroom reduces the amount of cleanroom floor space and its associated operating cost premium. A second advantage is that this strategy reduces the number of individual parts that must be cleaned prior to assembly, reducing the number of cleaning baskets, handling and, possibly, reducing the number of cleaners. The assemble then clean strategy also results in a part that is significantly cleaner because contamination generated during the assembly steps are more effectively removed that normally can be achieved by hand wiping after assembly in the cleanroom.

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

    PubMed

    Antus, Sándor

    2010-01-01

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

  4. 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.

  5. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination.

    PubMed

    Colloms, Sean D; Merrick, Christine A; Olorunniji, Femi J; Stark, W Marshall; Smith, Margaret C M; Osbourn, Anne; Keasling, Jay D; Rosser, Susan J

    2014-02-01

    Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by C31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. C31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.

  6. Theoretical Aspect of Assembly

    NASA Astrophysics Data System (ADS)

    Václav, Štefan; Jurko, Jozef; Božek, Pavol; Lecký, Šimon

    2016-09-01

    Assembly plays a decisive role in global production in terms of its share in the total costs of the products assembled and in terms of the number of people working in the field. The author of (1) indicates that the percentage of the workers in assembly out of the total number of the workers in manufacturing in the U.S.A. ranged from 26.3% (bicycles) to 45.6% (automobiles), while the cost of the product assembly represented typically more than 50% of the total costs. Despite the above-mentioned importance of assembly in the industry, the discontinuous production processes have not been paid adequate attention until recently. It was sufficient to manufacture parts and then an operative reasonably and inexpensively assembled each product manually. The authors of this paper would like to emphasise "the method of a systemic approach" which focuses upon identifying the key activities to meet the objective. Harmonious interrelations of the activities are often a source of greater profit than in a system where some activities are of the top level while the others are neglected (2). The aim of this paper is to describe theoretical aspects of all the typical activities of the assembly system.

  7. Synthesis and biological evaluation of novel pyrrolidine-2,5-dione derivatives as potential antidepressant agents. Part 1.

    PubMed

    Wróbel, Martyna Z; Chodkowski, Andrzej; Herold, Franciszek; Gomółka, Anna; Kleps, Jerzy; Mazurek, Aleksander P; Pluciński, Franciszek; Mazurek, Andrzej; Nowak, Gabriel; Siwek, Agata; Stachowicz, Katarzyna; Sławińska, Anna; Wolak, Małgorzata; Szewczyk, Bernadeta; Satała, Grzegorz; Bojarski, Andrzej J; Turło, Jadwiga

    2013-05-01

    A series of 3-(1H-indol-3-yl)pyrrolidine-2,5-dione derivatives was synthesized and their biological activity was evaluated. The chemical structures of the newly prepared compounds were confirmed by (1)H NMR, (13)C NMR and ESI-HRMS spectra data. All tested compounds proved to be potent 5-HT1A receptor and serotonin transporter protein (SERT) ligands. Among them, compounds 15, 18, 19 and 30 showed significant affinity for 5-HT1A and SERT. Computer docking simulations carried out for compounds 15, 31 and 32 to models of 5-HT1A receptor and SERT confirm the results of biological tests. Due to high affinity for the 5-HT1A receptor and moderate affinity for SERT, compounds 31, 32, 35, and 37 were evaluated for their affinity for D2L, 5-HT6, 5-HT7 and 5-HT2A receptors. In vivo tests, in turn, resulted in determining the functional activity of compounds 15, 18, 19 and 30 to the 5-HT1A receptor. The results of these tests indicate that all of the ligands possess properties characteristic of 5-HT1A receptor agonists.

  8. 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.

  9. Composition and effects of inhalable size fractions of atmospheric aerosols in the polluted atmosphere. Part II. In vitro biological potencies.

    PubMed

    Novák, Jiří; Hilscherová, Klára; Landlová, Linda; Čupr, Pavel; Kohút, Lukáš; Giesy, John P; Klánová, Jana

    2014-02-01

    Exposure to particulate matter (PM) in ambient air has been shown to lead to adverse health consequences. Six size fractions of PM with aerodynamic diameter smaller than 10μm (PM10) and gas phase were collected at six localities with different major pollution sources. Extracts of samples were assessed for AhR-mediated toxicity, (anti-)estrogenicity, (anti-)androgenicity and genotoxicity. The biological responses were interpreted relative to chemical characterization. Historically, for regulatory purposes, evaluation of air pollution was based mainly on assessment of the sum of PM10. In the case of AhR-mediated activity, PM1 was responsible for more than 75% of the activity of the particulate fraction from all localities. The assessed effects were correlated with concentrations of polycyclic aromatic hydrocarbons (PAH), organic carbon content and specific surface area of the PM. A significant proportion of biologically active chemicals seems to be present in the gas phase of air. The results suggest that an average daily exposure based just on the concentrations of contaminants contained in PM10, as regulated in EU legislation so far, is not a sufficient indicator of contaminants in air particulates and adoption of standards more similar to other countries and inclusion of other parameters besides mass should be considered. © 2013.

  10. 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.

  11. 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…

  12. 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…

  13. Wellhead assembly

    SciTech Connect

    Smith, J. D.; Szymczak, E. J.

    1985-05-07

    A wellhead assembly with an increased through bore for passing slightly oversized drill bits therethrough with a substantially reduced landing shoulder, and an improved landing assembly which transfers a portion of the stresses through the energizing ring and support ring into the wellhead body along the straight bore above said landing shoulder.

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

    PubMed

    Cock, Matthew J W

    2016-10-05

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

  15. 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. © 2014 American Academy of Forensic Sciences.

  16. Meniscal allograft transplantation. Part 1: systematic review of graft biology, graft shrinkage, graft extrusion, graft sizing, and graft fixation.

    PubMed

    Samitier, Gonzalo; Alentorn-Geli, Eduard; Taylor, Dean C; Rill, Brian; Lock, Terrence; Moutzouros, Vasilius; Kolowich, Patricia

    2015-01-01

    To provide a systematic review of the literature regarding five topics in meniscal allograft transplantation: graft biology, shrinkage, extrusion, sizing, and fixation. A systematic literature search was conducted using the PubMed (MEDLINE), ScienceDirect, and EBSCO-CINAHL databases. Articles were classified only in one topic, but information contained could be reported into other topics. Information was classified according to type of study (animal, in vitro human, and in vivo human) and level of evidence (for in vivo human studies). Sixty-two studies were finally included: 30 biology, 3 graft shrinkage, 11 graft extrusion, 17 graft size, and 6 graft fixation (some studies were categorized in more than one topic). These studies corresponded to 22 animal studies, 22 in vitro human studies, and 23 in vivo human studies (7 level II, 10 level III, and 6 level IV). The principal conclusions were as follows: (a) Donor cells decrease after MAT and grafts are repopulated with host cells form synovium; (b) graft preservation alters collagen network (deep freezing) and causes cell apoptosis with loss of viable cells (cryopreservation); (c) graft shrinkage occurs mainly in lyophilized and gamma-irradiated grafts (less with cryopreservation); (d) graft extrusion is common but has no clinical/functional implications; (e) overall, MRI is not superior to plain radiograph for graft sizing; (f) graft width size matching is more important than length size matching; (g) height appears to be the most important factor influencing meniscal size; (h) bone fixation better restores contact mechanics than suture fixation, but there are no differences for pullout strength or functional results; and (i) suture fixation has more risk of graft extrusion compared to bone fixation. Systematic review of level II-IV studies, Level IV.

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

    PubMed

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

    2014-09-10

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

  18. Body temperature variability (Part 1): a review of the history of body temperature and its variability due to site selection, biological rhythms, fitness, and aging.

    PubMed

    Kelly, Greg

    2006-12-01

    Body temperature is a complex, non-linear data point, subject to many sources of internal and external variation. While these sources of variation significantly complicate interpretation of temperature data, disregarding knowledge in favor of oversimplifying complex issues would represent a significant departure from practicing evidence-based medicine. Part 1 of this review outlines the historical work of Wunderlich on temperature and the origins of the concept that a healthy normal temperature is 98.6 degrees F (37.0 degrees C). Wunderlich's findings and methodology are reviewed and his results are contrasted with findings from modern clinical thermometry. Endogenous sources of temperature variability, including variations caused by site of measurement, circadian, menstrual, and annual biological rhythms, fitness, and aging are discussed. Part 2 will review the effects of exogenous masking agents - external factors in the environment, diet, or lifestyle that can influence body temperature, as well as temperature findings in disease states.

  19. 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.

  20. 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.

  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. © 2016 Authors; published by Portland Press Limited.

  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. Bio-inspired supramolecular hybrid dendrimers self-assembled from low-generation peptide dendrons for highly efficient gene delivery and biological tracking.

    PubMed

    Xu, Xianghui; Jian, Yeting; Li, Yunkun; Zhang, Xiao; Tu, Zhaoxu; Gu, Zhongwei

    2014-09-23

    Currently, supramolecular self-assembly of dendrons and dendrimers emerges as a powerful and challenging strategy for developing sophisticated nanostructures with excellent performances. Here we report a supramolecular hybrid strategy to fabricate a bio-inspired dendritic system as a versatile delivery nanoplatform. With a rational design, dual-functionalized low-generation peptide dendrons (PDs) self-assemble onto inorganic nanoparticles via coordination interactions to generate multifunctional supramolecular hybrid dendrimers (SHDs). These SHDs exhibit well-defined nanostructure, arginine-rich peptide corona, and fluorescent signaling properties. As expected, our bio-inspired supramolecular hybrid strategy largely enhances the gene transfection efficiency of SHDs approximately 50 000-fold as compared to single PDs at the same R/P ratio. Meanwhile the bio-inspired SHDs also (i) provide low cytotoxicity and serum resistance in gene delivery; (ii) provide inherent fluorescence for tracking intracellular pathways including cellular uptake, endosomal escape, and gene release; and (iii) work as an alternative reference for monitoring desired protein expression. More importantly, in vivo animal experiments demonstrate that SHDs offer considerable gene transfection efficiency (in muscular tissue and in HepG2 tumor xenografts) and real-time bioimaging capabilities. These SHDs will likely stimulate studies on bio-inspired supramolecular hybrid dendritic systems for biomedical applications both in vitro and in vivo.

  4. Observations on the biology of Afrotropical Hesperiidae (Lepidoptera). Part 7. Hesperiinae incertae sedis: grass and bamboo feeders.

    PubMed

    Cock, Matthew J W; Congdon, T Colin E

    2014-10-10

    Partial life histories for 17 Hesperiinae incertae sedis that feed on grasses or bamboos (Poaceae) are described and illustrated. The genera dealt with are: Astictopterus (from Evans' (1937) Astictopterus group), Prosopalpus, Kedestes (from Evans' (1937) Ampittia group), Ceratrichia, Pardaleodes, Ankola (From Evans' (1937) Ceratrichia and Acleros groups), Perrotia (part), Chondrolepis, and Monza (part) (all from Evans' Ploetzia genera group). The Poaceae-feeders comprise a relatively small proportion of the Afrotropical Hesperiinae fauna, particularly the mainland Afrotropical fauna. The caterpillars shown here are fairly homogeneous, with the head wider nearer the base, and lacking obvious setae on the body. Wax glands have been noted over most of the ventral surface A1-A8 in the final instar of Ceratrichia, Pardaleodes and Monza, but are absent in Chondrolepis, and either absent or not documented for other genera. The short double frontal projection of Tsitana uitenhaga is unusual, but pupae of the congeneric species have not been documented. The pupae of Kedestes spp. generally have extensive black or dark areas. The pupae of Pardaleodes and Ankola are very flimsy and collapse after emergence. All known pupae of Chondrolepis spp. have a short, blunt downturned frontal projection, not seen for any other Afrotropical genera, although Semalea spp. may have a short blunt projection. The remaining pupae are all generally similar and undistinguished. These are not substantial differences, but suggest that pupal characters may be useful in grouping some of the genera of Afrotropical Hesperiinae incertae sedis.

  5. 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.

  6. 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.

  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. 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.

  9. SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, part 2: biological evaluation.

    PubMed

    Mosmann, Tim R; Naim, Iftekhar; Rebhahn, Jonathan; Datta, Suprakash; Cavenaugh, James S; Weaver, Jason M; Sharma, Gaurav

    2014-05-01

    A multistage clustering and data processing method, SWIFT (detailed in a companion manuscript), has been developed to detect rare subpopulations in large, high-dimensional flow cytometry datasets. An iterative sampling procedure initially fits the data to multidimensional Gaussian distributions, then splitting and merging stages use a criterion of unimodality to optimize the detection of rare subpopulations, to converge on a consistent cluster number, and to describe non-Gaussian distributions. Probabilistic assignment of cells to clusters, visualization, and manipulation of clusters by their cluster medians, facilitate application of expert knowledge using standard flow cytometry programs. The dual problems of rigorously comparing similar complex samples, and enumerating absent or very rare cell subpopulations in negative controls, were solved by assigning cells in multiple samples to a cluster template derived from a single or combined sample. Comparison of antigen-stimulated and control human peripheral blood cell samples demonstrated that SWIFT could identify biologically significant subpopulations, such as rare cytokine-producing influenza-specific T cells. A sensitivity of better than one part per million was attained in very large samples. Results were highly consistent on biological replicates, yet the analysis was sensitive enough to show that multiple samples from the same subject were more similar than samples from different subjects. A companion manuscript (Part 1) details the algorithmic development of SWIFT.

  10. 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

  11. 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

  12. EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.

    PubMed

    Moore, Simon J; Lai, Hung-En; Kelwick, Richard J R; Chee, Soo Mei; Bell, David J; Polizzi, Karen Marie; Freemont, Paul S

    2016-10-21

    Golden Gate cloning is a prominent DNA assembly tool in synthetic biology for the assembly of plasmid constructs often used in combinatorial pathway optimization, with a number of assembly kits developed specifically for yeast and plant-based expression. However, its use for synthetic biology in commonly used bacterial systems such as Escherichia coli has surprisingly been overlooked. Here, we introduce EcoFlex a simplified modular package of DNA parts for a variety of applications in E. coli, cell-free protein synthesis, protein purification and hierarchical assembly of transcription units based on the MoClo assembly standard. The kit features a library of constitutive promoters, T7 expression, RBS strength variants, synthetic terminators, protein purification tags and fluorescence proteins. We validate EcoFlex by assembling a 68-part containing (20 genes) plasmid (31 kb), characterize in vivo and in vitro library parts, and perform combinatorial pathway assembly, using pooled libraries of either fluorescent proteins or the biosynthetic genes for the antimicrobial pigment violacein as a proof-of-concept. To minimize pathway screening, we also introduce a secondary module design site to simplify MoClo pathway optimization. In summary, EcoFlex provides a standardized and multifunctional kit for a variety of applications in E. coli synthetic biology.

  13. Mechanisms controlling primary and new production in a global ecosystem model - Part I: Validation of the biological simulation

    NASA Astrophysics Data System (ADS)

    Popova, E. E.; Coward, A. C.; Nurser, G. A.; de Cuevas, B.; Fasham, M. J. R.; Anderson, T. R.

    2006-12-01

    A global general circulation model coupled to a simple six-compartment ecosystem model is used to study the extent to which global variability in primary and export production can be realistically predicted on the basis of advanced parameterizations of upper mixed layer physics, without recourse to introducing extra complexity in model biology. The "K profile parameterization" (KPP) scheme employed, combined with 6-hourly external forcing, is able to capture short-term periodic and episodic events such as diurnal cycling and storm-induced deepening. The model realistically reproduces various features of global ecosystem dynamics that have been problematic in previous global modelling studies, using a single generic parameter set. The realistic simulation of deep convection in the North Atlantic, and lack of it in the North Pacific and Southern Oceans, leads to good predictions of chlorophyll and primary production in these contrasting areas. Realistic levels of primary production are predicted in the oligotrophic gyres due to high frequency external forcing of the upper mixed layer (accompanying paper Popova et al., 2006) and novel parameterizations of zooplankton excretion. Good agreement is shown between model and observations at various JGOFS time series sites: BATS, KERFIX, Papa and HOT. One exception is the northern North Atlantic where lower grazing rates are needed, perhaps related to the dominance of mesozooplankton there. The model is therefore not globally robust in the sense that additional parameterizations are needed to realistically simulate ecosystem dynamics in the North Atlantic. Nevertheless, the work emphasises the need to pay particular attention to the parameterization of mixed layer physics in global ocean ecosystem modelling as a prerequisite to increasing the complexity of ecosystem models.

  14. 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.

  15. Crew Assembly

    NASA Image and Video Library

    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 ...

  16. GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules

    PubMed Central

    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

  17. 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.

  18. 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.

  19. Slotting optimization of automated storage and retrieval system (AS/RS) for efficient delivery of parts in an assembly shop using genetic algorithm: A case Study

    NASA Astrophysics Data System (ADS)

    Yue, L.; Guan, Z.; He, C.; Luo, D.; Saif, U.

    2017-06-01

    In recent years, the competitive pressure on manufacturing companies shifted them from mass production to mass customization to produce large variety of products. It is a great challenge for companies nowadays to produce customized mixed flow mode of production to meet customized demand on time. Due to large variety of products, the storage system to deliver variety of products to production lines influences on the timely production of variety of products, as investigated from by simulation study of an inefficient storage system of a real Company, in the current research. Therefore, current research proposed a slotting optimization model with mixed model sequence to assemble in consideration of the final flow lines to optimize whole automated storage and retrieval system (AS/RS) and distribution system in the case company. Current research is aimed to minimize vertical height of centre of gravity of AS/RS and total time spent for taking the materials out from the AS/RS simultaneously. Genetic algorithm is adopted to solve the proposed problem and computational result shows significant improvement in stability and efficiency of AS/RS as compared to the existing method used in the case company.

  20. Military Handbook: Electrostatic Discharge Control Handbook for Protection of Electrical and Electronic Parts, Assemblies and Equipment (Excluding Electrically Initiated Explosive Devices (Metric)

    DTIC Science & Technology

    1994-07-31

    analysis. Trends in technology utilizing new materials, processes and design techniques, including increased packaging densities result in some parts being...Damaging electrostatic voltage levels are commonly generated by contact and subsequent separation of these materials by industrial processes and personnel...80 30. INTRODUCTION ....... ................... ... 80 30.1 General ....... ...................... ... 80 30.2 Fabrication process

  1. Biodegradable self-assembled PEG-PCL-PEG micelles for hydrophobic drug delivery, part 2: in vitro and in vivo toxicity evaluation

    NASA Astrophysics Data System (ADS)

    Gong, ChangYang; Wang, YuJun; Wang, XiuHong; Wei, XiaWei; Wu, QinJie; Wang, BiLan; Dong, PengWei; Chen, LiJuan; Luo, Feng; Qian, ZhiYong

    2011-02-01

    Polymeric micelles, prepared by self-assembly of biodegradable poly(ethylene glycol)-poly(ɛ-caprolactone)-poly(ethylene glycol) (PEG-PCL-PEG, PECE) copolymer in aqueous solution, were proved to be a potential carrier for hydrophobic drug honokiol in our previous contribution. In this study, the safety of blank PECE micelles was evaluated in vitro and in vivo before its further application in biomedical field. The average particle size of obtained micelle was 83.47 ± 0.44 nm, and polydisperse index was 0.27 ± 0.01. Also, the zeta potential of prepared micelles was about -0.41 ± 0.02 mV. Otherwise, cytotoxicity of PECE micelles was evaluated by cell viability assay using L929 cells, and in vitro hemolytic test was also performed. In vivo acute toxicity evaluation and histopathological study of PECE micelles were conducted in BALB/c mice by intravenous administration. Furthermore, serum chemistry profile and complete blood count test were performed. In acute toxicity test, the mice were observed continuously for 7 days. For histopathological study, samples including heart, liver, spleen, lung, and kidneys were histochemical prepared and stained with hematoxylin-eosin (H&E). No mortality or significant signs of acute toxicity was observed during the whole observation period, and there is no significant lesion to be shown in histopathological study of major organs. The maximal tolerance dose of PECE micelles (100 mg/mL) by intravenous administration was calculated to be higher than 10 g/kg body weight (b.w.). The results indicated that the obtained PECE micelles was non-toxic after intravenous administration, and could be a safe candidate for hydrophobic drug delivery system.

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

    PubMed

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

    2017-03-28

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

  3. In response to an open invitation for comments on AAAS project 2061's Benchmark books on science. Part 1: documentation of serious errors in cell biology.

    PubMed

    Ling, Gilbert

    2006-01-01

    Project 2061 was founded by the American Association for the Advancement of Science (AAAS) to improve secondary school science education. An in-depth study of ten 9 to 12th grade biology textbooks led to the verdict that none conveyed "Big Ideas" that would give coherence and meaning to the profusion of lavishly illustrated isolated details. However, neither the Project report itself nor the Benchmark books put out earlier by the Project carries what deserves the designation of "Big Ideas." Worse, in the two earliest-published Benchmark books, the basic unit of all life forms--the living cell--is described as a soup enclosed by a cell membrane, that determines what can enter or leave the cell. This is astonishing since extensive experimental evidence has unequivocally disproved this idea 60 years ago. A "new" version of the membrane theory brought in to replace the discredited (sieve) version is the pump model--currently taught as established truth in all high-school and college biology textbooks--was also unequivocally disproved 40 years ago. This comment is written partly in response to Bechmark's gracious open invitation for ideas to improve the books and through them, to improve US secondary school science education.

  4. 49 CFR 572.184 - Shoulder assembly.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Shoulder assembly. 572.184 Section 572.184... Dummy, 50th Percentile Adult Male § 572.184 Shoulder assembly. (a) The shoulder (175-3000) is part of...) of this section, the shoulder assembly shall meet performance requirements of paragraph (c) of...

  5. Preparation of PEGylated polymeric nanoprobes with aggregation-induced emission feature through the combination of chain transfer free radical polymerization and multicomponent reaction: Self-assembly, characterization and biological imaging applications.

    PubMed

    Wan, Qing; Liu, Meiying; Mao, Liucheng; Jiang, Ruming; Xu, Dazhuang; Huang, Hongye; Dai, Yanfeng; Deng, Fengjie; Zhang, Xiaoyong; Wei, Yen

    2017-03-01

    Self-assembly of amphiphilic luminescent copolymers is a general route to fabricate fluorescent polymeric microparticles (FPMs). In this work, the FPMs with aggregation-induced emission (AIE) feature were fabricated via the combination of the chain transfer free radical polymerization and "one-pot" multicomponent reaction, which conjugated the aldehyde-containing AIE active dye AIE (CHO-An-CHO) and amino-terminated hydrophilic polymer (ATPPEGMA) using mercaptoacetic acid (MTA) as the "lock" molecule. The structure, chemical compositions, optical properties as well as biological properties of the PPEGMA-An-PPEGMA FPMs were characterized and investigated by means of a series of techniques and experiments in detail. We demonstrated the final copolymers showed amphiphilic properties, strong yellow fluorescence and high water dispersibility. Biological evaluation suggested that PPEGMA-An-PPEGMA FPMs possess low cytotoxicity and can be used for cell imaging. More importantly, many other AIE active FPMs are expected to be fabricated using the similar strategy because of the good substrate and monomer applicability of the multicomponent reaction and chain transfer living radical polymerization. Therefore, we could conclude that the strategy described in this work should be of great interest for fabrication of multifunctional AIE active nanoprobes for biomedical applications.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Sabot assembly

    DOEpatents

    Bzorgi, Fariborz

    2016-11-08

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

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

    NASA Technical Reports Server (NTRS)

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

    2017-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2017-01-01

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

  13. 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.

  14. CAREERS IN BIOLOGY EDUCATION.

    ERIC Educational Resources Information Center

    KLINGE, PAUL

    THIS ENTIRE JOURNAL IS DEVOTED TO ARTICLES WHICH DESCRIBE VARIOUS CAREERS IN BIOLOGY EDUCATION. PART 1 CONTAINS ARTICLES ON CLASSROOM CAREERS IN BIOLOGY EDUCATION. THE ARTICLES DISCUSS (1) BIOLOGY TEACHING AT VARIOUS EDUCATIONAL LEVELS, (2) THE BIOLOGY TEACHER AS A RESEARCHER, AND (3) TEACHER AIDES FOR SCIENCE PROGRAMS. PART 2 PRESENTS ARTICLES ON…

  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. Toxic essential oils. Part IV: The essential oil of Achillea falcata L. as a source of biologically/pharmacologically active trans-sabinyl esters.

    PubMed

    Radulović, Niko S; Mladenović, Marko Z; Randjelovic, Pavle J; Stojanović, Nikola M; Dekić, Milan S; Blagojević, Polina D

    2015-06-01

    Herein we report on the comprehensive chemical analysis of the essential oils obtained from above- and underground parts of a previously unreported chemotype of Achillea falcata L. (Asteraceae) and, for the first time, on the biological/toxicological profile of its dominant/newly discovered volatile metabolites. Detailed spectral analyses, in combination with chemical synthesis and theoretical study, of selected constituents, enabled the identification of trans-sabinol and its esters - the formate, tiglate (new compounds), acetate, butanoate, isobutanoate, 2-methylbutanoate and 3-methylbutanoate - in both aerial and underground parts of A. falcata. Evaluation of acute toxicity in Artemia salina model, in vitro and in silico (molecular docking) evaluation of acetylcholinesterase inhibitory activity and in vivo (mice) evaluation of antinociceptive activity (hot plate, tail immersion and acetylcholine-induced abdominal writhing tests) of trans-sabinol and its esters suggested that they may interact with different targets in crustacean/mammalian organisms. Alongside moderate acute toxicity (LD50 (48 h) = 0.03-0.26 mmol/L), the tested compounds exert influence on both the peripheral and central nervous systems (in the hot plate test, trans-sabinyl tiglate, at 50 mg/kg, produced a 140% baseline increase 15 min after the treatment) and to moderately inhibit acetylcholinesterase (at the concentration of 20 µg/mL, these compounds caused a reduction of acetylcholinesterase activity up to 40%). Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. 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.

  18. 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.

  19. 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.

  20. Active Biological Materials

    NASA Astrophysics Data System (ADS)

    Fletcher, Daniel A.; Geissler, Phillip L.

    2009-05-01

    Cells make use of dynamic internal structures to control shape and create movement. By consuming energy to assemble into highly organized systems of interacting parts, these structures can generate force and resist compression, as well as adaptively change in response to their environment. Recent progress in reconstituting cytoskeletal structures in vitro has provided an opportunity to characterize the mechanics and dynamics of filament networks formed from purified proteins. Results indicate that a complex interplay between length scales and timescales underlies the mechanical responses of these systems and that energy consumption, as manifested in molecular motor activity and cytoskeletal filament growth, can drive transitions between distinct material states. This review discusses the basic characteristics of these active biological materials that set them apart from conventional materials and that create a rich array of unique behaviors.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. Dump assembly

    DOEpatents

    Goldmann, Louis H.

    1986-01-01

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

  6. 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

  7. Design of polymer motifs for nucleic acid recognition and assembly stabilization

    NASA Astrophysics Data System (ADS)

    Zhou, Zhun

    This dissertation describes the synthesis and assembly of bio-functional polymers and the applications of these polymers to drug encapsulation, delivery, and multivalent biomimetic macromolecular recognition between synthetic polymer and nucleic acids. The main content is divided into three parts: (1) polyacidic domains as strongly stabilizing design elements for aqueous phase polyacrylate diblock assembly; (2) small molecule/polymer recognition triggered macromolecular assembly and drug encapsulation; (3) trizaine derivatized polymer as a novel class of "bifacial polymer nucleic acid" (bPoNA) and applications of bPoNA to nanoparticle loading of DNA/RNA, silencing delivery as well as control of aptamer function. Through the studies in part (1) and part (2), it was demonstrated that well-designed polymer motifs are not only able to enhance assemblies driven by non-specific hydrophobic effect, but are also able to direct assemblies based on specific recognitions. In part (3) of this dissertation, this concept was further extended by the design of polyacrylate polymers that are capable of discrete and robust hybridization with nucleic acids. This surprising finding demonstrated both fundamental and practical applications. Overall, these studies provided insights into the rational design elements for improving the bio-functions of synthetic polymers, and significantly expanded the scope of biological applications in which polymers synthesized via controlled radical polymerization may play a role.

  8. A novel hybrid tobacco product that delivers a tobacco flavour note with vapour aerosol (Part 2): In vitro biological assessment and comparison with different tobacco-heating products.

    PubMed

    Breheny, Damien; Adamson, Jason; Azzopardi, David; Baxter, Andrew; Bishop, Emma; Carr, Tony; Crooks, Ian; Hewitt, Katherine; Jaunky, Tomasz; Larard, Sophie; Lowe, Frazer; Oke, Oluwatobiloba; Taylor, Mark; Santopietro, Simone; Thorne, David; Zainuddin, Benjamin; Gaça, Marianna; Liu, Chuan; Murphy, James; Proctor, Christopher

    2017-08-01

    This study assessed the toxicological and biological responses of aerosols from a novel hybrid tobacco product. Toxicological responses from the hybrid tobacco product were compared to those from a commercially available Tobacco Heating Product (c-THP), a prototype THP (p-THP) and a 3R4F reference cigarette, using in vitro test methods which were outlined as part of a framework to substantiate the risk reduction potential of novel tobacco and nicotine products. Exposure matrices used included total particulate matter (TPM), whole aerosol (WA), and aqueous aerosol extracts (AqE) obtained after machine-puffing the test products under the Health Canada Intense smoking regime. Levels of carbonyls and nicotine in these matrices were measured to understand the aerosol dosimetry of the products. The hybrid tobacco product tested negative across the in vitro assays including mutagenicity, genotoxicity, cytotoxicity, tumour promotion, oxidative stress and endothelial dysfunction. All the THPs tested demonstrated significantly reduced responses in these in vitro assays when compared to 3R4F. The findings suggest these products have the potential for reduced health risks. Further pre-clinical and clinical assessments are required to substantiate the risk reduction of these novel products at individual and population levels. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. 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

  10. Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

    PubMed Central

    Nakasugi, Kenlee; Crowhurst, Ross; Bally, Julia; Waterhouse, Peter

    2014-01-01

    Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assemble all possible transcripts from a transcriptome. Results In an effort to maximise the diversity and completeness of de novo assembled transcripts, we utilised four de novo transcriptome assemblers, TransAbyss, Trinity, SOAPdenovo-Trans, and Oases, using a range of k-mer sizes and different input RNA-seq read counts. We complemented the parameter space biologically by using RNA from 10 plant tissues. We then combined the output of all assemblies into a large super-set of sequences. Using a method from the EvidentialGene pipeline, the combined assembly was reduced from 9.9 million de novo assembled transcripts to about 235,000 of which about 50,000 were classified as primary. Metrics such as average bit-scores, feature response curves and the ability to distinguish paralogous or homeologous transcripts, indicated that the EvidentialGene processed assembly was of high quality. Of 35 RNA silencing gene transcripts, 34 were identified as assembled to full length, whereas in a previous assembly using only one assembler, 9 of these were partially assembled. Conclusions To achieve a high quality transcriptome, it is advantageous to implement and combine the output from as many different de novo assemblers as possible. We have in essence taking the ‘best’ output from each assembler while minimising sequence redundancy. We have also shown that simultaneous assessment of a variety of metrics, not just focused on contig length, is necessary to gauge the quality of assemblies. PMID

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

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

    PubMed

    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. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

  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. Self-Assembly of Biomolecular Soft Matter

    PubMed Central

    Zha, R. Helen; Palmer, Liam C.; Cui, Honggang; Bitton, Ronit

    2014-01-01

    Self-assembly programmed by molecular structure and guided dynamically by energy dissipation is a ubiquitous phenomenon in biological systems that build functional structures from the nanoscale to macroscopic dimensions. This paper describes examples of one-dimensional self-assembly of peptide amphiphiles and the consequent biological functions that emerge in these systems. We also discuss here hierarchical self-assembly of supramolecular peptide nanostructures and polysaccharides, and some new results are reported on supramolecular crystals formed by highly charged peptide amphiphiles. Reflecting on presentations at this Faraday Discussion, the paper ends with a discussion of some of the future opportunities and challenges of the field. PMID:24611266

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

    PubMed

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

    2008-03-01

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

  20. 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.

  1. Developing complex structures and functions through cell-directed assembly

    NASA Astrophysics Data System (ADS)

    Baca, Helen K.

    The integration of biological building blocks into functional platforms is important to applications across the field of nanotechnology. However, hybrid materials that incorporate biological units such as whole cells require functional bio/inorganic interfaces, benign synthesis conditions and fluidic support systems to avoid dehydration. Cell-directed assembly integrates biological materials in a uniformly nanostructured inorganic host that maintains cell accessibility, addressability, and viability in the absence of an external fluidic architecture. During immobilization of S. cerevisiae cells in a porous, lipid-templated silica matrix the cell forms its own novel interface through which it both directs assembly of the inorganic host phase and provides a fluid, membrane-like environment for the localization of proteins and nanocrystals in extended nanostructures. Characterization of the assembly process and the bio/nano interface through in-situ grazing incidence X-ray scattering, electron microscopy, and laser scanning confocal imaging, shows the cells profoundly alter the self-assembly pathway, creating around themselves multilayered phospholipid vesicles that interface coherently with the nanostructured silica host. The immobilized cells mediate their local pH and stress, collectively switching the silica mesophase. Replacing the cell with several cell models demonstrates that the living cell is necessary for the formation of the lipid interface and transformation of the inorganic phase, serving as a site for lipid aggregate nucleation and ordering. The living cell's response to osmotic stress is an important part of its ability to direct the structure of its local and global environments. Cell-directed assembly supports a highly biocompatible immobilization strategy that extends viability of immobilized cells to several weeks and creates cell-directed hierarchical structures that serve as stand-alone sensors through reporter protein expression, or organize

  2. 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

  3. KENNEDY SPACE CENTER, FLA. - James Harrison (left), Jack Nowling (center) and Amy Norris (right) pack up part of the debris stored in the Columbia Debris Hangar. An area of the Vehicle Assembly Building is being prepared to store the debris. About 83,000 pieces were shipped to KSC during search and recovery efforts in East Texas.

    NASA Image and Video Library

    2003-09-10

    KENNEDY SPACE CENTER, FLA. - James Harrison (left), Jack Nowling (center) and Amy Norris (right) pack up part of the debris stored in the Columbia Debris Hangar. An area of the Vehicle Assembly Building is being prepared to store the debris. About 83,000 pieces were shipped to KSC during search and recovery efforts in East Texas.

  4. KENNEDY SPACE CENTER, FLA. - In the Columbia Debris Hangar, Jack Nowling moves a box filled with part of the Columbia debris. About 83,000 pieces were shipped to KSC during search and recovery efforts in East Texas. An area of the Vehicle Assembly Building is being prepared to store the debris.

    NASA Image and Video Library

    2003-09-10

    KENNEDY SPACE CENTER, FLA. - In the Columbia Debris Hangar, Jack Nowling moves a box filled with part of the Columbia debris. About 83,000 pieces were shipped to KSC during search and recovery efforts in East Texas. An area of the Vehicle Assembly Building is being prepared to store the debris.

  5. KENNEDY SPACE CENTER, FLA. - The master assembler, crane crew, removes a five-meter telescope in Cocoa Beach, Fla., for repair. The tracking telescope is part of the Distant Object Attitude Measurement System (DOAMS) that provides optical support for launches from KSC and Cape Canaveral.

    NASA Image and Video Library

    2003-08-25

    KENNEDY SPACE CENTER, FLA. - The master assembler, crane crew, removes a five-meter telescope in Cocoa Beach, Fla., for repair. The tracking telescope is part of the Distant Object Attitude Measurement System (DOAMS) that provides optical support for launches from KSC and Cape Canaveral.

  6. 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

    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.

  7. 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

    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

  8. 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

  9. 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

  10. Biological Nanoplatforms for Self-Assembled Electronics

    DTIC Science & Technology

    2015-03-24

    Bacteriophages, viruses that infect bacteria , generate VLPs that are very stable in a variety of conditions. The amino acid sequences, and corresponding...coat protein surface did not cause morphological changes in the structure of the VLP. The radius of the modified VLPs is 28 nm, the same as that

  11. Biologically Self-Assembled Memristive Circuit Elements

    DTIC Science & Technology

    2010-01-01

    and sonication for 5 min ( Branson 1510). DNA Binding to TiO2 Nanoparticles DNA binding to TiO2 particles was determined by varying the...X. Li, D.A.A. Ohlberg, W. Wu, D.R. Stewart, and R.S. Williams . “A hybrid nanomemristor/transistor logic circuit capable of self-programming,” PNAS

  12. 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.

  13. 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.

  14. RETORT ASSEMBLY

    DOEpatents

    Loomis, C.C.; Ash, W.J.

    1957-11-26

    An improved retort assembly useful in the thermal reduction of volatilizable metals such as magnesium and calcium is described. In this process a high vacuum is maintained in the retort, however the retort must be heated to very high temperatures while at the same time the unloading end must bo cooled to condense the metal vapors, therefore the retention of the vacuum is frequently difficult due to the thermal stresses involved. This apparatus provides an extended condenser sleeve enclosed by the retort cover which forms the vacuum seal. Therefore, the seal is cooled by the fluid in the condenser sleeve and the extreme thermal stresses found in previous designs together with the deterioration of the sealing gasket caused by the high temperatures are avoided.

  15. 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.

  16. 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)

  17. 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)

  18. 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.

  19. 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.

  20. Space life sciences: biological research and space radiation. Proceedings of the F1.2, F1.3, F2.2 and F2.6 Symposia of COSPAR Scientific Commission F which were held during the Thirty-third COSPAR Scientific Assembly, Warsaw, Poland, July, 2000.

    PubMed

    2002-01-01

    This issue of Advances in Space Research contains a large number of manuscripts in the discipline of Space Life Sciences including papers from the following sessions of the Warsaw COSPAR Assembly: Gravity-related research with animals--past, present, future; The nervous system: space flight environmental factors effects--present results and new perspectives; Investigating space radiation effects at particle accelerators--biology and physics experiments; Perspectives on radiation risks on long space missions: deterministic and stochastic effects.

  1. Chemical reactions directed Peptide self-assembly.

    PubMed

    Rasale, Dnyaneshwar B; Das, Apurba K

    2015-05-13

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

  2. 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

  3. 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

  4. 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.

  5. Gold nanocage assemblies for selective second harmonic generation imaging of cancer cell.

    PubMed

    Demeritte, Teresa; Fan, Zhen; Sinha, Sudarson Sekhar; Duan, Jinsong; Pachter, Ruth; Ray, Paresh C

    2014-01-20

    Second harmonic generation (SHG) imaging using near infrared laser light is the key to improving penetration depths, leading to biological understanding. Unfortunately, currently SHG imaging techniques have limited capability due to the poor signal-to-noise ratio, resulting from the low SHG efficiency of available dyes. Targeted tumor imaging over nontargeted tissues is also a challenge that needs to be overcome. Driven by this need, in this study, the development of two-photon SHG imaging of live cancer cell lines selectively by enhancement of the nonlinear optical response of gold nanocage assemblies is reported. Experimental results show that two-photon scattering intensity can be increased by few orders of magnitude by just developing nanoparticle self-assembly. Theoretical modeling indicates that the field enhancement values for the nanocage assemblies can explain, in part, the enhanced nonlinear optical properties. Our experimental data also show that A9 RNA aptamer conjugated gold nanocage assemblies can be used for targeted SHG imaging of the LNCaP prostate cancer cell line. Experimental results with the HaCaT normal skin cell lines show that bioconjugated nanocage-based assemblies demonstrate SHG imaging that is highly selective and will be able to distinguish targeted cancer cell lines from other nontargeted cell types. After optimization, this reported SHG imaging assay could have considerable application for biology. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Nitrogenase Assembly: Strategies and Procedures.

    PubMed

    Sickerman, Nathaniel S; Hu, Yilin; Ribbe, Markus W

    2017-01-01

    Nitrogenase is a metalloenzyme system that plays a critical role in biological nitrogen fixation, and the study of how its metallocenters are assembled into functional entities to facilitate the catalytic reduction of dinitrogen to ammonia is an active area of interest. The diazotroph Azotobacter vinelandii is especially amenable to culturing and genetic manipulation, and this organism has provided the basis for many insights into the assembly of nitrogenase proteins and their respective metallocofactors. This chapter will cover the basic procedures necessary for growing A. vinelandii cultures and subsequent recombinant transformation and protein expression techniques. Furthermore, protocols for nitrogenase protein purification and substrate reduction activity assays are described. These methods provide a solid framework for the assessment of nitrogenase assembly and catalysis. © 2017 Elsevier Inc. All rights reserved.

  7. 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

  8. Drilling head assembly

    SciTech Connect

    De Wayne Wagoner, E.; Owen, E.D.

    1984-01-03

    An improved rotary drilling head assembly comprising a main housing having an axial bore therethrough; a stripper assembly disposed within the housing axial bore; and a stripper support assembly rotatingly supporting the stripper assembly. The stripper support assembly is removably attachable to the main housing and comprises an inner skirt member which is configured to extend about and to be supported on an exterior support surface of the main housing; an outer bearing housing configured to extend about and to be bearingly interconnected to the inner skirt member; a stripper clamp assembly clamping the stripper assembly to the outer bearing housing; and a clamping assembly removably attaching the inner skirt member to the exterior support surface such that the entire stripper support assembly of the drilling head assembly is removable from the housing as a unitary assembly by disengaging the clamping assembly.

  9. 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.

  10. 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.

  11. Electrical Connector Assembly

    DTIC Science & Technology

    2001-05-01

    hereinafter 5 appear, a feature of the invention is the provision of an 6 electrical connector assembly including a female connector 7 assembly comprising...urging of the male connector assembly 3 into the female connector assembly, a leading edge of ehe 4 retention ring engages the claw fingers forcing...assembly barrel portion to pass through the female connector 3 assembly annular wall central opening, and permitting entry of 9 the pin into the sleeve

  12. 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.

  13. 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.

  14. Bioinspired assembly of small molecules in cell milieu.

    PubMed

    Wang, Huaimin; Feng, Zhaoqianqi; Xu, Bing

    2017-03-30

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

  15. Amphiphiles for DNA Supramolecular Assemblies

    DTIC Science & Technology

    2005-11-15

    to drug or biomolecule delivery systems. In order to take advantage of forces that hold nucleic acid helices together, (Watson- Crick/Hoogsteen...supramolecular assemblies that highlight the underlying principles are evident in numerous biological (e.g., lipids) and synthetic (e.g., nanofibers ) systems.2...3). Additionally, they form hydrogels and organogels. The supramolecular systems obtained are promising in many aspects and could lead to new types

  16. 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

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

    PubMed

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

    2015-06-01

    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.

  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. EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors.

    PubMed

    Martella, Andrea; Matjusaitis, Mantas; Auxillos, Jamie; Pollard, Steven M; Cai, Yizhi

    2017-07-21

    Mammalian plasmid expression vectors are critical reagents underpinning many facets of research across biology, biomedical research, and the biotechnology industry. Traditional cloning methods often require laborious manual design and assembly of plasmids using tailored sequential cloning steps. This process can be protracted, complicated, expensive, and error-prone. New tools and strategies that facilitate the efficient design and production of bespoke vectors would help relieve a current bottleneck for researchers. To address this, we have developed an extensible mammalian modular assembly kit (EMMA). This enables rapid and efficient modular assembly of mammalian expression vectors in a one-tube, one-step golden-gate cloning reaction, using a standardized library of compatible genetic parts. The high modularity, flexibility, and extensibility of EMMA provide a simple method for the production of functionally diverse mammalian expression vectors. We demonstrate the value of this toolkit by constructing and validating a range of representative vectors, such as transient and stable expression vectors (transposon based vectors), targeting vectors, inducible systems, polycistronic expression cassettes, fusion proteins, and fluorescent reporters. The method also supports simple assembly combinatorial libraries and hierarchical assembly for production of larger multigenetic cargos. In summary, EMMA is compatible with automated production, and novel genetic parts can be easily incorporated, providing new opportunities for mammalian synthetic biology.

  20. Proceedings from the National Cancer Institute's Second International Workshop on the Biology, Prevention, and Treatment of Relapse after Hematopoietic Stem Cell Transplantation: Part I. Biology of relapse after transplantation.

    PubMed

    Gress, Ronald E; Miller, Jeffrey S; Battiwalla, Minoo; Bishop, Michael R; Giralt, Sergio A; Hardy, Nancy M; Kröger, Nicolaus; Wayne, Alan S; Landau, Dan A; Wu, Catherine J

    2013-11-01

    In the National Cancer Institute's Second Workshop on the Biology, Prevention, and Treatment of Relapse after Hematopoietic Stem Cell Transplantation, the Scientific/Educational Session on the Biology of Relapse discussed recent advances in understanding some of the host-, disease-, and transplantation-related contributions to relapse, emphasizing concepts with potential therapeutic implications. Relapse after hematopoietic stem cell transplantation (HSCT) represents tumor escape, from the cytotoxic effects of the conditioning regimen and from immunologic control mediated by reconstituted lymphocyte populations. Factors influencing the biology of the therapeutic graft-versus-malignancy (GVM) effect-and relapse-include conditioning regimen effects on lymphocyte populations and homeostasis, immunologic niches, and the tumor microenvironment; reconstitution of lymphocyte populations and establishment of functional immune competence; and genetic heterogeneity within the malignancy defining potential for clonal escape. Recent developments in T cell and natural killer cell homeostasis and reconstitution are reviewed, with implications for prevention and treatment of relapse, as is the application of modern genome sequencing to defining the biologic basis of GVM, clonal escape, and relapse after HSCT.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. Soybean meal enriched with microelements by biosorption--a new biological feed supplement for laying hens. Part I. Performance and egg traits.

    PubMed

    Witkowska, Z; Chojnacka, K; Korczyński, M; Świniarska, M; Saeid, A; Opaliński, S; Dobrzański, Z

    2014-05-15

    The aim of the study was to evaluate the effect of soybean meal enriched with Cu(II), Zn(II), Fe(II) and Cr(III) by biosorption on egg traits (egg weight, eggshell strength, eggshell thickness, yolk colour, albumen height) and performance of laying hens. Also, the effect of increased microelement doses in biological form on egg quality parameters and hens performance was investigated. A consumer questionnaire was undertaken to evaluate the organoleptic parameters of the eggs. Generally, our study showed that in the groups fed with the new biological supplement, egg quality parameters improved, including eggshell strength, eggshell thickness, albumen height and yolk colour. The biological form of microelements also improved the feed conversion rate, especially in the group fed with a biological form of Cr(III). Moreover, the new supplement improved organoleptic parameters of the eggs, in comparison to the inorganic form of microelements as well as to chelate. Enriched soybean meal could constitute an alternative for currently used feed additives with microelements. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2011-03-01

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

  10. 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.

  11. Probe tip heating assembly

    SciTech Connect

    Schmitz, Roger William; Oh, Yunje

    2016-10-25

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

  12. Statistical Tolerance and Clearance Analysis for Assembly

    NASA Technical Reports Server (NTRS)

    Lee, S.; Yi, C.

    1996-01-01

    Tolerance is inevitable because manufacturing exactly equal parts is known to be impossible. Furthermore, the specification of tolerances is an integral part of product design since tolerances directly affect the assemblability, functionality, manufacturability, and cost effectiveness of a product. In this paper, we present statistical tolerance and clearance analysis for the assembly. Our proposed work is expected to make the following contributions: (i) to help the designers to evaluate products for assemblability, (ii) to provide a new perspective to tolerance problems, and (iii) to provide a tolerance analysis tool which can be incorporated into a CAD or solid modeling system.

  13. Statistical Tolerance and Clearance Analysis for Assembly

    NASA Technical Reports Server (NTRS)

    Lee, S.; Yi, C.

    1996-01-01

    Tolerance is inevitable because manufacturing exactly equal parts is known to be impossible. Furthermore, the specification of tolerances is an integral part of product design since tolerances directly affect the assemblability, functionality, manufacturability, and cost effectiveness of a product. In this paper, we present statistical tolerance and clearance analysis for the assembly. Our proposed work is expected to make the following contributions: (i) to help the designers to evaluate products for assemblability, (ii) to provide a new perspective to tolerance problems, and (iii) to provide a tolerance analysis tool which can be incorporated into a CAD or solid modeling system.

  14. The PLOS ONE Synthetic Biology Collection: Six Years and Counting

    PubMed Central

    Peccoud, Jean; Isalan, Mark

    2012-01-01

    Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community. PMID:22916228

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

    PubMed

    Peccoud, Jean; Isalan, Mark

    2012-01-01

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

  16. 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.

  17. 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.

  18. 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.

  19. Short Synthetic Terminators for Assembly of Transcription Units in Vitro and Stable Chromosomal Integration in Yeast S. cerevisiae.

    PubMed

    MacPherson, Murray; Saka, Yasushi

    2017-01-20

    Assembly of synthetic genetic circuits is central to synthetic biology. Yeast S. cerevisiae, in particular, has proven to be an ideal chassis for synthetic genome assemblies by exploiting its efficient homologous recombination. However, this property of efficient homologous recombination poses a problem for multigene assemblies in yeast, since repeated usage of standard parts, such as transcriptional terminators, can lead to rearrangements of the repeats in assembled DNA constructs in vivo. To address this issue in developing a library of orthogonal genetic components for yeast, we designed a set of short synthetic terminators based on a consensus sequence with random linkers to avoid repetitive sequences. We constructed a series of expression vectors with these synthetic terminators for efficient assembly of synthetic genes using Gateway recombination reactions. We also constructed two BAC (bacterial artificial chromosome) vectors for assembling multiple transcription units with the synthetic terminators in vitro and their integration in the yeast genome. The tandem array of synthetic genes integrated in the genome by this method is highly stable because there are few homologous segments in the synthetic constructs. Using this system of assembly and genomic integration of transcription units, we tested the synthetic terminators and their influence on the proximal transcription units. Although all the synthetic terminators have the common consensus with the identical length, they showed different activities and impacts on the neighboring transcription units.

  20. 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.